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@@ -0,0 +1,529 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Collect_SILAC_XML</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
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+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module Collect_SILAC_XML
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== MODULE DESCRIPTION ==================== -->
+<h1 class="epydoc">Module Collect_SILAC_XML</h1><p class="nomargin-top"><span class="codelink"><a href="Collect_SILAC_XML-pysrc.html">source code</a></span></p>
+<p>Collect_SILAC_XML.py</p>
+ <p>Allow collection of SILAC XML file results after validation,
+ calculates statistics and generates a table with results, aggregating the
+ results for each protein (as an option)</p>
+ <p>Usage: python Collect_SILAC_XML.py -f <folder with XML SILAC
+ files> -s (switch to obtain the output in aggregated or summary
+ form)</p>
+ <p>Output is to stdout</p>
+ <p>First argument - folder with XML files Output - table in tab delimited
+ format containing the statistics for each validated protein, printed to
+ stdout</p>
+ <p>This script is provided "as is" and works well with
+ correctly formatted XML SILAC files. However, no exceptions have been
+ implemented and the code will fail if not fed correct data</p>
+ <p>Cosmin Saveanu, last modifications 2008-04-14 Genetique des
+ Interactions Macromoleculaires, Alain Jacquier's lab, Institut Pasteur,
+ CNRS-URA 2171, France csaveanu@pasteur.fr for any questions</p>
+
+<!-- ==================== CLASSES ==================== -->
+<a name="section-Classes"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Classes</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Classes"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="Collect_SILAC_XML.Usage-class.html" class="summary-name">Usage</a><br />
+ used for catching exceptions generated during command line
+ parameter parsing
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTIONS ==================== -->
+<a name="section-Functions"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Functions</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Functions"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="Mean"></a><span class="summary-sig-name">Mean</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Obtain the mean of the values from a list Returns 0 if the list is
+ empty</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#Mean">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="SumSquares"></a><span class="summary-sig-name">SumSquares</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Squares each value in the passed list, adds up these squares and
+ returns the result.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#SumSquares">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="Variance"></a><span class="summary-sig-name">Variance</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Calculates the variance for a sample Returns 100 if less than 2
+ values are provided</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#Variance">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="StdDev"></a><span class="summary-sig-name">StdDev</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Returns the standard deviation of the values in the passed list using
+ N-1 in the denominator (i.e., to estimate population stdev).</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#StdDev">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="Collect_SILAC_XML-module.html#Median" class="summary-sig-name">Median</a>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Returns the median of the passed list.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#Median">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="get_flist"></a><span class="summary-sig-name">get_flist</span>(<span class="summary-sig-arg">dirname</span>,
+ <span class="summary-sig-arg">ext</span>=<span class="summary-sig-default">".xml"</span>)</span><br />
+ Get all .ext file names from dirname, not recursive returns list of
+ complete paths for files</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#get_flist">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="Collect_SILAC_XML-module.html#GetValXML" class="summary-sig-name">GetValXML</a>(<span class="summary-sig-arg">data</span>,
+ <span class="summary-sig-arg">index</span>=<span class="summary-sig-default">0</span>,
+ <span class="summary-sig-arg">what</span>=<span class="summary-sig-default">'pepseq'</span>)</span><br />
+ Returns the text attribute of an entry in an ElementTree object based
+ on the XMLdict dictionary that maps numbers to tags - definition in
+ the init of the main frame.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#GetValXML">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="GenerateListDict"></a><span class="summary-sig-name">GenerateListDict</span>(<span class="summary-sig-arg">xmldata</span>)</span><br />
+ Recovers the data about a peptide in the XML SILAC file Returns a
+ dictionary, each peptide has an integer as key</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#GenerateListDict">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="CalcStatistics"></a><span class="summary-sig-name">CalcStatistics</span>(<span class="summary-sig-arg">datadict</span>)</span><br />
+ Returns statistics on a single data dictionary (corresponding to one
+ protein) as a multiple of strings <nr of valid peptides>,
+ <median>, <mean>, <SD></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#CalcStatistics">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="Collect_SILAC_XML-module.html#ExtractSILACDataFromXML" class="summary-sig-name">ExtractSILACDataFromXML</a>(<span class="summary-sig-arg">fname</span>,
+ <span class="summary-sig-arg">peptides_also</span>=<span class="summary-sig-default">True</span>)</span><br />
+ Parses an XML Silac file and returns information
+on all the validated peptides in the entry if peptides_also
+is True.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#ExtractSILACDataFromXML">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="main"></a><span class="summary-sig-name">main</span>(<span class="summary-sig-arg">argv</span>=<span class="summary-sig-default">None</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#main">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== VARIABLES ==================== -->
+<a name="section-Variables"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Variables</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Variables"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="Collect_SILAC_XML-module.html#XMLdict" class="summary-name">XMLdict</a> = <code title="{'pepseq': 0, 'mzh': 1, 'calc_mzh': 2, 'leucines': 3, 'mono_iso_int': \
+4, 'deuterated_intensity': 5, 'ratio': 6, 'validated': 7, 'local_bg': \
+8, 'corrected_ratio': 9}">{'pepseq': 0, 'mzh': 1, 'calc_mzh': 2, 'leucines': 3<code class="variable-ellipsis">...</code></code>
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTION DETAILS ==================== -->
+<a name="section-FunctionDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Function Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-FunctionDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="Median"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">Median</span>(<span class="sig-arg">inlist</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#Median">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns the median of the passed list. Returns 0 or the element if
+ less than 2 elements are passed to the function</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="GetValXML"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GetValXML</span>(<span class="sig-arg">data</span>,
+ <span class="sig-arg">index</span>=<span class="sig-default">0</span>,
+ <span class="sig-arg">what</span>=<span class="sig-default">'pepseq'</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#GetValXML">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns the text attribute of an entry in an ElementTree object based
+ on the XMLdict dictionary that maps numbers to tags - definition in the
+ init of the main frame. By default it returns the peptide sequence of the
+ first record.</p>
+ <p>pdatapos - indicates the position of the <pepdata> in the root
+ of the pepdata xml entry</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="ExtractSILACDataFromXML"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">ExtractSILACDataFromXML</span>(<span class="sig-arg">fname</span>,
+ <span class="sig-arg">peptides_also</span>=<span class="sig-default">True</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#ExtractSILACDataFromXML">source code</a></span>
+ </td>
+ </tr></table>
+
+ <pre class="literalblock">
+Parses an XML Silac file and returns information
+on all the validated peptides in the entry if peptides_also
+is True. The origin of the peptide (protein) is
+also recovered and used in the output. Uses:
+- GenerateListDict - to obtain the peptide data
+- CalcStatistics - to calculate protein SILAC statistics.
+Returns a string, formatted differently if peptides_also
+is true or false
+
+</pre>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== VARIABLES DETAILS ==================== -->
+<a name="section-VariablesDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Variables Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-VariablesDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="XMLdict"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <h3 class="epydoc">XMLdict</h3>
+
+ <dl class="fields">
+ </dl>
+ <dl class="fields">
+ <dt>Value:</dt>
+ <dd><table><tr><td><pre class="variable">
+{'pepseq': 0, 'mzh': 1, 'calc_mzh': 2, 'leucines': 3, 'mono_iso_int': <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+4, 'deuterated_intensity': 5, 'ratio': 6, 'validated': 7, 'local_bg': <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+8, 'corrected_ratio': 9}
+</pre></td></tr></table>
+</dd>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
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+ <!-- Tree link -->
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+
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+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
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+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
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+ <td align="right" class="footer">
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diff --git a/docs/Collect_SILAC_XML-pysrc.html b/docs/Collect_SILAC_XML-pysrc.html
new file mode 100644
index 0000000000000000000000000000000000000000..10e6c481853de6b52c9db4a8abd689734af56082
--- /dev/null
+++ b/docs/Collect_SILAC_XML-pysrc.html
@@ -0,0 +1,435 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Collect_SILAC_XML</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
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+ href="module-tree.html">Trees</a> </th>
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+ Module Collect_SILAC_XML
+ </span>
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+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
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+ onclick="toggle_private();">hide private</a>]</span></td></tr>
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+</table>
+<h1 class="epydoc">Source Code for <a href="Collect_SILAC_XML-module.html">Module Collect_SILAC_XML</a></h1>
+<pre class="py-src">
+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
+<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">Collect_SILAC_XML.py</tt> </tt>
+<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">Allow collection of SILAC XML file results after</tt> </tt>
+<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">validation, calculates statistics and generates</tt> </tt>
+<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">a table with results, aggregating the results</tt> </tt>
+<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">for each protein (as an option)</tt> </tt>
+<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">Usage: python Collect_SILAC_XML.py -f <folder with XML SILAC files> -s</tt> </tt>
+<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">(switch to obtain the output in aggregated or summary form)</tt> </tt>
+<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Output is to stdout</tt> </tt>
+<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">First argument - folder with XML files</tt> </tt>
+<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">Output - table in tab delimited format containing</tt> </tt>
+<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">the statistics for each validated protein, printed to stdout</tt> </tt>
+<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">This script is provided "as is" and works well with correctly</tt> </tt>
+<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">formatted XML SILAC files. However, no exceptions have been</tt> </tt>
+<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">implemented and the code will fail if not fed correct data</tt> </tt>
+<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">Cosmin Saveanu, last modifications 2008-04-14</tt> </tt>
+<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">Genetique des Interactions Macromoleculaires, </tt> </tt>
+<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">Alain Jacquier's lab, Institut Pasteur,</tt> </tt>
+<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">CNRS-URA 2171, France</tt> </tt>
+<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">csaveanu@pasteur.fr for any questions</tt> </tt>
+<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
+<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
+<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment">#import cElementTree as ET (for versions of Python < 2.5)</tt> </tt>
+<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">etree</tt><tt class="py-op">.</tt><tt class="py-name">cElementTree</tt> <tt class="py-keyword">as</tt> <tt class="py-name">ET</tt> <tt class="py-comment">#latest version integrated in Python 2.5</tt> </tt>
+<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">math</tt><tt class="py-op">,</tt> <tt class="py-name">getopt</tt> </tt>
+<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
+<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment">#a dictionary that holds the position of the different</tt> </tt>
+<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#informations available in the SILAC XML file</tt> </tt>
+<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#used by GetValXML</tt> </tt>
+<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-0" class="py-name" targets="Variable Collect_SILAC_XML.XMLdict=Collect_SILAC_XML-module.html#XMLdict"><a title="Collect_SILAC_XML.XMLdict" class="py-name" href="#" onclick="return doclink('link-0', 'XMLdict', 'link-0');">XMLdict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">:</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'mzh'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">'leucines'</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> </tt>
+<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> </tt>
+<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-string">'ratio'</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-string">'validated'</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">,</tt> </tt>
+<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-string">'local_bg'</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">:</tt><tt class="py-number">9</tt><tt class="py-op">}</tt> </tt>
+<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
+<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> </tt>
+<a name="Mean"></a><div id="Mean-def"><a name="L42"></a><tt class="py-lineno"> 42</tt> <a class="py-toggle" href="#" id="Mean-toggle" onclick="return toggle('Mean');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#Mean">Mean</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Mean-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Mean-expanded"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the mean of the values from a list</tt> </tt>
+<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> Returns 0 if the list is empty</tt> </tt>
+<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">sum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inlist</tt><tt class="py-op">:</tt> </tt>
+<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">sum</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt> <tt class="py-op">+</tt> <tt class="py-name">item</tt> </tt>
+<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sum</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
+</div><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> </tt>
+<a name="SumSquares"></a><div id="SumSquares-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="SumSquares-toggle" onclick="return toggle('SumSquares');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#SumSquares">SumSquares</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="SumSquares-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SumSquares-expanded"><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> Squares each value in the passed list, adds up these squares and</tt> </tt>
+<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> returns the result.</tt> </tt>
+<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">ss</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inlist</tt><tt class="py-op">:</tt> </tt>
+<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">ss</tt> <tt class="py-op">=</tt> <tt class="py-name">ss</tt> <tt class="py-op">+</tt> <tt class="py-name">item</tt><tt class="py-op">*</tt><tt class="py-name">item</tt> </tt>
+<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ss</tt> </tt>
+</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
+<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
+<a name="Variance"></a><div id="Variance-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="Variance-toggle" onclick="return toggle('Variance');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#Variance">Variance</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Variance-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Variance-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the variance for a sample </tt> </tt>
+<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> Returns 100 if less than 2 values are provided</tt> </tt>
+<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name" targets="Function Collect_SILAC_XML.Mean()=Collect_SILAC_XML-module.html#Mean,Function lilamsxml.Mean()=lilamsxml-module.html#Mean"><a title="Collect_SILAC_XML.Mean
+lilamsxml.Mean" class="py-name" href="#" onclick="return doclink('link-1', 'Mean', 'link-1');">Mean</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">ssq</tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name" targets="Function Collect_SILAC_XML.SumSquares()=Collect_SILAC_XML-module.html#SumSquares,Function lilamsxml.SumSquares()=lilamsxml-module.html#SumSquares"><a title="Collect_SILAC_XML.SumSquares
+lilamsxml.SumSquares" class="py-name" href="#" onclick="return doclink('link-2', 'SumSquares', 'link-2');">SumSquares</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-op">></tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">vari</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">ssq</tt> <tt class="py-op">-</tt> <tt class="py-name">n</tt><tt class="py-op">*</tt><tt class="py-name">mn</tt><tt class="py-op">*</tt><tt class="py-name">mn</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">vari</tt> <tt class="py-op">=</tt> <tt class="py-number">100</tt> </tt>
+<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">vari</tt> </tt>
+</div><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
+<a name="StdDev"></a><div id="StdDev-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="StdDev-toggle" onclick="return toggle('StdDev');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#StdDev">StdDev</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="StdDev-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StdDev-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> Returns the standard deviation of the values in the passed list</tt> </tt>
+<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> using N-1 in the denominator (i.e., to estimate population stdev).</tt> </tt>
+<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt id="link-3" class="py-name" targets="Function Collect_SILAC_XML.Variance()=Collect_SILAC_XML-module.html#Variance,Function lilamsxml.Variance()=lilamsxml-module.html#Variance"><a title="Collect_SILAC_XML.Variance
+lilamsxml.Variance" class="py-name" href="#" onclick="return doclink('link-3', 'Variance', 'link-3');">Variance</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
+<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
+<a name="Median"></a><div id="Median-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="Median-toggle" onclick="return toggle('Median');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#Median">Median</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Median-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Median-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> Returns the median of the passed list.</tt> </tt>
+<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> Returns 0 or the element if less than 2 elements</tt> </tt>
+<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> are passed to the function</tt> </tt>
+<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">newlist</tt> <tt class="py-op">=</tt> <tt class="py-name">inlist</tt> </tt>
+<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">newlist</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">%</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># if even number, simple mean of middles</tt> </tt>
+<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
+<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
+<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
+<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> </tt>
+<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">median</tt> </tt>
+</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
+<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
+<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
+<a name="get_flist"></a><div id="get_flist-def"><a name="L111"></a><tt class="py-lineno">111</tt> <a class="py-toggle" href="#" id="get_flist-toggle" onclick="return toggle('get_flist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#get_flist">get_flist</a><tt class="py-op">(</tt><tt class="py-param">dirname</tt><tt class="py-op">,</tt> <tt class="py-param">ext</tt> <tt class="py-op">=</tt> <tt class="py-string">".xml"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="get_flist-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="get_flist-expanded"><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> Get all .ext file names from dirname, not recursive</tt> </tt>
+<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> returns list of complete paths for files</tt> </tt>
+<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">outlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">f</tt> </tt>
+<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-comment">#we do nothing with the subfolders</tt> </tt>
+<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">extension</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">extension</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">ext</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">outlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
+<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">outlist</tt> </tt>
+</div><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
+<a name="GetValXML"></a><div id="GetValXML-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="GetValXML-toggle" onclick="return toggle('GetValXML');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#GetValXML">GetValXML</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">what</tt><tt class="py-op">=</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="GetValXML-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GetValXML-expanded"><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> Returns the text attribute of an entry in an ElementTree</tt> </tt>
+<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> object based on the XMLdict dictionary that maps</tt> </tt>
+<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> numbers to tags - definition in the init of the main</tt> </tt>
+<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> frame. By default it returns the peptide sequence of </tt> </tt>
+<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> the first record.</tt> </tt>
+<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> pdatapos - indicates the position of the <pepdata> in</tt> </tt>
+<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> the root of the pepdata xml entry</tt> </tt>
+<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">pdatapos</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
+<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-4" class="py-name"><a title="Collect_SILAC_XML.XMLdict" class="py-name" href="#" onclick="return doclink('link-4', 'XMLdict', 'link-0');">XMLdict</a></tt><tt class="py-op">[</tt><tt class="py-name">what</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> </tt>
+</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
+<a name="GenerateListDict"></a><div id="GenerateListDict-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="GenerateListDict-toggle" onclick="return toggle('GenerateListDict');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#GenerateListDict">GenerateListDict</a><tt class="py-op">(</tt><tt class="py-param">xmldata</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="GenerateListDict-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GenerateListDict-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> Recovers the data about a peptide in the XML SILAC file</tt> </tt>
+<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> Returns a dictionary, each peptide has an integer as key</tt> </tt>
+<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">entriesdict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
+<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">entriesdict</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-5" class="py-name" targets="Function Collect_SILAC_XML.GetValXML()=Collect_SILAC_XML-module.html#GetValXML,Method silacvalidator.MainFrame.GetValXML()=silacvalidator.MainFrame-class.html#GetValXML"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-5', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'pepseq'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-6', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'leucines'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt id="link-7" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-7', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'mzh'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-8', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-9', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-10', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-11', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'ratio'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt id="link-12" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-12', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-13', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'local_bg'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-14', 'GetValXML', 'link-5');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'validated'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">entriesdict</tt> </tt>
+</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
+<a name="CalcStatistics"></a><div id="CalcStatistics-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="CalcStatistics-toggle" onclick="return toggle('CalcStatistics');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#CalcStatistics">CalcStatistics</a><tt class="py-op">(</tt><tt class="py-param">datadict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="CalcStatistics-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CalcStatistics-expanded"><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> Returns statistics on a single data dictionary (corresponding to one protein)</tt> </tt>
+<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> as a multiple of strings <nr of valid peptides>, <median>, <mean>, <SD></tt> </tt>
+<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">yeslist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">yeskeylist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">datadict</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"YES"</tt><tt class="py-op">:</tt> </tt>
+<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">yeskeylist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt> </tt>
+<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">yeslist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment">#7 is calculated corrected ratio index</tt> </tt>
+<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Function Collect_SILAC_XML.Median()=Collect_SILAC_XML-module.html#Median,Function lilamsxml.Median()=lilamsxml-module.html#Median"><a title="Collect_SILAC_XML.Median
+lilamsxml.Median" class="py-name" href="#" onclick="return doclink('link-15', 'Median', 'link-15');">Median</a></tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
+<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">mean</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Collect_SILAC_XML.Mean
+lilamsxml.Mean" class="py-name" href="#" onclick="return doclink('link-16', 'Mean', 'link-1');">Mean</a></tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
+<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">stddev</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Function Collect_SILAC_XML.StdDev()=Collect_SILAC_XML-module.html#StdDev,Function lilamsxml.StdDev()=lilamsxml-module.html#StdDev"><a title="Collect_SILAC_XML.StdDev
+lilamsxml.StdDev" class="py-name" href="#" onclick="return doclink('link-17', 'StdDev', 'link-17');">StdDev</a></tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
+<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">nopep</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">yeslist</tt><tt class="py-op">)</tt> </tt>
+<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
+<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-string">"%d"</tt><tt class="py-op">%</tt><tt class="py-name">nopep</tt><tt class="py-op">,</tt> <tt class="py-string">"%.2f"</tt><tt class="py-op">%</tt><tt class="py-name">median</tt><tt class="py-op">,</tt> <tt class="py-string">"%.2f"</tt><tt class="py-op">%</tt><tt class="py-name">mean</tt><tt class="py-op">,</tt> <tt class="py-string">"%.4f"</tt><tt class="py-op">%</tt><tt class="py-name">stddev</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
+<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
+<a name="ExtractSILACDataFromXML"></a><div id="ExtractSILACDataFromXML-def"><a name="L184"></a><tt class="py-lineno">184</tt> <a class="py-toggle" href="#" id="ExtractSILACDataFromXML-toggle" onclick="return toggle('ExtractSILACDataFromXML');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#ExtractSILACDataFromXML">ExtractSILACDataFromXML</a><tt class="py-op">(</tt><tt class="py-param">fname</tt><tt class="py-op">,</tt> <tt class="py-param">peptides_also</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="ExtractSILACDataFromXML-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ExtractSILACDataFromXML-expanded"><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses an XML Silac file and returns information</tt> </tt>
+<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> on all the validated peptides in the entry if peptides_also</tt> </tt>
+<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> is True. The origin of the peptide (protein) is</tt> </tt>
+<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> also recovered and used in the output. Uses:</tt> </tt>
+<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> - GenerateListDict - to obtain the peptide data</tt> </tt>
+<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> - CalcStatistics - to calculate protein SILAC statistics. </tt> </tt>
+<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> Returns a string, formatted differently if peptides_also</tt> </tt>
+<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"> is true or false</tt> </tt>
+<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">tree</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">parse</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">)</tt> </tt>
+<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt class="py-name">getroot</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">fsplit</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">)</tt> </tt>
+<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">endofname</tt> <tt class="py-op">=</tt> <tt class="py-name">fsplit</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-comment">#the root is a <protdata> entry</tt> </tt>
+<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">prot_data</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">endofname</tt><tt class="py-op">,</tt> </tt>
+<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
+<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
+<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
+<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
+<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
+<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
+<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
+<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-comment">#print "> Mowse score: %s, database: %s, ppm tolerance: %s"%(data[0][3].text,</tt> </tt>
+<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># data[0][1].text, data[0][2].text)</tt> </tt>
+<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "> Spot identification: %s.\n"%data[0][0].text</tt> </tt>
+<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "> Identified protein: %s, accesion number: %s."%(data[2].text, data[1].text)</tt> </tt>
+<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "> Peptide coverage: %s percent, matched peptides: %s."%(data[0][4].text[:-1], data[0][5].text)</tt> </tt>
+<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">datadict</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name" targets="Function Collect_SILAC_XML.GenerateListDict()=Collect_SILAC_XML-module.html#GenerateListDict,Method silacvalidator.MainFrame.GenerateListDict()=silacvalidator.MainFrame-class.html#GenerateListDict"><a title="Collect_SILAC_XML.GenerateListDict
+silacvalidator.MainFrame.GenerateListDict" class="py-name" href="#" onclick="return doclink('link-18', 'GenerateListDict', 'link-18');">GenerateListDict</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
+<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">stats</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name" targets="Function Collect_SILAC_XML.CalcStatistics()=Collect_SILAC_XML-module.html#CalcStatistics"><a title="Collect_SILAC_XML.CalcStatistics" class="py-name" href="#" onclick="return doclink('link-19', 'CalcStatistics', 'link-19');">CalcStatistics</a></tt><tt class="py-op">(</tt><tt class="py-name">datadict</tt><tt class="py-op">)</tt> </tt>
+<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">stats_string</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">stats</tt><tt class="py-op">)</tt> </tt>
+<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">peptides_also</tt><tt class="py-op">:</tt> </tt>
+<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">peptide_info_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">peptkey</tt> <tt class="py-keyword">in</tt> <tt class="py-name">datadict</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">peptkey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"YES"</tt><tt class="py-op">:</tt> </tt>
+<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">peptide_info_list</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">prot_data</tt><tt class="py-op">,</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">datadict</tt><tt class="py-op">[</tt><tt class="py-name">peptkey</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">stats_string</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">peptide_info_list</tt><tt class="py-op">)</tt> </tt>
+<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">prot_data</tt><tt class="py-op">,</tt> <tt class="py-name">stats_string</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
+<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> </tt>
+<a name="Usage"></a><div id="Usage-def"><a name="L226"></a><tt class="py-lineno">226</tt> <a class="py-toggle" href="#" id="Usage-toggle" onclick="return toggle('Usage');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Collect_SILAC_XML.Usage-class.html">Usage</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Usage-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Usage-expanded"><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> used for catching exceptions generated</tt> </tt>
+<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> during command line parameter parsing</tt> </tt>
+<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="Usage.__init__"></a><div id="Usage.__init__-def"><a name="L231"></a><tt class="py-lineno">231</tt> <a class="py-toggle" href="#" id="Usage.__init__-toggle" onclick="return toggle('Usage.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML.Usage-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">msg</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Usage.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Usage.__init__-expanded"><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Variable silacvalidator.msg=silacvalidator-module.html#msg"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-20', 'msg', 'link-20');">msg</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-21', 'msg', 'link-20');">msg</a></tt> </tt>
+</div></div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
+<a name="main"></a><div id="main-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Collect_SILAC_XML-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-param">argv</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt class="py-name">foldername</tt><tt class="py-op">,</tt> <tt class="py-name">aggregate</tt> </tt>
+<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
+<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">argv</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
+<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">argv</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt> </tt>
+<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">opts</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">getopt</tt><tt class="py-op">.</tt><tt class="py-name">getopt</tt><tt class="py-op">(</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"hsf:"</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">"help"</tt><tt class="py-op">,</tt> <tt class="py-string">"summary"</tt><tt class="py-op">,</tt> </tt>
+<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-string">"XMLfolder="</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">getopt</tt><tt class="py-op">.</tt><tt class="py-name">error</tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-22', 'msg', 'link-20');">msg</a></tt><tt class="py-op">:</tt> </tt>
+<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-23" class="py-name" targets="Class Collect_SILAC_XML.Usage=Collect_SILAC_XML.Usage-class.html,Class lilamsxml.Usage=lilamsxml.Usage-class.html"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-23', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-24', 'msg', 'link-20');">msg</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-comment"># option processing</tt> </tt>
+<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">foldername</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
+<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">aggregate</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">option</tt><tt class="py-op">,</tt> <tt class="py-name">value</tt> <tt class="py-keyword">in</tt> <tt class="py-name">opts</tt><tt class="py-op">:</tt> </tt>
+<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-h"</tt><tt class="py-op">,</tt> <tt class="py-string">"--help"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-25" class="py-name"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-25', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">(</tt><tt class="py-name">__doc__</tt><tt class="py-op">)</tt> </tt>
+<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-s"</tt><tt class="py-op">,</tt> <tt class="py-string">"--summary"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">aggregate</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
+<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-f"</tt><tt class="py-op">,</tt> <tt class="py-string">"--XMLfolder"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">foldername</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
+<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
+<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">""</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">foldername</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-26" class="py-name"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-26', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">(</tt><tt class="py-string">"no input folder!"</tt><tt class="py-op">)</tt> </tt>
+<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">flist</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name" targets="Function Collect_SILAC_XML.get_flist()=Collect_SILAC_XML-module.html#get_flist"><a title="Collect_SILAC_XML.get_flist" class="py-name" href="#" onclick="return doclink('link-27', 'get_flist', 'link-27');">get_flist</a></tt><tt class="py-op">(</tt><tt class="py-name">foldername</tt><tt class="py-op">)</tt> </tt>
+<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> </tt>
+<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">header_identif</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"file_name"</tt><tt class="py-op">,</tt> </tt>
+<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-string">"Mowse_score"</tt><tt class="py-op">,</tt> </tt>
+<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-string">"Database"</tt><tt class="py-op">,</tt> </tt>
+<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-string">"ppm_tolerance"</tt><tt class="py-op">,</tt> </tt>
+<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-string">"Spot_identification"</tt><tt class="py-op">,</tt> </tt>
+<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-string">"Identified_protein"</tt><tt class="py-op">,</tt> </tt>
+<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-string">"Accesion_number"</tt><tt class="py-op">,</tt> </tt>
+<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-string">"Peptide_coverage"</tt><tt class="py-op">,</tt> </tt>
+<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-string">"%_matched_peptides"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">header_stats</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"Number_of_valid_peptides"</tt><tt class="py-op">,</tt> </tt>
+<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-string">"Median_ratio"</tt><tt class="py-op">,</tt> <tt class="py-string">"Mean_ratio"</tt><tt class="py-op">,</tt> </tt>
+<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-string">"Std_Dev"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">aggregate</tt><tt class="py-op">:</tt> </tt>
+<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">header_pep</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">,</tt> </tt>
+<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-string">'leucines'</tt><tt class="py-op">,</tt> </tt>
+<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-string">'mzh'</tt><tt class="py-op">,</tt> </tt>
+<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">,</tt> </tt>
+<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">,</tt> </tt>
+<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">,</tt> </tt>
+<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-string">'ratio'</tt><tt class="py-op">,</tt> </tt>
+<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">,</tt> </tt>
+<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-string">'local_bg'</tt><tt class="py-op">,</tt> </tt>
+<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-string">'validated'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">header</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">header_identif</tt><tt class="py-op">,</tt> <tt class="py-name">header_pep</tt><tt class="py-op">,</tt> <tt class="py-name">header_stats</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">header</tt> <tt class="py-op">=</tt> <tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">header_identif</tt><tt class="py-op">,</tt> <tt class="py-name">header_stats</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">header</tt> </tt>
+<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">fname</tt> <tt class="py-keyword">in</tt> <tt class="py-name">flist</tt><tt class="py-op">:</tt> </tt>
+<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-28" class="py-name" targets="Function Collect_SILAC_XML.ExtractSILACDataFromXML()=Collect_SILAC_XML-module.html#ExtractSILACDataFromXML"><a title="Collect_SILAC_XML.ExtractSILACDataFromXML" class="py-name" href="#" onclick="return doclink('link-28', 'ExtractSILACDataFromXML', 'link-28');">ExtractSILACDataFromXML</a></tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">,</tt> <tt class="py-name">peptides_also</tt><tt class="py-op">=</tt> <tt class="py-keyword">not</tt> <tt class="py-name">aggregate</tt><tt class="py-op">)</tt> </tt>
+<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt>
+<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
+<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> </tt>
+<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-29" class="py-name"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-29', 'Usage', 'link-23');">Usage</a></tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">:</tt> </tt>
+<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">": "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-30', 'msg', 'link-20');">msg</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-string">"\t for help use --help or -h"</tt> </tt>
+<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">2</tt> </tt>
+</div><a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
+<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
+<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt id="link-31" class="py-name" targets="Function Collect_SILAC_XML.main()=Collect_SILAC_XML-module.html#main,Function lilamsxml.main()=lilamsxml-module.html#main"><a title="Collect_SILAC_XML.main
+lilamsxml.main" class="py-name" href="#" onclick="return doclink('link-31', 'main', 'link-31');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt><script type="text/javascript">
+<!--
+expandto(location.href);
+// -->
+</script>
+</pre>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
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+ <!-- Tree link -->
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+
+ <!-- Project homepage -->
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+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
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+ </tr>
+</table>
+
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+ <!--
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+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/Collect_SILAC_XML.Usage-class.html b/docs/Collect_SILAC_XML.Usage-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..16f42d46945ed18bc94416cb58509d0a25eeb0b7
--- /dev/null
+++ b/docs/Collect_SILAC_XML.Usage-class.html
@@ -0,0 +1,250 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Collect_SILAC_XML.Usage</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
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+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="Collect_SILAC_XML-module.html">Module Collect_SILAC_XML</a> ::
+ Class Usage
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class Usage</h1><p class="nomargin-top"><span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#Usage">source code</a></span></p>
+<pre class="base-tree">
+ object --+
+ |
+exceptions.BaseException --+
+ |
+ exceptions.Exception --+
+ |
+ <strong class="uidshort">Usage</strong>
+</pre>
+
+<hr />
+<p>used for catching exceptions generated during command line parameter
+ parsing</p>
+
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="Collect_SILAC_XML.Usage-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">msg</span>)</span><br />
+ x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#Usage.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>exceptions.Exception</code></b>:
+ <code>__new__</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>exceptions.BaseException</code></b>:
+ <code>__delattr__</code>,
+ <code>__getattribute__</code>,
+ <code>__getitem__</code>,
+ <code>__getslice__</code>,
+ <code>__reduce__</code>,
+ <code>__repr__</code>,
+ <code>__setattr__</code>,
+ <code>__setstate__</code>,
+ <code>__str__</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
+ <code>__hash__</code>,
+ <code>__reduce_ex__</code>
+ </p>
+ </td>
+ </tr>
+</table>
+<!-- ==================== PROPERTIES ==================== -->
+<a name="section-Properties"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Properties</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Properties"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>exceptions.BaseException</code></b>:
+ <code>args</code>,
+ <code>message</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
+ <code>__class__</code>
+ </p>
+ </td>
+ </tr>
+</table>
+<!-- ==================== METHOD DETAILS ==================== -->
+<a name="section-MethodDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Method Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-MethodDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="__init__"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">msg</span>)</span>
+ <br /><em class="fname">(Constructor)</em>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="Collect_SILAC_XML-pysrc.html#Usage.__init__">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>x.__init__(...) initializes x; see x.__class__.__doc__ for
+ signature</p>
+ <dl class="fields">
+ <dt>Overrides:
+ object.__init__
+ <dd><em class="note">(inherited documentation)</em></dd>
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/MSFit_to_txt-module.html b/docs/MSFit_to_txt-module.html
new file mode 100644
index 0000000000000000000000000000000000000000..2a06d25cf53f0013bb858bcdab841f6d46153ceb
--- /dev/null
+++ b/docs/MSFit_to_txt-module.html
@@ -0,0 +1,294 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>MSFit_to_txt</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module MSFit_to_txt
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== MODULE DESCRIPTION ==================== -->
+<h1 class="epydoc">Module MSFit_to_txt</h1><p class="nomargin-top"><span class="codelink"><a href="MSFit_to_txt-pysrc.html">source code</a></span></p>
+<p>MSFit to Table v 0.2</p>
+ <p>New version, based on HTMLparser</p>
+ <p>A tool with GUI to collect data from a series of MSFit HTML
+ identification files in a unique table</p>
+ <p>Written using wxPython in Python, August 2004, Cosmin Modified to be
+ more general and flexible, Sept 2004 Included the HTML parser in the
+ script, 2008-04-29</p>
+ <p>Alain Jacquier's laboratory, Institut Pasteur, Paris, France</p>
+ <p>INSTRUCTIONS:</p>
+ <p>Place the files with .html or .htm extension in a folder From the File
+ menu select Choose directory... You will be able to see a list of the
+ html files in your directory</p>
+ <p>From the File menu choose Collect to..., the global file will be saved
+ under the name you specify.</p>
+
+<!-- ==================== CLASSES ==================== -->
+<a name="section-Classes"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Classes</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Classes"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="MSFit_to_txt.MSFit32ParserProt-class.html" class="summary-name">MSFit32ParserProt</a><br />
+ A parser for MSFit HTML results to obtain a dictionary of data
+ corresponding to the page Only protein information is retained
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="MSFit_to_txt.MainFrame-class.html" class="summary-name">MainFrame</a>
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTIONS ==================== -->
+<a name="section-Functions"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Functions</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Functions"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="Read_Dir"></a><span class="summary-sig-name">Read_Dir</span>(<span class="summary-sig-arg">dirname</span>)</span><br />
+ Recover information for all the files in a folder, recursively
+ Collect data in a list of complete path names, returned</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#Read_Dir">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="WriteListToFile"></a><span class="summary-sig-name">WriteListToFile</span>(<span class="summary-sig-arg">filename</span>,
+ <span class="summary-sig-arg">outlist</span>)</span><br />
+ Writes a list of lists to a tab delimited text file</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#WriteListToFile">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== VARIABLES ==================== -->
+<a name="section-Variables"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Variables</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Variables"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="pepseqRE"></a><span class="summary-name">pepseqRE</span> = <code title="r"sequence=([A-Z]+)\*?\\"">r"sequence=([A-Z]+)\*?\\"</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="peplinePATT"></a><span class="summary-name">peplinePATT</span> = <code title="re.compile(pepseqRE)">re.compile(pepseqRE)</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="pepseqmodRE"></a><span class="summary-name">pepseqmodRE</span> = <code title="r"\)([A-Z]+)\*?\("">r"\)([A-Z]+)\*?\("</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="peplinePATTmod"></a><span class="summary-name">peplinePATTmod</span> = <code title="re.compile(pepseqmodRE)">re.compile(pepseqmodRE)</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_ABOUT"></a><span class="summary-name">ID_ABOUT</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_EXIT"></a><span class="summary-name">ID_EXIT</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_COLLECTTO"></a><span class="summary-name">ID_COLLECTTO</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_CHOOSEDIR"></a><span class="summary-name">ID_CHOOSEDIR</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="app"></a><span class="summary-name">app</span> = <code title="wx.PySimpleApp()">wx.PySimpleApp()</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="frame"></a><span class="summary-name">frame</span> = <code title="MainFrame(None,-1, "MSFit to txt v. 0.2")">MainFrame(None,-1, "MSFit to txt v. 0.2")</code>
+ </td>
+ </tr>
+</table>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/MSFit_to_txt-pysrc.html b/docs/MSFit_to_txt-pysrc.html
new file mode 100644
index 0000000000000000000000000000000000000000..09b5fc57e393be5b58f0c950a0cf89e12d5d2421
--- /dev/null
+++ b/docs/MSFit_to_txt-pysrc.html
@@ -0,0 +1,481 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>MSFit_to_txt</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module MSFit_to_txt
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<h1 class="epydoc">Source Code for <a href="MSFit_to_txt-module.html">Module MSFit_to_txt</a></h1>
+<pre class="py-src">
+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env pythonw</tt> </tt>
+<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""</tt> </tt>
+<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">MSFit to Table v 0.2</tt> </tt>
+<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">New version, based on HTMLparser</tt> </tt>
+<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">A tool with GUI to collect data from </tt> </tt>
+<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">a series of MSFit HTML identification files</tt> </tt>
+<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">in a unique table</tt> </tt>
+<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Written using wxPython in Python, August 2004, Cosmin</tt> </tt>
+<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Modified to be more general and flexible, Sept 2004</tt> </tt>
+<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">Included the HTML parser in the script, 2008-04-29</tt> </tt>
+<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">Alain Jacquier's laboratory, Institut Pasteur, Paris, France</tt> </tt>
+<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">INSTRUCTIONS:</tt> </tt>
+<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">Place the files with .html or .htm extension in a folder</tt> </tt>
+<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">From the File menu select Choose directory...</tt> </tt>
+<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">You will be able to see a list of the html files in your directory</tt> </tt>
+<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">From the File menu choose Collect to..., the global file will</tt> </tt>
+<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">be saved under the name you specify.</tt> </tt>
+<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
+<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">string</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt> </tt>
+<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">string</tt> <tt class="py-keyword">import</tt> <tt class="py-name">lstrip</tt><tt class="py-op">,</tt> <tt class="py-name">rstrip</tt> </tt>
+<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment">#from MsFitHTMLparse02 import MSFit32ParserProt #now included</tt> </tt>
+<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt class="py-name">HTMLParser</tt> <tt class="py-keyword">import</tt> <tt class="py-name">HTMLParser</tt> </tt>
+<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
+<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable MSFit_to_txt.pepseqRE=MSFit_to_txt-module.html#pepseqRE,Variable lilamsxml.pepseqRE=lilamsxml-module.html#pepseqRE"><a title="MSFit_to_txt.pepseqRE
+lilamsxml.pepseqRE" class="py-name" href="#" onclick="return doclink('link-0', 'pepseqRE', 'link-0');">pepseqRE</a></tt> <tt class="py-op">=</tt> <tt class="py-string">r"sequence=([A-Z]+)\*?\\"</tt> </tt>
+<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable MSFit_to_txt.peplinePATT=MSFit_to_txt-module.html#peplinePATT,Variable lilamsxml.peplinePATT=lilamsxml-module.html#peplinePATT"><a title="MSFit_to_txt.peplinePATT
+lilamsxml.peplinePATT" class="py-name" href="#" onclick="return doclink('link-1', 'peplinePATT', 'link-1');">peplinePATT</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt id="link-2" class="py-name"><a title="MSFit_to_txt.pepseqRE
+lilamsxml.pepseqRE" class="py-name" href="#" onclick="return doclink('link-2', 'pepseqRE', 'link-0');">pepseqRE</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable MSFit_to_txt.pepseqmodRE=MSFit_to_txt-module.html#pepseqmodRE,Variable lilamsxml.pepseqmodRE=lilamsxml-module.html#pepseqmodRE"><a title="MSFit_to_txt.pepseqmodRE
+lilamsxml.pepseqmodRE" class="py-name" href="#" onclick="return doclink('link-3', 'pepseqmodRE', 'link-3');">pepseqmodRE</a></tt> <tt class="py-op">=</tt> <tt class="py-string">r"\)([A-Z]+)\*?\("</tt> </tt>
+<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable MSFit_to_txt.peplinePATTmod=MSFit_to_txt-module.html#peplinePATTmod,Variable lilamsxml.peplinePATTmod=lilamsxml-module.html#peplinePATTmod"><a title="MSFit_to_txt.peplinePATTmod
+lilamsxml.peplinePATTmod" class="py-name" href="#" onclick="return doclink('link-4', 'peplinePATTmod', 'link-4');">peplinePATTmod</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="MSFit_to_txt.pepseqmodRE
+lilamsxml.pepseqmodRE" class="py-name" href="#" onclick="return doclink('link-5', 'pepseqmodRE', 'link-3');">pepseqmodRE</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
+<a name="MSFit32ParserProt"></a><div id="MSFit32ParserProt-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="MSFit32ParserProt-toggle" onclick="return toggle('MSFit32ParserProt');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="MSFit_to_txt.MSFit32ParserProt-class.html">MSFit32ParserProt</a><tt class="py-op">(</tt><tt class="py-base-class">HTMLParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32ParserProt-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MSFit32ParserProt-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> A parser for MSFit HTML results to obtain a</tt> </tt>
+<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> dictionary of data corresponding to the page</tt> </tt>
+<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> Only protein information is retained</tt> </tt>
+<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="MSFit32ParserProt.reset"></a><div id="MSFit32ParserProt.reset-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <a class="py-toggle" href="#" id="MSFit32ParserProt.reset-toggle" onclick="return toggle('MSFit32ParserProt.reset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MSFit32ParserProt-class.html#reset">reset</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32ParserProt.reset-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32ParserProt.reset-expanded"><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">HTMLParser</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method MSFit_to_txt.MSFit32ParserProt.reset()=MSFit_to_txt.MSFit32ParserProt-class.html#reset,Method lilamsxml.MSFit32Parser.reset()=lilamsxml.MSFit32Parser-class.html#reset"><a title="MSFit_to_txt.MSFit32ParserProt.reset
+lilamsxml.MSFit32Parser.reset" class="py-name" href="#" onclick="return doclink('link-6', 'reset', 'link-6');">reset</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
+<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-comment">#list of text contained between tags</tt> </tt>
+<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">comments</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-comment">#list of comment texts</tt> </tt>
+<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-comment">#true if the text to be handled</tt> </tt>
+<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#follows a comment</tt> </tt>
+<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accesionRE</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'> (.+)'</tt><tt class="py-op">)</tt> </tt>
+<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-comment">#allows extraction of ORF name from the first table</tt> </tt>
+<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-comment">#two variables to allow start of scanning for peptide sequences in file</tt> </tt>
+<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequence</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequencemod</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
+<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+</div><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-comment">#contains the list of sequences of all peptides</tt> </tt>
+<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="MSFit32ParserProt.handle_starttag"></a><div id="MSFit32ParserProt.handle_starttag-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="MSFit32ParserProt.handle_starttag-toggle" onclick="return toggle('MSFit32ParserProt.handle_starttag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_starttag">handle_starttag</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32ParserProt.handle_starttag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32ParserProt.handle_starttag-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-comment">#print tag, attrs</tt> </tt>
+<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
+</div><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
+<a name="MSFit32ParserProt.handle_comment"></a><div id="MSFit32ParserProt.handle_comment-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="MSFit32ParserProt.handle_comment-toggle" onclick="return toggle('MSFit32ParserProt.handle_comment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_comment">handle_comment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32ParserProt.handle_comment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32ParserProt.handle_comment-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> Overrides the handle_comment method</tt> </tt>
+<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> Builds a list of all the found comments</tt> </tt>
+<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> If a comment is found, the aftercomment</tt> </tt>
+<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> variable is set to True</tt> </tt>
+<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">comments</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">tag</tt><tt class="py-op">)</tt> </tt>
+<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+</div><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-comment">#if tag == 'delta_mass':</tt> </tt>
+<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.seeksequence = True</tt> </tt>
+<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
+<a name="MSFit32ParserProt.handle_data"></a><div id="MSFit32ParserProt.handle_data-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="MSFit32ParserProt.handle_data-toggle" onclick="return toggle('MSFit32ParserProt.handle_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_data">handle_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32ParserProt.handle_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32ParserProt.handle_data-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> Overrides the handle_data method</tt> </tt>
+<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> writes to a list the text following</tt> </tt>
+<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> any comment - modifies self.parsedlist</tt> </tt>
+<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-comment">#print "text", text</tt> </tt>
+<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt><tt class="py-op">:</tt> </tt>
+<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">cleantext</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-string">'\n\r ./'</tt><tt class="py-op">)</tt> </tt>
+<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">comments</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">cleantext</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-comment">#append the last comment and the text that follows</tt> </tt>
+<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-comment">#don't get any other value until the next comment</tt> </tt>
+<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#appears</tt> </tt>
+<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#however obtain the sequence of a peptide if we are in an in_mass tags</tt> </tt>
+<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
+</div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
+<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
+<a name="MSFit32ParserProt.get_dictionary"></a><div id="MSFit32ParserProt.get_dictionary-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="MSFit32ParserProt.get_dictionary-toggle" onclick="return toggle('MSFit32ParserProt.get_dictionary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MSFit32ParserProt-class.html#get_dictionary">get_dictionary</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32ParserProt.get_dictionary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32ParserProt.get_dictionary-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> Reorganizes data and treats some special cases</tt> </tt>
+<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> of data found after comment tags</tt> </tt>
+<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> Should be called after closing the parser</tt> </tt>
+<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">reccounter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">secreccounter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">list_out</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">list</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt> </tt>
+<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">details</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">passedrank1</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
+<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">list</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'rank'</tt><tt class="py-op">:</tt> </tt>
+<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">passedrank1</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op"><></tt> <tt class="py-string">'fraction_matched'</tt><tt class="py-op">:</tt> </tt>
+<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-comment">#we are not at the beginning of the details</tt> </tt>
+<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#sometimes proteins have equal ranks</tt> </tt>
+<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#we build the data dictionary for the identified proteins</tt> </tt>
+<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">reccounter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">{</tt><tt class="py-string">'protdata'</tt><tt class="py-op">:</tt><tt class="py-op">{</tt><tt class="py-string">'rank'</tt><tt class="py-op">:</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">}</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
+<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">details</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-comment">#we are at the beginning of the details</tt> </tt>
+<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">details</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">secreccounter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">details</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">passedrank1</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment">#not yet in details but passed the first rank tags</tt> </tt>
+<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#take care first of the accesion numbers</tt> </tt>
+<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'accession_number'</tt><tt class="py-op">:</tt> </tt>
+<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">matches</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accesionRE</tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">matches</tt><tt class="py-op">:</tt> </tt>
+<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">matches</tt><tt class="py-op">.</tt><tt class="py-name">groups</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">entries</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">reccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">details</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-comment">#we are in the details, we may build the peptide masses lists</tt> </tt>
+<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'protein_coverage'</tt><tt class="py-op">:</tt> </tt>
+<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">secreccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list_out</tt> </tt>
+</div></div><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
+<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment">###################################</tt> </tt>
+<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##### INTERFACE ###################</tt> </tt>
+<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###################################</tt> </tt>
+<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-op">[</tt><tt class="py-name">ID_CHOOSEDIR</tt><tt class="py-op">,</tt> </tt>
+<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-name">ID_COLLECTTO</tt><tt class="py-op">,</tt> </tt>
+<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> </tt>
+<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> </tt>
+<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">init_ctrls</tt><tt class="py-op">:</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">NewId</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
+<a name="Read_Dir"></a><div id="Read_Dir-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="Read_Dir-toggle" onclick="return toggle('Read_Dir');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt-module.html#Read_Dir">Read_Dir</a><tt class="py-op">(</tt><tt class="py-param">dirname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Read_Dir-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Read_Dir-expanded"><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> Recover information for all the files in a folder, recursively</tt> </tt>
+<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> Collect data in a list of complete path names, returned</tt> </tt>
+<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">filelist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">f</tt> </tt>
+<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt id="link-7" class="py-name" targets="Function MSFit_to_txt.Read_Dir()=MSFit_to_txt-module.html#Read_Dir"><a title="MSFit_to_txt.Read_Dir" class="py-name" href="#" onclick="return doclink('link-7', 'Read_Dir', 'link-7');">Read_Dir</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
+<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">extension</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">extension</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">".html"</tt><tt class="py-op">,</tt> <tt class="py-string">".htm"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">filelist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
+<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">filelist</tt> </tt>
+</div><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
+<a name="WriteListToFile"></a><div id="WriteListToFile-def"><a name="L166"></a><tt class="py-lineno">166</tt> <a class="py-toggle" href="#" id="WriteListToFile-toggle" onclick="return toggle('WriteListToFile');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt-module.html#WriteListToFile">WriteListToFile</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">outlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="WriteListToFile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WriteListToFile-expanded"><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> Writes a list of lists to a tab delimited text file</tt> </tt>
+<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">fout</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
+<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt class="py-name">outlist</tt><tt class="py-op">:</tt> </tt>
+<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">element</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entry</tt><tt class="py-op">:</tt> </tt>
+<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">fout</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">element</tt><tt class="py-op">+</tt><tt class="py-string">'\t'</tt><tt class="py-op">)</tt> </tt>
+<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">fout</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
+<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">fout</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
+</div><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
+<a name="MainFrame"></a><div id="MainFrame-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="MainFrame-toggle" onclick="return toggle('MainFrame');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="MSFit_to_txt.MainFrame-class.html">MainFrame</a><tt class="py-op">(</tt><tt class="py-base-class">wx</tt><tt class="py-op">.</tt><tt class="py-base-class">Frame</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MainFrame-expanded"><a name="MainFrame.__init__"></a><div id="MainFrame.__init__-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="MainFrame.__init__-toggle" onclick="return toggle('MainFrame.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MainFrame-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Frame</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Collect_SILAC_XML.Usage.__init__()=Collect_SILAC_XML.Usage-class.html#__init__,Method MSFit_to_txt.MainFrame.__init__()=MSFit_to_txt.MainFrame-class.html#__init__,Method lilamslaunchGUI.MainFrame.__init__()=lilamslaunchGUI.MainFrame-class.html#__init__,Method lilamsxml.DataIntObj.__init__()=lilamsxml.DataIntObj-class.html#__init__,Method lilamsxml.Usage.__init__()=lilamsxml.Usage-class.html#__init__,Method silacvalidator.MainFrame.__init__()=silacvalidator.MainFrame-class.html#__init__,Method silacvalidator.PepListCtrl.__init__()=silacvalidator.PepListCtrl-class.html#__init__,Method silacvalidator.PepListCtrlPanel.__init__()=silacvalidator.PepListCtrlPanel-class.html#__init__"><a title="Collect_SILAC_XML.Usage.__init__
+MSFit_to_txt.MainFrame.__init__
+lilamslaunchGUI.MainFrame.__init__
+lilamsxml.DataIntObj.__init__
+lilamsxml.Usage.__init__
+silacvalidator.MainFrame.__init__
+silacvalidator.PepListCtrl.__init__
+silacvalidator.PepListCtrlPanel.__init__" class="py-name" href="#" onclick="return doclink('link-8', '__init__', 'link-8');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt class="py-name">id</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">,</tt> </tt>
+<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultPosition</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">600</tt><tt class="py-op">,</tt> <tt class="py-number">600</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
+<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">temp_outfile</tt> <tt class="py-op">=</tt> <tt class="py-string">"temp_data"</tt> </tt>
+<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-string">"."</tt> </tt>
+<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt>
+<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment">#default directory for saving, will be modified after first save</tt> </tt>
+<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.maxy = 0</tt> </tt>
+<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-comment"># Create the menu bar and items</tt> </tt>
+<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MenuBar</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt>
+<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_CHOOSEDIR</tt><tt class="py-op">,</tt> <tt class="py-string">'Ch&oose folder...\tCtrl+O'</tt><tt class="py-op">,</tt> <tt class="py-string">'Choose folder with html MSFit files'</tt><tt class="py-op">)</tt> </tt>
+<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_COLLECTTO</tt><tt class="py-op">,</tt> <tt class="py-string">'Collec&t data to...\tCtrl+S'</tt><tt class="py-op">,</tt> <tt class="py-string">'Parse files and save data to the specified file'</tt><tt class="py-op">)</tt> </tt>
+<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> <tt class="py-string">'&Quit\tCtrl+Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'Exit program'</tt><tt class="py-op">)</tt> </tt>
+<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
+<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">helpmenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">helpmenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> <tt class="py-string">'About...\tCtrl+H'</tt><tt class="py-op">,</tt> <tt class="py-string">'About this program'</tt><tt class="py-op">)</tt> </tt>
+<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
+<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-comment"># Bind the events to methods </tt> </tt>
+<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_CHOOSEDIR</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnChooseFolder()=MSFit_to_txt.MainFrame-class.html#OnChooseFolder"><a title="MSFit_to_txt.MainFrame.OnChooseFolder" class="py-name" href="#" onclick="return doclink('link-9', 'OnChooseFolder', 'link-9');">OnChooseFolder</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnFileExit()=MSFit_to_txt.MainFrame-class.html#OnFileExit,Method lilamslaunchGUI.MainFrame.OnFileExit()=lilamslaunchGUI.MainFrame-class.html#OnFileExit,Method silacvalidator.MainFrame.OnFileExit()=silacvalidator.MainFrame-class.html#OnFileExit"><a title="MSFit_to_txt.MainFrame.OnFileExit
+lilamslaunchGUI.MainFrame.OnFileExit
+silacvalidator.MainFrame.OnFileExit" class="py-name" href="#" onclick="return doclink('link-10', 'OnFileExit', 'link-10');">OnFileExit</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_COLLECTTO</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnCollectData()=MSFit_to_txt.MainFrame-class.html#OnCollectData"><a title="MSFit_to_txt.MainFrame.OnCollectData" class="py-name" href="#" onclick="return doclink('link-11', 'OnCollectData', 'link-11');">OnCollectData</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnHelpAbout()=MSFit_to_txt.MainFrame-class.html#OnHelpAbout,Method lilamslaunchGUI.MainFrame.OnHelpAbout()=lilamslaunchGUI.MainFrame-class.html#OnHelpAbout,Method silacvalidator.MainFrame.OnHelpAbout()=silacvalidator.MainFrame-class.html#OnHelpAbout"><a title="MSFit_to_txt.MainFrame.OnHelpAbout
+lilamslaunchGUI.MainFrame.OnHelpAbout
+silacvalidator.MainFrame.OnHelpAbout" class="py-name" href="#" onclick="return doclink('link-12', 'OnHelpAbout', 'link-12');">OnHelpAbout</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
+<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment"># Attach menus to the menubar</tt> </tt>
+<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">filemenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&File'</tt><tt class="py-op">)</tt> </tt>
+<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">helpmenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&Help'</tt><tt class="py-op">)</tt> </tt>
+<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
+<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">SetMenuBar</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">)</tt> </tt>
+<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
+<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-comment">#Disable by default the Save data as menu</tt> </tt>
+<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_COLLECTTO</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> </tt>
+<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">autoscale</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
+<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-comment"># A status bar to tell people what's happening</tt> </tt>
+<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">CreateStatusBar</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> </tt>
+<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ListCtrl</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LC_REPORT</tt><tt class="py-op">|</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">SUNKEN_BORDER</tt><tt class="py-op">)</tt> </tt>
+<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">lc</tt> </tt>
+<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumn</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"Number"</tt><tt class="py-op">)</tt> </tt>
+<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumn</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"File name"</tt><tt class="py-op">)</tt> </tt>
+<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">SetColumnWidth</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">100</tt><tt class="py-op">)</tt> </tt>
+<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">SetColumnWidth</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">400</tt><tt class="py-op">)</tt> </tt>
+<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Show</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnChooseFolder"></a><div id="MainFrame.OnChooseFolder-def"><a name="L231"></a><tt class="py-lineno">231</tt> <a class="py-toggle" href="#" id="MainFrame.OnChooseFolder-toggle" onclick="return toggle('MainFrame.OnChooseFolder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MainFrame-class.html#OnChooseFolder">OnChooseFolder</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnChooseFolder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnChooseFolder-expanded"><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-docstring"> Shows a directory select dialog, allows to set the self.defaultdirname</tt> </tt>
+<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"> to a value where data collection will occur, also enables the menu item</tt> </tt>
+<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"> corresponding to data collection.</tt> </tt>
+<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DirDialog</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name" targets="Variable MSFit_to_txt.frame=MSFit_to_txt-module.html#frame,Variable lilamslaunchGUI.frame=lilamslaunchGUI-module.html#frame,Variable silacvalidator.frame=silacvalidator-module.html#frame"><a title="MSFit_to_txt.frame
+lilamslaunchGUI.frame
+silacvalidator.frame" class="py-name" href="#" onclick="return doclink('link-13', 'frame', 'link-13');">frame</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Choose a folder with MSFit files:"</tt><tt class="py-op">,</tt> </tt>
+<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DD_DEFAULT_STYLE</tt><tt class="py-op">)</tt> </tt>
+<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-comment"># If the user selects OK, then we process the dialog's data.</tt> </tt>
+<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># This is done by getting the path data from the dialog - BEFORE</tt> </tt>
+<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># we destroy it. </tt> </tt>
+<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-comment">#log.WriteText('You selected: %s\n' % dlg.GetPath())</tt> </tt>
+<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetPath</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-comment"># Only destroy a dialog after you're done with it.</tt> </tt>
+<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_COLLECTTO</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="MSFit_to_txt.Read_Dir" class="py-name" href="#" onclick="return doclink('link-14', 'Read_Dir', 'link-7');">Read_Dir</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">)</tt> </tt>
+<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">DeleteAllItems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-comment">#self.txtout.WriteText("You chose "+self.defaultdirname+" that contains the following html files:\n\n")</tt> </tt>
+<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">counter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">filename</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">:</tt> </tt>
+<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">filepath</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">InsertStringItem</tt><tt class="py-op">(</tt><tt class="py-name">counter</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">counter</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">counter</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">filepath</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">counter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">SetStatusText</tt><tt class="py-op">(</tt><tt class="py-string">"Now choose where to save the output file (File>Collect data to...)"</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.ProcessFiles"></a><div id="MainFrame.ProcessFiles-def"><a name="L259"></a><tt class="py-lineno">259</tt> <a class="py-toggle" href="#" id="MainFrame.ProcessFiles-toggle" onclick="return toggle('MainFrame.ProcessFiles');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MainFrame-class.html#ProcessFiles">ProcessFiles</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filelist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.ProcessFiles-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.ProcessFiles-expanded"><a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">biglist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">outlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">progcounter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">progbar</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ProgressDialog</tt><tt class="py-op">(</tt><tt class="py-string">"Quantitating peptides..."</tt><tt class="py-op">,</tt> <tt class="py-string">"Working..."</tt><tt class="py-op">,</tt> </tt>
+<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">maximum</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">,</tt> </tt>
+<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">style</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">PD_CAN_ABORT</tt><tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">PD_APP_MODAL</tt><tt class="py-op">)</tt> </tt>
+<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">filelist</tt><tt class="py-op">:</tt> </tt>
+<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">shortname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
+<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">htmlpage</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">close</tt> </tt>
+<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
+<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Class MSFit_to_txt.MSFit32ParserProt=MSFit_to_txt.MSFit32ParserProt-class.html"><a title="MSFit_to_txt.MSFit32ParserProt" class="py-name" href="#" onclick="return doclink('link-15', 'MSFit32ParserProt', 'link-15');">MSFit32ParserProt</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">feed</tt><tt class="py-op">(</tt><tt class="py-name">htmlpage</tt><tt class="py-op">)</tt> </tt>
+<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> </tt>
+<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">biglist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method MSFit_to_txt.MSFit32ParserProt.get_dictionary()=MSFit_to_txt.MSFit32ParserProt-class.html#get_dictionary,Method lilamsxml.MSFit32Parser.get_dictionary()=lilamsxml.MSFit32Parser-class.html#get_dictionary"><a title="MSFit_to_txt.MSFit32ParserProt.get_dictionary
+lilamsxml.MSFit32Parser.get_dictionary" class="py-name" href="#" onclick="return doclink('link-16', 'get_dictionary', 'link-16');">get_dictionary</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
+<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">progbar</tt><tt class="py-op">.</tt><tt class="py-name">Update</tt><tt class="py-op">(</tt><tt class="py-name">progcounter</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">progcounter</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">" "</tt><tt class="py-op">+</tt><tt class="py-name">shortname</tt><tt class="py-op">+</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
+<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">progcounter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> </tt>
+<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
+<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-comment">#print len(biglist)</tt> </tt>
+<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">progbar</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
+<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entrieslist</tt> <tt class="py-keyword">in</tt> <tt class="py-name">biglist</tt><tt class="py-op">:</tt> </tt>
+<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-comment">#print entrieslist</tt> </tt>
+<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">dict</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entrieslist</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
+<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-comment">#print dict</tt> </tt>
+<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">outlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">entrieslist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'rank'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
+<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protein_coverage'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protein_mw'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
+<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protein_pI'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'accession_number'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
+<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'entry_name'</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">outlist</tt> </tt>
+</div><a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnCollectData"></a><div id="MainFrame.OnCollectData-def"><a name="L298"></a><tt class="py-lineno">298</tt> <a class="py-toggle" href="#" id="MainFrame.OnCollectData-toggle" onclick="return toggle('MainFrame.OnCollectData');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MainFrame-class.html#OnCollectData">OnCollectData</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnCollectData-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnCollectData-expanded"><a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> Save data to a specified text file (new)</tt> </tt>
+<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"Tab delimited text file (*.txt)|*.txt|"</tt>\ </tt>
+<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-string">"All files (*.*)|*.*"</tt> </tt>
+<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-comment">#might be os.getcwd()</tt> </tt>
+<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt> </tt>
+<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">message</tt><tt class="py-op">=</tt><tt class="py-string">"Save collected data as ..."</tt><tt class="py-op">,</tt> <tt class="py-name">defaultDir</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> </tt>
+<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-name">defaultFile</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">=</tt><tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">SAVE</tt> </tt>
+<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
+<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">SetFilterIndex</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-comment">#self.dirname=dlg.GetDirectory()</tt> </tt>
+<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.defaultdirname = self.dirname</tt> </tt>
+<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetPath</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-comment">#print "You selected", path </tt> </tt>
+<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-comment">#filelist = Read_Dir(self.defaultdirname)</tt> </tt>
+<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">outlist</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method MSFit_to_txt.MainFrame.ProcessFiles()=MSFit_to_txt.MainFrame-class.html#ProcessFiles"><a title="MSFit_to_txt.MainFrame.ProcessFiles" class="py-name" href="#" onclick="return doclink('link-17', 'ProcessFiles', 'link-17');">ProcessFiles</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">)</tt> </tt>
+<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt id="link-18" class="py-name" targets="Function MSFit_to_txt.WriteListToFile()=MSFit_to_txt-module.html#WriteListToFile"><a title="MSFit_to_txt.WriteListToFile" class="py-name" href="#" onclick="return doclink('link-18', 'WriteListToFile', 'link-18');">WriteListToFile</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">,</tt> <tt class="py-name">outlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> </tt>
+<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Error. Maybe the output file is in use..."</tt><tt class="py-op">,</tt> <tt class="py-string">'Problem saving data'</tt><tt class="py-op">,</tt> </tt>
+<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OK</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_INFORMATION</tt><tt class="py-op">)</tt> </tt>
+<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnHelpAbout"></a><div id="MainFrame.OnHelpAbout-def"><a name="L326"></a><tt class="py-lineno">326</tt> <a class="py-toggle" href="#" id="MainFrame.OnHelpAbout-toggle" onclick="return toggle('MainFrame.OnHelpAbout');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MainFrame-class.html#OnHelpAbout">OnHelpAbout</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnHelpAbout-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnHelpAbout-expanded"><a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt><tt class="py-op">.</tt><tt class="py-name">dialogs</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ScrolledMessageDialog</tt> </tt>
+<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">about</tt> <tt class="py-op">=</tt> <tt class="py-name">ScrolledMessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">__doc__</tt><tt class="py-op">,</tt> <tt class="py-string">"About..."</tt><tt class="py-op">)</tt> </tt>
+<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">about</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFileExit"></a><div id="MainFrame.OnFileExit-def"><a name="L331"></a><tt class="py-lineno">331</tt> <a class="py-toggle" href="#" id="MainFrame.OnFileExit-toggle" onclick="return toggle('MainFrame.OnFileExit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="MSFit_to_txt.MainFrame-class.html#OnFileExit">OnFileExit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnFileExit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnFileExit-expanded"><a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div></div><a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt>
+<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> </tt>
+<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt id="link-19" class="py-name" targets="Variable MSFit_to_txt.app=MSFit_to_txt-module.html#app,Variable lilamslaunchGUI.app=lilamslaunchGUI-module.html#app,Variable silacvalidator.app=silacvalidator-module.html#app"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-19', 'app', 'link-19');">app</a></tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">PySimpleApp</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt id="link-20" class="py-name"><a title="MSFit_to_txt.frame
+lilamslaunchGUI.frame
+silacvalidator.frame" class="py-name" href="#" onclick="return doclink('link-20', 'frame', 'link-13');">frame</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name" targets="Class MSFit_to_txt.MainFrame=MSFit_to_txt.MainFrame-class.html,Class lilamslaunchGUI.MainFrame=lilamslaunchGUI.MainFrame-class.html,Class silacvalidator.MainFrame=silacvalidator.MainFrame-class.html"><a title="MSFit_to_txt.MainFrame
+lilamslaunchGUI.MainFrame
+silacvalidator.MainFrame" class="py-name" href="#" onclick="return doclink('link-21', 'MainFrame', 'link-21');">MainFrame</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"MSFit to txt v. 0.2"</tt><tt class="py-op">)</tt> </tt>
+<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt id="link-22" class="py-name"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-22', 'app', 'link-19');">app</a></tt><tt class="py-op">.</tt><tt class="py-name">SetTopWindow</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="MSFit_to_txt.frame
+lilamslaunchGUI.frame
+silacvalidator.frame" class="py-name" href="#" onclick="return doclink('link-23', 'frame', 'link-13');">frame</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt id="link-24" class="py-name"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-24', 'app', 'link-19');">app</a></tt><tt class="py-op">.</tt><tt class="py-name">MainLoop</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> </tt><script type="text/javascript">
+<!--
+expandto(location.href);
+// -->
+</script>
+</pre>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:24 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/MSFit_to_txt.MSFit32ParserProt-class.html b/docs/MSFit_to_txt.MSFit32ParserProt-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..a69fd39c802eb3d9ca2d295066cf8e17687f14b7
--- /dev/null
+++ b/docs/MSFit_to_txt.MSFit32ParserProt-class.html
@@ -0,0 +1,409 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>MSFit_to_txt.MSFit32ParserProt</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="MSFit_to_txt-module.html">Module MSFit_to_txt</a> ::
+ Class MSFit32ParserProt
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class MSFit32ParserProt</h1><p class="nomargin-top"><span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt">source code</a></span></p>
+<pre class="base-tree">
+markupbase.ParserBase --+
+ |
+ HTMLParser.HTMLParser --+
+ |
+ <strong class="uidshort">MSFit32ParserProt</strong>
+</pre>
+
+<hr />
+<p>A parser for MSFit HTML results to obtain a dictionary of data
+ corresponding to the page Only protein information is retained</p>
+
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#reset" class="summary-sig-name">reset</a>(<span class="summary-sig-arg">self</span>)</span><br />
+ Reset this instance.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.reset">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_starttag" class="summary-sig-name">handle_starttag</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">tag</span>,
+ <span class="summary-sig-arg">attrs</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.handle_starttag">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_comment" class="summary-sig-name">handle_comment</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">tag</span>)</span><br />
+ Overrides the handle_comment method Builds a list of all the found
+ comments If a comment is found, the aftercomment variable is set to
+ True</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.handle_comment">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_data" class="summary-sig-name">handle_data</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">text</span>)</span><br />
+ Overrides the handle_data method writes to a list the text following
+ any comment - modifies self.parsedlist</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.handle_data">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="get_dictionary"></a><span class="summary-sig-name">get_dictionary</span>(<span class="summary-sig-arg">self</span>)</span><br />
+ Reorganizes data and treats some special cases of data found after
+ comment tags Should be called after closing the parser</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.get_dictionary">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>HTMLParser.HTMLParser</code></b>:
+ <code>__init__</code>,
+ <code>check_for_whole_start_tag</code>,
+ <code>clear_cdata_mode</code>,
+ <code>close</code>,
+ <code>error</code>,
+ <code>feed</code>,
+ <code>get_starttag_text</code>,
+ <code>goahead</code>,
+ <code>handle_charref</code>,
+ <code>handle_decl</code>,
+ <code>handle_endtag</code>,
+ <code>handle_entityref</code>,
+ <code>handle_pi</code>,
+ <code>handle_startendtag</code>,
+ <code>parse_endtag</code>,
+ <code>parse_pi</code>,
+ <code>parse_starttag</code>,
+ <code>set_cdata_mode</code>,
+ <code>unescape</code>,
+ <code>unknown_decl</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b>:
+ <code>getpos</code>,
+ <code>parse_comment</code>,
+ <code>parse_declaration</code>,
+ <code>parse_marked_section</code>,
+ <code>updatepos</code>
+ </p>
+ <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b> (private):
+ <code>_parse_doctype_attlist</code>,
+ <code>_parse_doctype_element</code>,
+ <code>_parse_doctype_entity</code>,
+ <code>_parse_doctype_notation</code>,
+ <code>_parse_doctype_subset</code>,
+ <code>_scan_name</code>
+ </p></div>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS VARIABLES ==================== -->
+<a name="section-ClassVariables"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Class Variables</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-ClassVariables"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>HTMLParser.HTMLParser</code></b>:
+ <code>CDATA_CONTENT_ELEMENTS</code>
+ </p>
+ <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b> (private):
+ <code>_decl_otherchars</code>
+ </p></div>
+ </td>
+ </tr>
+</table>
+<!-- ==================== METHOD DETAILS ==================== -->
+<a name="section-MethodDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Method Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-MethodDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="reset"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">reset</span>(<span class="sig-arg">self</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.reset">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Reset this instance. Loses all unprocessed data.</p>
+ <dl class="fields">
+ <dt>Overrides:
+ markupbase.ParserBase.reset
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<a name="handle_starttag"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">handle_starttag</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">tag</span>,
+ <span class="sig-arg">attrs</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.handle_starttag">source code</a></span>
+ </td>
+ </tr></table>
+
+
+ <dl class="fields">
+ <dt>Overrides:
+ HTMLParser.HTMLParser.handle_starttag
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<a name="handle_comment"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">handle_comment</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">tag</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.handle_comment">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Overrides the handle_comment method Builds a list of all the found
+ comments If a comment is found, the aftercomment variable is set to
+ True</p>
+ <dl class="fields">
+ <dt>Overrides:
+ HTMLParser.HTMLParser.handle_comment
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<a name="handle_data"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">handle_data</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">text</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="MSFit_to_txt-pysrc.html#MSFit32ParserProt.handle_data">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Overrides the handle_data method writes to a list the text following
+ any comment - modifies self.parsedlist</p>
+ <dl class="fields">
+ <dt>Overrides:
+ HTMLParser.HTMLParser.handle_data
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/MSFit_to_txt.MainFrame-class.html b/docs/MSFit_to_txt.MainFrame-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..92df2672bb65a11f0471a0734e53c8bfc1adc3a1
--- /dev/null
+++ b/docs/MSFit_to_txt.MainFrame-class.html
@@ -0,0 +1,237 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>MSFit_to_txt.MainFrame</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="MSFit_to_txt-module.html">Module MSFit_to_txt</a> ::
+ Class MainFrame
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class MainFrame</h1><p class="nomargin-top"><span class="codelink"><a href="MSFit_to_txt-pysrc.html#MainFrame">source code</a></span></p>
+<pre class="base-tree">
+wx.Frame --+
+ |
+ <strong class="uidshort">MainFrame</strong>
+</pre>
+
+<hr />
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">parent</span>,
+ <span class="summary-sig-arg">id</span>,
+ <span class="summary-sig-arg">title</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MainFrame.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnChooseFolder"></a><span class="summary-sig-name">OnChooseFolder</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Shows a directory select dialog, allows to set the
+ self.defaultdirname to a value where data collection will occur, also
+ enables the menu item corresponding to data collection.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MainFrame.OnChooseFolder">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="ProcessFiles"></a><span class="summary-sig-name">ProcessFiles</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">filelist</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MainFrame.ProcessFiles">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnCollectData"></a><span class="summary-sig-name">OnCollectData</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Save data to a specified text file (new)</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MainFrame.OnCollectData">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnHelpAbout"></a><span class="summary-sig-name">OnHelpAbout</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MainFrame.OnHelpAbout">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFileExit"></a><span class="summary-sig-name">OnFileExit</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="MSFit_to_txt-pysrc.html#MainFrame.OnFileExit">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/api-objects.txt b/docs/api-objects.txt
new file mode 100644
index 0000000000000000000000000000000000000000..83d4bcfcfd4ca9a5354fae5de5eefa2e9558c0e4
--- /dev/null
+++ b/docs/api-objects.txt
@@ -0,0 +1,158 @@
+Collect_SILAC_XML Collect_SILAC_XML-module.html
+Collect_SILAC_XML.StdDev Collect_SILAC_XML-module.html#StdDev
+Collect_SILAC_XML.XMLdict Collect_SILAC_XML-module.html#XMLdict
+Collect_SILAC_XML.get_flist Collect_SILAC_XML-module.html#get_flist
+Collect_SILAC_XML.ExtractSILACDataFromXML Collect_SILAC_XML-module.html#ExtractSILACDataFromXML
+Collect_SILAC_XML.Median Collect_SILAC_XML-module.html#Median
+Collect_SILAC_XML.SumSquares Collect_SILAC_XML-module.html#SumSquares
+Collect_SILAC_XML.GetValXML Collect_SILAC_XML-module.html#GetValXML
+Collect_SILAC_XML.CalcStatistics Collect_SILAC_XML-module.html#CalcStatistics
+Collect_SILAC_XML.Variance Collect_SILAC_XML-module.html#Variance
+Collect_SILAC_XML.main Collect_SILAC_XML-module.html#main
+Collect_SILAC_XML.GenerateListDict Collect_SILAC_XML-module.html#GenerateListDict
+Collect_SILAC_XML.Mean Collect_SILAC_XML-module.html#Mean
+MSFit_to_txt MSFit_to_txt-module.html
+MSFit_to_txt.frame MSFit_to_txt-module.html#frame
+MSFit_to_txt.peplinePATT MSFit_to_txt-module.html#peplinePATT
+MSFit_to_txt.peplinePATTmod MSFit_to_txt-module.html#peplinePATTmod
+MSFit_to_txt.WriteListToFile MSFit_to_txt-module.html#WriteListToFile
+MSFit_to_txt.Read_Dir MSFit_to_txt-module.html#Read_Dir
+MSFit_to_txt.app MSFit_to_txt-module.html#app
+MSFit_to_txt.pepseqmodRE MSFit_to_txt-module.html#pepseqmodRE
+MSFit_to_txt.pepseqRE MSFit_to_txt-module.html#pepseqRE
+lilamslaunchGUI lilamslaunchGUI-module.html
+lilamslaunchGUI.ReadFromFile lilamslaunchGUI-module.html#ReadFromFile
+lilamslaunchGUI.frame lilamslaunchGUI-module.html#frame
+lilamslaunchGUI.app lilamslaunchGUI-module.html#app
+lilamsxml lilamsxml-module.html
+lilamsxml.WriteMToFile lilamsxml-module.html#WriteMToFile
+lilamsxml.GetPeak lilamsxml-module.html#GetPeak
+lilamsxml.PepCompare lilamsxml-module.html#PepCompare
+lilamsxml.GetIsotopeSeries lilamsxml-module.html#GetIsotopeSeries
+lilamsxml.WriteMToString lilamsxml-module.html#WriteMToString
+lilamsxml.RunIPC lilamsxml-module.html#RunIPC
+lilamsxml.MzIntGet lilamsxml-module.html#MzIntGet
+lilamsxml.peplinePATTmod lilamsxml-module.html#peplinePATTmod
+lilamsxml.CrowlToMax lilamsxml-module.html#CrowlToMax
+lilamsxml.GetBackground lilamsxml-module.html#GetBackground
+lilamsxml.StdDev lilamsxml-module.html#StdDev
+lilamsxml.main lilamsxml-module.html#main
+lilamsxml.CalcMonoMz lilamsxml-module.html#CalcMonoMz
+lilamsxml.pepseqmodRE lilamsxml-module.html#pepseqmodRE
+lilamsxml.ParseMSFIT lilamsxml-module.html#ParseMSFIT
+lilamsxml.ReadFromFileFloats lilamsxml-module.html#ReadFromFileFloats
+lilamsxml.Median lilamsxml-module.html#Median
+lilamsxml.pepseqRE lilamsxml-module.html#pepseqRE
+lilamsxml.IsDifference lilamsxml-module.html#IsDifference
+lilamsxml.ProcessSpectrum lilamsxml-module.html#ProcessSpectrum
+lilamsxml.Variance lilamsxml-module.html#Variance
+lilamsxml.Mean lilamsxml-module.html#Mean
+lilamsxml.WriteListToString lilamsxml-module.html#WriteListToString
+lilamsxml.SumSquares lilamsxml-module.html#SumSquares
+lilamsxml.peplinePATT lilamsxml-module.html#peplinePATT
+lilamsxml.CorrectIsotopicSeries lilamsxml-module.html#CorrectIsotopicSeries
+lilamsxml.GetPeaksFromValue lilamsxml-module.html#GetPeaksFromValue
+silacvalidator silacvalidator-module.html
+silacvalidator.getSmallUpArrowData silacvalidator-module.html#getSmallUpArrowData
+silacvalidator.map_pos_inlist silacvalidator-module.html#map_pos_inlist
+silacvalidator.get_flist_xml silacvalidator-module.html#get_flist_xml
+silacvalidator.app silacvalidator-module.html#app
+silacvalidator.frame silacvalidator-module.html#frame
+silacvalidator.get_flist_txt silacvalidator-module.html#get_flist_txt
+silacvalidator.getSmallDnArrowImage silacvalidator-module.html#getSmallDnArrowImage
+silacvalidator.getSmallUpArrowBitmap silacvalidator-module.html#getSmallUpArrowBitmap
+silacvalidator.getSmallDnArrowBitmap silacvalidator-module.html#getSmallDnArrowBitmap
+silacvalidator.msg silacvalidator-module.html#msg
+silacvalidator.getSmallDnArrowData silacvalidator-module.html#getSmallDnArrowData
+silacvalidator.getSmallUpArrowImage silacvalidator-module.html#getSmallUpArrowImage
+silacvalidator.ReadFromFileArray silacvalidator-module.html#ReadFromFileArray
+Collect_SILAC_XML.Usage Collect_SILAC_XML.Usage-class.html
+Collect_SILAC_XML.Usage.__init__ Collect_SILAC_XML.Usage-class.html#__init__
+MSFit_to_txt.MSFit32ParserProt MSFit_to_txt.MSFit32ParserProt-class.html
+MSFit_to_txt.MSFit32ParserProt.handle_starttag MSFit_to_txt.MSFit32ParserProt-class.html#handle_starttag
+MSFit_to_txt.MSFit32ParserProt.handle_comment MSFit_to_txt.MSFit32ParserProt-class.html#handle_comment
+MSFit_to_txt.MSFit32ParserProt.reset MSFit_to_txt.MSFit32ParserProt-class.html#reset
+MSFit_to_txt.MSFit32ParserProt.get_dictionary MSFit_to_txt.MSFit32ParserProt-class.html#get_dictionary
+MSFit_to_txt.MSFit32ParserProt.handle_data MSFit_to_txt.MSFit32ParserProt-class.html#handle_data
+MSFit_to_txt.MainFrame MSFit_to_txt.MainFrame-class.html
+MSFit_to_txt.MainFrame.OnChooseFolder MSFit_to_txt.MainFrame-class.html#OnChooseFolder
+MSFit_to_txt.MainFrame.OnFileExit MSFit_to_txt.MainFrame-class.html#OnFileExit
+MSFit_to_txt.MainFrame.ProcessFiles MSFit_to_txt.MainFrame-class.html#ProcessFiles
+MSFit_to_txt.MainFrame.OnHelpAbout MSFit_to_txt.MainFrame-class.html#OnHelpAbout
+MSFit_to_txt.MainFrame.OnCollectData MSFit_to_txt.MainFrame-class.html#OnCollectData
+MSFit_to_txt.MainFrame.__init__ MSFit_to_txt.MainFrame-class.html#__init__
+lilamslaunchGUI.MainFrame lilamslaunchGUI.MainFrame-class.html
+lilamslaunchGUI.MainFrame.OnGo lilamslaunchGUI.MainFrame-class.html#OnGo
+lilamslaunchGUI.MainFrame.OnFileOpenORFs lilamslaunchGUI.MainFrame-class.html#OnFileOpenORFs
+lilamslaunchGUI.MainFrame.OnFileExit lilamslaunchGUI.MainFrame-class.html#OnFileExit
+lilamslaunchGUI.MainFrame.__init__ lilamslaunchGUI.MainFrame-class.html#__init__
+lilamslaunchGUI.MainFrame.OnHelpAbout lilamslaunchGUI.MainFrame-class.html#OnHelpAbout
+lilamslaunchGUI.MainFrame.OnFileOpenPairs lilamslaunchGUI.MainFrame-class.html#OnFileOpenPairs
+lilamslaunchGUI.MainFrame.OnLilamsChoose lilamslaunchGUI.MainFrame-class.html#OnLilamsChoose
+lilamslaunchGUI.MainFrame.OnIPCChoose lilamslaunchGUI.MainFrame-class.html#OnIPCChoose
+lilamsxml.DataIntObj lilamsxml.DataIntObj-class.html
+lilamsxml.DataIntObj.calc_statistics lilamsxml.DataIntObj-class.html#calc_statistics
+lilamsxml.DataIntObj.get_data lilamsxml.DataIntObj-class.html#get_data
+lilamsxml.DataIntObj.calc_ratios lilamsxml.DataIntObj-class.html#calc_ratios
+lilamsxml.DataIntObj.filter_peaks lilamsxml.DataIntObj-class.html#filter_peaks
+lilamsxml.DataIntObj.return_resultsXML lilamsxml.DataIntObj-class.html#return_resultsXML
+lilamsxml.DataIntObj.__init__ lilamsxml.DataIntObj-class.html#__init__
+lilamsxml.DataIntObj.return_results lilamsxml.DataIntObj-class.html#return_results
+lilamsxml.MSFit32Parser lilamsxml.MSFit32Parser-class.html
+lilamsxml.MSFit32Parser.handle_starttag lilamsxml.MSFit32Parser-class.html#handle_starttag
+lilamsxml.MSFit32Parser.handle_comment lilamsxml.MSFit32Parser-class.html#handle_comment
+lilamsxml.MSFit32Parser.reset lilamsxml.MSFit32Parser-class.html#reset
+lilamsxml.MSFit32Parser.get_dictionary lilamsxml.MSFit32Parser-class.html#get_dictionary
+lilamsxml.MSFit32Parser.handle_data lilamsxml.MSFit32Parser-class.html#handle_data
+lilamsxml.Usage lilamsxml.Usage-class.html
+lilamsxml.Usage.__init__ lilamsxml.Usage-class.html#__init__
+silacvalidator.MainFrame silacvalidator.MainFrame-class.html
+silacvalidator.MainFrame.OnInvalidate silacvalidator.MainFrame-class.html#OnInvalidate
+silacvalidator.MainFrame.PlotFile silacvalidator.MainFrame-class.html#PlotFile
+silacvalidator.MainFrame.OnMDoubleClick silacvalidator.MainFrame-class.html#OnMDoubleClick
+silacvalidator.MainFrame.OnXMLSave silacvalidator.MainFrame-class.html#OnXMLSave
+silacvalidator.MainFrame.GetValXML silacvalidator.MainFrame-class.html#GetValXML
+silacvalidator.MainFrame.OnEnableGrid silacvalidator.MainFrame-class.html#OnEnableGrid
+silacvalidator.MainFrame.PlotSpectrumXML silacvalidator.MainFrame-class.html#PlotSpectrumXML
+silacvalidator.MainFrame.OnHelpAbout silacvalidator.MainFrame-class.html#OnHelpAbout
+silacvalidator.MainFrame.OnSpectrumSave silacvalidator.MainFrame-class.html#OnSpectrumSave
+silacvalidator.MainFrame.SetXMLValidated silacvalidator.MainFrame-class.html#SetXMLValidated
+silacvalidator.MainFrame.PlotArray silacvalidator.MainFrame-class.html#PlotArray
+silacvalidator.MainFrame.__init__ silacvalidator.MainFrame-class.html#__init__
+silacvalidator.MainFrame.OnSetLocalBg silacvalidator.MainFrame-class.html#OnSetLocalBg
+silacvalidator.MainFrame.XMLOpen silacvalidator.MainFrame-class.html#XMLOpen
+silacvalidator.MainFrame.resetDefaults silacvalidator.MainFrame-class.html#resetDefaults
+silacvalidator.MainFrame.OnXMLOpen silacvalidator.MainFrame-class.html#OnXMLOpen
+silacvalidator.MainFrame.OnSaveImage silacvalidator.MainFrame-class.html#OnSaveImage
+silacvalidator.MainFrame.OnFileClose silacvalidator.MainFrame-class.html#OnFileClose
+silacvalidator.MainFrame.OnFileExit silacvalidator.MainFrame-class.html#OnFileExit
+silacvalidator.MainFrame.OnPlotClear silacvalidator.MainFrame-class.html#OnPlotClear
+silacvalidator.MainFrame.OnFileOpen silacvalidator.MainFrame-class.html#OnFileOpen
+silacvalidator.MainFrame.GenerateListDict silacvalidator.MainFrame-class.html#GenerateListDict
+silacvalidator.MainFrame.OnReset silacvalidator.MainFrame-class.html#OnReset
+silacvalidator.MainFrame.OnEnableLegend silacvalidator.MainFrame-class.html#OnEnableLegend
+silacvalidator.MainFrame.OnPlotScale silacvalidator.MainFrame-class.html#OnPlotScale
+silacvalidator.MainFrame.OnEnableZoom silacvalidator.MainFrame-class.html#OnEnableZoom
+silacvalidator.MainFrame.MapUniqueKey silacvalidator.MainFrame-class.html#MapUniqueKey
+silacvalidator.MainFrame.OnValidate silacvalidator.MainFrame-class.html#OnValidate
+silacvalidator.MainFrame.OnMLeftDown silacvalidator.MainFrame-class.html#OnMLeftDown
+silacvalidator.MainFrame.OnItemSelected silacvalidator.MainFrame-class.html#OnItemSelected
+silacvalidator.MainFrame.OnNextFile silacvalidator.MainFrame-class.html#OnNextFile
+silacvalidator.MainFrame.SpectrumSave silacvalidator.MainFrame-class.html#SpectrumSave
+silacvalidator.MainFrame.OnPlotRedraw silacvalidator.MainFrame-class.html#OnPlotRedraw
+silacvalidator.MainFrame.OnFullUnzoom silacvalidator.MainFrame-class.html#OnFullUnzoom
+silacvalidator.MainFrame.OnPrevFile silacvalidator.MainFrame-class.html#OnPrevFile
+silacvalidator.MainFrame.PopulateList silacvalidator.MainFrame-class.html#PopulateList
+silacvalidator.PepListCtrl silacvalidator.PepListCtrl-class.html
+silacvalidator.PepListCtrl.__init__ silacvalidator.PepListCtrl-class.html#__init__
+silacvalidator.PepListCtrlPanel silacvalidator.PepListCtrlPanel-class.html
+silacvalidator.PepListCtrlPanel.getColumnText silacvalidator.PepListCtrlPanel-class.html#getColumnText
+silacvalidator.PepListCtrlPanel.SetBg silacvalidator.PepListCtrlPanel-class.html#SetBg
+silacvalidator.PepListCtrlPanel.OnItemSelected silacvalidator.PepListCtrlPanel-class.html#OnItemSelected
+silacvalidator.PepListCtrlPanel.OnColClick silacvalidator.PepListCtrlPanel-class.html#OnColClick
+silacvalidator.PepListCtrlPanel.OnSize silacvalidator.PepListCtrlPanel-class.html#OnSize
+silacvalidator.PepListCtrlPanel.GetListCtrl silacvalidator.PepListCtrlPanel-class.html#GetListCtrl
+silacvalidator.PepListCtrlPanel.PopulateList silacvalidator.PepListCtrlPanel-class.html#PopulateList
+silacvalidator.PepListCtrlPanel.__init__ silacvalidator.PepListCtrlPanel-class.html#__init__
+silacvalidator.PepListCtrlPanel.GetSortImages silacvalidator.PepListCtrlPanel-class.html#GetSortImages
+silacvalidator.PepListCtrlPanel.SetValidated silacvalidator.PepListCtrlPanel-class.html#SetValidated
diff --git a/docs/class-tree.html b/docs/class-tree.html
new file mode 100644
index 0000000000000000000000000000000000000000..ddf6a27f73449342a576a50aa199e6e0adc17971
--- /dev/null
+++ b/docs/class-tree.html
@@ -0,0 +1,153 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Class Hierarchy</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Trees </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%"> </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<center><b>
+ [ <a href="module-tree.html">Module Hierarchy</a>
+ | <a href="class-tree.html">Class Hierarchy</a> ]
+</b></center><br />
+<h1 class="epydoc">Class Hierarchy</h1>
+<ul class="nomargin-top">
+ <li> <strong class="uidlink">wx.lib.mixins.listctrl.ColumnSorterMixin</strong>:
+ <em class="summary">A mixin class that handles sorting of a wx.ListCtrl in REPORT mode
+ when the column header is clicked on.</em>
+ </li>
+ <li> <strong class="uidlink"><a href="lilamsxml.DataIntObj-class.html">lilamsxml.DataIntObj</a></strong>:
+ <em class="summary">A data structure to handle SILAC difference results and calculate
+ statistics</em>
+ </li>
+ <li> <strong class="uidlink">wx.lib.plot.wx.Frame</strong>
+ </li>
+ <li> <strong class="uidlink">wx.Frame</strong>
+ </li>
+ <li> <strong class="uidlink">wx.Frame</strong>
+ </li>
+ <li> <strong class="uidlink">wx.lib.plot.wx.ListCtrl</strong>
+ </li>
+ <li> <strong class="uidlink">wx.lib.mixins.listctrl.ListCtrlAutoWidthMixin</strong>:
+ <em class="summary">A mix-in class that automatically resizes the last column to take up
+the remaining width of the wx.ListCtrl.</em>
+ </li>
+ <li> <strong class="uidlink">wx.lib.plot.wx.Panel</strong>
+ </li>
+ <li> <strong class="uidlink">markupbase.ParserBase</strong>:
+ <em class="summary">Parser base class which provides some common support methods used
+ by the SGML/HTML and XHTML parsers.</em>
+ </li>
+ <li> <strong class="uidlink">object</strong>:
+ <em class="summary">The most base type</em>
+ <ul>
+ <li> <strong class="uidlink">exceptions.BaseException</strong>:
+ <em class="summary">Common base class for all exceptions</em>
+ <ul>
+ <li> <strong class="uidlink">exceptions.Exception</strong>:
+ <em class="summary">Common base class for all non-exit exceptions.</em>
+ <ul>
+ <li> <strong class="uidlink"><a href="Collect_SILAC_XML.Usage-class.html">Collect_SILAC_XML.Usage</a></strong>:
+ <em class="summary">used for catching exceptions generated during command line
+ parameter parsing</em>
+ </li>
+ <li> <strong class="uidlink"><a href="lilamsxml.Usage-class.html">lilamsxml.Usage</a></strong>:
+ <em class="summary">used for catching exceptions generated during command line
+ parameter parsing</em>
+ </li>
+ </ul>
+ </li>
+ </ul>
+ </li>
+ </ul>
+ </li>
+</ul>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Trees </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/crarr.png b/docs/crarr.png
new file mode 100644
index 0000000000000000000000000000000000000000..26b43c52433b71e72a9a478c52d446278335f0e4
Binary files /dev/null and b/docs/crarr.png differ
diff --git a/docs/epydoc.conf b/docs/epydoc.conf
new file mode 100644
index 0000000000000000000000000000000000000000..84f0be85e0ec3eeccad1a41dc568a2bd9ea111f1
--- /dev/null
+++ b/docs/epydoc.conf
@@ -0,0 +1,100 @@
+[epydoc] # Epydoc section marker (required by ConfigParser)
+
+# Information about the project.
+name: Lilams docs
+
+# The list of modules to document. Modules can be named using
+# dotted names, module filenames, or package directory names.
+# This option may be repeated.
+modules: ../src/lilamslaunchGUI.py, ../src/lilamsxml.py, ../src/silacvalidator.py, ../src/Collect_SILAC_XML.py, ../src/MSFit_to_txt.py
+
+# Write html output to the directory "docs", Should be one
+# of: html, text, latex, dvi, ps, pdf.
+output: html
+target: ../docs/
+
+# docformat
+# The default markup language for docstrings, for modules that do
+# not define __docformat__. Defaults to epytext.
+docformat: epytext
+
+# css
+# The CSS stylesheet for HTML output. Can be the name of a builtin
+# stylesheet, or the name of a file.
+css: white
+
+# url
+# The documented project's URL.
+url: http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html
+
+# link
+# HTML code for the project link in the navigation bar. If left
+# unspecified, the project link will be generated based on the
+# project's name and URL.
+#link: <a href="somewhere">My Cool Project</a>
+
+# top
+# The "top" page for the documentation. Can be a URL, the name
+# of a module or class, or one of the special names "trees.html",
+# "indices.html", or "help.html"
+top: help.html
+
+# help
+# An alternative help file. The named file should contain the
+# body of an HTML file; navigation bars will be added to it.
+#help: helpfile.html
+
+# frames
+# Whether or not to include a frames-based table of contents.
+frames: no
+
+# private
+# Whether or not to inclue private variables. (Even if included,
+# private variables will be hidden by default.)
+private: yes
+
+# imports
+# Whether or not to list each module's imports.
+#imports: yes
+
+# verbosity
+# An integer indicating how verbose epydoc should be. The default
+# value is 0; negative values will supress warnings and errors;
+# positive values will give more verbose output.
+verbosity: 0
+
+# parse
+# Whether or not parsing should be used to examine objects.
+parse: yes
+
+# introspect
+# Whether or not introspection should be used to examine objects.
+introspect: no
+
+# graph
+# The list of graph types that should be automatically included
+# in the output. Graphs are generated using the Graphviz "dot"
+# executable. Graph types include: "classtree", "callgraph",
+# "umlclass". Use "all" to include all graph types
+# graph: all
+
+# dotpath
+# The path to the Graphviz "dot" executable, used to generate
+# graphs.
+#dotpath: /usr/local/bin/dot
+#dotpath: /Volumes/Apps/Graphviz.app/Contents/MacOS/dot
+
+# sourcecode
+# Whether or not to include syntax highlighted source code in
+# the output (HTML only).
+sourcecode: yes
+
+# pstat
+# The name of one or more pstat files (generated by the profile
+# or hotshot module). These are used to generate call graphs.
+pstat: profile.out
+
+# separate-classes
+# Whether each class should be listed in its own section when
+# generating LaTeX or PDF output.
+separate-classes: no
diff --git a/docs/epydoc.css b/docs/epydoc.css
new file mode 100644
index 0000000000000000000000000000000000000000..86d417068248fa6aad14b794b0b8614764b1e454
--- /dev/null
+++ b/docs/epydoc.css
@@ -0,0 +1,322 @@
+
+
+/* Epydoc CSS Stylesheet
+ *
+ * This stylesheet can be used to customize the appearance of epydoc's
+ * HTML output.
+ *
+ */
+
+/* Default Colors & Styles
+ * - Set the default foreground & background color with 'body'; and
+ * link colors with 'a:link' and 'a:visited'.
+ * - Use bold for decision list terms.
+ * - The heading styles defined here are used for headings *within*
+ * docstring descriptions. All headings used by epydoc itself use
+ * either class='epydoc' or class='toc' (CSS styles for both
+ * defined below).
+ */
+body { background: #ffffff; color: #000000; }
+p { margin-top: 0.5em; margin-bottom: 0.5em; }
+a:link { color: #0000ff; }
+a:visited { color: #204080; }
+dt { font-weight: bold; }
+h1 { font-size: +140%; font-style: italic;
+ font-weight: bold; }
+h2 { font-size: +125%; font-style: italic;
+ font-weight: bold; }
+h3 { font-size: +110%; font-style: italic;
+ font-weight: normal; }
+code { font-size: 100%; }
+/* N.B.: class, not pseudoclass */
+a.link { font-family: monospace; }
+
+/* Page Header & Footer
+ * - The standard page header consists of a navigation bar (with
+ * pointers to standard pages such as 'home' and 'trees'); a
+ * breadcrumbs list, which can be used to navigate to containing
+ * classes or modules; options links, to show/hide private
+ * variables and to show/hide frames; and a page title (using
+ * <h1>). The page title may be followed by a link to the
+ * corresponding source code (using 'span.codelink').
+ * - The footer consists of a navigation bar, a timestamp, and a
+ * pointer to epydoc's homepage.
+ */
+h1.epydoc { margin: 0; font-size: +140%; font-weight: bold; }
+h2.epydoc { font-size: +130%; font-weight: bold; }
+h3.epydoc { font-size: +115%; font-weight: bold;
+ margin-top: 0.2em; }
+td h3.epydoc { font-size: +115%; font-weight: bold;
+ margin-bottom: 0; }
+table.navbar { background: #a0c0ff; color: #000000;
+ border: 2px groove #c0d0d0; }
+table.navbar table { color: #000000; }
+th.navbar-select { background: #70b0ff;
+ color: #000000; }
+table.navbar a { text-decoration: none; }
+table.navbar a:link { color: #0000ff; }
+table.navbar a:visited { color: #204080; }
+span.breadcrumbs { font-size: 85%; font-weight: bold; }
+span.options { font-size: 70%; }
+span.codelink { font-size: 85%; }
+td.footer { font-size: 85%; }
+
+/* Table Headers
+ * - Each summary table and details section begins with a 'header'
+ * row. This row contains a section title (marked by
+ * 'span.table-header') as well as a show/hide private link
+ * (marked by 'span.options', defined above).
+ * - Summary tables that contain user-defined groups mark those
+ * groups using 'group header' rows.
+ */
+td.table-header { background: #70b0ff; color: #000000;
+ border: 1px solid #608090; }
+td.table-header table { color: #000000; }
+td.table-header table a:link { color: #0000ff; }
+td.table-header table a:visited { color: #204080; }
+span.table-header { font-size: 120%; font-weight: bold; }
+th.group-header { background: #c0e0f8; color: #000000;
+ text-align: left; font-style: italic;
+ font-size: 115%;
+ border: 1px solid #608090; }
+
+/* Summary Tables (functions, variables, etc)
+ * - Each object is described by a single row of the table with
+ * two cells. The left cell gives the object's type, and is
+ * marked with 'code.summary-type'. The right cell gives the
+ * object's name and a summary description.
+ * - CSS styles for the table's header and group headers are
+ * defined above, under 'Table Headers'
+ */
+table.summary { border-collapse: collapse;
+ background: #e8f0f8; color: #000000;
+ border: 1px solid #608090;
+ margin-bottom: 0.5em; }
+td.summary { border: 1px solid #608090; }
+code.summary-type { font-size: 85%; }
+table.summary a:link { color: #0000ff; }
+table.summary a:visited { color: #204080; }
+
+
+/* Details Tables (functions, variables, etc)
+ * - Each object is described in its own div.
+ * - A single-row summary table w/ table-header is used as
+ * a header for each details section (CSS style for table-header
+ * is defined above, under 'Table Headers').
+ */
+table.details { border-collapse: collapse;
+ background: #e8f0f8; color: #000000;
+ border: 1px solid #608090;
+ margin: .2em 0 0 0; }
+table.details table { color: #000000; }
+table.details a:link { color: #0000ff; }
+table.details a:visited { color: #204080; }
+
+/* Fields */
+dl.fields { margin-left: 2em; margin-top: 1em;
+ margin-bottom: 1em; }
+dl.fields dd ul { margin-left: 0em; padding-left: 0em; }
+dl.fields dd ul li ul { margin-left: 2em; padding-left: 0em; }
+div.fields { margin-left: 2em; }
+div.fields p { margin-bottom: 0.5em; }
+
+/* Index tables (identifier index, term index, etc)
+ * - link-index is used for indices containing lists of links
+ * (namely, the identifier index & term index).
+ * - index-where is used in link indices for the text indicating
+ * the container/source for each link.
+ * - metadata-index is used for indices containing metadata
+ * extracted from fields (namely, the bug index & todo index).
+ */
+table.link-index { border-collapse: collapse;
+ background: #e8f0f8; color: #000000;
+ border: 1px solid #608090; }
+td.link-index { border-width: 0px; }
+table.link-index a:link { color: #0000ff; }
+table.link-index a:visited { color: #204080; }
+span.index-where { font-size: 70%; }
+table.metadata-index { border-collapse: collapse;
+ background: #e8f0f8; color: #000000;
+ border: 1px solid #608090;
+ margin: .2em 0 0 0; }
+td.metadata-index { border-width: 1px; border-style: solid; }
+table.metadata-index a:link { color: #0000ff; }
+table.metadata-index a:visited { color: #204080; }
+
+/* Function signatures
+ * - sig* is used for the signature in the details section.
+ * - .summary-sig* is used for the signature in the summary
+ * table, and when listing property accessor functions.
+ * */
+.sig-name { color: #006080; }
+.sig-arg { color: #008060; }
+.sig-default { color: #602000; }
+.summary-sig { font-family: monospace; }
+.summary-sig-name { color: #006080; font-weight: bold; }
+table.summary a.summary-sig-name:link
+ { color: #006080; font-weight: bold; }
+table.summary a.summary-sig-name:visited
+ { color: #006080; font-weight: bold; }
+.summary-sig-arg { color: #006040; }
+.summary-sig-default { color: #501800; }
+
+/* Subclass list
+ */
+ul.subclass-list { display: inline; }
+ul.subclass-list li { display: inline; }
+
+/* To render variables, classes etc. like functions */
+table.summary .summary-name { color: #006080; font-weight: bold;
+ font-family: monospace; }
+table.summary
+ a.summary-name:link { color: #006080; font-weight: bold;
+ font-family: monospace; }
+table.summary
+ a.summary-name:visited { color: #006080; font-weight: bold;
+ font-family: monospace; }
+
+/* Variable values
+ * - In the 'variable details' sections, each varaible's value is
+ * listed in a 'pre.variable' box. The width of this box is
+ * restricted to 80 chars; if the value's repr is longer than
+ * this it will be wrapped, using a backslash marked with
+ * class 'variable-linewrap'. If the value's repr is longer
+ * than 3 lines, the rest will be ellided; and an ellipsis
+ * marker ('...' marked with 'variable-ellipsis') will be used.
+ * - If the value is a string, its quote marks will be marked
+ * with 'variable-quote'.
+ * - If the variable is a regexp, it is syntax-highlighted using
+ * the re* CSS classes.
+ */
+pre.variable { padding: .5em; margin: 0;
+ background: #dce4ec; color: #000000;
+ border: 1px solid #708890; }
+.variable-linewrap { color: #604000; font-weight: bold; }
+.variable-ellipsis { color: #604000; font-weight: bold; }
+.variable-quote { color: #604000; font-weight: bold; }
+.variable-group { color: #008000; font-weight: bold; }
+.variable-op { color: #604000; font-weight: bold; }
+.variable-string { color: #006030; }
+.variable-unknown { color: #a00000; font-weight: bold; }
+.re { color: #000000; }
+.re-char { color: #006030; }
+.re-op { color: #600000; }
+.re-group { color: #003060; }
+.re-ref { color: #404040; }
+
+/* Base tree
+ * - Used by class pages to display the base class hierarchy.
+ */
+pre.base-tree { font-size: 80%; margin: 0; }
+
+/* Frames-based table of contents headers
+ * - Consists of two frames: one for selecting modules; and
+ * the other listing the contents of the selected module.
+ * - h1.toc is used for each frame's heading
+ * - h2.toc is used for subheadings within each frame.
+ */
+h1.toc { text-align: center; font-size: 105%;
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+ margin: 0.5em 0 0 -0.3em; }
+
+/* Syntax Highlighting for Source Code
+ * - doctest examples are displayed in a 'pre.py-doctest' block.
+ * If the example is in a details table entry, then it will use
+ * the colors specified by the 'table pre.py-doctest' line.
+ * - Source code listings are displayed in a 'pre.py-src' block.
+ * Each line is marked with 'span.py-line' (used to draw a line
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+ * The expand/collapse block toggle button is displayed with
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+ * modify the font size of the text.)
+ * - If a source code page is opened with an anchor, then the
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+.py-param { color: #000060; }
+.py-docstring { color: #006030; }
+.py-decorator { color: #804020; }
+/* Use this if you don't want links to names underlined: */
+/*a.py-name { text-decoration: none; }*/
+
+/* Graphs & Diagrams
+ * - These CSS styles are used for graphs & diagrams generated using
+ * Graphviz dot. 'img.graph-without-title' is used for bare
+ * diagrams (to remove the border created by making the image
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+ */
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+img.graph-with-title { border: 1px solid #000000; }
+span.graph-title { font-weight: bold; }
+span.graph-caption { }
+
+/* General-purpose classes
+ * - 'p.indent-wrapped-lines' defines a paragraph whose first line
+ * is not indented, but whose subsequent lines are.
+ * - The 'nomargin-top' class is used to remove the top margin (e.g.
+ * from lists). The 'nomargin' class is used to remove both the
+ * top and bottom margin (but not the left or right margin --
+ * for lists, that would cause the bullets to disappear.)
+ */
+p.indent-wrapped-lines { padding: 0 0 0 7em; text-indent: -7em;
+ margin: 0; }
+.nomargin-top { margin-top: 0; }
+.nomargin { margin-top: 0; margin-bottom: 0; }
+
+/* HTML Log */
+div.log-block { padding: 0; margin: .5em 0 .5em 0;
+ background: #e8f0f8; color: #000000;
+ border: 1px solid #000000; }
+div.log-error { padding: .1em .3em .1em .3em; margin: 4px;
+ background: #ffb0b0; color: #000000;
+ border: 1px solid #000000; }
+div.log-warning { padding: .1em .3em .1em .3em; margin: 4px;
+ background: #ffffb0; color: #000000;
+ border: 1px solid #000000; }
+div.log-info { padding: .1em .3em .1em .3em; margin: 4px;
+ background: #b0ffb0; color: #000000;
+ border: 1px solid #000000; }
+h2.log-hdr { background: #70b0ff; color: #000000;
+ margin: 0; padding: 0em 0.5em 0em 0.5em;
+ border-bottom: 1px solid #000000; font-size: 110%; }
+p.log { font-weight: bold; margin: .5em 0 .5em 0; }
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index 0000000000000000000000000000000000000000..e787dbcf4718f1b897de64c7749ed98969031b4c
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+ }
+ // Update all table rows containing private objects. Note, we
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+ // this should be (block vs table-row), and "" just gives the
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+ }
+ }
+ // Update all list items containing private objects.
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+ if (elt) { elt.innerHTML = "-"; }
+}
+
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+ if (elt) elt.style.display = "none";
+ var elt = document.getElementById(id+"-collapsed-linenums");
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+ var elt = document.getElementById(id+"-toggle");
+ if (elt) { elt.innerHTML = "+"; }
+ var elt = document.getElementById(id+"-collapsed");
+ if (elt) {
+ elt.style.display = "block";
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+ var indent = elt.getAttribute("indent");
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+ var s = "<tt class='py-lineno'>";
+ for (var i=0; i<pad.length; i++) { s += " " }
+ s += "</tt>";
+ s += " <tt class='py-line'>";
+ for (var i=0; i<indent.length; i++) { s += " " }
+ s += "<a href='#' onclick='expand(\"" + id;
+ s += "\");return false'>...</a></tt><br />";
+ elt.innerHTML = s;
+ }
+}
+
+function toggle(id) {
+ elt = document.getElementById(id+"-toggle");
+ if (elt.innerHTML == "-")
+ collapse(id);
+ else
+ expand(id);
+ return false;
+}
+
+function highlight(id) {
+ var elt = document.getElementById(id+"-def");
+ if (elt) elt.className = "py-highlight-hdr";
+ var elt = document.getElementById(id+"-expanded");
+ if (elt) elt.className = "py-highlight";
+ var elt = document.getElementById(id+"-collapsed");
+ if (elt) elt.className = "py-highlight";
+}
+
+function num_lines(s) {
+ var n = 1;
+ var pos = s.indexOf("\n");
+ while ( pos > 0) {
+ n += 1;
+ pos = s.indexOf("\n", pos+1);
+ }
+ return n;
+}
+
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+ var elts = document.getElementsByTagName("div");
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+ var elt = elts[i];
+ var split = elt.id.indexOf("-");
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+ if (num_lines(elt.innerHTML) > min_lines)
+ collapse(elt.id.substring(0, split));
+ }
+}
+
+function expandto(href) {
+ var start = href.indexOf("#")+1;
+ if (start != 0 && start != href.length) {
+ if (href.substring(start, href.length) != "-") {
+ collapse_all(4);
+ pos = href.indexOf(".", start);
+ while (pos != -1) {
+ var id = href.substring(start, pos);
+ expand(id);
+ pos = href.indexOf(".", pos+1);
+ }
+ var id = href.substring(start, href.length);
+ expand(id);
+ highlight(id);
+ }
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+}
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+ parent.removeChild(parent.childNodes.item(0));
+ }
+}
+
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+ var elt = document.getElementById(id);
+
+ // If we already opened the box, then destroy it.
+ // (This case should never occur, but leave it in just in case.)
+ if (elt.childNodes.length > 1) {
+ elt.removeChild(elt.childNodes.item(0));
+ }
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+ var box1 = document.createElement("div");
+ box1.style.position = "relative";
+ box1.style.display = "inline";
+ box1.style.top = 0;
+ box1.style.left = 0;
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+ shadow.style.position = "absolute";
+ shadow.style.left = "-1.3em";
+ shadow.style.top = "-1.3em";
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+ box2.style.border = "1px solid #a0a0a0";
+ box2.style.left = "-.2em";
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+ box2.style.background = "white";
+ box2.style.padding = ".3em .4em .3em .4em";
+ box2.style.fontStyle = "normal";
+ box2.onmouseout=auto_kill_doclink;
+ box2.parentID = id;
+
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+ var targets_elt = document.getElementById(targets_id);
+ var targets = targets_elt.getAttribute("targets");
+ var links = "";
+ target_list = targets.split(",");
+ for (var i=0; i<target_list.length; i++) {
+ var target = target_list[i].split("=");
+ links += "<li><a href='" + target[1] +
+ "' style='text-decoration:none'>" +
+ target[0] + "</a></li>";
+ }
+
+ // Put it all together.
+ elt.insertBefore(box1, elt.childNodes.item(0));
+ //box1.appendChild(box2);
+ box1.appendChild(shadow);
+ shadow.appendChild(box2);
+ box2.innerHTML =
+ "Which <b>"+name+"</b> do you want to see documentation for?" +
+ "<ul style='margin-bottom: 0;'>" +
+ links +
+ "<li><a href='#' style='text-decoration:none' " +
+ "onclick='kill_doclink(\""+id+"\");return false;'>"+
+ "<i>None of the above</i></a></li></ul>";
+ }
+ return false;
+}
+
+function get_anchor() {
+ var href = location.href;
+ var start = href.indexOf("#")+1;
+ if ((start != 0) && (start != href.length))
+ return href.substring(start, href.length);
+ }
+function redirect_url(dottedName) {
+ // Scan through each element of the "pages" list, and check
+ // if "name" matches with any of them.
+ for (var i=0; i<pages.length; i++) {
+
+ // Each page has the form "<pagename>-m" or "<pagename>-c";
+ // extract the <pagename> portion & compare it to dottedName.
+ var pagename = pages[i].substring(0, pages[i].length-2);
+ if (pagename == dottedName.substring(0,pagename.length)) {
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+ // We've found a page that matches `dottedName`;
+ // construct its URL, using leftover `dottedName`
+ // content to form an anchor.
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+ if (dottedName.length > pagename.length)
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diff --git a/docs/help.html b/docs/help.html
new file mode 100644
index 0000000000000000000000000000000000000000..af0493adada22703cb25c0ae6722878b91d24b28
--- /dev/null
+++ b/docs/help.html
@@ -0,0 +1,268 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Help</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Help </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%"> </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+
+<h1 class="epydoc"> API Documentation </h1>
+
+<p> This document contains the API (Application Programming Interface)
+documentation for Lilams docs. Documentation for the Python
+objects defined by the project is divided into separate pages for each
+package, module, and class. The API documentation also includes two
+pages containing information about the project as a whole: a trees
+page, and an index page. </p>
+
+<h2> Object Documentation </h2>
+
+ <p>Each <strong>Package Documentation</strong> page contains: </p>
+ <ul>
+ <li> A description of the package. </li>
+ <li> A list of the modules and sub-packages contained by the
+ package. </li>
+ <li> A summary of the classes defined by the package. </li>
+ <li> A summary of the functions defined by the package. </li>
+ <li> A summary of the variables defined by the package. </li>
+ <li> A detailed description of each function defined by the
+ package. </li>
+ <li> A detailed description of each variable defined by the
+ package. </li>
+ </ul>
+
+ <p>Each <strong>Module Documentation</strong> page contains:</p>
+ <ul>
+ <li> A description of the module. </li>
+ <li> A summary of the classes defined by the module. </li>
+ <li> A summary of the functions defined by the module. </li>
+ <li> A summary of the variables defined by the module. </li>
+ <li> A detailed description of each function defined by the
+ module. </li>
+ <li> A detailed description of each variable defined by the
+ module. </li>
+ </ul>
+
+ <p>Each <strong>Class Documentation</strong> page contains: </p>
+ <ul>
+ <li> A class inheritance diagram. </li>
+ <li> A list of known subclasses. </li>
+ <li> A description of the class. </li>
+ <li> A summary of the methods defined by the class. </li>
+ <li> A summary of the instance variables defined by the class. </li>
+ <li> A summary of the class (static) variables defined by the
+ class. </li>
+ <li> A detailed description of each method defined by the
+ class. </li>
+ <li> A detailed description of each instance variable defined by the
+ class. </li>
+ <li> A detailed description of each class (static) variable defined
+ by the class. </li>
+ </ul>
+
+<h2> Project Documentation </h2>
+
+ <p> The <strong>Trees</strong> page contains the module and class hierarchies: </p>
+ <ul>
+ <li> The <em>module hierarchy</em> lists every package and module, with
+ modules grouped into packages. At the top level, and within each
+ package, modules and sub-packages are listed alphabetically. </li>
+ <li> The <em>class hierarchy</em> lists every class, grouped by base
+ class. If a class has more than one base class, then it will be
+ listed under each base class. At the top level, and under each base
+ class, classes are listed alphabetically. </li>
+ </ul>
+
+ <p> The <strong>Index</strong> page contains indices of terms and
+ identifiers: </p>
+ <ul>
+ <li> The <em>term index</em> lists every term indexed by any object's
+ documentation. For each term, the index provides links to each
+ place where the term is indexed. </li>
+ <li> The <em>identifier index</em> lists the (short) name of every package,
+ module, class, method, function, variable, and parameter. For each
+ identifier, the index provides a short description, and a link to
+ its documentation. </li>
+ </ul>
+
+<h2> The Table of Contents </h2>
+
+<p> The table of contents occupies the two frames on the left side of
+the window. The upper-left frame displays the <em>project
+contents</em>, and the lower-left frame displays the <em>module
+contents</em>: </p>
+
+<table class="help summary" border="1" cellspacing="0" cellpadding="3">
+ <tr style="height: 30%">
+ <td align="center" style="font-size: small">
+ Project<br />Contents<hr />...</td>
+ <td align="center" style="font-size: small" rowspan="2" width="70%">
+ API<br />Documentation<br />Frame<br /><br /><br />
+ </td>
+ </tr>
+ <tr>
+ <td align="center" style="font-size: small">
+ Module<br />Contents<hr /> <br />...<br />
+ </td>
+ </tr>
+</table><br />
+
+<p> The <strong>project contents frame</strong> contains a list of all packages
+and modules that are defined by the project. Clicking on an entry
+will display its contents in the module contents frame. Clicking on a
+special entry, labeled "Everything," will display the contents of
+the entire project. </p>
+
+<p> The <strong>module contents frame</strong> contains a list of every
+submodule, class, type, exception, function, and variable defined by a
+module or package. Clicking on an entry will display its
+documentation in the API documentation frame. Clicking on the name of
+the module, at the top of the frame, will display the documentation
+for the module itself. </p>
+
+<p> The "<strong>frames</strong>" and "<strong>no frames</strong>" buttons below the top
+navigation bar can be used to control whether the table of contents is
+displayed or not. </p>
+
+<h2> The Navigation Bar </h2>
+
+<p> A navigation bar is located at the top and bottom of every page.
+It indicates what type of page you are currently viewing, and allows
+you to go to related pages. The following table describes the labels
+on the navigation bar. Note that not some labels (such as
+[Parent]) are not displayed on all pages. </p>
+
+<table class="summary" border="1" cellspacing="0" cellpadding="3" width="100%">
+<tr class="summary">
+ <th>Label</th>
+ <th>Highlighted when...</th>
+ <th>Links to...</th>
+</tr>
+ <tr><td valign="top"><strong>[Parent]</strong></td>
+ <td valign="top"><em>(never highlighted)</em></td>
+ <td valign="top"> the parent of the current package </td></tr>
+ <tr><td valign="top"><strong>[Package]</strong></td>
+ <td valign="top">viewing a package</td>
+ <td valign="top">the package containing the current object
+ </td></tr>
+ <tr><td valign="top"><strong>[Module]</strong></td>
+ <td valign="top">viewing a module</td>
+ <td valign="top">the module containing the current object
+ </td></tr>
+ <tr><td valign="top"><strong>[Class]</strong></td>
+ <td valign="top">viewing a class </td>
+ <td valign="top">the class containing the current object</td></tr>
+ <tr><td valign="top"><strong>[Trees]</strong></td>
+ <td valign="top">viewing the trees page</td>
+ <td valign="top"> the trees page </td></tr>
+ <tr><td valign="top"><strong>[Index]</strong></td>
+ <td valign="top">viewing the index page</td>
+ <td valign="top"> the index page </td></tr>
+ <tr><td valign="top"><strong>[Help]</strong></td>
+ <td valign="top">viewing the help page</td>
+ <td valign="top"> the help page </td></tr>
+</table>
+
+<p> The "<strong>show private</strong>" and "<strong>hide private</strong>" buttons below
+the top navigation bar can be used to control whether documentation
+for private objects is displayed. Private objects are usually defined
+as objects whose (short) names begin with a single underscore, but do
+not end with an underscore. For example, "<code>_x</code>",
+"<code>__pprint</code>", and "<code>epydoc.epytext._tokenize</code>"
+are private objects; but "<code>re.sub</code>",
+"<code>__init__</code>", and "<code>type_</code>" are not. However,
+if a module defines the "<code>__all__</code>" variable, then its
+contents are used to decide which objects are private. </p>
+
+<p> A timestamp below the bottom navigation bar indicates when each
+page was last updated. </p>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Help </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/identifier-index.html b/docs/identifier-index.html
new file mode 100644
index 0000000000000000000000000000000000000000..1ef89151970ded219ff01ac4148caa20e42784ce
--- /dev/null
+++ b/docs/identifier-index.html
@@ -0,0 +1,694 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Identifier Index</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Indices </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%"> </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<table border="0" width="100%">
+<tr valign="bottom"><td>
+<h1 class="epydoc">Identifier Index</h1>
+</td><td>
+[
+ <a href="#A">A</a>
+ B
+ <a href="#C">C</a>
+ <a href="#D">D</a>
+ <a href="#E">E</a>
+ <a href="#F">F</a>
+ <a href="#G">G</a>
+ <a href="#H">H</a>
+ <a href="#I">I</a>
+ J
+ K
+ <a href="#L">L</a>
+ <a href="#M">M</a>
+ N
+ <a href="#O">O</a>
+ <a href="#P">P</a>
+ Q
+ <a href="#R">R</a>
+ <a href="#S">S</a>
+ T
+ <a href="#U">U</a>
+ <a href="#V">V</a>
+ <a href="#W">W</a>
+ <a href="#X">X</a>
+ Y
+ Z
+ <a href="#_">_</a>
+]
+</td></table>
+<table border="0" width="100%">
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="A">A</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#app">app</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI-module.html#app">app</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI-module.html">lilamslaunchGUI</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#app">app</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="C">C</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html#calc_ratios">calc_ratios()</a><br />
+<span class="index-where">(in <a href="lilamsxml.DataIntObj-class.html">DataIntObj</a>)</span></td>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#CalcStatistics">CalcStatistics()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#CrowlToMax">CrowlToMax()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html#calc_statistics">calc_statistics()</a><br />
+<span class="index-where">(in <a href="lilamsxml.DataIntObj-class.html">DataIntObj</a>)</span></td>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#CalcMonoMz">CalcMonoMz()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#CorrectIsotopicSeries">CorrectIsotopicSeries()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="D">D</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html">DataIntObj</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="E">E</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#ExtractSILACDataFromXML">ExtractSILACDataFromXML()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="F">F</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html#filter_peaks">filter_peaks()</a><br />
+<span class="index-where">(in <a href="lilamsxml.DataIntObj-class.html">DataIntObj</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI-module.html#frame">frame</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI-module.html">lilamslaunchGUI</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#frame">frame</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#frame">frame</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="G">G</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#GenerateListDict">GenerateListDict()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#GetBackground">GetBackground()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#getSmallDnArrowImage">getSmallDnArrowImage()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#GenerateListDict">GenerateListDict()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#getColumnText">getColumnText()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#getSmallUpArrowBitmap">getSmallUpArrowBitmap()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html#get_data">get_data()</a><br />
+<span class="index-where">(in <a href="lilamsxml.DataIntObj-class.html">DataIntObj</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#GetIsotopeSeries">GetIsotopeSeries()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#getSmallUpArrowData">getSmallUpArrowData()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#get_dictionary">get_dictionary()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MSFit32ParserProt-class.html">MSFit32ParserProt</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#GetListCtrl">GetListCtrl()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#getSmallUpArrowImage">getSmallUpArrowImage()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml.MSFit32Parser-class.html#get_dictionary">get_dictionary()</a><br />
+<span class="index-where">(in <a href="lilamsxml.MSFit32Parser-class.html">MSFit32Parser</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#GetPeak">GetPeak()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#GetSortImages">GetSortImages()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#get_flist">get_flist()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#GetPeaksFromValue">GetPeaksFromValue()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#GetValXML">GetValXML()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#get_flist_txt">get_flist_txt()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#getSmallDnArrowBitmap">getSmallDnArrowBitmap()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#GetValXML">GetValXML()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#get_flist_xml">get_flist_xml()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#getSmallDnArrowData">getSmallDnArrowData()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="H">H</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_comment">handle_comment()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MSFit32ParserProt-class.html">MSFit32ParserProt</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_data">handle_data()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MSFit32ParserProt-class.html">MSFit32ParserProt</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#handle_starttag">handle_starttag()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MSFit32ParserProt-class.html">MSFit32ParserProt</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml.MSFit32Parser-class.html#handle_comment">handle_comment()</a><br />
+<span class="index-where">(in <a href="lilamsxml.MSFit32Parser-class.html">MSFit32Parser</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.MSFit32Parser-class.html#handle_data">handle_data()</a><br />
+<span class="index-where">(in <a href="lilamsxml.MSFit32Parser-class.html">MSFit32Parser</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.MSFit32Parser-class.html#handle_starttag">handle_starttag()</a><br />
+<span class="index-where">(in <a href="lilamsxml.MSFit32Parser-class.html">MSFit32Parser</a>)</span></td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="I">I</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#IsDifference">IsDifference()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="L">L</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI-module.html">lilamslaunchGUI</a></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html">lilamsxml</a></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="M">M</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#main">main()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#MapUniqueKey">MapUniqueKey()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MSFit32ParserProt-class.html">MSFit32ParserProt</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#main">main()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#Mean">Mean()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html">MSFit_to_txt</a></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MainFrame-class.html">MainFrame</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#Mean">Mean()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#msg">msg</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI-module.html">lilamslaunchGUI</a>)</span></td>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#Median">Median()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#MzIntGet">MzIntGet()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html">MainFrame</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#Median">Median()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#map_pos_inlist">map_pos_inlist()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.MSFit32Parser-class.html">MSFit32Parser</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="O">O</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MainFrame-class.html#OnChooseFolder">OnChooseFolder()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnFullUnzoom">OnFullUnzoom()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnPlotClear">OnPlotClear()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#OnColClick">OnColClick()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#OnGo">OnGo()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnPlotRedraw">OnPlotRedraw()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MainFrame-class.html#OnCollectData">OnCollectData()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MainFrame-class.html#OnHelpAbout">OnHelpAbout()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnPlotScale">OnPlotScale()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnEnableGrid">OnEnableGrid()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#OnHelpAbout">OnHelpAbout()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnPrevFile">OnPrevFile()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnEnableLegend">OnEnableLegend()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnHelpAbout">OnHelpAbout()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnReset">OnReset()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnEnableZoom">OnEnableZoom()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnInvalidate">OnInvalidate()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnSaveImage">OnSaveImage()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnFileClose">OnFileClose()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#OnIPCChoose">OnIPCChoose()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnSetLocalBg">OnSetLocalBg()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MainFrame-class.html#OnFileExit">OnFileExit()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnItemSelected">OnItemSelected()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#OnSize">OnSize()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#OnFileExit">OnFileExit()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#OnItemSelected">OnItemSelected()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnSpectrumSave">OnSpectrumSave()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnFileExit">OnFileExit()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#OnLilamsChoose">OnLilamsChoose()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnValidate">OnValidate()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnFileOpen">OnFileOpen()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnMDoubleClick">OnMDoubleClick()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnXMLOpen">OnXMLOpen()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#OnFileOpenORFs">OnFileOpenORFs()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnMLeftDown">OnMLeftDown()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnXMLSave">OnXMLSave()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#OnFileOpenPairs">OnFileOpenPairs()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#OnNextFile">OnNextFile()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="P">P</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#ParseMSFIT">ParseMSFIT()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#PlotSpectrumXML">PlotSpectrumXML()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#PepCompare">PepCompare()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#pepseqmodRE">pepseqmodRE</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#PopulateList">PopulateList()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#peplinePATT">peplinePATT</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#pepseqmodRE">pepseqmodRE</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#PopulateList">PopulateList()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#peplinePATT">peplinePATT</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#pepseqRE">pepseqRE</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MainFrame-class.html#ProcessFiles">ProcessFiles()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MainFrame-class.html">MainFrame</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#peplinePATTmod">peplinePATTmod</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#pepseqRE">pepseqRE</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#ProcessSpectrum">ProcessSpectrum()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#peplinePATTmod">peplinePATTmod</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#PlotArray">PlotArray()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrl-class.html">PepListCtrl</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#PlotFile">PlotFile()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="R">R</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#Read_Dir">Read_Dir()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MSFit32ParserProt-class.html#reset">reset()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MSFit32ParserProt-class.html">MSFit32ParserProt</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html#return_resultsXML">return_resultsXML()</a><br />
+<span class="index-where">(in <a href="lilamsxml.DataIntObj-class.html">DataIntObj</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI-module.html#ReadFromFile">ReadFromFile()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI-module.html">lilamslaunchGUI</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.MSFit32Parser-class.html#reset">reset()</a><br />
+<span class="index-where">(in <a href="lilamsxml.MSFit32Parser-class.html">MSFit32Parser</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#RunIPC">RunIPC()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html#ReadFromFileArray">ReadFromFileArray()</a><br />
+<span class="index-where">(in <a href="silacvalidator-module.html">silacvalidator</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#resetDefaults">resetDefaults()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#ReadFromFileFloats">ReadFromFileFloats()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html#return_results">return_results()</a><br />
+<span class="index-where">(in <a href="lilamsxml.DataIntObj-class.html">DataIntObj</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="S">S</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#SetBg">SetBg()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator-module.html">silacvalidator</a></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#StdDev">StdDev()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#SetValidated">SetValidated()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#SpectrumSave">SpectrumSave()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#SumSquares">SumSquares()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#SetXMLValidated">SetXMLValidated()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#StdDev">StdDev()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#SumSquares">SumSquares()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="U">U</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML.Usage-class.html">Usage</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.Usage-class.html">Usage</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="V">V</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#Variance">Variance()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#Variance">Variance()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="W">W</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt-module.html#WriteListToFile">WriteListToFile()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt-module.html">MSFit_to_txt</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#WriteMToFile">WriteMToFile()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#WriteListToString">WriteListToString()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml-module.html#WriteMToString">WriteMToString()</a><br />
+<span class="index-where">(in <a href="lilamsxml-module.html">lilamsxml</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="X">X</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML-module.html#XMLdict">XMLdict</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#XMLOpen">XMLOpen()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+<tr><td class="link-index"> </td><td class="link-index"> </td><td class="link-index"> </td></tr>
+</table>
+</td></tr>
+<tr valign="top"><td valign="top" width="1%"><h2 class="epydoc"><a name="_">_</a></h2></td>
+<td valign="top">
+<table class="link-index" width="100%" border="1">
+<tr>
+<td width="33%" class="link-index"><a href="Collect_SILAC_XML.Usage-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="Collect_SILAC_XML.Usage-class.html">Usage</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.DataIntObj-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="lilamsxml.DataIntObj-class.html">DataIntObj</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrl-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrl-class.html">PepListCtrl</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="MSFit_to_txt.MainFrame-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="MSFit_to_txt.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="lilamsxml.Usage-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="lilamsxml.Usage-class.html">Usage</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.PepListCtrlPanel-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a>)</span></td>
+</tr>
+<tr>
+<td width="33%" class="link-index"><a href="lilamslaunchGUI.MainFrame-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"><a href="silacvalidator.MainFrame-class.html#__init__">__init__()</a><br />
+<span class="index-where">(in <a href="silacvalidator.MainFrame-class.html">MainFrame</a>)</span></td>
+<td width="33%" class="link-index"> </td>
+</tr>
+</table>
+</td></tr>
+</table>
+<br /><br /><!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Indices </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/index.html b/docs/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..6af102b1ca506172ab15fdfd0f04de17ffebed83
--- /dev/null
+++ b/docs/index.html
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Module Hierarchy</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Trees </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%"> </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<center><b>
+ [ <a href="module-tree.html">Module Hierarchy</a>
+ | <a href="class-tree.html">Class Hierarchy</a> ]
+</b></center><br />
+<h1 class="epydoc">Module Hierarchy</h1>
+<ul class="nomargin-top">
+ <li> <strong class="uidlink"><a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a></strong>: <em class="summary">Collect_SILAC_XML.py</em> </li>
+ <li> <strong class="uidlink"><a href="MSFit_to_txt-module.html">MSFit_to_txt</a></strong>: <em class="summary">MSFit to Table v 0.2</em> </li>
+ <li> <strong class="uidlink"><a href="lilamslaunchGUI-module.html">lilamslaunchGUI</a></strong>: <em class="summary">LilamslaunchGUI.py is a GUI for the lilamsxml.py script Allows
+ interactive choosing of a file containing pairs of Spectrum/MSfit
+ file names (complete path) and of a file containing ORF names of
+ interest</em> </li>
+ <li> <strong class="uidlink"><a href="lilamsxml-module.html">lilamsxml</a></strong>: <em class="summary">lilamsxml.py - python script for the analysis of SILAC experiments
+ with MALDI spectra and MSFit protein identifications</em> </li>
+ <li> <strong class="uidlink"><a href="silacvalidator-module.html">silacvalidator</a></strong>: <em class="summary">SILAC validator v.</em> </li>
+</ul>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Trees </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/lilamslaunchGUI-module.html b/docs/lilamslaunchGUI-module.html
new file mode 100644
index 0000000000000000000000000000000000000000..35231000137e466f8d414f0c648e13e3dbf08d72
--- /dev/null
+++ b/docs/lilamslaunchGUI-module.html
@@ -0,0 +1,295 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>lilamslaunchGUI</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module lilamslaunchGUI
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== MODULE DESCRIPTION ==================== -->
+<h1 class="epydoc">Module lilamslaunchGUI</h1><p class="nomargin-top"><span class="codelink"><a href="lilamslaunchGUI-pysrc.html">source code</a></span></p>
+<p>LilamslaunchGUI.py is a GUI for the lilamsxml.py script Allows
+ interactive choosing of a file containing pairs of Spectrum/MSfit file
+ names (complete path) and of a file containing ORF names of interest</p>
+ <p>The output consists of xml files with the same name as the msfit html
+ files used for quantitation.</p>
+ <p>Cosmin, IP - September 2004 Modified in Jan 2008 to be able to locate
+ the lilamsxml script and the ipc executable path Updated the import of
+ the ElementTree XML module to use the one integrated in Python 2.5</p>
+
+<!-- ==================== CLASSES ==================== -->
+<a name="section-Classes"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Classes</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Classes"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="lilamslaunchGUI.MainFrame-class.html" class="summary-name">MainFrame</a>
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTIONS ==================== -->
+<a name="section-Functions"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Functions</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Functions"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamslaunchGUI-module.html#ReadFromFile" class="summary-sig-name">ReadFromFile</a>(<span class="summary-sig-arg">filename</span>,
+ <span class="summary-sig-arg">skip</span>=<span class="summary-sig-default">0</span>)</span><br />
+ Obtain data from a tab delimited file into a list</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#ReadFromFile">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== VARIABLES ==================== -->
+<a name="section-Variables"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Variables</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Variables"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_LILAMS"></a><span class="summary-name">ID_LILAMS</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_IPC"></a><span class="summary-name">ID_IPC</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_ORFS"></a><span class="summary-name">ID_ORFS</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_PAIRS"></a><span class="summary-name">ID_PAIRS</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_ABOUT"></a><span class="summary-name">ID_ABOUT</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_EXIT"></a><span class="summary-name">ID_EXIT</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_GO"></a><span class="summary-name">ID_GO</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="app"></a><span class="summary-name">app</span> = <code title="wx.PySimpleApp()">wx.PySimpleApp()</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="frame"></a><span class="summary-name">frame</span> = <code title="MainFrame(None,-1, "LilamsXML launcher v. 0.2")">MainFrame(None,-1, "LilamsXML launcher v. 0.2")</code>
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTION DETAILS ==================== -->
+<a name="section-FunctionDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Function Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-FunctionDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="ReadFromFile"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">ReadFromFile</span>(<span class="sig-arg">filename</span>,
+ <span class="sig-arg">skip</span>=<span class="sig-default">0</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamslaunchGUI-pysrc.html#ReadFromFile">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Obtain data from a tab delimited file into a list</p>
+ <p>Needs the import string statement The <skip> parameter indicate
+ the number of lines not read.</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/lilamslaunchGUI-pysrc.html b/docs/lilamslaunchGUI-pysrc.html
new file mode 100644
index 0000000000000000000000000000000000000000..7a173aa56a836a366d5d8f55b5dff3bbf4efc065
--- /dev/null
+++ b/docs/lilamslaunchGUI-pysrc.html
@@ -0,0 +1,386 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ <title>lilamslaunchGUI</title>
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+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
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+<table width="100%" cellpadding="0" cellspacing="0">
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+ <td width="100%">
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+ Module lilamslaunchGUI
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<h1 class="epydoc">Source Code for <a href="lilamslaunchGUI-module.html">Module lilamslaunchGUI</a></h1>
+<pre class="py-src">
+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env pythonw</tt> </tt>
+<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""</tt> </tt>
+<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">LilamslaunchGUI.py is a GUI for the lilamsxml.py script</tt> </tt>
+<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">Allows interactive choosing of a file containing</tt> </tt>
+<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">pairs of Spectrum/MSfit file names (complete path)</tt> </tt>
+<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">and of a file containing ORF names of interest</tt> </tt>
+<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">The output consists of xml files with the same name</tt> </tt>
+<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">as the msfit html files used for quantitation.</tt> </tt>
+<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Cosmin, IP - September 2004</tt> </tt>
+<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Modified in Jan 2008 to be able to locate the</tt> </tt>
+<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">lilamsxml script and the ipc executable path</tt> </tt>
+<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">Updated the import of the ElementTree XML module</tt> </tt>
+<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">to use the one integrated in Python 2.5</tt> </tt>
+<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
+<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
+<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">string</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt> </tt>
+<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">string</tt> <tt class="py-keyword">import</tt> <tt class="py-name">lstrip</tt><tt class="py-op">,</tt> <tt class="py-name">rstrip</tt> </tt>
+<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment">#from elementtree import ElementTree as ET</tt> </tt>
+<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#import cElementTree as ET</tt> </tt>
+<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">etree</tt><tt class="py-op">.</tt><tt class="py-name">cElementTree</tt> <tt class="py-keyword">as</tt> <tt class="py-name">ET</tt> </tt>
+<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment">#works with Python 2.5 and higher</tt> </tt>
+<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="ReadFromFile"></a><div id="ReadFromFile-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="ReadFromFile-toggle" onclick="return toggle('ReadFromFile');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI-module.html#ReadFromFile">ReadFromFile</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">skip</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="ReadFromFile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ReadFromFile-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> Obtain data from a tab delimited file into a list</tt> </tt>
+<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> Needs the import string statement</tt> </tt>
+<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> The <skip> parameter indicate the number of lines not</tt> </tt>
+<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> read.</tt> </tt>
+<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">=</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
+<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">skip</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
+<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">'\t'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">data</tt> </tt>
+</div><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-comment">#the returned data will be in string format</tt> </tt>
+<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
+<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment">#generate IDs for the interface</tt> </tt>
+<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-op">[</tt><tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> <tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> <tt class="py-name">ID_PAIRS</tt><tt class="py-op">,</tt> <tt class="py-name">ID_ORFS</tt><tt class="py-op">,</tt> <tt class="py-name">ID_IPC</tt><tt class="py-op">,</tt> <tt class="py-name">ID_LILAMS</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">init_ctrls</tt><tt class="py-op">:</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">NewId</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt>
+<a name="MainFrame"></a><div id="MainFrame-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="MainFrame-toggle" onclick="return toggle('MainFrame');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html">MainFrame</a><tt class="py-op">(</tt><tt class="py-base-class">wx</tt><tt class="py-op">.</tt><tt class="py-base-class">Frame</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MainFrame-expanded"><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.__init__"></a><div id="MainFrame.__init__-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="MainFrame.__init__-toggle" onclick="return toggle('MainFrame.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Frame</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Method Collect_SILAC_XML.Usage.__init__()=Collect_SILAC_XML.Usage-class.html#__init__,Method MSFit_to_txt.MainFrame.__init__()=MSFit_to_txt.MainFrame-class.html#__init__,Method lilamslaunchGUI.MainFrame.__init__()=lilamslaunchGUI.MainFrame-class.html#__init__,Method lilamsxml.DataIntObj.__init__()=lilamsxml.DataIntObj-class.html#__init__,Method lilamsxml.Usage.__init__()=lilamsxml.Usage-class.html#__init__,Method silacvalidator.MainFrame.__init__()=silacvalidator.MainFrame-class.html#__init__,Method silacvalidator.PepListCtrl.__init__()=silacvalidator.PepListCtrl-class.html#__init__,Method silacvalidator.PepListCtrlPanel.__init__()=silacvalidator.PepListCtrlPanel-class.html#__init__"><a title="Collect_SILAC_XML.Usage.__init__
+MSFit_to_txt.MainFrame.__init__
+lilamslaunchGUI.MainFrame.__init__
+lilamsxml.DataIntObj.__init__
+lilamsxml.Usage.__init__
+silacvalidator.MainFrame.__init__
+silacvalidator.PepListCtrl.__init__
+silacvalidator.PepListCtrlPanel.__init__" class="py-name" href="#" onclick="return doclink('link-0', '__init__', 'link-0');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt class="py-name">id</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">,</tt> </tt>
+<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultPosition</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">600</tt><tt class="py-op">,</tt> <tt class="py-number">200</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
+<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-comment">#default directory for saving, will be modified after first save</tt> </tt>
+<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-string">"."</tt> </tt>
+<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
+<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orffilename_ok</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pairsfilename_ok</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ipc_path</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
+<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lilams_path</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
+<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt>
+<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-comment"># Create the menu bar and items</tt> </tt>
+<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MenuBar</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
+<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_PAIRS</tt><tt class="py-op">,</tt> <tt class="py-string">'&Open file with pairs...'</tt><tt class="py-op">,</tt> <tt class="py-string">'Open a file that contains pairs of complete file names separated by tabs - spectrum file .. Msfit identification file'</tt><tt class="py-op">)</tt> </tt>
+<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_ORFS</tt><tt class="py-op">,</tt> <tt class="py-string">'Open f&ile with ORFs...'</tt><tt class="py-op">,</tt> <tt class="py-string">'Open a list of ORFs to be considered for calculations'</tt><tt class="py-op">)</tt> </tt>
+<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_IPC</tt><tt class="py-op">,</tt> <tt class="py-string">'Choose &IPC location...'</tt><tt class="py-op">,</tt> <tt class="py-string">'Choose the ipc program path.'</tt><tt class="py-op">)</tt> </tt>
+<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_LILAMS</tt><tt class="py-op">,</tt> <tt class="py-string">'Choose Li&lams.py location...'</tt><tt class="py-op">,</tt> <tt class="py-string">'Choose the lilamsxml script.'</tt><tt class="py-op">)</tt> </tt>
+<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-string">'&Run...\tCtrl+R'</tt><tt class="py-op">,</tt> <tt class="py-string">'Run: perform calculations on the dataset'</tt><tt class="py-op">)</tt> </tt>
+<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> <tt class="py-string">'&Quit\tCtrl+Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'Exit program'</tt><tt class="py-op">)</tt> </tt>
+<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
+<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">helpmenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">helpmenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> <tt class="py-string">'About...\tCtrl+E'</tt><tt class="py-op">,</tt> <tt class="py-string">'About this program'</tt><tt class="py-op">)</tt> </tt>
+<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
+<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-comment"># Bind the events to methods </tt> </tt>
+<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_PAIRS</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method lilamslaunchGUI.MainFrame.OnFileOpenPairs()=lilamslaunchGUI.MainFrame-class.html#OnFileOpenPairs"><a title="lilamslaunchGUI.MainFrame.OnFileOpenPairs" class="py-name" href="#" onclick="return doclink('link-1', 'OnFileOpenPairs', 'link-1');">OnFileOpenPairs</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_ORFS</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method lilamslaunchGUI.MainFrame.OnFileOpenORFs()=lilamslaunchGUI.MainFrame-class.html#OnFileOpenORFs"><a title="lilamslaunchGUI.MainFrame.OnFileOpenORFs" class="py-name" href="#" onclick="return doclink('link-2', 'OnFileOpenORFs', 'link-2');">OnFileOpenORFs</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_IPC</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method lilamslaunchGUI.MainFrame.OnIPCChoose()=lilamslaunchGUI.MainFrame-class.html#OnIPCChoose"><a title="lilamslaunchGUI.MainFrame.OnIPCChoose" class="py-name" href="#" onclick="return doclink('link-3', 'OnIPCChoose', 'link-3');">OnIPCChoose</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_LILAMS</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method lilamslaunchGUI.MainFrame.OnLilamsChoose()=lilamslaunchGUI.MainFrame-class.html#OnLilamsChoose"><a title="lilamslaunchGUI.MainFrame.OnLilamsChoose" class="py-name" href="#" onclick="return doclink('link-4', 'OnLilamsChoose', 'link-4');">OnLilamsChoose</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method lilamslaunchGUI.MainFrame.OnGo()=lilamslaunchGUI.MainFrame-class.html#OnGo"><a title="lilamslaunchGUI.MainFrame.OnGo" class="py-name" href="#" onclick="return doclink('link-5', 'OnGo', 'link-5');">OnGo</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnFileExit()=MSFit_to_txt.MainFrame-class.html#OnFileExit,Method lilamslaunchGUI.MainFrame.OnFileExit()=lilamslaunchGUI.MainFrame-class.html#OnFileExit,Method silacvalidator.MainFrame.OnFileExit()=silacvalidator.MainFrame-class.html#OnFileExit"><a title="MSFit_to_txt.MainFrame.OnFileExit
+lilamslaunchGUI.MainFrame.OnFileExit
+silacvalidator.MainFrame.OnFileExit" class="py-name" href="#" onclick="return doclink('link-6', 'OnFileExit', 'link-6');">OnFileExit</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnHelpAbout()=MSFit_to_txt.MainFrame-class.html#OnHelpAbout,Method lilamslaunchGUI.MainFrame.OnHelpAbout()=lilamslaunchGUI.MainFrame-class.html#OnHelpAbout,Method silacvalidator.MainFrame.OnHelpAbout()=silacvalidator.MainFrame-class.html#OnHelpAbout"><a title="MSFit_to_txt.MainFrame.OnHelpAbout
+lilamslaunchGUI.MainFrame.OnHelpAbout
+silacvalidator.MainFrame.OnHelpAbout" class="py-name" href="#" onclick="return doclink('link-7', 'OnHelpAbout', 'link-7');">OnHelpAbout</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
+<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-comment"># Attach menus to the menubar</tt> </tt>
+<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">filemenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&File'</tt><tt class="py-op">)</tt> </tt>
+<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">helpmenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&Help'</tt><tt class="py-op">)</tt> </tt>
+<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
+<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">SetMenuBar</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">)</tt> </tt>
+<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-comment">#disable by default the Run menu</tt> </tt>
+<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
+<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-comment"># A status bar to tell people what's happening</tt> </tt>
+<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">CreateStatusBar</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Show</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFileOpenORFs"></a><div id="MainFrame.OnFileOpenORFs-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="MainFrame.OnFileOpenORFs-toggle" onclick="return toggle('MainFrame.OnFileOpenORFs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#OnFileOpenORFs">OnFileOpenORFs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the name of the file with the ORFs list</tt> </tt>
+<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> Set the self.orfname_ok to True</tt> </tt>
+<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"Text file (*.txt)|*.txt|"</tt>\ </tt>
+<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-string">"All files (*.*)|*.*"</tt> </tt>
+<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Choose the interesting ORFs list text file"</tt><tt class="py-op">,</tt> </tt>
+<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OPEN</tt><tt class="py-op">)</tt> </tt>
+<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetFilename</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">dirname</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetDirectory</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> </tt>
+<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orffilename</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orffilename_ok</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
+<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orffilename_ok</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orffilename_ok</tt> <tt class="py-op">==</tt> <tt class="py-name">True</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pairsfilename_ok</tt> <tt class="py-op">==</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
+<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFileOpenPairs"></a><div id="MainFrame.OnFileOpenPairs-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="MainFrame.OnFileOpenPairs-toggle" onclick="return toggle('MainFrame.OnFileOpenPairs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#OnFileOpenPairs">OnFileOpenPairs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnFileOpenPairs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnFileOpenPairs-expanded"><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the name of the file with the pairs</tt> </tt>
+<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> spectrum files/msfit files - complete paths</tt> </tt>
+<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"Tab delimited text file (*.txt)|*.txt|"</tt>\ </tt>
+<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-string">"All files (*.*)|*.*"</tt> </tt>
+<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Choose the tab delimited text file with spectra/msfit"</tt><tt class="py-op">,</tt> </tt>
+<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OPEN</tt><tt class="py-op">)</tt> </tt>
+<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetFilename</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">dirname</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetDirectory</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> </tt>
+<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pairsfilename</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-comment">#self.menubar.Enable(ID_SAVEDATA, 0)</tt> </tt>
+<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pairsfilename_ok</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
+<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pairsfilename_ok</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
+<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orffilename_ok</tt> <tt class="py-op">==</tt> <tt class="py-name">True</tt> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pairsfilename_ok</tt> <tt class="py-op">==</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
+<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_GO</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnIPCChoose"></a><div id="MainFrame.OnIPCChoose-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="MainFrame.OnIPCChoose-toggle" onclick="return toggle('MainFrame.OnIPCChoose');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#OnIPCChoose">OnIPCChoose</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the path to the IPC executable with a dialog</tt> </tt>
+<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> Set the self.ipc_path</tt> </tt>
+<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"All files (*.*)|*.*"</tt> </tt>
+<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Choose the interesting ORFs list text file"</tt><tt class="py-op">,</tt> </tt>
+<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-string">"/usr/local/"</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OPEN</tt><tt class="py-op">)</tt> </tt>
+<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetFilename</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">dirname</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetDirectory</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ipc_path</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-comment">#self.menubar.Enable(ID_SAVEDATA, 0)</tt> </tt>
+<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="MainFrame.OnLilamsChoose"></a><div id="MainFrame.OnLilamsChoose-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="MainFrame.OnLilamsChoose-toggle" onclick="return toggle('MainFrame.OnLilamsChoose');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#OnLilamsChoose">OnLilamsChoose</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the path to the python program used for calculations with a dialog</tt> </tt>
+<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> Set the self.lilams_path</tt> </tt>
+<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"Python files (*.py)|*.py"</tt> </tt>
+<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Choose the lilams xml python script to run"</tt><tt class="py-op">,</tt> </tt>
+<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-string">"."</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OPEN</tt><tt class="py-op">)</tt> </tt>
+<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetFilename</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">dirname</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetDirectory</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lilams_path</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-comment">#self.menubar.Enable(ID_SAVEDATA, 0)</tt> </tt>
+<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="MainFrame.OnGo"></a><div id="MainFrame.OnGo-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="MainFrame.OnGo-toggle" onclick="return toggle('MainFrame.OnGo');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#OnGo">OnGo</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnGo-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnGo-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-comment">#scriptname = r"python lilamsxml.py"</tt> </tt>
+<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">scriptname</tt> <tt class="py-op">=</tt> <tt class="py-string">"python "</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lilams_path</tt> </tt>
+<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">ipccommand</tt> <tt class="py-op">=</tt> <tt class="py-string">"-c "</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ipc_path</tt> </tt>
+<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
+<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">""</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ipc_path</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lilams_path</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
+<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment">#HTMLbasepath = "/Volumes/Fire/CosminF/200409September/SILAC_Rlp24/Msfit/"</tt> </tt>
+<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#SPECTRAbasepath = "/Volumes/Fire/CosminF/200409September/SILAC_Rlp24/Spectra/"</tt> </tt>
+<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#datalist = ReadFromFile(HTMLbasepath+"Results/pairsspectmsfitOK.txt")</tt> </tt>
+<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">datalist</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Function lilamslaunchGUI.ReadFromFile()=lilamslaunchGUI-module.html#ReadFromFile"><a title="lilamslaunchGUI.ReadFromFile" class="py-name" href="#" onclick="return doclink('link-8', 'ReadFromFile', 'link-8');">ReadFromFile</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pairsfilename</tt><tt class="py-op">)</tt> </tt>
+<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
+<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-comment">#orffilename = HTMLbasepath+"Results/listeORFpreriboetcontam.tab"</tt> </tt>
+<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">orffilecomm</tt> <tt class="py-op">=</tt> <tt class="py-string">"-p "</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orffilename</tt> </tt>
+<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt>
+<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">datalist</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"pairs of files to be analysed"</tt> </tt>
+<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-comment">#print datalist</tt> </tt>
+<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print datalist</tt> </tt>
+<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">paircounter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ProgressDialog</tt><tt class="py-op">(</tt><tt class="py-string">"Quantitating peptides..."</tt><tt class="py-op">,</tt> <tt class="py-string">"Working..."</tt><tt class="py-op">,</tt> <tt class="py-name">maximum</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">datalist</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">,</tt> </tt>
+<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">style</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">PD_CAN_ABORT</tt><tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">PD_APP_MODAL</tt><tt class="py-op">)</tt> </tt>
+<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
+<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pair</tt> <tt class="py-keyword">in</tt> <tt class="py-name">datalist</tt><tt class="py-op">:</tt> </tt>
+<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment">#generate as many xml files as html files are present</tt> </tt>
+<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-comment">#the pair contains the name of the spectrum file and the name of the msfit file</tt> </tt>
+<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">spectrumname</tt> <tt class="py-op">=</tt> <tt class="py-string">"-s "</tt> <tt class="py-op">+</tt> <tt class="py-name">pair</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">identifname</tt> <tt class="py-op">=</tt> <tt class="py-string">"-i "</tt> <tt class="py-op">+</tt> <tt class="py-name">pair</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
+<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">tailspecfile</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">pair</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">splittedid</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">tailspecfile</tt><tt class="py-op">)</tt> </tt>
+<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">splittedpath</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">pair</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">splittedfname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">splittedpath</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">xmlfname</tt> <tt class="py-op">=</tt> <tt class="py-name">splittedfname</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"_"</tt> <tt class="py-op">+</tt><tt class="py-name">splittedid</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">".xml"</tt> </tt>
+<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">resultfname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">splittedpath</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">xmlfname</tt><tt class="py-op">)</tt> </tt>
+<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
+<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">pipe_s</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">popen</tt><tt class="py-op">(</tt><tt class="py-string">"%s %s %s %s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">scriptname</tt><tt class="py-op">,</tt> <tt class="py-name">spectrumname</tt><tt class="py-op">,</tt> <tt class="py-name">identifname</tt><tt class="py-op">,</tt> </tt>
+<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">ipccommand</tt><tt class="py-op">,</tt> <tt class="py-name">orffilecomm</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">pipe_s</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-comment">#the result is an xml formatted string</tt> </tt>
+<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">result</tt> <tt class="py-op"><></tt> <tt class="py-string">"nodata"</tt><tt class="py-op">:</tt> </tt>
+<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">fileout</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">resultfname</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
+<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">fileout</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">result</tt><tt class="py-op">)</tt> </tt>
+<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">fileout</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">paircounter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">paircounter</tt><tt class="py-op">,</tt> <tt class="py-name">pair</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">pair</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"done..."</tt> </tt>
+<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Update</tt><tt class="py-op">(</tt><tt class="py-name">paircounter</tt><tt class="py-op">,</tt> <tt class="py-string">"Done "</tt><tt class="py-op">+</tt> <tt class="py-name">xmlfname</tt> <tt class="py-op">+</tt><tt class="py-string">"."</tt><tt class="py-op">)</tt> </tt>
+<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">pair</tt><tt class="py-op">,</tt> <tt class="py-string">"didn't work"</tt> </tt>
+<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
+<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">'IPC path and lilams script must be specified'</tt><tt class="py-op">,</tt> </tt>
+<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-string">'Alert'</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OK</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_INFORMATION</tt><tt class="py-op">)</tt> </tt>
+<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">result</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
+<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnHelpAbout"></a><div id="MainFrame.OnHelpAbout-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="MainFrame.OnHelpAbout-toggle" onclick="return toggle('MainFrame.OnHelpAbout');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#OnHelpAbout">OnHelpAbout</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnHelpAbout-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnHelpAbout-expanded"><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt><tt class="py-op">.</tt><tt class="py-name">dialogs</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ScrolledMessageDialog</tt> </tt>
+<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">about</tt> <tt class="py-op">=</tt> <tt class="py-name">ScrolledMessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">__doc__</tt><tt class="py-op">,</tt> <tt class="py-string">"About..."</tt><tt class="py-op">)</tt> </tt>
+<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">about</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFileExit"></a><div id="MainFrame.OnFileExit-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="MainFrame.OnFileExit-toggle" onclick="return toggle('MainFrame.OnFileExit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamslaunchGUI.MainFrame-class.html#OnFileExit">OnFileExit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnFileExit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MainFrame.OnFileExit-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div></div><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
+<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> </tt>
+<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> </tt>
+<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt id="link-9" class="py-name" targets="Variable MSFit_to_txt.app=MSFit_to_txt-module.html#app,Variable lilamslaunchGUI.app=lilamslaunchGUI-module.html#app,Variable silacvalidator.app=silacvalidator-module.html#app"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-9', 'app', 'link-9');">app</a></tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">PySimpleApp</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt id="link-10" class="py-name" targets="Variable MSFit_to_txt.frame=MSFit_to_txt-module.html#frame,Variable lilamslaunchGUI.frame=lilamslaunchGUI-module.html#frame,Variable silacvalidator.frame=silacvalidator-module.html#frame"><a title="MSFit_to_txt.frame
+lilamslaunchGUI.frame
+silacvalidator.frame" class="py-name" href="#" onclick="return doclink('link-10', 'frame', 'link-10');">frame</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Class MSFit_to_txt.MainFrame=MSFit_to_txt.MainFrame-class.html,Class lilamslaunchGUI.MainFrame=lilamslaunchGUI.MainFrame-class.html,Class silacvalidator.MainFrame=silacvalidator.MainFrame-class.html"><a title="MSFit_to_txt.MainFrame
+lilamslaunchGUI.MainFrame
+silacvalidator.MainFrame" class="py-name" href="#" onclick="return doclink('link-11', 'MainFrame', 'link-11');">MainFrame</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"LilamsXML launcher v. 0.2"</tt><tt class="py-op">)</tt> </tt>
+<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt id="link-12" class="py-name"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-12', 'app', 'link-9');">app</a></tt><tt class="py-op">.</tt><tt class="py-name">SetTopWindow</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="MSFit_to_txt.frame
+lilamslaunchGUI.frame
+silacvalidator.frame" class="py-name" href="#" onclick="return doclink('link-13', 'frame', 'link-10');">frame</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt id="link-14" class="py-name"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-14', 'app', 'link-9');">app</a></tt><tt class="py-op">.</tt><tt class="py-name">MainLoop</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> </tt><script type="text/javascript">
+<!--
+expandto(location.href);
+// -->
+</script>
+</pre>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:24 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/lilamslaunchGUI.MainFrame-class.html b/docs/lilamslaunchGUI.MainFrame-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..da49a506cb752a50c241cca9093054540b9a2722
--- /dev/null
+++ b/docs/lilamslaunchGUI.MainFrame-class.html
@@ -0,0 +1,275 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>lilamslaunchGUI.MainFrame</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="lilamslaunchGUI-module.html">Module lilamslaunchGUI</a> ::
+ Class MainFrame
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class MainFrame</h1><p class="nomargin-top"><span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame">source code</a></span></p>
+<pre class="base-tree">
+wx.Frame --+
+ |
+ <strong class="uidshort">MainFrame</strong>
+</pre>
+
+<hr />
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">parent</span>,
+ <span class="summary-sig-arg">id</span>,
+ <span class="summary-sig-arg">title</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFileOpenORFs"></a><span class="summary-sig-name">OnFileOpenORFs</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Obtain the name of the file with the ORFs list Set the
+ self.orfname_ok to True</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.OnFileOpenORFs">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFileOpenPairs"></a><span class="summary-sig-name">OnFileOpenPairs</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Obtain the name of the file with the pairs spectrum files/msfit files
+ - complete paths</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.OnFileOpenPairs">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnIPCChoose"></a><span class="summary-sig-name">OnIPCChoose</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Obtain the path to the IPC executable with a dialog Set the
+ self.ipc_path</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.OnIPCChoose">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnLilamsChoose"></a><span class="summary-sig-name">OnLilamsChoose</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Obtain the path to the python program used for calculations with a
+ dialog Set the self.lilams_path</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.OnLilamsChoose">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnGo"></a><span class="summary-sig-name">OnGo</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.OnGo">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnHelpAbout"></a><span class="summary-sig-name">OnHelpAbout</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.OnHelpAbout">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFileExit"></a><span class="summary-sig-name">OnFileExit</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamslaunchGUI-pysrc.html#MainFrame.OnFileExit">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
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+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
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+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
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+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
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+</html>
diff --git a/docs/lilamsxml-module.html b/docs/lilamsxml-module.html
new file mode 100644
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+++ b/docs/lilamsxml-module.html
@@ -0,0 +1,1023 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>lilamsxml</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module lilamsxml
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== MODULE DESCRIPTION ==================== -->
+<h1 class="epydoc">Module lilamsxml</h1><p class="nomargin-top"><span class="codelink"><a href="lilamsxml-pysrc.html">source code</a></span></p>
+<p>lilamsxml.py - python script for the analysis of SILAC experiments
+ with MALDI spectra and MSFit protein identifications</p>
+ <p>first version - September 2003 this version - September 2004 slightly
+ revised in oct 2005 and jan 2008</p>
+ <p>Allows generation of XML output containing the whole information used
+ for quantitations As a result, the output of this script is an XML-like
+ string with <pepdata>...</pepdata> as delimiters.</p>
+ <p>Uses HTMLparser to parse the MSFit files. While much slower, this
+ method is much more flexible</p>
+ <p>GIM - Institut Pasteur first argument - spectrum (text format)
+ (--spectrum, -s) second argument - Msfit file (html format) (--msfithtml,
+ -i) third argument - a list of ORFs that will be quantified (--orflist,
+ -p) fourth argument - the path to the ipc, Isotope Pattern Calculator
+ executable (--ipc_path, -c) as it may vary in localization</p>
+ <p>Returns the results to the stdout with the peptide sequence and
+ differences between observed peak intensities and their theoretical
+ intensities. By default 10 peak differences from a family of peaks are
+ returned this takes in account 0, 1, 2 or 3 leucines Makes use of the
+ external IPC program for calculating peak mass distributions. The program
+ should be installed locally.</p>
+ <p>Modified on 20080130 to handle the absence of a mowse score Will
+ report 1, if a Mowse score is present. April 2008, integrated the HTML
+ parser in the script</p>
+ <p>Cosmin SAVEANU, Genetique des Interactions Macromoleculaires Alain
+ Jacquier's lab, Institut Pasteur, CNRS-URA 2171</p>
+
+<!-- ==================== CLASSES ==================== -->
+<a name="section-Classes"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Classes</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Classes"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="lilamsxml.MSFit32Parser-class.html" class="summary-name">MSFit32Parser</a><br />
+ A parser for MSFit HTML (version 3.2) results to obtain a dictionary
+ of data corresponding to the page, first entry only
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="lilamsxml.DataIntObj-class.html" class="summary-name">DataIntObj</a><br />
+ A data structure to handle SILAC difference results and calculate
+ statistics
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="lilamsxml.Usage-class.html" class="summary-name">Usage</a><br />
+ used for catching exceptions generated during command line
+ parameter parsing
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTIONS ==================== -->
+<a name="section-Functions"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Functions</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Functions"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#ParseMSFIT" class="summary-sig-name">ParseMSFIT</a>(<span class="summary-sig-arg">msfitfilehandle</span>)</span><br />
+ Parses an MSFit generated html identification file</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#ParseMSFIT">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#CalcMonoMz" class="summary-sig-name">CalcMonoMz</a>(<span class="summary-sig-arg">pepseq</span>)</span><br />
+ Returns the m/zH+ for a peptide</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#CalcMonoMz">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="Mean"></a><span class="summary-sig-name">Mean</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Obtain the mean of the values from a list</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#Mean">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="SumSquares"></a><span class="summary-sig-name">SumSquares</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Squares each value in the passed list, adds up these squares and
+ returns the result.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#SumSquares">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="Variance"></a><span class="summary-sig-name">Variance</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Calculates the variance for a sample Returns 1 if less than 2 values
+ are provided</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#Variance">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="StdDev"></a><span class="summary-sig-name">StdDev</span>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Returns the standard deviation of the values in the passed list using
+ N-1 in the denominator (i.e., to estimate population stdev).</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#StdDev">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#Median" class="summary-sig-name">Median</a>(<span class="summary-sig-arg">inlist</span>)</span><br />
+ Returns the median of the passed list.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#Median">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#ReadFromFileFloats" class="summary-sig-name">ReadFromFileFloats</a>(<span class="summary-sig-arg">fhandle</span>,
+ <span class="summary-sig-arg">skip</span>=<span class="summary-sig-default">0</span>)</span><br />
+ Obtain data from a tab delimited file into a list of floats</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#ReadFromFileFloats">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="WriteMToFile"></a><span class="summary-sig-name">WriteMToFile</span>(<span class="summary-sig-arg">matrix</span>,
+ <span class="summary-sig-arg">file_handle</span>)</span><br />
+ Writes the content of a matrix (list of lists) to a tab delimited
+ text file</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#WriteMToFile">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="WriteMToString"></a><span class="summary-sig-name">WriteMToString</span>(<span class="summary-sig-arg">matrix</span>)</span><br />
+ Returns the content of a matrix to a tab delimited string</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#WriteMToString">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="WriteListToString"></a><span class="summary-sig-name">WriteListToString</span>(<span class="summary-sig-arg">list</span>,
+ <span class="summary-sig-arg">format</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#WriteListToString">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#GetPeak" class="summary-sig-name">GetPeak</a>(<span class="summary-sig-arg">data</span>,
+ <span class="summary-sig-arg">peakx</span>,
+ <span class="summary-sig-arg">lo</span>=<span class="summary-sig-default">0</span>,
+ <span class="summary-sig-arg">hi</span>=<span class="summary-sig-default">41357</span>)</span><br />
+ Obtain the x y index for the pair most closely to the peak mass in
+ the list of data: mass-intensity</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#GetPeak">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#CrowlToMax" class="summary-sig-name">CrowlToMax</a>(<span class="summary-sig-arg">peakindex</span>,
+ <span class="summary-sig-arg">howmuch</span>,
+ <span class="summary-sig-arg">data</span>)</span><br />
+ Returns the most probable position of a maximum around a given index</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#CrowlToMax">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#GetBackground" class="summary-sig-name">GetBackground</a>(<span class="summary-sig-arg">monoindex</span>,
+ <span class="summary-sig-arg">points</span>,
+ <span class="summary-sig-arg">data</span>,
+ <span class="summary-sig-arg">level</span>=<span class="summary-sig-default">0.05</span>)</span><br />
+ Define the background as the average of the <level>% lowest
+ intensity values; uses function Mean</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#GetBackground">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#GetIsotopeSeries" class="summary-sig-name">GetIsotopeSeries</a>(<span class="summary-sig-arg">monoindex</span>,
+ <span class="summary-sig-arg">howmany</span>,
+ <span class="summary-sig-arg">data</span>)</span><br />
+ Returns a list of intensities in a series of peaks</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#GetIsotopeSeries">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#GetPeaksFromValue" class="summary-sig-name">GetPeaksFromValue</a>(<span class="summary-sig-arg">monopeak</span>,
+ <span class="summary-sig-arg">data</span>,
+ <span class="summary-sig-arg">bground</span>=<span class="summary-sig-default">100</span>,
+ <span class="summary-sig-arg">nbisotopes</span>=<span class="summary-sig-default">14</span>,
+ <span class="summary-sig-arg">crowlnb</span>=<span class="summary-sig-default">5</span>)</span><br />
+ Generates the list (amu and intensities) from a peak amu value</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#GetPeaksFromValue">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#RunIPC" class="summary-sig-name">RunIPC</a>(<span class="summary-sig-arg">peptide</span>,
+ <span class="summary-sig-arg">howmany</span>,
+ <span class="summary-sig-arg">monoisoint</span>,
+ <span class="summary-sig-arg">ipc_path</span>)</span><br />
+ Runs the external program IPC -> theoretical isotopic distribution</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#RunIPC">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="IsDifference"></a><span class="summary-sig-name">IsDifference</span>(<span class="summary-sig-arg">difference</span>,
+ <span class="summary-sig-arg">dif</span>,
+ <span class="summary-sig-arg">tolerated</span>)</span><br />
+ Returns 1 if the <difference> is in the tolerated range around
+ <dif> accepts an error, the <tolerated> parameter</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#IsDifference">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#PepCompare" class="summary-sig-name">PepCompare</a>(<span class="summary-sig-arg">pepmz</span>,
+ <span class="summary-sig-arg">pepseq</span>)</span><br />
+ Evaluates the measured mass of a peptide to see if its deuterated or
+ not</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#PepCompare">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#CorrectIsotopicSeries" class="summary-sig-name">CorrectIsotopicSeries</a>(<span class="summary-sig-arg">pepmz</span>,
+ <span class="summary-sig-arg">pepseq</span>,
+ <span class="summary-sig-arg">data</span>,
+ <span class="summary-sig-arg">peaks</span>,
+ <span class="summary-sig-arg">ipc_path</span>)</span><br />
+ Calculates the theoretical intensities of the first 4 peaks for
+ peptides with 1 Leucine, the pepmz corresponds to the nondeuterated
+ form.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#CorrectIsotopicSeries">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml-module.html#MzIntGet" class="summary-sig-name">MzIntGet</a>(<span class="summary-sig-arg">data</span>,
+ <span class="summary-sig-arg">pepmz</span>,
+ <span class="summary-sig-arg">plusminus</span>=<span class="summary-sig-default">15</span>)</span><br />
+ Obtain the list of mz-int pairs from the spectrum data</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#MzIntGet">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="ProcessSpectrum"></a><span class="summary-sig-name">ProcessSpectrum</span>(<span class="summary-sig-arg">spectrahandle</span>,
+ <span class="summary-sig-arg">msfithandle</span>,
+ <span class="summary-sig-arg">orflisthandle</span>,
+ <span class="summary-sig-arg">ipc_path</span>)</span><br />
+ A function to simplify the aspect of Main uses handles to file or
+ file-like objects Returns the results in list/string form May also be
+ used in a CGI</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#ProcessSpectrum">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="main"></a><span class="summary-sig-name">main</span>(<span class="summary-sig-arg">argv</span>=<span class="summary-sig-default">None</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#main">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== VARIABLES ==================== -->
+<a name="section-Variables"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Variables</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Variables"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="pepseqRE"></a><span class="summary-name">pepseqRE</span> = <code title="r"sequence=([A-Z]+)\*?\\"">r"sequence=([A-Z]+)\*?\\"</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="peplinePATT"></a><span class="summary-name">peplinePATT</span> = <code title="re.compile(pepseqRE)">re.compile(pepseqRE)</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="pepseqmodRE"></a><span class="summary-name">pepseqmodRE</span> = <code title="r"\)([A-Z]+)\*?\("">r"\)([A-Z]+)\*?\("</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="peplinePATTmod"></a><span class="summary-name">peplinePATTmod</span> = <code title="re.compile(pepseqmodRE)">re.compile(pepseqmodRE)</code>
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTION DETAILS ==================== -->
+<a name="section-FunctionDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Function Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-FunctionDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="ParseMSFIT"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">ParseMSFIT</span>(<span class="sig-arg">msfitfilehandle</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#ParseMSFIT">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Parses an MSFit generated html identification file</p>
+ <p>Returns a list of dictionaries with 2 entries: dict key = protdata -
+ with many subkeys dict key = pepdata with subkeys 'matched' - a list m/z
+ - sequence, and 'unmatched' - a simple list</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="CalcMonoMz"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">CalcMonoMz</span>(<span class="sig-arg">pepseq</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#CalcMonoMz">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns the m/zH+ for a peptide</p>
+ <p>Using the monoisotopic masses of aminoacid residues calculates the
+ monoisotopic mass of a peptide with a given sequence. Variations may be
+ implemented by the use of modified aminoacid masses</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="Median"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">Median</span>(<span class="sig-arg">inlist</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#Median">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns the median of the passed list. Returns 0 or the element if
+ less than 2 elements are passed to the function</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="ReadFromFileFloats"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">ReadFromFileFloats</span>(<span class="sig-arg">fhandle</span>,
+ <span class="sig-arg">skip</span>=<span class="sig-default">0</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#ReadFromFileFloats">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Obtain data from a tab delimited file into a list of floats</p>
+ <p>Needs the import string statement The <skip> parameter indicate
+ the number of lines not read. This version uses a filehandle for calls
+ Entry file has the format (with or without a header): 1000.0450 tab 158
+ 1000.0650 tab 190 ... ...</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="GetPeak"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GetPeak</span>(<span class="sig-arg">data</span>,
+ <span class="sig-arg">peakx</span>,
+ <span class="sig-arg">lo</span>=<span class="sig-default">0</span>,
+ <span class="sig-arg">hi</span>=<span class="sig-default">41357</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#GetPeak">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Obtain the x y index for the pair most closely to the peak mass in the
+ list of data: mass-intensity</p>
+ <p>Uses a binary search algorithm since the list is sorted 41357 is the
+ number of datapoints from a typical exported spectrum between 700 and
+ 3000 Da</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="CrowlToMax"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">CrowlToMax</span>(<span class="sig-arg">peakindex</span>,
+ <span class="sig-arg">howmuch</span>,
+ <span class="sig-arg">data</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#CrowlToMax">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns the most probable position of a maximum around a given
+ index</p>
+ <p>Go around to see if the peak is really at the maximum value, otherwise
+ leave it as it was <howmuch> the number of values tested around the
+ actual value - 10 should be good</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="GetBackground"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GetBackground</span>(<span class="sig-arg">monoindex</span>,
+ <span class="sig-arg">points</span>,
+ <span class="sig-arg">data</span>,
+ <span class="sig-arg">level</span>=<span class="sig-default">0.05</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#GetBackground">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Define the background as the average of the <level>% lowest
+ intensity values; uses function Mean</p>
+ <p><monoindex> - position of the monoisotopic peak <points>
+ points considered <data> list of floats m/z, intensity
+ <level> percent of points that might be considered in
+ background</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="GetIsotopeSeries"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GetIsotopeSeries</span>(<span class="sig-arg">monoindex</span>,
+ <span class="sig-arg">howmany</span>,
+ <span class="sig-arg">data</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#GetIsotopeSeries">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns a list of intensities in a series of peaks</p>
+ <p>Starting from the monoisotopic peak obtain maximum peaks at 1 Da
+ distance intervals; uses function CrowlToMax to recenter on real peaks
+ <howmany> defines the number of peaks to be retrieved
+ <monoindex> the mass of the firs peak in the series <data> a
+ list containing floats in pairs: mass/intensity</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="GetPeaksFromValue"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GetPeaksFromValue</span>(<span class="sig-arg">monopeak</span>,
+ <span class="sig-arg">data</span>,
+ <span class="sig-arg">bground</span>=<span class="sig-default">100</span>,
+ <span class="sig-arg">nbisotopes</span>=<span class="sig-default">14</span>,
+ <span class="sig-arg">crowlnb</span>=<span class="sig-default">5</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#GetPeaksFromValue">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Generates the list (amu and intensities) from a peak amu value</p>
+ <p>returns the family of peaks (amu and intensities) starting from a
+ value of a peak measured in the spectra; uses functions GetPeak,
+ GetBackground, GetIsotopeSeries, CrowlToMax monopeak - the mass of the
+ monoisotopic peak bground - number of points around the peak to be
+ considered for calculating the background nbisotopes - number of peaks
+ returned for a family crowlnb - number of points tested to see if a peak
+ is a peak</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="RunIPC"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">RunIPC</span>(<span class="sig-arg">peptide</span>,
+ <span class="sig-arg">howmany</span>,
+ <span class="sig-arg">monoisoint</span>,
+ <span class="sig-arg">ipc_path</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#RunIPC">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Runs the external program IPC -> theoretical isotopic
+ distribution</p>
+ <p>Returns a list of peptide masses+H and intensities at 1 Da distance,
+ normalized to the intensity of the monoisoint peak. Theoretical
+ distribution of the peak intensities is calculated by IPC, its path is
+ indicated by <ipc_path> needs os and string import.</p>
+ <p>How to test: pep = "AADGGHGGHHILL" hmany = 6 rlist = []
+ rlist = RunIPC(pep, hmany)</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="PepCompare"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">PepCompare</span>(<span class="sig-arg">pepmz</span>,
+ <span class="sig-arg">pepseq</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#PepCompare">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Evaluates the measured mass of a peptide to see if its deuterated or
+ not</p>
+ <p>Returns a dictionary containing the corrected pepmz if deuterated, the
+ peptide sequence (unchanged), and two flags MODIFIED if MetOX or other
+ has been found and IGNORE if no known modification was found. It also
+ calculates the number of leucines and reports it as a fifth element
+ NBLEU. Uses CalcMonoMz and IsDifference.</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="CorrectIsotopicSeries"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">CorrectIsotopicSeries</span>(<span class="sig-arg">pepmz</span>,
+ <span class="sig-arg">pepseq</span>,
+ <span class="sig-arg">data</span>,
+ <span class="sig-arg">peaks</span>,
+ <span class="sig-arg">ipc_path</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#CorrectIsotopicSeries">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Calculates the theoretical intensities of the first 4 peaks for
+ peptides with 1 Leucine, the pepmz corresponds to the nondeuterated
+ form.</p>
+ <p>This function is called only when the NBLEU of a peptide is 1
+ Otherwise, the differences in m/z between non-deuterated and deuterated
+ peptides are larger, the contribution of secondary peaks to the
+ quantification is less important (ignored) Returns a list of differences
+ between the measured and theoretical intensities for the peaks normalized
+ to the monoisotopic peak. Uses most of the functions previously defined
+ by calls to GetPeaksFromValue and RunIPC. The first elements of the
+ returned list are the peptide sequence, mz and the intensity of the
+ monoisotopic peak</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="MzIntGet"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">MzIntGet</span>(<span class="sig-arg">data</span>,
+ <span class="sig-arg">pepmz</span>,
+ <span class="sig-arg">plusminus</span>=<span class="sig-default">15</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#MzIntGet">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Obtain the list of mz-int pairs from the spectrum data</p>
+ <p>Returns tuple of two lists</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
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+
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+ </tr></table></th>
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diff --git a/docs/lilamsxml-pysrc.html b/docs/lilamsxml-pysrc.html
new file mode 100644
index 0000000000000000000000000000000000000000..aea7ed69938ca5112f6df65b9cb2fa85e18c9982
--- /dev/null
+++ b/docs/lilamsxml-pysrc.html
@@ -0,0 +1,1094 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>lilamsxml</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
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+ bgcolor="#a0c0ff" cellspacing="0">
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+ href="module-tree.html">Trees</a> </th>
+
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+
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+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module lilamsxml
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<h1 class="epydoc">Source Code for <a href="lilamsxml-module.html">Module lilamsxml</a></h1>
+<pre class="py-src">
+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt>
+<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""</tt> </tt>
+<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">lilamsxml.py - python script for the analysis</tt> </tt>
+<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">of SILAC experiments with MALDI spectra</tt> </tt>
+<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">and MSFit protein identifications</tt> </tt>
+<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">first version - September 2003</tt> </tt>
+<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">this version - September 2004</tt> </tt>
+<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">slightly revised in oct 2005 and jan 2008</tt> </tt>
+<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Allows generation of XML output containing</tt> </tt>
+<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">the whole information used for quantitations</tt> </tt>
+<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">As a result, the output of this script is an </tt> </tt>
+<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">XML-like string with <pepdata>...</pepdata></tt> </tt>
+<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">as delimiters.</tt> </tt>
+<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">Uses HTMLparser to parse the MSFit files. While much</tt> </tt>
+<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">slower, this method is much more flexible</tt> </tt>
+<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">GIM - Institut Pasteur</tt> </tt>
+<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">first argument - spectrum (text format) (--spectrum, -s)</tt> </tt>
+<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring">second argument - Msfit file (html format) (--msfithtml, -i)</tt> </tt>
+<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">third argument - a list of ORFs that will be quantified (--orflist, -p)</tt> </tt>
+<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">fourth argument - the path to the ipc, Isotope Pattern Calculator</tt> </tt>
+<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">executable (--ipc_path, -c) as it may vary in localization</tt> </tt>
+<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">Returns the results to the stdout with the peptide sequence and differences</tt> </tt>
+<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring">between observed peak intensities and their theoretical intensities.</tt> </tt>
+<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">By default 10 peak differences from a family of peaks are returned</tt> </tt>
+<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">this takes in account 0, 1, 2 or 3 leucines</tt> </tt>
+<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">Makes use of the external IPC program for calculating</tt> </tt>
+<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">peak mass distributions. The program should be installed locally.</tt> </tt>
+<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring">Modified on 20080130 to handle the absence of a mowse score</tt> </tt>
+<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">Will report 1, if a Mowse score is present. April 2008, integrated the</tt> </tt>
+<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring">HTML parser in the script</tt> </tt>
+<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring">Cosmin SAVEANU, Genetique des Interactions Macromoleculaires</tt> </tt>
+<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring">Alain Jacquier's lab, Institut Pasteur, CNRS-URA 2171</tt> </tt>
+<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
+<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">string</tt><tt class="py-op">,</tt> <tt class="py-name">copy</tt><tt class="py-op">,</tt> <tt class="py-name">math</tt><tt class="py-op">,</tt> <tt class="py-name">getopt</tt> </tt>
+<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">HTMLParser</tt> <tt class="py-keyword">import</tt> <tt class="py-name">HTMLParser</tt> </tt>
+<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment">#import cElementTree as ET</tt> </tt>
+<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">etree</tt><tt class="py-op">.</tt><tt class="py-name">cElementTree</tt> <tt class="py-keyword">as</tt> <tt class="py-name">ET</tt> <tt class="py-comment">#latest version integrated in Python 2.5</tt> </tt>
+<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
+<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment">#############################################</tt> </tt>
+<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">####### MSFit html file parser #########</tt> </tt>
+<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#############################################</tt> </tt>
+<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># regular expressions used to isolate the elements of</tt> </tt>
+<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># parsed HTML files when extracting peptide and protein</tt> </tt>
+<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># information from MSFit files</tt> </tt>
+<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-0" class="py-name" targets="Variable MSFit_to_txt.pepseqRE=MSFit_to_txt-module.html#pepseqRE,Variable lilamsxml.pepseqRE=lilamsxml-module.html#pepseqRE"><a title="MSFit_to_txt.pepseqRE
+lilamsxml.pepseqRE" class="py-name" href="#" onclick="return doclink('link-0', 'pepseqRE', 'link-0');">pepseqRE</a></tt> <tt class="py-op">=</tt> <tt class="py-string">r"sequence=([A-Z]+)\*?\\"</tt> </tt>
+<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable MSFit_to_txt.peplinePATT=MSFit_to_txt-module.html#peplinePATT,Variable lilamsxml.peplinePATT=lilamsxml-module.html#peplinePATT"><a title="MSFit_to_txt.peplinePATT
+lilamsxml.peplinePATT" class="py-name" href="#" onclick="return doclink('link-1', 'peplinePATT', 'link-1');">peplinePATT</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt id="link-2" class="py-name"><a title="MSFit_to_txt.pepseqRE
+lilamsxml.pepseqRE" class="py-name" href="#" onclick="return doclink('link-2', 'pepseqRE', 'link-0');">pepseqRE</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable MSFit_to_txt.pepseqmodRE=MSFit_to_txt-module.html#pepseqmodRE,Variable lilamsxml.pepseqmodRE=lilamsxml-module.html#pepseqmodRE"><a title="MSFit_to_txt.pepseqmodRE
+lilamsxml.pepseqmodRE" class="py-name" href="#" onclick="return doclink('link-3', 'pepseqmodRE', 'link-3');">pepseqmodRE</a></tt> <tt class="py-op">=</tt> <tt class="py-string">r"\)([A-Z]+)\*?\("</tt> </tt>
+<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable MSFit_to_txt.peplinePATTmod=MSFit_to_txt-module.html#peplinePATTmod,Variable lilamsxml.peplinePATTmod=lilamsxml-module.html#peplinePATTmod"><a title="MSFit_to_txt.peplinePATTmod
+lilamsxml.peplinePATTmod" class="py-name" href="#" onclick="return doclink('link-4', 'peplinePATTmod', 'link-4');">peplinePATTmod</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt id="link-5" class="py-name"><a title="MSFit_to_txt.pepseqmodRE
+lilamsxml.pepseqmodRE" class="py-name" href="#" onclick="return doclink('link-5', 'pepseqmodRE', 'link-3');">pepseqmodRE</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
+<a name="MSFit32Parser"></a><div id="MSFit32Parser-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="MSFit32Parser-toggle" onclick="return toggle('MSFit32Parser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="lilamsxml.MSFit32Parser-class.html">MSFit32Parser</a><tt class="py-op">(</tt><tt class="py-base-class">HTMLParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32Parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MSFit32Parser-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> A parser for MSFit HTML (version 3.2) results to obtain a</tt> </tt>
+<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> dictionary of data corresponding to the page, first entry only</tt> </tt>
+<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> Regular expression needed to extract sequences</tt> </tt>
+<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> of peptides from MSFit lines are compiled outside</tt> </tt>
+<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> functions to avoid repetition of re compilations</tt> </tt>
+<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="MSFit32Parser.reset"></a><div id="MSFit32Parser.reset-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="MSFit32Parser.reset-toggle" onclick="return toggle('MSFit32Parser.reset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.MSFit32Parser-class.html#reset">reset</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32Parser.reset-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32Parser.reset-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">HTMLParser</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method MSFit_to_txt.MSFit32ParserProt.reset()=MSFit_to_txt.MSFit32ParserProt-class.html#reset,Method lilamsxml.MSFit32Parser.reset()=lilamsxml.MSFit32Parser-class.html#reset"><a title="MSFit_to_txt.MSFit32ParserProt.reset
+lilamsxml.MSFit32Parser.reset" class="py-name" href="#" onclick="return doclink('link-6', 'reset', 'link-6');">reset</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
+<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt> <tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment">#list of text chunks contained between tags</tt> </tt>
+<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">comments</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment">#list of comment texts, this is </tt> </tt>
+<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-comment">#true if the text to be handled follows a comment</tt> </tt>
+<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accesionRE</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'> (.+)'</tt><tt class="py-op">)</tt> </tt>
+<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-comment">#allows extraction of ORF name from the first table</tt> </tt>
+<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment">#two variables to allow start of scanning for peptide sequences in file</tt> </tt>
+<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequence</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequencemod</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
+<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
+<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+</div><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-comment">#contains the list of sequences of all peptides</tt> </tt>
+<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="MSFit32Parser.handle_starttag"></a><div id="MSFit32Parser.handle_starttag-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="MSFit32Parser.handle_starttag-toggle" onclick="return toggle('MSFit32Parser.handle_starttag');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.MSFit32Parser-class.html#handle_starttag">handle_starttag</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32Parser.handle_starttag-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32Parser.handle_starttag-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment">#print tag, attrs</tt> </tt>
+<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">tag</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"nobr"</tt><tt class="py-op">:</tt> </tt>
+<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequencemod</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
+<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tag</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"script"</tt><tt class="py-op">:</tt> </tt>
+<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequence</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
+<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequencemod</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequence</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-name">False</tt> </tt>
+</div><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> </tt>
+<a name="MSFit32Parser.handle_comment"></a><div id="MSFit32Parser.handle_comment-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="MSFit32Parser.handle_comment-toggle" onclick="return toggle('MSFit32Parser.handle_comment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.MSFit32Parser-class.html#handle_comment">handle_comment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">tag</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32Parser.handle_comment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32Parser.handle_comment-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> Overrides the handle_comment method</tt> </tt>
+<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> Builds a list of all the found comments</tt> </tt>
+<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> If a comment is found, the aftercomment</tt> </tt>
+<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> variable is set to True</tt> </tt>
+<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">comments</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">tag</tt><tt class="py-op">)</tt> </tt>
+<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+</div><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-comment">#if tag == 'delta_mass':</tt> </tt>
+<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.seeksequence = True</tt> </tt>
+<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
+<a name="MSFit32Parser.handle_data"></a><div id="MSFit32Parser.handle_data-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="MSFit32Parser.handle_data-toggle" onclick="return toggle('MSFit32Parser.handle_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.MSFit32Parser-class.html#handle_data">handle_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32Parser.handle_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32Parser.handle_data-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> Overrides the handle_data method</tt> </tt>
+<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> writes to a list the text following</tt> </tt>
+<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> any comment - modifies self.parsedlist</tt> </tt>
+<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-comment">#print "text", text</tt> </tt>
+<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt><tt class="py-op">:</tt> </tt>
+<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">cleantext</tt> <tt class="py-op">=</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-string">'\n\r ./'</tt><tt class="py-op">)</tt> </tt>
+<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">comments</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">cleantext</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-comment">#append the last comment and the text that follows</tt> </tt>
+<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">aftercomment</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment">#don't get any other value until the next comment appears</tt> </tt>
+<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#however obtain the sequence of a peptide if we are in an in_mass tags</tt> </tt>
+<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequence</tt><tt class="py-op">:</tt> </tt>
+<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">pepmatch</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="MSFit_to_txt.peplinePATT
+lilamsxml.peplinePATT" class="py-name" href="#" onclick="return doclink('link-7', 'peplinePATT', 'link-1');">peplinePATT</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
+<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pepmatch</tt><tt class="py-op">:</tt> </tt>
+<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pepmatch</tt><tt class="py-op">.</tt><tt class="py-name">groups</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seeksequencemod</tt><tt class="py-op">:</tt> </tt>
+<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">pepmatch</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="MSFit_to_txt.peplinePATTmod
+lilamsxml.peplinePATTmod" class="py-name" href="#" onclick="return doclink('link-8', 'peplinePATTmod', 'link-4');">peplinePATTmod</a></tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
+<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pepmatch</tt><tt class="py-op">:</tt> </tt>
+<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pepmatch</tt><tt class="py-op">.</tt><tt class="py-name">groups</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
+</div><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
+<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
+<a name="MSFit32Parser.get_dictionary"></a><div id="MSFit32Parser.get_dictionary-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="MSFit32Parser.get_dictionary-toggle" onclick="return toggle('MSFit32Parser.get_dictionary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.MSFit32Parser-class.html#get_dictionary">get_dictionary</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MSFit32Parser.get_dictionary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MSFit32Parser.get_dictionary-expanded"><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> Reorganizes data and treats some special cases</tt> </tt>
+<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> of data found after comment tags</tt> </tt>
+<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> Should be called after closing the parser</tt> </tt>
+<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">reccounter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">secreccounter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">list_out</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">list</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt> </tt>
+<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">details</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">passedrank1</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">seq_counter</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment">#a counter for the list of sequences, append to matched masses</tt> </tt>
+<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> </tt>
+<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">list</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'rank'</tt><tt class="py-op">:</tt> </tt>
+<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">passedrank1</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op"><></tt> <tt class="py-string">'fraction_matched'</tt><tt class="py-op">:</tt> </tt>
+<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-comment">#we are not at the beginning of the details</tt> </tt>
+<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#sometimes proteins have equal ranks</tt> </tt>
+<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#we build the data dictionary for the identified proteins</tt> </tt>
+<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">reccounter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">{</tt><tt class="py-string">'protdata'</tt><tt class="py-op">:</tt><tt class="py-op">{</tt><tt class="py-string">'rank'</tt><tt class="py-op">:</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">}</tt><tt class="py-op">,</tt> \ </tt>
+<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-string">'pepdata'</tt><tt class="py-op">:</tt><tt class="py-op">{</tt><tt class="py-string">'matched'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'unmatched'</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">}</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
+<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">details</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">reccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'comment'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">reccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'database'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">reccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'parent_mass_tolerance'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> </tt>
+<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-comment">#we are at the beginning of the details</tt> </tt>
+<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">details</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">secreccounter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">details</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">passedrank1</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-comment">#not yet in details but passed the first rank tags</tt> </tt>
+<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#take care first of the accesion numbers</tt> </tt>
+<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'accession_number'</tt><tt class="py-op">:</tt> </tt>
+<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">matches</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">accesionRE</tt><tt class="py-op">.</tt><tt class="py-name">search</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parsedlist</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">matches</tt><tt class="py-op">:</tt> </tt>
+<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">matches</tt><tt class="py-op">.</tt><tt class="py-name">groups</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">entries</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">reccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">details</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-comment">#we are in the details, we may build the peptide masses lists</tt> </tt>
+<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'protein_coverage'</tt><tt class="py-op">:</tt> </tt>
+<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">secreccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'in_mass'</tt><tt class="py-op">:</tt> </tt>
+<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'matched_mass'</tt><tt class="py-op">:</tt> </tt>
+<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-comment">#we are in the matched masses</tt> </tt>
+<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">secreccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'pepdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'matched'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seqlist</tt><tt class="py-op">[</tt><tt class="py-name">seq_counter</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> </tt>
+<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">seq_counter</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
+<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment">#print seq_counter</tt> </tt>
+<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">list_out</tt><tt class="py-op">[</tt><tt class="py-name">secreccounter</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'pepdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'unmatched'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt>
+<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> </tt>
+<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">list_out</tt> </tt>
+</div></div><a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
+<a name="ParseMSFIT"></a><div id="ParseMSFIT-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="ParseMSFIT-toggle" onclick="return toggle('ParseMSFIT');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#ParseMSFIT">ParseMSFIT</a><tt class="py-op">(</tt><tt class="py-param">msfitfilehandle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="ParseMSFIT-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ParseMSFIT-expanded"><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> Parses an MSFit generated html identification file</tt> </tt>
+<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of dictionaries with 2 entries:</tt> </tt>
+<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"> dict key = protdata - with many subkeys</tt> </tt>
+<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> dict key = pepdata with subkeys 'matched' - a list</tt> </tt>
+<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> m/z - sequence, and 'unmatched' - a simple list</tt> </tt>
+<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">htmlpage</tt> <tt class="py-op">=</tt> <tt class="py-name">msfitfilehandle</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name" targets="Class lilamsxml.MSFit32Parser=lilamsxml.MSFit32Parser-class.html"><a title="lilamsxml.MSFit32Parser" class="py-name" href="#" onclick="return doclink('link-9', 'MSFit32Parser', 'link-9');">MSFit32Parser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">feed</tt><tt class="py-op">(</tt><tt class="py-name">htmlpage</tt><tt class="py-op">)</tt> </tt>
+<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method MSFit_to_txt.MSFit32ParserProt.get_dictionary()=MSFit_to_txt.MSFit32ParserProt-class.html#get_dictionary,Method lilamsxml.MSFit32Parser.get_dictionary()=lilamsxml.MSFit32Parser-class.html#get_dictionary"><a title="MSFit_to_txt.MSFit32ParserProt.get_dictionary
+lilamsxml.MSFit32Parser.get_dictionary" class="py-name" href="#" onclick="return doclink('link-10', 'get_dictionary', 'link-10');">get_dictionary</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> </tt>
+<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment">#####################################################</tt> </tt>
+<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##### STATISTICAL AND COMPUTATIONAL FUNCTIONS ######</tt> </tt>
+<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#####################################################</tt> </tt>
+<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="CalcMonoMz"></a><div id="CalcMonoMz-def"><a name="L212"></a><tt class="py-lineno">212</tt> <a class="py-toggle" href="#" id="CalcMonoMz-toggle" onclick="return toggle('CalcMonoMz');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#CalcMonoMz">CalcMonoMz</a><tt class="py-op">(</tt><tt class="py-param">pepseq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="CalcMonoMz-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CalcMonoMz-expanded"><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> Returns the m/zH+ for a peptide</tt> </tt>
+<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> Using the monoisotopic masses of aminoacid residues calculates the </tt> </tt>
+<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"> monoisotopic mass of a peptide with a given sequence. Variations </tt> </tt>
+<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-docstring"> may be implemented by the use of modified aminoacid masses</tt> </tt>
+<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">Daamass</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"G"</tt><tt class="py-op">:</tt><tt class="py-number">57.02147</tt><tt class="py-op">,</tt> <tt class="py-string">"A"</tt><tt class="py-op">:</tt><tt class="py-number">71.03712</tt><tt class="py-op">,</tt> <tt class="py-string">"S"</tt><tt class="py-op">:</tt><tt class="py-number">87.03203</tt><tt class="py-op">,</tt> </tt>
+<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-string">"P"</tt><tt class="py-op">:</tt><tt class="py-number">97.05277</tt><tt class="py-op">,</tt> <tt class="py-string">"V"</tt><tt class="py-op">:</tt><tt class="py-number">99.06842</tt><tt class="py-op">,</tt> <tt class="py-string">"T"</tt><tt class="py-op">:</tt><tt class="py-number">101.04768</tt><tt class="py-op">,</tt> </tt>
+<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-string">"C"</tt><tt class="py-op">:</tt><tt class="py-number">103.00919</tt><tt class="py-op">,</tt> <tt class="py-string">"carbamidomethyl"</tt><tt class="py-op">:</tt><tt class="py-number">57.02146</tt><tt class="py-op">,</tt> </tt>
+<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-string">"carboxymethyl"</tt><tt class="py-op">:</tt><tt class="py-number">58.00547</tt><tt class="py-op">,</tt> <tt class="py-string">"acrylamide"</tt><tt class="py-op">:</tt><tt class="py-number">71.05511</tt><tt class="py-op">,</tt> </tt>
+<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-string">"I"</tt><tt class="py-op">:</tt><tt class="py-number">113.08407</tt><tt class="py-op">,</tt> <tt class="py-string">"L"</tt><tt class="py-op">:</tt><tt class="py-number">113.08407</tt><tt class="py-op">,</tt> <tt class="py-string">"N"</tt><tt class="py-op">:</tt><tt class="py-number">114.04293</tt><tt class="py-op">,</tt> </tt>
+<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-string">"D"</tt><tt class="py-op">:</tt><tt class="py-number">115.02695</tt><tt class="py-op">,</tt> <tt class="py-string">"Q"</tt><tt class="py-op">:</tt><tt class="py-number">128.05858</tt><tt class="py-op">,</tt> <tt class="py-string">"K"</tt><tt class="py-op">:</tt><tt class="py-number">128.09497</tt><tt class="py-op">,</tt> </tt>
+<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-string">"E"</tt><tt class="py-op">:</tt><tt class="py-number">129.0426</tt><tt class="py-op">,</tt> <tt class="py-string">"M"</tt><tt class="py-op">:</tt><tt class="py-number">131.04049</tt><tt class="py-op">,</tt> <tt class="py-string">"MOxidized"</tt><tt class="py-op">:</tt><tt class="py-number">147.0354</tt><tt class="py-op">,</tt> </tt>
+<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-string">"H"</tt><tt class="py-op">:</tt><tt class="py-number">137.05891</tt><tt class="py-op">,</tt> <tt class="py-string">"F"</tt><tt class="py-op">:</tt><tt class="py-number">147.06842</tt><tt class="py-op">,</tt> <tt class="py-string">"R"</tt><tt class="py-op">:</tt><tt class="py-number">156.10112</tt><tt class="py-op">,</tt> </tt>
+<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-string">"Y"</tt><tt class="py-op">:</tt><tt class="py-number">163.06333</tt><tt class="py-op">,</tt> <tt class="py-string">"W"</tt><tt class="py-op">:</tt><tt class="py-number">186.07932</tt><tt class="py-op">,</tt> <tt class="py-string">"water"</tt><tt class="py-op">:</tt><tt class="py-number">18.01056</tt><tt class="py-op">,</tt> <tt class="py-string">"Hplus"</tt><tt class="py-op">:</tt><tt class="py-number">1.007825</tt><tt class="py-op">,</tt> </tt>
+<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-string">"Oxygen16"</tt><tt class="py-op">:</tt><tt class="py-number">15.99491</tt><tt class="py-op">}</tt> </tt>
+<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">mass</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">aminoacid</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pepseq</tt><tt class="py-op">:</tt> </tt>
+<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">mass</tt><tt class="py-op">+=</tt><tt class="py-name">Daamass</tt><tt class="py-op">[</tt><tt class="py-name">aminoacid</tt><tt class="py-op">]</tt> </tt>
+<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">mass</tt><tt class="py-op">+=</tt><tt class="py-name">Daamass</tt><tt class="py-op">[</tt><tt class="py-string">"water"</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">Daamass</tt><tt class="py-op">[</tt><tt class="py-string">"Hplus"</tt><tt class="py-op">]</tt> <tt class="py-comment">#add the water and charged H+</tt> </tt>
+<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">mass</tt> </tt>
+</div><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> </tt>
+<a name="Mean"></a><div id="Mean-def"><a name="L236"></a><tt class="py-lineno">236</tt> <a class="py-toggle" href="#" id="Mean-toggle" onclick="return toggle('Mean');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#Mean">Mean</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Mean-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Mean-expanded"><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the mean of the values from a list</tt> </tt>
+<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">sum</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inlist</tt><tt class="py-op">:</tt> </tt>
+<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">sum</tt> <tt class="py-op">=</tt> <tt class="py-name">sum</tt> <tt class="py-op">+</tt> <tt class="py-name">item</tt> </tt>
+<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">></tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sum</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
+</div><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
+<a name="SumSquares"></a><div id="SumSquares-def"><a name="L248"></a><tt class="py-lineno">248</tt> <a class="py-toggle" href="#" id="SumSquares-toggle" onclick="return toggle('SumSquares');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#SumSquares">SumSquares</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="SumSquares-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SumSquares-expanded"><a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-docstring"> Squares each value in the passed list, adds up these squares and</tt> </tt>
+<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-docstring"> returns the result.</tt> </tt>
+<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">ss</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inlist</tt><tt class="py-op">:</tt> </tt>
+<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">ss</tt> <tt class="py-op">=</tt> <tt class="py-name">ss</tt> <tt class="py-op">+</tt> <tt class="py-name">item</tt><tt class="py-op">*</tt><tt class="py-name">item</tt> </tt>
+<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ss</tt> </tt>
+</div><a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> </tt>
+<a name="Variance"></a><div id="Variance-def"><a name="L258"></a><tt class="py-lineno">258</tt> <a class="py-toggle" href="#" id="Variance-toggle" onclick="return toggle('Variance');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#Variance">Variance</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Variance-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Variance-expanded"><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the variance for a sample </tt> </tt>
+<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-docstring"> Returns 1 if less than 2 values are provided</tt> </tt>
+<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name" targets="Function Collect_SILAC_XML.Mean()=Collect_SILAC_XML-module.html#Mean,Function lilamsxml.Mean()=lilamsxml-module.html#Mean"><a title="Collect_SILAC_XML.Mean
+lilamsxml.Mean" class="py-name" href="#" onclick="return doclink('link-11', 'Mean', 'link-11');">Mean</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">ssq</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name" targets="Function Collect_SILAC_XML.SumSquares()=Collect_SILAC_XML-module.html#SumSquares,Function lilamsxml.SumSquares()=lilamsxml-module.html#SumSquares"><a title="Collect_SILAC_XML.SumSquares
+lilamsxml.SumSquares" class="py-name" href="#" onclick="return doclink('link-12', 'SumSquares', 'link-12');">SumSquares</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">n</tt> <tt class="py-op">></tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">vari</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">ssq</tt> <tt class="py-op">-</tt> <tt class="py-name">n</tt><tt class="py-op">*</tt><tt class="py-name">mn</tt><tt class="py-op">*</tt><tt class="py-name">mn</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">vari</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">vari</tt> </tt>
+</div><a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt>
+<a name="StdDev"></a><div id="StdDev-def"><a name="L272"></a><tt class="py-lineno">272</tt> <a class="py-toggle" href="#" id="StdDev-toggle" onclick="return toggle('StdDev');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#StdDev">StdDev</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="StdDev-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StdDev-expanded"><a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-docstring"> Returns the standard deviation of the values in the passed list</tt> </tt>
+<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-docstring"> using N-1 in the denominator (i.e., to estimate population stdev).</tt> </tt>
+<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name" targets="Function Collect_SILAC_XML.Variance()=Collect_SILAC_XML-module.html#Variance,Function lilamsxml.Variance()=lilamsxml-module.html#Variance"><a title="Collect_SILAC_XML.Variance
+lilamsxml.Variance" class="py-name" href="#" onclick="return doclink('link-13', 'Variance', 'link-13');">Variance</a></tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
+<a name="Median"></a><div id="Median-def"><a name="L279"></a><tt class="py-lineno">279</tt> <a class="py-toggle" href="#" id="Median-toggle" onclick="return toggle('Median');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#Median">Median</a><tt class="py-op">(</tt><tt class="py-param">inlist</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Median-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Median-expanded"><a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-docstring"> Returns the median of the passed list.</tt> </tt>
+<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-docstring"> Returns 0 or the element if less than 2 elements</tt> </tt>
+<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-docstring"> are passed to the function</tt> </tt>
+<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">newlist</tt> <tt class="py-op">=</tt> <tt class="py-name">copy</tt><tt class="py-op">.</tt><tt class="py-name">deepcopy</tt><tt class="py-op">(</tt><tt class="py-name">inlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">newlist</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt> <tt class="py-op">%</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># if even number, simple mean of middles</tt> </tt>
+<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
+<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
+<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">newlist</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
+<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">median</tt> <tt class="py-op">=</tt> <tt class="py-name">newlist</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt> </tt>
+<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">median</tt> </tt>
+</div><a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> </tt>
+<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-comment">#############################################</tt> </tt>
+<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">####### I/O functions ####################</tt> </tt>
+<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#############################################</tt> </tt>
+<a name="ReadFromFileFloats"></a><div id="ReadFromFileFloats-def"><a name="L302"></a><tt class="py-lineno">302</tt> <a class="py-toggle" href="#" id="ReadFromFileFloats-toggle" onclick="return toggle('ReadFromFileFloats');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#ReadFromFileFloats">ReadFromFileFloats</a><tt class="py-op">(</tt><tt class="py-param">fhandle</tt><tt class="py-op">,</tt> <tt class="py-param">skip</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="ReadFromFileFloats-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ReadFromFileFloats-expanded"><a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> Obtain data from a tab delimited file into a list of floats</tt> </tt>
+<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> Needs the import string statement</tt> </tt>
+<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-docstring"> The <skip> parameter indicate the number of lines not</tt> </tt>
+<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-docstring"> read. This version uses a filehandle for calls</tt> </tt>
+<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-docstring"> Entry file has the format (with or without a header):</tt> </tt>
+<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-docstring"> 1000.0450 tab 158</tt> </tt>
+<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-docstring"> 1000.0650 tab 190</tt> </tt>
+<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
+<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
+<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">skip</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-name">fhandle</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">fhandle</tt><tt class="py-op">:</tt> </tt>
+<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">'\t'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">data</tt> </tt>
+</div><a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-comment">#the returned data will be in float format</tt> </tt>
+<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> </tt>
+<a name="WriteMToFile"></a><div id="WriteMToFile-def"><a name="L324"></a><tt class="py-lineno">324</tt> <a class="py-toggle" href="#" id="WriteMToFile-toggle" onclick="return toggle('WriteMToFile');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#WriteMToFile">WriteMToFile</a><tt class="py-op">(</tt><tt class="py-param">matrix</tt><tt class="py-op">,</tt> <tt class="py-param">file_handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="WriteMToFile-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WriteMToFile-expanded"><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-docstring"> Writes the content of a matrix (list of lists) to a </tt> </tt>
+<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-docstring"> tab delimited text file</tt> </tt>
+<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">matrix</tt><tt class="py-op">:</tt> </tt>
+<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
+<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">file_handle</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">file_handle</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'\t'</tt><tt class="py-op">)</tt> </tt>
+<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-name">file_handle</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> </tt>
+<a name="WriteMToString"></a><div id="WriteMToString-def"><a name="L335"></a><tt class="py-lineno">335</tt> <a class="py-toggle" href="#" id="WriteMToString-toggle" onclick="return toggle('WriteMToString');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#WriteMToString">WriteMToString</a><tt class="py-op">(</tt><tt class="py-param">matrix</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="WriteMToString-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WriteMToString-expanded"><a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-docstring"> Returns the content of a matrix to a tab delimited</tt> </tt>
+<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-docstring"> string</tt> </tt>
+<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
+<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">matrix</tt><tt class="py-op">:</tt> </tt>
+<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
+<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\t'</tt> </tt>
+<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt>
+<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
+</div><a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> </tt>
+<a name="WriteListToString"></a><div id="WriteListToString-def"><a name="L347"></a><tt class="py-lineno">347</tt> <a class="py-toggle" href="#" id="WriteListToString-toggle" onclick="return toggle('WriteListToString');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#WriteListToString">WriteListToString</a><tt class="py-op">(</tt><tt class="py-param">list</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="WriteListToString-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WriteListToString-expanded"><a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
+<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">item</tt> <tt class="py-keyword">in</tt> <tt class="py-name">list</tt><tt class="py-op">:</tt> </tt>
+<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-name">format</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">" "</tt> </tt>
+<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
+</div><a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
+<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-comment">###############################################</tt> </tt>
+<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">######### SPECTRA ANALYSIS functions ##########</tt> </tt>
+<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">###############################################</tt> </tt>
+<a name="GetPeak"></a><div id="GetPeak-def"><a name="L356"></a><tt class="py-lineno">356</tt> <a class="py-toggle" href="#" id="GetPeak-toggle" onclick="return toggle('GetPeak');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#GetPeak">GetPeak</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">peakx</tt><tt class="py-op">,</tt> <tt class="py-param">lo</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">hi</tt><tt class="py-op">=</tt><tt class="py-number">41357</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="GetPeak-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GetPeak-expanded"><a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the x y index for the pair most closely to the peak mass</tt> </tt>
+<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-docstring"> in the list of data: mass-intensity</tt> </tt>
+<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-docstring"> Uses a binary search algorithm since the list is sorted</tt> </tt>
+<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-docstring"> 41357 is the number of datapoints from a typical exported spectrum </tt> </tt>
+<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-docstring"> between 700 and 3000 Da</tt> </tt>
+<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">mindif</tt> <tt class="py-op">=</tt> <tt class="py-number">0.037</tt> <tt class="py-comment">#it depends on the minimal distance between values</tt> </tt>
+<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-comment">#should be larger than half that minimal distance</tt> </tt>
+<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#hi = len(data)</tt> </tt>
+<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#lo = 0</tt> </tt>
+<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dif</tt> <tt class="py-op">=</tt> <tt class="py-number">10000.0</tt> </tt>
+<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
+<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-name">mindif</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">middle</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">hi</tt><tt class="py-op">-</tt><tt class="py-name">lo</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> <tt class="py-op">+</tt><tt class="py-name">lo</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-name">dif</tt> <tt class="py-op">=</tt> <tt class="py-name">peakx</tt> <tt class="py-op">-</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">middle</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dif</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
+<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dif</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">middle</tt> </tt>
+<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">middle</tt> </tt>
+<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">middle</tt> </tt>
+</div><a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> </tt>
+<a name="CrowlToMax"></a><div id="CrowlToMax-def"><a name="L382"></a><tt class="py-lineno">382</tt> <a class="py-toggle" href="#" id="CrowlToMax-toggle" onclick="return toggle('CrowlToMax');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#CrowlToMax">CrowlToMax</a><tt class="py-op">(</tt><tt class="py-param">peakindex</tt><tt class="py-op">,</tt> <tt class="py-param">howmuch</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="CrowlToMax-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CrowlToMax-expanded"><a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-docstring"> Returns the most probable position of a maximum around a given index</tt> </tt>
+<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-docstring"> Go around to see if the peak is really at the maximum value, otherwise</tt> </tt>
+<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"><tt class="py-docstring"> leave it as it was</tt> </tt>
+<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"><tt class="py-docstring"> <howmuch> the number of values tested around the actual value - 10 should be good</tt> </tt>
+<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-name">peak_int</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peakindex</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-name">newmax</tt> <tt class="py-op">=</tt> <tt class="py-name">peakindex</tt> </tt>
+<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-comment">#initialize with the value of the peak index, will be changed later</tt> </tt>
+<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">peakindex</tt><tt class="py-op">-</tt><tt class="py-name">howmuch</tt><tt class="py-op">,</tt> <tt class="py-name">peakindex</tt><tt class="py-op">+</tt><tt class="py-name">howmuch</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">peak_int</tt> <tt class="py-op"><=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
+<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-name">newmax</tt> <tt class="py-op">=</tt> <tt class="py-name">i</tt> </tt>
+<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">peak_int</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">newmax</tt> </tt>
+</div><a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> </tt>
+<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> </tt>
+<a name="GetBackground"></a><div id="GetBackground-def"><a name="L400"></a><tt class="py-lineno">400</tt> <a class="py-toggle" href="#" id="GetBackground-toggle" onclick="return toggle('GetBackground');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#GetBackground">GetBackground</a><tt class="py-op">(</tt><tt class="py-param">monoindex</tt><tt class="py-op">,</tt> <tt class="py-param">points</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">level</tt><tt class="py-op">=</tt><tt class="py-number">0.05</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="GetBackground-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GetBackground-expanded"><a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-docstring"> Define the background as the average of the <level>% lowest</tt> </tt>
+<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-docstring"> intensity values; uses function Mean</tt> </tt>
+<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"> <monoindex> - position of the monoisotopic peak</tt> </tt>
+<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-docstring"> <points> points considered</tt> </tt>
+<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"> <data> list of floats m/z, intensity</tt> </tt>
+<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-docstring"> <level> percent of points that might be considered in background</tt> </tt>
+<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">intensities</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">monoindex</tt><tt class="py-op">,</tt> <tt class="py-name">monoindex</tt><tt class="py-op">+</tt><tt class="py-name">points</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-name">intensities</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-name">intensities</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-name">smallestval_list</tt> <tt class="py-op">=</tt> <tt class="py-name">intensities</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">intensities</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">level</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
+<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-14" class="py-name"><a title="Collect_SILAC_XML.Mean
+lilamsxml.Mean" class="py-name" href="#" onclick="return doclink('link-14', 'Mean', 'link-11');">Mean</a></tt><tt class="py-op">(</tt><tt class="py-name">smallestval_list</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> </tt>
+<a name="GetIsotopeSeries"></a><div id="GetIsotopeSeries-def"><a name="L417"></a><tt class="py-lineno">417</tt> <a class="py-toggle" href="#" id="GetIsotopeSeries-toggle" onclick="return toggle('GetIsotopeSeries');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#GetIsotopeSeries">GetIsotopeSeries</a><tt class="py-op">(</tt><tt class="py-param">monoindex</tt><tt class="py-op">,</tt> <tt class="py-param">howmany</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="GetIsotopeSeries-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GetIsotopeSeries-expanded"><a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of intensities in a series of peaks</tt> </tt>
+<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-docstring"> Starting from the monoisotopic peak obtain maximum peaks at 1 Da</tt> </tt>
+<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-docstring"> distance intervals; uses function CrowlToMax to recenter on real peaks</tt> </tt>
+<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-docstring"> <howmany> defines the number of peaks to be retrieved</tt> </tt>
+<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"><tt class="py-docstring"> <monoindex> the mass of the firs peak in the series</tt> </tt>
+<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-docstring"> <data> a list containing floats in pairs: mass/intensity</tt> </tt>
+<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-comment"># calculate average distance for a dalton in the range of monoindex, between</tt> </tt>
+<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 15 and 30 values/dalton normally</tt> </tt>
+<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">distforonedalton</tt> <tt class="py-op">=</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-number">100</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">monoindex</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">monoindex</tt><tt class="py-op">+</tt><tt class="py-number">100</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> </tt>
+<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">peaklist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">howmany</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-name">peakindex</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Function lilamsxml.CrowlToMax()=lilamsxml-module.html#CrowlToMax"><a title="lilamsxml.CrowlToMax" class="py-name" href="#" onclick="return doclink('link-15', 'CrowlToMax', 'link-15');">CrowlToMax</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">monoindex</tt> <tt class="py-op">+</tt> <tt class="py-name">i</tt><tt class="py-op">*</tt><tt class="py-name">distforonedalton</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">distforonedalton</tt><tt class="py-op">/</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
+<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-comment">#we accept deviations of distforonedalton/3 - that is 0,33 Da - this can be modified</tt> </tt>
+<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#in general, the peptides are singly charged</tt> </tt>
+<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">peakvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peakindex</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-name">peakamu</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peakindex</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-name">peaklist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">peakamu</tt><tt class="py-op">,</tt> <tt class="py-name">peakvalue</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">peaklist</tt> </tt>
+</div><a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> </tt>
+<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> </tt>
+<a name="GetPeaksFromValue"></a><div id="GetPeaksFromValue-def"><a name="L442"></a><tt class="py-lineno">442</tt> <a class="py-toggle" href="#" id="GetPeaksFromValue-toggle" onclick="return toggle('GetPeaksFromValue');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#GetPeaksFromValue">GetPeaksFromValue</a><tt class="py-op">(</tt><tt class="py-param">monopeak</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">bground</tt> <tt class="py-op">=</tt> <tt class="py-number">100</tt><tt class="py-op">,</tt> <tt class="py-param">nbisotopes</tt> <tt class="py-op">=</tt> <tt class="py-number">14</tt><tt class="py-op">,</tt> <tt class="py-param">crowlnb</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="GetPeaksFromValue-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GetPeaksFromValue-expanded"><a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-docstring"> Generates the list (amu and intensities) from a peak amu value</tt> </tt>
+<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-docstring"> returns the family of peaks (amu and intensities) starting</tt> </tt>
+<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-docstring"> from a value of a peak measured in the spectra;</tt> </tt>
+<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-docstring"> uses functions GetPeak, GetBackground, GetIsotopeSeries,</tt> </tt>
+<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-docstring"> CrowlToMax</tt> </tt>
+<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-docstring"> monopeak - the mass of the monoisotopic peak</tt> </tt>
+<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-docstring"> bground - number of points around the peak to be considered</tt> </tt>
+<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-docstring"> for calculating the background</tt> </tt>
+<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-docstring"> nbisotopes - number of peaks returned for a family</tt> </tt>
+<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-docstring"> crowlnb - number of points tested to see if a peak is a peak</tt> </tt>
+<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-name">resultlst</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-comment">#see if we may find the peak around that value</tt> </tt>
+<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">peak_pos</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Function lilamsxml.GetPeak()=lilamsxml-module.html#GetPeak"><a title="lilamsxml.GetPeak" class="py-name" href="#" onclick="return doclink('link-16', 'GetPeak', 'link-16');">GetPeak</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">monopeak</tt><tt class="py-op">,</tt> <tt class="py-name">hi</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-comment">#test to see if there is no peak higher at 5 values around</tt> </tt>
+<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">real_peakpos</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="lilamsxml.CrowlToMax" class="py-name" href="#" onclick="return doclink('link-17', 'CrowlToMax', 'link-15');">CrowlToMax</a></tt><tt class="py-op">(</tt><tt class="py-name">peak_pos</tt><tt class="py-op">,</tt> <tt class="py-name">crowlnb</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
+<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-name">background</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name" targets="Function lilamsxml.GetBackground()=lilamsxml-module.html#GetBackground"><a title="lilamsxml.GetBackground" class="py-name" href="#" onclick="return doclink('link-18', 'GetBackground', 'link-18');">GetBackground</a></tt><tt class="py-op">(</tt><tt class="py-name">real_peakpos</tt><tt class="py-op">,</tt> <tt class="py-name">bground</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
+<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-name">peak_list</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name" targets="Function lilamsxml.GetIsotopeSeries()=lilamsxml-module.html#GetIsotopeSeries"><a title="lilamsxml.GetIsotopeSeries" class="py-name" href="#" onclick="return doclink('link-19', 'GetIsotopeSeries', 'link-19');">GetIsotopeSeries</a></tt><tt class="py-op">(</tt><tt class="py-name">real_peakpos</tt><tt class="py-op">,</tt> <tt class="py-name">nbisotopes</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
+<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> </tt>
+<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">element</tt> <tt class="py-keyword">in</tt> <tt class="py-name">peak_list</tt><tt class="py-op">:</tt> </tt>
+<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">resultlst</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">background</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> </tt>
+<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">resultlst</tt> </tt>
+</div><a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> </tt>
+<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"><tt class="py-comment">### INTERFACE WITH Isotope Pattern Calculator IPC ###</tt> </tt>
+<a name="RunIPC"></a><div id="RunIPC-def"><a name="L470"></a><tt class="py-lineno">470</tt> <a class="py-toggle" href="#" id="RunIPC-toggle" onclick="return toggle('RunIPC');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#RunIPC">RunIPC</a><tt class="py-op">(</tt><tt class="py-param">peptide</tt><tt class="py-op">,</tt> <tt class="py-param">howmany</tt><tt class="py-op">,</tt> <tt class="py-param">monoisoint</tt><tt class="py-op">,</tt> <tt class="py-param">ipc_path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="RunIPC-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RunIPC-expanded"><a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"><tt class="py-docstring"> Runs the external program IPC -> theoretical isotopic distribution</tt> </tt>
+<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of peptide masses+H and intensities at 1 Da distance,</tt> </tt>
+<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"><tt class="py-docstring"> normalized to the intensity of the monoisoint peak. Theoretical distribution</tt> </tt>
+<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"><tt class="py-docstring"> of the peak intensities is calculated by IPC, its path is indicated by <ipc_path></tt> </tt>
+<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"><tt class="py-docstring"> needs os and string import.</tt> </tt>
+<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"><tt class="py-docstring"> How to test:</tt> </tt>
+<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"><tt class="py-docstring"> pep = "AADGGHGGHHILL"</tt> </tt>
+<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-docstring"> hmany = 6</tt> </tt>
+<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"><tt class="py-docstring"> rlist = []</tt> </tt>
+<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"><tt class="py-docstring"> rlist = RunIPC(pep, hmany)</tt> </tt>
+<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-name">HMASS</tt> <tt class="py-op">=</tt> <tt class="py-number">1.007825</tt> <tt class="py-comment">#to be added to the peaks for m/z calculations</tt> </tt>
+<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-comment">#ipccommand = r"/usr/local/ipc-1.1/ipc" #example of hardcoded path to ipc executable</tt> </tt>
+<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ipccommand</tt> <tt class="py-op">=</tt> <tt class="py-name">ipc_path</tt> </tt>
+<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-name">ipciterations</tt> <tt class="py-op">=</tt> <tt class="py-string">"-f 500"</tt> </tt>
+<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-name">ipcresolution</tt> <tt class="py-op">=</tt> <tt class="py-string">"-d 1"</tt> <tt class="py-comment">#this will sum the intensities of peaks at less than 0.1 Da apart</tt> </tt>
+<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-name">ipcpeptide</tt> <tt class="py-op">=</tt> <tt class="py-string">"-a "</tt> <tt class="py-op">+</tt> <tt class="py-name">peptide</tt> </tt>
+<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> </tt>
+<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-name">pipe_ipc</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">popen</tt><tt class="py-op">(</tt><tt class="py-string">"%s %s %s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">ipccommand</tt><tt class="py-op">,</tt> <tt class="py-name">ipciterations</tt><tt class="py-op">,</tt> <tt class="py-name">ipcresolution</tt><tt class="py-op">,</tt> <tt class="py-name">ipcpeptide</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-name">pipe_ipc</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt class="py-name">out_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-name">res_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">howmany</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-name">out_list</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">pipe_ipc</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> </tt>
+<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">elm</tt> <tt class="py-keyword">in</tt> <tt class="py-name">out_list</tt><tt class="py-op">:</tt> </tt>
+<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-name">amustr</tt> <tt class="py-op">=</tt> <tt class="py-name">elm</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">percentstr</tt> <tt class="py-op">=</tt> <tt class="py-name">elm</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
+<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-name">res_list</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">amustr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">HMASS</tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">percentstr</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-comment">#the elements 1 and 3 are the amu and the relative abundance</tt> </tt>
+<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#the [0:-1] chops the last character (comma)</tt> </tt>
+<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-name">norm_lst</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment">#normalized list in function of the intensity of the first peak</tt> </tt>
+<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">res_list</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-name">norm_lst</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">res_list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">res_list</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">monoisoint</tt><tt class="py-op">/</tt><tt class="py-name">res_list</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> </tt>
+<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">norm_lst</tt> </tt>
+</div><a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> </tt>
+<a name="IsDifference"></a><div id="IsDifference-def"><a name="L512"></a><tt class="py-lineno">512</tt> <a class="py-toggle" href="#" id="IsDifference-toggle" onclick="return toggle('IsDifference');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#IsDifference">IsDifference</a><tt class="py-op">(</tt><tt class="py-param">difference</tt><tt class="py-op">,</tt> <tt class="py-param">dif</tt><tt class="py-op">,</tt> <tt class="py-param">tolerated</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="IsDifference-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IsDifference-expanded"><a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"><tt class="py-docstring"> Returns 1 if the <difference> is in the tolerated range around <dif></tt> </tt>
+<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"><tt class="py-docstring"> accepts an error, the <tolerated> parameter</tt> </tt>
+<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">difference</tt><tt class="py-op">></tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">-</tt><tt class="py-name">tolerated</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">difference</tt> <tt class="py-op"><</tt><tt class="py-op">(</tt><tt class="py-name">dif</tt><tt class="py-op">+</tt><tt class="py-name">tolerated</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
+<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
+</div><a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> </tt>
+<a name="PepCompare"></a><div id="PepCompare-def"><a name="L522"></a><tt class="py-lineno">522</tt> <a class="py-toggle" href="#" id="PepCompare-toggle" onclick="return toggle('PepCompare');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#PepCompare">PepCompare</a><tt class="py-op">(</tt><tt class="py-param">pepmz</tt><tt class="py-op">,</tt> <tt class="py-param">pepseq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepCompare-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PepCompare-expanded"><a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"><tt class="py-docstring"> Evaluates the measured mass of a peptide to see if its deuterated or not</tt> </tt>
+<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"><tt class="py-docstring"> Returns a dictionary containing the corrected pepmz if deuterated,</tt> </tt>
+<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"><tt class="py-docstring"> the peptide sequence (unchanged), and two flags MODIFIED if MetOX or other</tt> </tt>
+<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"><tt class="py-docstring"> has been found and IGNORE if no known modification was found. It also calculates</tt> </tt>
+<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"><tt class="py-docstring"> the number of leucines and reports it as a fifth element NBLEU.</tt> </tt>
+<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"><tt class="py-docstring"> Uses CalcMonoMz and IsDifference.</tt> </tt>
+<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-name">HPLUS</tt> <tt class="py-op">=</tt> <tt class="py-number">1.007825</tt> </tt>
+<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">tolerated</tt> <tt class="py-op">=</tt> <tt class="py-number">0.3</tt> <tt class="py-comment">#daltons</tt> </tt>
+<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-name">theor_mz</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name" targets="Function lilamsxml.CalcMonoMz()=lilamsxml-module.html#CalcMonoMz"><a title="lilamsxml.CalcMonoMz" class="py-name" href="#" onclick="return doclink('link-20', 'CalcMonoMz', 'link-20');">CalcMonoMz</a></tt><tt class="py-op">(</tt><tt class="py-name">pepseq</tt><tt class="py-op">)</tt> </tt>
+<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-name">modif_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"MetOX"</tt><tt class="py-op">:</tt><tt class="py-number">15.9949</tt><tt class="py-op">}</tt> </tt>
+<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-name">deut_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"NotD"</tt><tt class="py-op">:</tt> <tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-string">"1LeuD3"</tt><tt class="py-op">:</tt> <tt class="py-number">3.023</tt><tt class="py-op">,</tt> <tt class="py-string">"2LeuD3"</tt> <tt class="py-op">:</tt> <tt class="py-number">6.047</tt><tt class="py-op">,</tt> <tt class="py-string">"3LeuD3"</tt><tt class="py-op">:</tt> <tt class="py-number">9.07</tt><tt class="py-op">,</tt> <tt class="py-string">"4LeuD3"</tt><tt class="py-op">:</tt> <tt class="py-number">12.094</tt><tt class="py-op">}</tt> </tt>
+<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> </tt>
+<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-comment">#test if the peptide is the deuterated form (up to 4 Leu)</tt> </tt>
+<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">diff_mz</tt> <tt class="py-op">=</tt> <tt class="py-name">pepmz</tt> <tt class="py-op">-</tt> <tt class="py-name">theor_mz</tt> </tt>
+<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-name">MODIFIED</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-name">IGNORE</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-name">NBLEU</tt> <tt class="py-op">=</tt> <tt class="py-name">pepseq</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'L'</tt><tt class="py-op">)</tt> </tt>
+<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> </tt>
+<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-name">FOUND</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">mod</tt> <tt class="py-keyword">in</tt> <tt class="py-name">modif_dict</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">dif</tt> <tt class="py-keyword">in</tt> <tt class="py-name">deut_dict</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-21" class="py-name" targets="Function lilamsxml.IsDifference()=lilamsxml-module.html#IsDifference"><a title="lilamsxml.IsDifference" class="py-name" href="#" onclick="return doclink('link-21', 'IsDifference', 'link-21');">IsDifference</a></tt><tt class="py-op">(</tt><tt class="py-name">diff_mz</tt><tt class="py-op">,</tt> <tt class="py-name">deut_dict</tt><tt class="py-op">[</tt><tt class="py-name">dif</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">tolerated</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-name">pepmz</tt> <tt class="py-op">=</tt> <tt class="py-name">pepmz</tt> <tt class="py-op">-</tt> <tt class="py-name">deut_dict</tt><tt class="py-op">[</tt><tt class="py-name">dif</tt><tt class="py-op">]</tt> </tt>
+<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-name">FOUND</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
+<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-22" class="py-name"><a title="lilamsxml.IsDifference" class="py-name" href="#" onclick="return doclink('link-22', 'IsDifference', 'link-21');">IsDifference</a></tt><tt class="py-op">(</tt><tt class="py-name">diff_mz</tt><tt class="py-op">,</tt> <tt class="py-name">deut_dict</tt><tt class="py-op">[</tt><tt class="py-name">dif</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">modif_dict</tt><tt class="py-op">[</tt><tt class="py-name">mod</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">tolerated</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-name">pepmz</tt> <tt class="py-op">=</tt> <tt class="py-name">pepmz</tt> <tt class="py-op">-</tt> <tt class="py-name">deut_dict</tt><tt class="py-op">[</tt><tt class="py-name">dif</tt><tt class="py-op">]</tt> </tt>
+<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-name">MODIFIED</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-name">FOUND</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
+<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">FOUND</tt><tt class="py-op">:</tt> </tt>
+<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-comment">#none of the tested modifications or deuteration accounted for the mass difference</tt> </tt>
+<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">IGNORE</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">{</tt><tt class="py-string">"pepmz"</tt><tt class="py-op">:</tt><tt class="py-name">pepmz</tt><tt class="py-op">,</tt> <tt class="py-string">"pepseq"</tt><tt class="py-op">:</tt><tt class="py-name">pepseq</tt><tt class="py-op">,</tt> <tt class="py-string">"MODIFIED"</tt><tt class="py-op">:</tt><tt class="py-name">MODIFIED</tt><tt class="py-op">,</tt> <tt class="py-string">"IGNORE"</tt><tt class="py-op">:</tt><tt class="py-name">IGNORE</tt><tt class="py-op">,</tt> <tt class="py-string">"NBLEU"</tt><tt class="py-op">:</tt><tt class="py-name">NBLEU</tt><tt class="py-op">}</tt> </tt>
+</div><a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> </tt>
+<a name="CorrectIsotopicSeries"></a><div id="CorrectIsotopicSeries-def"><a name="L561"></a><tt class="py-lineno">561</tt> <a class="py-toggle" href="#" id="CorrectIsotopicSeries-toggle" onclick="return toggle('CorrectIsotopicSeries');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#CorrectIsotopicSeries">CorrectIsotopicSeries</a><tt class="py-op">(</tt><tt class="py-param">pepmz</tt><tt class="py-op">,</tt> <tt class="py-param">pepseq</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">peaks</tt><tt class="py-op">,</tt> <tt class="py-param">ipc_path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="CorrectIsotopicSeries-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CorrectIsotopicSeries-expanded"><a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the theoretical intensities of the first 4 peaks</tt> </tt>
+<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"><tt class="py-docstring"> for peptides with 1 Leucine, the pepmz corresponds to the nondeuterated form.</tt> </tt>
+<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"><tt class="py-docstring"> This function is called only when the NBLEU of a peptide is 1</tt> </tt>
+<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"><tt class="py-docstring"> Otherwise, the differences in m/z between non-deuterated and deuterated</tt> </tt>
+<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"><tt class="py-docstring"> peptides are larger, the contribution of secondary peaks to the quantification</tt> </tt>
+<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"><tt class="py-docstring"> is less important (ignored)</tt> </tt>
+<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of differences between the measured and theoretical</tt> </tt>
+<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"><tt class="py-docstring"> intensities for the peaks normalized to the monoisotopic peak.</tt> </tt>
+<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"><tt class="py-docstring"> Uses most of the functions previously defined by calls to </tt> </tt>
+<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"><tt class="py-docstring"> GetPeaksFromValue and RunIPC. The first elements of the returned</tt> </tt>
+<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"><tt class="py-docstring"> list are the peptide sequence, mz and the intensity of the monoisotopic peak</tt> </tt>
+<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-name">theor_mz</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="lilamsxml.CalcMonoMz" class="py-name" href="#" onclick="return doclink('link-23', 'CalcMonoMz', 'link-20');">CalcMonoMz</a></tt><tt class="py-op">(</tt><tt class="py-name">pepseq</tt><tt class="py-op">)</tt> </tt>
+<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-name">mz_difference</tt> <tt class="py-op">=</tt> <tt class="py-name">pepmz</tt> <tt class="py-op">-</tt> <tt class="py-name">theor_mz</tt> </tt>
+<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt class="py-name">measured_lst</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name" targets="Function lilamsxml.GetPeaksFromValue()=lilamsxml-module.html#GetPeaksFromValue"><a title="lilamsxml.GetPeaksFromValue" class="py-name" href="#" onclick="return doclink('link-24', 'GetPeaksFromValue', 'link-24');">GetPeaksFromValue</a></tt><tt class="py-op">(</tt><tt class="py-name">pepmz</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">nbisotopes</tt><tt class="py-op">=</tt><tt class="py-name">peaks</tt><tt class="py-op">)</tt> </tt>
+<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-comment">#recover the peaks on a range of 6 daltons from the monoisotopic peak</tt> </tt>
+<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">monointensity</tt> <tt class="py-op">=</tt> <tt class="py-name">measured_lst</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pepseq</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">"L"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-name">theor_lst</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name" targets="Function lilamsxml.RunIPC()=lilamsxml-module.html#RunIPC"><a title="lilamsxml.RunIPC" class="py-name" href="#" onclick="return doclink('link-25', 'RunIPC', 'link-25');">RunIPC</a></tt><tt class="py-op">(</tt><tt class="py-name">pepseq</tt><tt class="py-op">,</tt> <tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-name">monointensity</tt><tt class="py-op">,</tt> <tt class="py-name">ipc_path</tt><tt class="py-op">)</tt> </tt>
+<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-comment">#obtain the calculated list of pairs (mz, Intensity) based on the monointensity value given</tt> </tt>
+<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-name">dif_lstint</tt><tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">pepseq</tt><tt class="py-op">]</tt> </tt>
+<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-name">dif_lstint</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">pepmz</tt><tt class="py-op">)</tt> </tt>
+<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> </tt>
+<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">measured_lst</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-comment">#we only substract from the measured values the peaks 4, 5, 6</tt> </tt>
+<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">pepseq</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">"L"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">i</tt> <tt class="py-op"><</tt> <tt class="py-number">3</tt> <tt class="py-keyword">or</tt> <tt class="py-name">i</tt> <tt class="py-op">></tt> <tt class="py-number">5</tt><tt class="py-op">:</tt> </tt>
+<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-name">dif_lstint</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">measured_lst</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-name">dif_lstint</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">measured_lst</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">theor_lst</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-name">dif_lstint</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">measured_lst</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> </tt>
+<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">dif_lstint</tt> </tt>
+</div><a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> </tt>
+<a name="MzIntGet"></a><div id="MzIntGet-def"><a name="L600"></a><tt class="py-lineno">600</tt> <a class="py-toggle" href="#" id="MzIntGet-toggle" onclick="return toggle('MzIntGet');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#MzIntGet">MzIntGet</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">pepmz</tt><tt class="py-op">,</tt> <tt class="py-param">plusminus</tt><tt class="py-op">=</tt><tt class="py-number">15</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MzIntGet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MzIntGet-expanded"><a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the list of mz-int pairs</tt> </tt>
+<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"><tt class="py-docstring"> from the spectrum data</tt> </tt>
+<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"><tt class="py-docstring"> Returns tuple of two lists</tt> </tt>
+<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt class="py-name">mzdata</tt><tt class="py-op">,</tt> <tt class="py-name">intdata</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> </tt>
+<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> <tt class="py-name">peakindex</tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="lilamsxml.GetPeak" class="py-name" href="#" onclick="return doclink('link-26', 'GetPeak', 'link-16');">GetPeak</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">pepmz</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">hi</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-name">distforonedalton</tt> <tt class="py-op">=</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">round</tt><tt class="py-op">(</tt><tt class="py-number">100</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peakindex</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">peakindex</tt><tt class="py-op">+</tt><tt class="py-number">100</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-name">minindex</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">peakindex</tt> <tt class="py-op">-</tt> <tt class="py-name">distforonedalton</tt><tt class="py-op">*</tt><tt class="py-name">plusminus</tt><tt class="py-op">)</tt> </tt>
+<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-name">maxindex</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">peakindex</tt> <tt class="py-op">+</tt> <tt class="py-name">distforonedalton</tt><tt class="py-op">*</tt><tt class="py-name">plusminus</tt> <tt class="py-op">+</tt> <tt class="py-number">6</tt><tt class="py-op">*</tt><tt class="py-name">distforonedalton</tt><tt class="py-op">)</tt> </tt>
+<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">minindex</tt><tt class="py-op">,</tt> <tt class="py-name">maxindex</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-name">mzdata</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-name">intdata</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-keyword">return</tt><tt class="py-op">(</tt><tt class="py-name">mzdata</tt><tt class="py-op">,</tt> <tt class="py-name">intdata</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> </tt>
+<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"><tt class="py-comment">##################################</tt> </tt>
+<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#### Processing data structure ###</tt> </tt>
+<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##################################</tt> </tt>
+<a name="DataIntObj"></a><div id="DataIntObj-def"><a name="L621"></a><tt class="py-lineno">621</tt> <a class="py-toggle" href="#" id="DataIntObj-toggle" onclick="return toggle('DataIntObj');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html">DataIntObj</a><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DataIntObj-expanded"><a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"><tt class="py-docstring"> A data structure to handle SILAC</tt> </tt>
+<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"><tt class="py-docstring"> difference results and calculate</tt> </tt>
+<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"><tt class="py-docstring"> statistics</tt> </tt>
+<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="DataIntObj.__init__"></a><div id="DataIntObj.__init__-def"><a name="L627"></a><tt class="py-lineno">627</tt> <a class="py-toggle" href="#" id="DataIntObj.__init__-toggle" onclick="return toggle('DataIntObj.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataIntObj.__init__-expanded"><a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">nmbentries</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
+<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
+<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
+<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-comment">#dictionaries with unique keys formed by pepseq+mzh</tt> </tt>
+<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">deleted</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+</div><a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> </tt>
+<a name="DataIntObj.get_data"></a><div id="DataIntObj.get_data-def"><a name="L635"></a><tt class="py-lineno">635</tt> <a class="py-toggle" href="#" id="DataIntObj.get_data-toggle" onclick="return toggle('DataIntObj.get_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html#get_data">get_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt> <tt class="py-op">,</tt> <tt class="py-param">matrix</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj.get_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataIntObj.get_data-expanded"><a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"><tt class="py-docstring"> transforms the matrix obtained by several</tt> </tt>
+<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"><tt class="py-docstring"> calls to DiffMeasTheor into internal data</tt> </tt>
+<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">element</tt> <tt class="py-keyword">in</tt> <tt class="py-name">matrix</tt><tt class="py-op">:</tt> </tt>
+<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-name">listdiff</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">element</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt class="py-comment">#first element is pepseq, second element modif pepmz</tt> </tt>
+<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">listdiff</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-name">intdict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">:</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"mzh"</tt><tt class="py-op">:</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-string">"calcmzh"</tt><tt class="py-op">:</tt><tt id="link-27" class="py-name"><a title="lilamsxml.CalcMonoMz" class="py-name" href="#" onclick="return doclink('link-27', 'CalcMonoMz', 'link-20');">CalcMonoMz</a></tt><tt class="py-op">(</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-string">"int0"</tt><tt class="py-op">:</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-string">"BADPEAKS"</tt><tt class="py-op">:</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
+<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-string">"listdiff"</tt><tt class="py-op">:</tt><tt class="py-name">listdiff</tt><tt class="py-op">}</tt> </tt>
+<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-name">intdict</tt><tt class="py-op">[</tt><tt class="py-string">"massdiff"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">intdict</tt><tt class="py-op">[</tt><tt class="py-string">"mzh"</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">intdict</tt><tt class="py-op">[</tt><tt class="py-string">"calcmzh"</tt><tt class="py-op">]</tt> </tt>
+<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt class="py-name">intdict</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">intdict</tt><tt class="py-op">[</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">count</tt><tt class="py-op">(</tt><tt class="py-string">'L'</tt><tt class="py-op">)</tt> </tt>
+<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-string">'_'</tt><tt class="py-op">+</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">element</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">intdict</tt> </tt>
+<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> </tt>
+</div><a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> </tt>
+<a name="DataIntObj.filter_peaks"></a><div id="DataIntObj.filter_peaks-def"><a name="L655"></a><tt class="py-lineno">655</tt> <a class="py-toggle" href="#" id="DataIntObj.filter_peaks-toggle" onclick="return toggle('DataIntObj.filter_peaks');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html#filter_peaks">filter_peaks</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj.filter_peaks-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataIntObj.filter_peaks-expanded"><a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-docstring"> Eliminates from self.data the peaks for which</tt> </tt>
+<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"><tt class="py-docstring"> the peak 3 or multiple is higher than 2 or multiple</tt> </tt>
+<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"><tt class="py-docstring"> Decides whether to take the non-deuterated or the</tt> </tt>
+<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"><tt class="py-docstring"> deuterated form in function of the intensity of the</tt> </tt>
+<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"><tt class="py-docstring"> corresponding peaks</tt> </tt>
+<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt class="py-name">entrieslist</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entrykey</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entrieslist</tt><tt class="py-op">:</tt> </tt>
+<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt class="py-comment">#print self.data[entrykey]</tt> </tt>
+<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">peak2</tt><tt class="py-op">,</tt> <tt class="py-name">peak3</tt><tt class="py-op">,</tt> <tt class="py-name">peakdx2</tt><tt class="py-op">,</tt> <tt class="py-name">peakdx3</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-number">0.0</tt><tt class="py-op">,</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-name">nbleu</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt> </tt>
+<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nbleu</tt> <tt class="py-op"><=</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
+<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-comment">#treat maximum 4 leucines</tt> </tt>
+<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">13</tt><tt class="py-op">:</tt> </tt>
+<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-name">peak2</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-name">peak3</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
+<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-name">peakdx2</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">nbleu</tt><tt class="py-op">*</tt><tt class="py-number">3</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt class="py-name">peakdx3</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">nbleu</tt><tt class="py-op">*</tt><tt class="py-number">3</tt><tt class="py-op">+</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
+<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> <tt class="py-comment">#print peak2, peak3, peakdx2, peakdx3, "peaks"</tt> </tt>
+<a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">peak2</tt><tt class="py-op">+</tt><tt class="py-name">peak3</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-op">(</tt><tt class="py-name">peakdx2</tt><tt class="py-op">+</tt><tt class="py-name">peakdx3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> <tt class="py-comment">#work only with the highest value pair</tt> </tt>
+<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">peak3</tt> <tt class="py-op">></tt> <tt class="py-name">peak2</tt><tt class="py-op">:</tt> </tt>
+<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt> </tt>
+<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">deleted</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">entrykey</tt><tt class="py-op">)</tt> </tt>
+<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-comment">#"Considered unreliable", entrykey</tt> </tt>
+<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">peakdx3</tt> <tt class="py-op">></tt> <tt class="py-name">peakdx2</tt><tt class="py-op">:</tt> </tt>
+<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt> </tt>
+<a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">deleted</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">entrykey</tt><tt class="py-op">)</tt> </tt>
+<a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"> <tt class="py-comment">#"Considered unreliable", entrykey</tt> </tt>
+<a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt> </tt>
+<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"> <tt class="py-comment">#"List too short", entrykey</tt> </tt>
+<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">entrykey</tt><tt class="py-op">]</tt> </tt>
+<a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"> <tt class="py-comment">#"More than 4 leucines", entrykey</tt> </tt>
+<a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> </tt>
+</div><a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"> </tt>
+<a name="DataIntObj.calc_ratios"></a><div id="DataIntObj.calc_ratios-def"><a name="L695"></a><tt class="py-lineno">695</tt> <a class="py-toggle" href="#" id="DataIntObj.calc_ratios-toggle" onclick="return toggle('DataIntObj.calc_ratios');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html#calc_ratios">calc_ratios</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj.calc_ratios-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataIntObj.calc_ratios-expanded"><a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-docstring"> Calculates the ratios deut/nondeuterated peptides</tt> </tt>
+<a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"><tt class="py-docstring"> in a mix based on peptide sequence (0, 1-4 leucines)</tt> </tt>
+<a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"> <tt class="py-name">entrieslist</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"> </tt>
+<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entrieslist</tt><tt class="py-op">:</tt> </tt>
+<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"> <tt class="py-name">nbleu</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt> </tt>
+<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"> <tt class="py-name">monoisoint</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nbleu</tt> <tt class="py-op"><></tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">monoisoint</tt> <tt class="py-op"><></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">nbleu</tt><tt class="py-op">*</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-name">monoisoint</tt> </tt>
+<a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt> </tt>
+</div><a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> </tt>
+<a name="DataIntObj.calc_statistics"></a><div id="DataIntObj.calc_statistics-def"><a name="L711"></a><tt class="py-lineno">711</tt> <a class="py-toggle" href="#" id="DataIntObj.calc_statistics-toggle" onclick="return toggle('DataIntObj.calc_statistics');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html#calc_statistics">calc_statistics</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj.calc_statistics-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataIntObj.calc_statistics-expanded"><a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"><tt class="py-docstring"> Median, average and StdDev for the fractions calculated for</tt> </tt>
+<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"><tt class="py-docstring"> peptides with 1, 2, 3 or 4 leucines</tt> </tt>
+<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"> <tt class="py-name">frlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> <tt class="py-name">entrieslist</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">entrieslist</tt><tt class="py-op">:</tt> </tt>
+<a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt class="py-name">nbleu</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt> </tt>
+<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">nbleu</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">nbleu</tt> <tt class="py-op"><</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"> <tt class="py-name">frlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"Median"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-28" class="py-name" targets="Function Collect_SILAC_XML.Median()=Collect_SILAC_XML-module.html#Median,Function lilamsxml.Median()=lilamsxml-module.html#Median"><a title="Collect_SILAC_XML.Median
+lilamsxml.Median" class="py-name" href="#" onclick="return doclink('link-28', 'Median', 'link-28');">Median</a></tt><tt class="py-op">(</tt><tt class="py-name">frlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"Mean"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-29" class="py-name"><a title="Collect_SILAC_XML.Mean
+lilamsxml.Mean" class="py-name" href="#" onclick="return doclink('link-29', 'Mean', 'link-11');">Mean</a></tt><tt class="py-op">(</tt><tt class="py-name">frlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"StdDev"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-30" class="py-name" targets="Function Collect_SILAC_XML.StdDev()=Collect_SILAC_XML-module.html#StdDev,Function lilamsxml.StdDev()=lilamsxml-module.html#StdDev"><a title="Collect_SILAC_XML.StdDev
+lilamsxml.StdDev" class="py-name" href="#" onclick="return doclink('link-30', 'StdDev', 'link-30');">StdDev</a></tt><tt class="py-op">(</tt><tt class="py-name">frlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"Nbvalues"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">frlist</tt><tt class="py-op">)</tt> </tt>
+<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt class="py-comment">#print self.statistics</tt> </tt>
+<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt> </tt>
+</div><a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> </tt>
+<a name="DataIntObj.return_resultsXML"></a><div id="DataIntObj.return_resultsXML-def"><a name="L730"></a><tt class="py-lineno">730</tt> <a class="py-toggle" href="#" id="DataIntObj.return_resultsXML-toggle" onclick="return toggle('DataIntObj.return_resultsXML');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html#return_resultsXML">return_resultsXML</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">spectr_dict</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj.return_resultsXML-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataIntObj.return_resultsXML-expanded"><a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"><tt class="py-docstring"> The results are returned in very simple XML-like format</tt> </tt>
+<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"><tt class="py-docstring"> that should be compatible with Silacvalidator.py (interactive visualization</tt> </tt>
+<a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"><tt class="py-docstring"> of the results)</tt> </tt>
+<a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-comment">#res = [["Pepseq", "mz", "mzcalc", "Leucines", "MonoisoIntensity", "DeuteratedIntensity",</tt> </tt>
+<a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#"Deuterated_fraction"]]</tt> </tt>
+<a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Add primary data</tt> </tt>
+<a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">root</tt><tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">Element</tt><tt class="py-op">(</tt><tt class="py-string">"protdata"</tt><tt class="py-op">)</tt> </tt>
+<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-name">idroot</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">,</tt> <tt class="py-string">"id_parameters"</tt><tt class="py-op">)</tt> </tt>
+<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"> <tt class="py-name">comm</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">idroot</tt><tt class="py-op">,</tt> <tt class="py-string">"spot_id"</tt><tt class="py-op">)</tt> </tt>
+<a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"> <tt class="py-name">comm</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"comment"</tt><tt class="py-op">]</tt> </tt>
+<a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"> <tt class="py-name">dbase</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">idroot</tt><tt class="py-op">,</tt> <tt class="py-string">"database"</tt><tt class="py-op">)</tt> </tt>
+<a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"> <tt class="py-name">dbase</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"database"</tt><tt class="py-op">]</tt> </tt>
+<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"> <tt class="py-name">ppm</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">idroot</tt><tt class="py-op">,</tt> <tt class="py-string">"ppm_tolerance"</tt><tt class="py-op">)</tt> </tt>
+<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"> <tt class="py-name">ppm</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"parent_mass_tolerance"</tt><tt class="py-op">]</tt> </tt>
+<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"> <tt class="py-name">mowse</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">idroot</tt><tt class="py-op">,</tt> <tt class="py-string">"mowse_score"</tt><tt class="py-op">)</tt> </tt>
+<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"> <tt class="py-name">mowse</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"mowse_score"</tt><tt class="py-op">]</tt> </tt>
+<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"> <tt class="py-name">mowse</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"1.0"</tt> </tt>
+<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> <tt class="py-name">protcovg</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">idroot</tt><tt class="py-op">,</tt> <tt class="py-string">"pep_coverage"</tt><tt class="py-op">)</tt> </tt>
+<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"> <tt class="py-name">protcovg</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"protein_coverage"</tt><tt class="py-op">]</tt> </tt>
+<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"> <tt class="py-name">matchedpep</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">idroot</tt><tt class="py-op">,</tt> <tt class="py-string">"no_matched_pept"</tt><tt class="py-op">)</tt> </tt>
+<a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"> <tt class="py-name">matchedpep</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"pepdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"matched"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"> <tt class="py-name">accnb</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">,</tt> <tt class="py-string">"accession_number"</tt><tt class="py-op">)</tt> </tt>
+<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"> <tt class="py-name">accnb</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"accession_number"</tt><tt class="py-op">]</tt> </tt>
+<a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> <tt class="py-name">enname</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">,</tt> <tt class="py-string">"entry_name"</tt><tt class="py-op">)</tt> </tt>
+<a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"> <tt class="py-name">enname</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"entry_name"</tt><tt class="py-op">]</tt> </tt>
+<a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"> <tt class="py-name">protmw</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">,</tt> <tt class="py-string">"prot_mw"</tt><tt class="py-op">)</tt> </tt>
+<a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"> <tt class="py-name">protmw</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"protein_mw"</tt><tt class="py-op">]</tt> </tt>
+<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"> <tt class="py-name">protpi</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">,</tt> <tt class="py-string">"prot_pi"</tt><tt class="py-op">)</tt> </tt>
+<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"> <tt class="py-name">protpi</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">"protdata"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"protein_pI"</tt><tt class="py-op">]</tt> </tt>
+<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"> </tt>
+<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"> <tt class="py-name">pepdataroot</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">,</tt> <tt class="py-string">"pepdata"</tt><tt class="py-op">)</tt> </tt>
+<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"> </tt>
+<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">peprec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"> <tt class="py-name">nbleu</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt> </tt>
+<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nbleu</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"> <tt class="py-name">deuterated</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">nbleu</tt><tt class="py-op">*</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
+<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"> <tt class="py-name">deuterated</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> </tt>
+<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> <tt class="py-name">pepentry</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepdataroot</tt><tt class="py-op">,</tt> <tt class="py-string">"measured"</tt><tt class="py-op">)</tt> </tt>
+<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> <tt class="py-name">pepseq</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"pepseq"</tt><tt class="py-op">)</tt> </tt>
+<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"> <tt class="py-name">pepseq</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">]</tt> </tt>
+<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> <tt class="py-name">mzh</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"mzh"</tt><tt class="py-op">)</tt> </tt>
+<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-name">mzh</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%.4f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"mzh"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"> <tt class="py-name">calcmzh</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"calc_mzh"</tt><tt class="py-op">)</tt> </tt>
+<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-name">calcmzh</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%.4f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"calcmzh"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-name">Lnumber</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"leucines"</tt><tt class="py-op">)</tt> </tt>
+<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-name">Lnumber</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-name">int0</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"mono_iso_intensity"</tt><tt class="py-op">)</tt> </tt>
+<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-name">int0</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%.0f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"int0"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> <tt class="py-name">intd</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"deuterated_intensity"</tt><tt class="py-op">)</tt> </tt>
+<a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> <tt class="py-name">intd</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%.0f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">deuterated</tt><tt class="py-op">)</tt> </tt>
+<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> <tt class="py-name">ratio</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"ratio"</tt><tt class="py-op">)</tt> </tt>
+<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"> <tt class="py-name">ratio</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%.2f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"> <tt class="py-name">validated</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"validated"</tt><tt class="py-op">)</tt> </tt>
+<a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"> <tt class="py-name">validated</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"UNKNOWN"</tt> </tt>
+<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"> <tt class="py-comment">#lookedat = ET.SubElement(pepentry, "looked_at")</tt> </tt>
+<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#lookedat.text = "NO"</tt> </tt>
+<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">local_bg</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"local_bg"</tt><tt class="py-op">)</tt> </tt>
+<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt class="py-name">local_bg</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"0.0000"</tt> </tt>
+<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> <tt class="py-name">corr_ratio</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"corrected_ratio"</tt><tt class="py-op">)</tt> </tt>
+<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> <tt class="py-name">corr_ratio</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%.2f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> <tt class="py-name">spec_piece</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">pepentry</tt><tt class="py-op">,</tt> <tt class="py-string">"spectrum"</tt><tt class="py-op">)</tt> </tt>
+<a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"> <tt class="py-name">mzspec</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">spec_piece</tt><tt class="py-op">,</tt> <tt class="py-string">"mz_list"</tt><tt class="py-op">)</tt> </tt>
+<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"> <tt class="py-name">mzspec</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name" targets="Function lilamsxml.WriteListToString()=lilamsxml-module.html#WriteListToString"><a title="lilamsxml.WriteListToString" class="py-name" href="#" onclick="return doclink('link-31', 'WriteListToString', 'link-31');">WriteListToString</a></tt><tt class="py-op">(</tt><tt class="py-name">spectr_dict</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"%.4f"</tt><tt class="py-op">)</tt> </tt>
+<a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> <tt class="py-name">intspec</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">SubElement</tt><tt class="py-op">(</tt><tt class="py-name">spec_piece</tt><tt class="py-op">,</tt> <tt class="py-string">"int_list"</tt><tt class="py-op">)</tt> </tt>
+<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"> <tt class="py-name">intspec</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="lilamsxml.WriteListToString" class="py-name" href="#" onclick="return doclink('link-32', 'WriteListToString', 'link-31');">WriteListToString</a></tt><tt class="py-op">(</tt><tt class="py-name">spectr_dict</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"%.4f"</tt><tt class="py-op">)</tt> </tt>
+<a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"> </tt>
+<a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">tostring</tt><tt class="py-op">(</tt><tt class="py-name">root</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"> </tt>
+<a name="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"> </tt>
+<a name="DataIntObj.return_results"></a><div id="DataIntObj.return_results-def"><a name="L806"></a><tt class="py-lineno">806</tt> <a class="py-toggle" href="#" id="DataIntObj.return_results-toggle" onclick="return toggle('DataIntObj.return_results');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.DataIntObj-class.html#return_results">return_results</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="DataIntObj.return_results-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DataIntObj.return_results-expanded"><a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"><tt class="py-docstring"> Return the results as as a list of lists</tt> </tt>
+<a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-string">"Pepseq"</tt><tt class="py-op">,</tt> <tt class="py-string">"mz"</tt><tt class="py-op">,</tt> <tt class="py-string">"mzcalc"</tt><tt class="py-op">,</tt> <tt class="py-string">"Leucines"</tt><tt class="py-op">,</tt> <tt class="py-string">"MonoisoIntensity"</tt><tt class="py-op">,</tt> <tt class="py-string">"DeuteratedIntensity"</tt><tt class="py-op">,</tt> </tt>
+<a name="L811"></a><tt class="py-lineno">811</tt> <tt class="py-line"> <tt class="py-string">"Deuterated_fraction"</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
+<a name="L812"></a><tt class="py-lineno">812</tt> <tt class="py-line"> <tt class="py-comment">#Add primary data</tt> </tt>
+<a name="L813"></a><tt class="py-lineno">813</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">peprec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L814"></a><tt class="py-lineno">814</tt> <tt class="py-line"> <tt class="py-name">nbleu</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt> </tt>
+<a name="L815"></a><tt class="py-lineno">815</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">nbleu</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L816"></a><tt class="py-lineno">816</tt> <tt class="py-line"> <tt class="py-name">deuterated</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"listdiff"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">nbleu</tt><tt class="py-op">*</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
+<a name="L817"></a><tt class="py-lineno">817</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L818"></a><tt class="py-lineno">818</tt> <tt class="py-line"> <tt class="py-name">deuterated</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L819"></a><tt class="py-lineno">819</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"%.4f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"mzh"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L820"></a><tt class="py-lineno">820</tt> <tt class="py-line"> <tt class="py-string">"%.4f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"calcmzh"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"Lnumber"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
+<a name="L821"></a><tt class="py-lineno">821</tt> <tt class="py-line"> <tt class="py-string">"%.0f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"int0"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"%.0f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">deuterated</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L822"></a><tt class="py-lineno">822</tt> <tt class="py-line"> <tt class="py-string">"%.2f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">results</tt><tt class="py-op">[</tt><tt class="py-name">peprec</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L823"></a><tt class="py-lineno">823</tt> <tt class="py-line"> </tt>
+<a name="L824"></a><tt class="py-lineno">824</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"Nbofvalues"</tt><tt class="py-op">,</tt> <tt class="py-string">"Median"</tt><tt class="py-op">,</tt> <tt class="py-string">"Mean"</tt><tt class="py-op">,</tt> <tt class="py-string">"StdDev"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L825"></a><tt class="py-lineno">825</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"%s"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"Nbvalues"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L826"></a><tt class="py-lineno">826</tt> <tt class="py-line"> <tt class="py-string">"%.2f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"Median"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L827"></a><tt class="py-lineno">827</tt> <tt class="py-line"> <tt class="py-string">"%.2f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"Mean"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L828"></a><tt class="py-lineno">828</tt> <tt class="py-line"> <tt class="py-string">"%.4f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">statistics</tt><tt class="py-op">[</tt><tt class="py-string">"StdDev"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L829"></a><tt class="py-lineno">829</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
+</div></div><a name="L830"></a><tt class="py-lineno">830</tt> <tt class="py-line"> </tt>
+<a name="L831"></a><tt class="py-lineno">831</tt> <tt class="py-line"> </tt>
+<a name="L832"></a><tt class="py-lineno">832</tt> <tt class="py-line"><tt class="py-comment">#######################</tt> </tt>
+<a name="L833"></a><tt class="py-lineno">833</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#######################</tt> </tt>
+<a name="ProcessSpectrum"></a><div id="ProcessSpectrum-def"><a name="L834"></a><tt class="py-lineno">834</tt> <a class="py-toggle" href="#" id="ProcessSpectrum-toggle" onclick="return toggle('ProcessSpectrum');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#ProcessSpectrum">ProcessSpectrum</a><tt class="py-op">(</tt><tt class="py-param">spectrahandle</tt><tt class="py-op">,</tt> <tt class="py-param">msfithandle</tt><tt class="py-op">,</tt> <tt class="py-param">orflisthandle</tt><tt class="py-op">,</tt> <tt class="py-param">ipc_path</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="ProcessSpectrum-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ProcessSpectrum-expanded"><a name="L835"></a><tt class="py-lineno">835</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L836"></a><tt class="py-lineno">836</tt> <tt class="py-line"><tt class="py-docstring"> A function to simplify the aspect of Main</tt> </tt>
+<a name="L837"></a><tt class="py-lineno">837</tt> <tt class="py-line"><tt class="py-docstring"> uses handles to file or file-like objects</tt> </tt>
+<a name="L838"></a><tt class="py-lineno">838</tt> <tt class="py-line"><tt class="py-docstring"> Returns the results in list/string form</tt> </tt>
+<a name="L839"></a><tt class="py-lineno">839</tt> <tt class="py-line"><tt class="py-docstring"> May also be used in a CGI</tt> </tt>
+<a name="L840"></a><tt class="py-lineno">840</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L841"></a><tt class="py-lineno">841</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt class="py-name">calc_res</tt> </tt>
+<a name="L842"></a><tt class="py-lineno">842</tt> <tt class="py-line"> <tt class="py-name">calc_res</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
+<a name="L843"></a><tt class="py-lineno">843</tt> <tt class="py-line"> <tt class="py-comment">#insert data from the spectra in a list of floats</tt> </tt>
+<a name="L844"></a><tt class="py-lineno">844</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">data_num</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name" targets="Function lilamsxml.ReadFromFileFloats()=lilamsxml-module.html#ReadFromFileFloats"><a title="lilamsxml.ReadFromFileFloats" class="py-name" href="#" onclick="return doclink('link-33', 'ReadFromFileFloats', 'link-33');">ReadFromFileFloats</a></tt><tt class="py-op">(</tt><tt class="py-name">spectrahandle</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L845"></a><tt class="py-lineno">845</tt> <tt class="py-line"> <tt class="py-name">data_num_minmz</tt> <tt class="py-op">=</tt> <tt class="py-name">data_num</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L846"></a><tt class="py-lineno">846</tt> <tt class="py-line"> <tt class="py-name">data_num_maxmz</tt> <tt class="py-op">=</tt> <tt class="py-name">data_num</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L847"></a><tt class="py-lineno">847</tt> <tt class="py-line"> <tt class="py-comment">#parse the HTML file</tt> </tt>
+<a name="L848"></a><tt class="py-lineno">848</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">parseddict</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name" targets="Function lilamsxml.ParseMSFIT()=lilamsxml-module.html#ParseMSFIT"><a title="lilamsxml.ParseMSFIT" class="py-name" href="#" onclick="return doclink('link-34', 'ParseMSFIT', 'link-34');">ParseMSFIT</a></tt><tt class="py-op">(</tt><tt class="py-name">msfithandle</tt><tt class="py-op">)</tt> </tt>
+<a name="L849"></a><tt class="py-lineno">849</tt> <tt class="py-line"> <tt class="py-name">orflist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L850"></a><tt class="py-lineno">850</tt> <tt class="py-line"> </tt>
+<a name="L851"></a><tt class="py-lineno">851</tt> <tt class="py-line"> <tt class="py-comment">#the next lines are only necessary if the entries were not </tt> </tt>
+<a name="L852"></a><tt class="py-lineno">852</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#well formated in the database. To be modified otherwise.</tt> </tt>
+<a name="L853"></a><tt class="py-lineno">853</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">###############################################</tt> </tt>
+<a name="L854"></a><tt class="py-lineno">854</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">orflisthandle</tt><tt class="py-op">:</tt> </tt>
+<a name="L855"></a><tt class="py-lineno">855</tt> <tt class="py-line"> <tt class="py-name">orflist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L856"></a><tt class="py-lineno">856</tt> <tt class="py-line"> <tt class="py-comment">###############################################</tt> </tt>
+<a name="L857"></a><tt class="py-lineno">857</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L858"></a><tt class="py-lineno">858</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt class="py-name">parseddict</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L859"></a><tt class="py-lineno">859</tt> <tt class="py-line"> <tt class="py-name">proteinrank</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'rank'</tt><tt class="py-op">]</tt> </tt>
+<a name="L860"></a><tt class="py-lineno">860</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">'protdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'accession_number'</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-name">orflist</tt><tt class="py-op">:</tt> </tt>
+<a name="L861"></a><tt class="py-lineno">861</tt> <tt class="py-line"> </tt>
+<a name="L862"></a><tt class="py-lineno">862</tt> <tt class="py-line"> <tt class="py-name">peplist</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">[</tt><tt class="py-string">'pepdata'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">'matched'</tt><tt class="py-op">]</tt> </tt>
+<a name="L863"></a><tt class="py-lineno">863</tt> <tt class="py-line"> <tt class="py-comment">#the list of pairs mzh/pepseq for a given protein</tt> </tt>
+<a name="L864"></a><tt class="py-lineno">864</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">result_matrix</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L865"></a><tt class="py-lineno">865</tt> <tt class="py-line"> <tt class="py-name">spectrum_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
+<a name="L866"></a><tt class="py-lineno">866</tt> <tt class="py-line"> <tt class="py-name">PLUSMINUS</tt> <tt class="py-op">=</tt> <tt class="py-number">25</tt> </tt>
+<a name="L867"></a><tt class="py-lineno">867</tt> <tt class="py-line"> <tt class="py-comment">#the number of daltons around the monoisotopic peak to be retrieved</tt> </tt>
+<a name="L868"></a><tt class="py-lineno">868</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">peptide</tt> <tt class="py-keyword">in</tt> <tt class="py-name">peplist</tt><tt class="py-op">:</tt> </tt>
+<a name="L869"></a><tt class="py-lineno">869</tt> <tt class="py-line"> <tt class="py-name">difflist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L870"></a><tt class="py-lineno">870</tt> <tt class="py-line"> <tt class="py-name">peptidesequence</tt> <tt class="py-op">=</tt> <tt class="py-name">peptide</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L871"></a><tt class="py-lineno">871</tt> <tt class="py-line"> <tt class="py-name">inputpepmz</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">peptide</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L872"></a><tt class="py-lineno">872</tt> <tt class="py-line"> <tt class="py-name">decision_dict</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name" targets="Function lilamsxml.PepCompare()=lilamsxml-module.html#PepCompare"><a title="lilamsxml.PepCompare" class="py-name" href="#" onclick="return doclink('link-35', 'PepCompare', 'link-35');">PepCompare</a></tt><tt class="py-op">(</tt><tt class="py-name">inputpepmz</tt><tt class="py-op">,</tt> <tt class="py-name">peptidesequence</tt><tt class="py-op">)</tt> </tt>
+<a name="L873"></a><tt class="py-lineno">873</tt> <tt class="py-line"> <tt class="py-comment">#if the peptide entry is a deuterated peptide or if its mass is already in the </tt> </tt>
+<a name="L874"></a><tt class="py-lineno">874</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#result_matrix (DUPLICATED = 1), no calculation is performed</tt> </tt>
+<a name="L875"></a><tt class="py-lineno">875</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L876"></a><tt class="py-lineno">876</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"IGNORE"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L877"></a><tt class="py-lineno">877</tt> <tt class="py-line"> <tt class="py-name">DUPLICATED</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L878"></a><tt class="py-lineno">878</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">result_matrix</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L879"></a><tt class="py-lineno">879</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">result_matrix</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"pepmz"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">0.5</tt><tt class="py-op">:</tt> </tt>
+<a name="L880"></a><tt class="py-lineno">880</tt> <tt class="py-line"> <tt class="py-comment">#look for pepmz similar in the range +-0.5 Da to the one tested. </tt> </tt>
+<a name="L881"></a><tt class="py-lineno">881</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#If it exists do not run CorrectIsotopicSeries</tt> </tt>
+<a name="L882"></a><tt class="py-lineno">882</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">DUPLICATED</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L883"></a><tt class="py-lineno">883</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
+<a name="L884"></a><tt class="py-lineno">884</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">DUPLICATED</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L885"></a><tt class="py-lineno">885</tt> <tt class="py-line"> <tt class="py-comment">#test also if the range of mass from the spectrum is OK, otherwise stop</tt> </tt>
+<a name="L886"></a><tt class="py-lineno">886</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"pepmz"</tt><tt class="py-op">]</tt> <tt class="py-op">></tt> <tt class="py-name">data_num_minmz</tt> <tt class="py-keyword">and</tt>\ </tt>
+<a name="L887"></a><tt class="py-lineno">887</tt> <tt class="py-line"> <tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"pepmz"</tt><tt class="py-op">]</tt> <tt class="py-op"><</tt> <tt class="py-name">data_num_maxmz</tt><tt class="py-op">:</tt> </tt>
+<a name="L888"></a><tt class="py-lineno">888</tt> <tt class="py-line"> <tt class="py-name">difflist</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name" targets="Function lilamsxml.CorrectIsotopicSeries()=lilamsxml-module.html#CorrectIsotopicSeries"><a title="lilamsxml.CorrectIsotopicSeries" class="py-name" href="#" onclick="return doclink('link-36', 'CorrectIsotopicSeries', 'link-36');">CorrectIsotopicSeries</a></tt><tt class="py-op">(</tt><tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"pepmz"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> \ </tt>
+<a name="L889"></a><tt class="py-lineno">889</tt> <tt class="py-line"> <tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">data_num</tt><tt class="py-op">,</tt> <tt class="py-number">16</tt><tt class="py-op">,</tt> <tt class="py-name">ipc_path</tt><tt class="py-op">)</tt> </tt>
+<a name="L890"></a><tt class="py-lineno">890</tt> <tt class="py-line"> <tt class="py-name">result_matrix</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">difflist</tt><tt class="py-op">)</tt> </tt>
+<a name="L891"></a><tt class="py-lineno">891</tt> <tt class="py-line"> <tt class="py-name">spectrum_dict</tt><tt class="py-op">[</tt><tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name" targets="Function lilamsxml.MzIntGet()=lilamsxml-module.html#MzIntGet"><a title="lilamsxml.MzIntGet" class="py-name" href="#" onclick="return doclink('link-37', 'MzIntGet', 'link-37');">MzIntGet</a></tt><tt class="py-op">(</tt><tt class="py-name">data_num</tt><tt class="py-op">,</tt> </tt>
+<a name="L892"></a><tt class="py-lineno">892</tt> <tt class="py-line"> <tt class="py-name">decision_dict</tt><tt class="py-op">[</tt><tt class="py-string">"pepmz"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">PLUSMINUS</tt><tt class="py-op">)</tt> </tt>
+<a name="L893"></a><tt class="py-lineno">893</tt> <tt class="py-line"> </tt>
+<a name="L894"></a><tt class="py-lineno">894</tt> <tt class="py-line"> <tt class="py-name">rawdiff</tt><tt class="py-op">=</tt> <tt id="link-38" class="py-name" targets="Class lilamsxml.DataIntObj=lilamsxml.DataIntObj-class.html"><a title="lilamsxml.DataIntObj" class="py-name" href="#" onclick="return doclink('link-38', 'DataIntObj', 'link-38');">DataIntObj</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L895"></a><tt class="py-lineno">895</tt> <tt class="py-line"> <tt class="py-name">rawdiff</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method lilamsxml.DataIntObj.get_data()=lilamsxml.DataIntObj-class.html#get_data"><a title="lilamsxml.DataIntObj.get_data" class="py-name" href="#" onclick="return doclink('link-39', 'get_data', 'link-39');">get_data</a></tt><tt class="py-op">(</tt><tt class="py-name">result_matrix</tt><tt class="py-op">)</tt> </tt>
+<a name="L896"></a><tt class="py-lineno">896</tt> <tt class="py-line"> <tt class="py-name">rawdiff</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method lilamsxml.DataIntObj.filter_peaks()=lilamsxml.DataIntObj-class.html#filter_peaks"><a title="lilamsxml.DataIntObj.filter_peaks" class="py-name" href="#" onclick="return doclink('link-40', 'filter_peaks', 'link-40');">filter_peaks</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L897"></a><tt class="py-lineno">897</tt> <tt class="py-line"> <tt class="py-name">rawdiff</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method lilamsxml.DataIntObj.calc_ratios()=lilamsxml.DataIntObj-class.html#calc_ratios"><a title="lilamsxml.DataIntObj.calc_ratios" class="py-name" href="#" onclick="return doclink('link-41', 'calc_ratios', 'link-41');">calc_ratios</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L898"></a><tt class="py-lineno">898</tt> <tt class="py-line"> <tt class="py-name">pepresults</tt> <tt class="py-op">=</tt> <tt class="py-name">rawdiff</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method lilamsxml.DataIntObj.return_resultsXML()=lilamsxml.DataIntObj-class.html#return_resultsXML"><a title="lilamsxml.DataIntObj.return_resultsXML" class="py-name" href="#" onclick="return doclink('link-42', 'return_resultsXML', 'link-42');">return_resultsXML</a></tt><tt class="py-op">(</tt><tt class="py-name">spectrum_dict</tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">)</tt> </tt>
+<a name="L899"></a><tt class="py-lineno">899</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L900"></a><tt class="py-lineno">900</tt> <tt class="py-line"> <tt class="py-name">pepresults</tt> <tt class="py-op">=</tt> <tt class="py-string">"nodata"</tt> </tt>
+<a name="L901"></a><tt class="py-lineno">901</tt> <tt class="py-line"> </tt>
+<a name="L902"></a><tt class="py-lineno">902</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">pepresults</tt> </tt>
+</div><a name="L903"></a><tt class="py-lineno">903</tt> <tt class="py-line"> </tt>
+<a name="L904"></a><tt class="py-lineno">904</tt> <tt class="py-line"><tt class="py-comment">####################</tt> </tt>
+<a name="L905"></a><tt class="py-lineno">905</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">####### MAIN #######</tt> </tt>
+<a name="L906"></a><tt class="py-lineno">906</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">####################</tt> </tt>
+<a name="Usage"></a><div id="Usage-def"><a name="L907"></a><tt class="py-lineno">907</tt> <a class="py-toggle" href="#" id="Usage-toggle" onclick="return toggle('Usage');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="lilamsxml.Usage-class.html">Usage</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Usage-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Usage-expanded"><a name="L908"></a><tt class="py-lineno">908</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L909"></a><tt class="py-lineno">909</tt> <tt class="py-line"><tt class="py-docstring"> used for catching exceptions generated</tt> </tt>
+<a name="L910"></a><tt class="py-lineno">910</tt> <tt class="py-line"><tt class="py-docstring"> during command line parameter parsing</tt> </tt>
+<a name="L911"></a><tt class="py-lineno">911</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="Usage.__init__"></a><div id="Usage.__init__-def"><a name="L912"></a><tt class="py-lineno">912</tt> <a class="py-toggle" href="#" id="Usage.__init__-toggle" onclick="return toggle('Usage.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml.Usage-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">msg</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="Usage.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Usage.__init__-expanded"><a name="L913"></a><tt class="py-lineno">913</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Variable silacvalidator.msg=silacvalidator-module.html#msg"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-43', 'msg', 'link-43');">msg</a></tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-44', 'msg', 'link-43');">msg</a></tt> </tt>
+</div></div><a name="L914"></a><tt class="py-lineno">914</tt> <tt class="py-line"> </tt>
+<a name="main"></a><div id="main-def"><a name="L915"></a><tt class="py-lineno">915</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="lilamsxml-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-param">argv</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L916"></a><tt class="py-lineno">916</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt class="py-name">fname_spectra</tt><tt class="py-op">,</tt> <tt class="py-name">fname_msfit</tt><tt class="py-op">,</tt> <tt class="py-name">fname_orflist</tt><tt class="py-op">,</tt> <tt class="py-name">ipc_command_path</tt> </tt>
+<a name="L917"></a><tt class="py-lineno">917</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt class="py-name">spectrumhandle</tt><tt class="py-op">,</tt> <tt class="py-name">msfithandle</tt><tt class="py-op">,</tt> <tt class="py-name">orflisthandle</tt> </tt>
+<a name="L918"></a><tt class="py-lineno">918</tt> <tt class="py-line"> <tt class="py-name">spectrumhandle</tt><tt class="py-op">,</tt> <tt class="py-name">msfithandle</tt><tt class="py-op">,</tt> <tt class="py-name">orflisthandle</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdin</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdin</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdin</tt> </tt>
+<a name="L919"></a><tt class="py-lineno">919</tt> <tt class="py-line"> </tt>
+<a name="L920"></a><tt class="py-lineno">920</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">argv</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
+<a name="L921"></a><tt class="py-lineno">921</tt> <tt class="py-line"> <tt class="py-name">argv</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt> </tt>
+<a name="L922"></a><tt class="py-lineno">922</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L923"></a><tt class="py-lineno">923</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L924"></a><tt class="py-lineno">924</tt> <tt class="py-line"> <tt class="py-name">opts</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">getopt</tt><tt class="py-op">.</tt><tt class="py-name">getopt</tt><tt class="py-op">(</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"hs:i:p:c:"</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">"help"</tt><tt class="py-op">,</tt> <tt class="py-string">"spectrum="</tt><tt class="py-op">,</tt> </tt>
+<a name="L925"></a><tt class="py-lineno">925</tt> <tt class="py-line"> <tt class="py-string">"msfithtml="</tt><tt class="py-op">,</tt> <tt class="py-string">'orflist='</tt><tt class="py-op">,</tt> <tt class="py-string">"ipc_path="</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L926"></a><tt class="py-lineno">926</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">getopt</tt><tt class="py-op">.</tt><tt class="py-name">error</tt><tt class="py-op">,</tt> <tt id="link-45" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-45', 'msg', 'link-43');">msg</a></tt><tt class="py-op">:</tt> </tt>
+<a name="L927"></a><tt class="py-lineno">927</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-46" class="py-name" targets="Class Collect_SILAC_XML.Usage=Collect_SILAC_XML.Usage-class.html,Class lilamsxml.Usage=lilamsxml.Usage-class.html"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-46', 'Usage', 'link-46');">Usage</a></tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-47', 'msg', 'link-43');">msg</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L928"></a><tt class="py-lineno">928</tt> <tt class="py-line"> <tt class="py-comment"># option processing</tt> </tt>
+<a name="L929"></a><tt class="py-lineno">929</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L930"></a><tt class="py-lineno">930</tt> <tt class="py-line"> <tt class="py-name">fname_spectra</tt><tt class="py-op">,</tt> <tt class="py-name">fname_msfit</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt> </tt>
+<a name="L931"></a><tt class="py-lineno">931</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">option</tt><tt class="py-op">,</tt> <tt class="py-name">value</tt> <tt class="py-keyword">in</tt> <tt class="py-name">opts</tt><tt class="py-op">:</tt> </tt>
+<a name="L932"></a><tt class="py-lineno">932</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-h"</tt><tt class="py-op">,</tt> <tt class="py-string">"--help"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L933"></a><tt class="py-lineno">933</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-48" class="py-name"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-48', 'Usage', 'link-46');">Usage</a></tt><tt class="py-op">(</tt><tt class="py-name">__doc__</tt><tt class="py-op">)</tt> </tt>
+<a name="L934"></a><tt class="py-lineno">934</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-s"</tt><tt class="py-op">,</tt> <tt class="py-string">"--spectrum"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L935"></a><tt class="py-lineno">935</tt> <tt class="py-line"> <tt class="py-name">fname_spectra</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
+<a name="L936"></a><tt class="py-lineno">936</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-i"</tt><tt class="py-op">,</tt> <tt class="py-string">"--msfithtml"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L937"></a><tt class="py-lineno">937</tt> <tt class="py-line"> <tt class="py-name">fname_msfit</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
+<a name="L938"></a><tt class="py-lineno">938</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-p"</tt><tt class="py-op">,</tt> <tt class="py-string">"--orflist"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L939"></a><tt class="py-lineno">939</tt> <tt class="py-line"> <tt class="py-name">fname_orflist</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
+<a name="L940"></a><tt class="py-lineno">940</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">option</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"-c"</tt><tt class="py-op">,</tt> <tt class="py-string">"--ipc_path"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L941"></a><tt class="py-lineno">941</tt> <tt class="py-line"> <tt class="py-name">ipc_command_path</tt> <tt class="py-op">=</tt> <tt class="py-name">value</tt> </tt>
+<a name="L942"></a><tt class="py-lineno">942</tt> <tt class="py-line"> </tt>
+<a name="L943"></a><tt class="py-lineno">943</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">fname_spectra</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> <tt class="py-keyword">or</tt> <tt class="py-name">fname_msfit</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> <tt class="py-keyword">or</tt> <tt class="py-name">fname_orflist</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L944"></a><tt class="py-lineno">944</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-49" class="py-name"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-49', 'Usage', 'link-46');">Usage</a></tt><tt class="py-op">(</tt><tt class="py-string">"no input filenames!"</tt><tt class="py-op">)</tt> </tt>
+<a name="L945"></a><tt class="py-lineno">945</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L946"></a><tt class="py-lineno">946</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L947"></a><tt class="py-lineno">947</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L948"></a><tt class="py-lineno">948</tt> <tt class="py-line"> <tt class="py-name">spectrumhandle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname_spectra</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
+<a name="L949"></a><tt class="py-lineno">949</tt> <tt class="py-line"> <tt class="py-name">msfithandle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname_msfit</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
+<a name="L950"></a><tt class="py-lineno">950</tt> <tt class="py-line"> <tt class="py-name">orflisthandle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname_orflist</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
+<a name="L951"></a><tt class="py-lineno">951</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-50" class="py-name" targets="Function lilamsxml.ProcessSpectrum()=lilamsxml-module.html#ProcessSpectrum"><a title="lilamsxml.ProcessSpectrum" class="py-name" href="#" onclick="return doclink('link-50', 'ProcessSpectrum', 'link-50');">ProcessSpectrum</a></tt><tt class="py-op">(</tt><tt class="py-name">spectrumhandle</tt><tt class="py-op">,</tt> <tt class="py-name">msfithandle</tt><tt class="py-op">,</tt> <tt class="py-name">orflisthandle</tt><tt class="py-op">,</tt> <tt class="py-name">ipc_command_path</tt><tt class="py-op">)</tt> </tt>
+<a name="L952"></a><tt class="py-lineno">952</tt> <tt class="py-line"> <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
+<a name="L953"></a><tt class="py-lineno">953</tt> <tt class="py-line"> <tt class="py-name">spectrumhandle</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L954"></a><tt class="py-lineno">954</tt> <tt class="py-line"> <tt class="py-name">msfithandle</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L955"></a><tt class="py-lineno">955</tt> <tt class="py-line"> <tt class="py-name">orflisthandle</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L956"></a><tt class="py-lineno">956</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-51" class="py-name"><a title="Collect_SILAC_XML.Usage
+lilamsxml.Usage" class="py-name" href="#" onclick="return doclink('link-51', 'Usage', 'link-46');">Usage</a></tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">:</tt> </tt>
+<a name="L957"></a><tt class="py-lineno">957</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">": "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">err</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-52', 'msg', 'link-43');">msg</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L958"></a><tt class="py-lineno">958</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-string">"\t for help use --help or -h"</tt> </tt>
+<a name="L959"></a><tt class="py-lineno">959</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">2</tt> </tt>
+</div><a name="L960"></a><tt class="py-lineno">960</tt> <tt class="py-line"> </tt>
+<a name="L961"></a><tt class="py-lineno">961</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
+<a name="L962"></a><tt class="py-lineno">962</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt id="link-53" class="py-name" targets="Function Collect_SILAC_XML.main()=Collect_SILAC_XML-module.html#main,Function lilamsxml.main()=lilamsxml-module.html#main"><a title="Collect_SILAC_XML.main
+lilamsxml.main" class="py-name" href="#" onclick="return doclink('link-53', 'main', 'link-53');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L963"></a><tt class="py-lineno">963</tt> <tt class="py-line"> </tt><script type="text/javascript">
+<!--
+expandto(location.href);
+// -->
+</script>
+</pre>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
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+ </tr></table></th>
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+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
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+ </td>
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+ >http://epydoc.sourceforge.net</a>
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+ <!--
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+ // visible); but by default, we want to hide them. So hide
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+ checkCookie();
+ // -->
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+</body>
+</html>
diff --git a/docs/lilamsxml.DataIntObj-class.html b/docs/lilamsxml.DataIntObj-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..e75d98f83498db122de6acfc29857fbf8d1008ac
--- /dev/null
+++ b/docs/lilamsxml.DataIntObj-class.html
@@ -0,0 +1,254 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>lilamsxml.DataIntObj</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
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+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
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+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
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+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="lilamsxml-module.html">Module lilamsxml</a> ::
+ Class DataIntObj
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class DataIntObj</h1><p class="nomargin-top"><span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj">source code</a></span></p>
+<p>A data structure to handle SILAC difference results and calculate
+ statistics</p>
+
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="get_data"></a><span class="summary-sig-name">get_data</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">matrix</span>)</span><br />
+ transforms the matrix obtained by several calls to DiffMeasTheor into
+ internal data</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj.get_data">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="filter_peaks"></a><span class="summary-sig-name">filter_peaks</span>(<span class="summary-sig-arg">self</span>)</span><br />
+ Eliminates from self.data the peaks for which the peak 3 or multiple
+ is higher than 2 or multiple Decides whether to take the
+ non-deuterated or the deuterated form in function of the intensity of
+ the corresponding peaks</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj.filter_peaks">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="calc_ratios"></a><span class="summary-sig-name">calc_ratios</span>(<span class="summary-sig-arg">self</span>)</span><br />
+ Calculates the ratios deut/nondeuterated peptides in a mix based on
+ peptide sequence (0, 1-4 leucines)</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj.calc_ratios">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="calc_statistics"></a><span class="summary-sig-name">calc_statistics</span>(<span class="summary-sig-arg">self</span>)</span><br />
+ Median, average and StdDev for the fractions calculated for peptides
+ with 1, 2, 3 or 4 leucines</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj.calc_statistics">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="return_resultsXML"></a><span class="summary-sig-name">return_resultsXML</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">spectr_dict</span>,
+ <span class="summary-sig-arg">record</span>)</span><br />
+ The results are returned in very simple XML-like format that should
+ be compatible with Silacvalidator.py (interactive visualization of
+ the results)</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj.return_resultsXML">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="return_results"></a><span class="summary-sig-name">return_results</span>(<span class="summary-sig-arg">self</span>)</span><br />
+ Return the results as as a list of lists</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#DataIntObj.return_results">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
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+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
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+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/lilamsxml.MSFit32Parser-class.html b/docs/lilamsxml.MSFit32Parser-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..2f49f34d2a3a539a813d20d01bc04fbee44f94d1
--- /dev/null
+++ b/docs/lilamsxml.MSFit32Parser-class.html
@@ -0,0 +1,412 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>lilamsxml.MSFit32Parser</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
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+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="lilamsxml-module.html">Module lilamsxml</a> ::
+ Class MSFit32Parser
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class MSFit32Parser</h1><p class="nomargin-top"><span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser">source code</a></span></p>
+<pre class="base-tree">
+markupbase.ParserBase --+
+ |
+ HTMLParser.HTMLParser --+
+ |
+ <strong class="uidshort">MSFit32Parser</strong>
+</pre>
+
+<hr />
+<p>A parser for MSFit HTML (version 3.2) results to obtain a dictionary
+ of data corresponding to the page, first entry only</p>
+ <p>Regular expression needed to extract sequences of peptides from MSFit
+ lines are compiled outside functions to avoid repetition of re
+ compilations</p>
+
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml.MSFit32Parser-class.html#reset" class="summary-sig-name">reset</a>(<span class="summary-sig-arg">self</span>)</span><br />
+ Reset this instance.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.reset">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml.MSFit32Parser-class.html#handle_starttag" class="summary-sig-name">handle_starttag</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">tag</span>,
+ <span class="summary-sig-arg">attrs</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.handle_starttag">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml.MSFit32Parser-class.html#handle_comment" class="summary-sig-name">handle_comment</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">tag</span>)</span><br />
+ Overrides the handle_comment method Builds a list of all the found
+ comments If a comment is found, the aftercomment variable is set to
+ True</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.handle_comment">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml.MSFit32Parser-class.html#handle_data" class="summary-sig-name">handle_data</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">text</span>)</span><br />
+ Overrides the handle_data method writes to a list the text following
+ any comment - modifies self.parsedlist</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.handle_data">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="get_dictionary"></a><span class="summary-sig-name">get_dictionary</span>(<span class="summary-sig-arg">self</span>)</span><br />
+ Reorganizes data and treats some special cases of data found after
+ comment tags Should be called after closing the parser</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.get_dictionary">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>HTMLParser.HTMLParser</code></b>:
+ <code>__init__</code>,
+ <code>check_for_whole_start_tag</code>,
+ <code>clear_cdata_mode</code>,
+ <code>close</code>,
+ <code>error</code>,
+ <code>feed</code>,
+ <code>get_starttag_text</code>,
+ <code>goahead</code>,
+ <code>handle_charref</code>,
+ <code>handle_decl</code>,
+ <code>handle_endtag</code>,
+ <code>handle_entityref</code>,
+ <code>handle_pi</code>,
+ <code>handle_startendtag</code>,
+ <code>parse_endtag</code>,
+ <code>parse_pi</code>,
+ <code>parse_starttag</code>,
+ <code>set_cdata_mode</code>,
+ <code>unescape</code>,
+ <code>unknown_decl</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b>:
+ <code>getpos</code>,
+ <code>parse_comment</code>,
+ <code>parse_declaration</code>,
+ <code>parse_marked_section</code>,
+ <code>updatepos</code>
+ </p>
+ <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b> (private):
+ <code>_parse_doctype_attlist</code>,
+ <code>_parse_doctype_element</code>,
+ <code>_parse_doctype_entity</code>,
+ <code>_parse_doctype_notation</code>,
+ <code>_parse_doctype_subset</code>,
+ <code>_scan_name</code>
+ </p></div>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS VARIABLES ==================== -->
+<a name="section-ClassVariables"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Class Variables</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-ClassVariables"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>HTMLParser.HTMLParser</code></b>:
+ <code>CDATA_CONTENT_ELEMENTS</code>
+ </p>
+ <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>markupbase.ParserBase</code></b> (private):
+ <code>_decl_otherchars</code>
+ </p></div>
+ </td>
+ </tr>
+</table>
+<!-- ==================== METHOD DETAILS ==================== -->
+<a name="section-MethodDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Method Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-MethodDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="reset"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">reset</span>(<span class="sig-arg">self</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.reset">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Reset this instance. Loses all unprocessed data.</p>
+ <dl class="fields">
+ <dt>Overrides:
+ markupbase.ParserBase.reset
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<a name="handle_starttag"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">handle_starttag</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">tag</span>,
+ <span class="sig-arg">attrs</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.handle_starttag">source code</a></span>
+ </td>
+ </tr></table>
+
+
+ <dl class="fields">
+ <dt>Overrides:
+ HTMLParser.HTMLParser.handle_starttag
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<a name="handle_comment"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">handle_comment</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">tag</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.handle_comment">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Overrides the handle_comment method Builds a list of all the found
+ comments If a comment is found, the aftercomment variable is set to
+ True</p>
+ <dl class="fields">
+ <dt>Overrides:
+ HTMLParser.HTMLParser.handle_comment
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<a name="handle_data"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">handle_data</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">text</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#MSFit32Parser.handle_data">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Overrides the handle_data method writes to a list the text following
+ any comment - modifies self.parsedlist</p>
+ <dl class="fields">
+ <dt>Overrides:
+ HTMLParser.HTMLParser.handle_data
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/lilamsxml.Usage-class.html b/docs/lilamsxml.Usage-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..698da937fd3d1c18fa2314ac465c64cdaf19453d
--- /dev/null
+++ b/docs/lilamsxml.Usage-class.html
@@ -0,0 +1,250 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>lilamsxml.Usage</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="lilamsxml-module.html">Module lilamsxml</a> ::
+ Class Usage
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class Usage</h1><p class="nomargin-top"><span class="codelink"><a href="lilamsxml-pysrc.html#Usage">source code</a></span></p>
+<pre class="base-tree">
+ object --+
+ |
+exceptions.BaseException --+
+ |
+ exceptions.Exception --+
+ |
+ <strong class="uidshort">Usage</strong>
+</pre>
+
+<hr />
+<p>used for catching exceptions generated during command line parameter
+ parsing</p>
+
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="lilamsxml.Usage-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">msg</span>)</span><br />
+ x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="lilamsxml-pysrc.html#Usage.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>exceptions.Exception</code></b>:
+ <code>__new__</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>exceptions.BaseException</code></b>:
+ <code>__delattr__</code>,
+ <code>__getattribute__</code>,
+ <code>__getitem__</code>,
+ <code>__getslice__</code>,
+ <code>__reduce__</code>,
+ <code>__repr__</code>,
+ <code>__setattr__</code>,
+ <code>__setstate__</code>,
+ <code>__str__</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
+ <code>__hash__</code>,
+ <code>__reduce_ex__</code>
+ </p>
+ </td>
+ </tr>
+</table>
+<!-- ==================== PROPERTIES ==================== -->
+<a name="section-Properties"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Properties</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Properties"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>exceptions.BaseException</code></b>:
+ <code>args</code>,
+ <code>message</code>
+ </p>
+ <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
+ <code>__class__</code>
+ </p>
+ </td>
+ </tr>
+</table>
+<!-- ==================== METHOD DETAILS ==================== -->
+<a name="section-MethodDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Method Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-MethodDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="__init__"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">msg</span>)</span>
+ <br /><em class="fname">(Constructor)</em>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="lilamsxml-pysrc.html#Usage.__init__">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>x.__init__(...) initializes x; see x.__class__.__doc__ for
+ signature</p>
+ <dl class="fields">
+ <dt>Overrides:
+ object.__init__
+ <dd><em class="note">(inherited documentation)</em></dd>
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/module-tree.html b/docs/module-tree.html
new file mode 100644
index 0000000000000000000000000000000000000000..6af102b1ca506172ab15fdfd0f04de17ffebed83
--- /dev/null
+++ b/docs/module-tree.html
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Module Hierarchy</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Trees </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%"> </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<center><b>
+ [ <a href="module-tree.html">Module Hierarchy</a>
+ | <a href="class-tree.html">Class Hierarchy</a> ]
+</b></center><br />
+<h1 class="epydoc">Module Hierarchy</h1>
+<ul class="nomargin-top">
+ <li> <strong class="uidlink"><a href="Collect_SILAC_XML-module.html">Collect_SILAC_XML</a></strong>: <em class="summary">Collect_SILAC_XML.py</em> </li>
+ <li> <strong class="uidlink"><a href="MSFit_to_txt-module.html">MSFit_to_txt</a></strong>: <em class="summary">MSFit to Table v 0.2</em> </li>
+ <li> <strong class="uidlink"><a href="lilamslaunchGUI-module.html">lilamslaunchGUI</a></strong>: <em class="summary">LilamslaunchGUI.py is a GUI for the lilamsxml.py script Allows
+ interactive choosing of a file containing pairs of Spectrum/MSfit
+ file names (complete path) and of a file containing ORF names of
+ interest</em> </li>
+ <li> <strong class="uidlink"><a href="lilamsxml-module.html">lilamsxml</a></strong>: <em class="summary">lilamsxml.py - python script for the analysis of SILAC experiments
+ with MALDI spectra and MSFit protein identifications</em> </li>
+ <li> <strong class="uidlink"><a href="silacvalidator-module.html">silacvalidator</a></strong>: <em class="summary">SILAC validator v.</em> </li>
+</ul>
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th bgcolor="#70b0f0" class="navbar-select"
+ > Trees </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
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+</table>
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+ <!--
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+ checkCookie();
+ // -->
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+</body>
+</html>
diff --git a/docs/redirect.html b/docs/redirect.html
new file mode 100644
index 0000000000000000000000000000000000000000..b563d57af8b15e0c3d8693ae22b2a655f6bbb392
--- /dev/null
+++ b/docs/redirect.html
@@ -0,0 +1,38 @@
+<html><head><title>Epydoc Redirect Page</title>
+<meta http-equiv="cache-control" content="no-cache" />
+<meta http-equiv="expires" content="0" />
+<meta http-equiv="pragma" content="no-cache" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+<body>
+<script type="text/javascript">
+<!--
+var pages = ["silacvalidator.PepListCtrlPanel-c", "MSFit_to_txt.MSFit32ParserProt-c", "silacvalidator.PepListCtrl-c", "lilamslaunchGUI.MainFrame-c", "silacvalidator.MainFrame-c", "Collect_SILAC_XML.Usage-c", "lilamsxml.MSFit32Parser-c", "MSFit_to_txt.MainFrame-c", "lilamsxml.DataIntObj-c", "Collect_SILAC_XML-m", "lilamslaunchGUI-m", "lilamsxml.Usage-c", "silacvalidator-m", "MSFit_to_txt-m", "lilamsxml-m"];
+var dottedName = get_anchor();
+if (dottedName) {
+ var target = redirect_url(dottedName);
+ if (target) window.location.replace(target);
+}
+// -->
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+
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+
+<p>When javascript is enabled, this page will redirect URLs of
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+
+<script type="text/javascript">
+<!--
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+}
+// -->
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+
+</body>
+</html>
diff --git a/docs/silacvalidator-module.html b/docs/silacvalidator-module.html
new file mode 100644
index 0000000000000000000000000000000000000000..9cf7e5aab922f9b15729281167a769e94a01bbd1
--- /dev/null
+++ b/docs/silacvalidator-module.html
@@ -0,0 +1,624 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>silacvalidator</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module silacvalidator
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== MODULE DESCRIPTION ==================== -->
+<h1 class="epydoc">Module silacvalidator</h1><p class="nomargin-top"><span class="codelink"><a href="silacvalidator-pysrc.html">source code</a></span></p>
+<p>SILAC validator v. 0.2, silacvalidator.py requires Python (2.5 or
+ higher), wxPython and numpy (Numeric or numarray) (ElementTree is now
+ included in Python 2.5)</p>
+ <p>INSTRUCTIONS:</p>
+ <p>This application recognizes XML files, as generated by lilamsXML.
+ These files are obtained from a spectrum (in text format) and a MsFit3.2
+ results file (in html for- mat). Only the first entry in the file is
+ quantified and generates an xml file. After opening an XML file, the
+ first peptide-associated spectrum is displayed in the interactive plot
+ window. You can zoom by drawing a rectangle with the left mouse click and
+ unzoom with the menu >Plot>Full Unzoom. When clicking anywhere on
+ the plot, the m/z value and intensity are shown in the status bar. To
+ associate a local background to a spectrum double-click on the maximum
+ and minimum of the peak considered as background. The difference of the
+ two values is shown in the status bar. By clicking on the <Set
+ Bgrnd.> button the last va- lue of the local background is inserted in
+ the peptide table and the corrected ratio is automatically calculated. To
+ validate the peptide quantification click on the <Validate>
+ button.</p>
+ <p>Clicking on the column titles allows sorting of the peptide list by
+ any criteria. A visualisation program for XML files generated by
+ lilamsxml. Allows validation of SILAC experiments, peptide by
+ peptide.</p>
+ <p>Written using wxPython, numarray, ElementTree et al., in Python,
+ September 2004. Modified in January 2008, to be able to save in text
+ format individual spectra regions. Several ergonomy amelioration also
+ done and debugged the Next/Previous commands. THIS PROGRAM CONTAINS BUGS,
+ SOME OF THEM IN THE UPSTREAM LIBRARIES!</p>
+ <p>Cosmin Saveanu in Alain Jacquier's laboratory, Institut Pasteur,
+ CNRS-URA2171.</p>
+ <p>Many thanks to all the people contributing to the development of tools
+ like wxPython, Python itself, ElementTree, and wx.lib.plot and the
+ wonderful examples to get inspiration (and sometimes copy/paste)
+ from.</p>
+ <p>This program may be freely distributed as long as correct references
+ to it are provided, with this included note.</p>
+
+<!-- ==================== CLASSES ==================== -->
+<a name="section-Classes"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Classes</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Classes"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="silacvalidator.MainFrame-class.html" class="summary-name">MainFrame</a><br />
+ The application main frame.
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="silacvalidator.PepListCtrl-class.html" class="summary-name">PepListCtrl</a>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="silacvalidator.PepListCtrlPanel-class.html" class="summary-name">PepListCtrlPanel</a>
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTIONS ==================== -->
+<a name="section-Functions"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Functions</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Functions"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator-module.html#get_flist_xml" class="summary-sig-name">get_flist_xml</a>(<span class="summary-sig-arg">dirname</span>)</span><br />
+ get all .xml file names from dirname, not recursive return only the
+ file name, not the path</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#get_flist_xml">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="get_flist_txt"></a><span class="summary-sig-name">get_flist_txt</span>(<span class="summary-sig-arg">dirname</span>)</span><br />
+ get all .txt file names from dirname, not recursive return only the
+ file name, not the path</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#get_flist_txt">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="map_pos_inlist"></a><span class="summary-sig-name">map_pos_inlist</span>(<span class="summary-sig-arg">flist</span>,
+ <span class="summary-sig-arg">fname</span>)</span><br />
+ Obtain the index of a file name in a file list If file name not found
+ return 0 as the position Used in XMLOpen, generated a value for
+ <self.where> about the current position of a file in the file
+ list obtained with <get_flist_xml>.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#map_pos_inlist">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator-module.html#ReadFromFileArray" class="summary-sig-name">ReadFromFileArray</a>(<span class="summary-sig-arg">file</span>,
+ <span class="summary-sig-arg">skip</span>=<span class="summary-sig-default">0</span>)</span><br />
+ Obtain floats from a tab delimited file into a numarray array The
+ <skip> parameter indicate the number of lines not read.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#ReadFromFileArray">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="getSmallUpArrowData"></a><span class="summary-sig-name">getSmallUpArrowData</span>()</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#getSmallUpArrowData">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="getSmallUpArrowBitmap"></a><span class="summary-sig-name">getSmallUpArrowBitmap</span>()</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#getSmallUpArrowBitmap">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="getSmallUpArrowImage"></a><span class="summary-sig-name">getSmallUpArrowImage</span>()</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#getSmallUpArrowImage">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="getSmallDnArrowData"></a><span class="summary-sig-name">getSmallDnArrowData</span>()</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#getSmallDnArrowData">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="getSmallDnArrowBitmap"></a><span class="summary-sig-name">getSmallDnArrowBitmap</span>()</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#getSmallDnArrowBitmap">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="getSmallDnArrowImage"></a><span class="summary-sig-name">getSmallDnArrowImage</span>()</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#getSmallDnArrowImage">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== VARIABLES ==================== -->
+<a name="section-Variables"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Variables</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-Variables"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a href="silacvalidator-module.html#msg" class="summary-name">msg</a> = <code title=""""This program requires the Numeric or numarray
+ module to function - in fact is a requirement for the
+ wx.lib.plot module. Please install either Numeric or
+ numarray.
+ """">"""This program requires the Numeric or numar<code class="variable-ellipsis">...</code></code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_BTN3"></a><span class="summary-name">ID_BTN3</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_BTN2"></a><span class="summary-name">ID_BTN2</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_BTN1"></a><span class="summary-name">ID_BTN1</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_PREVF"></a><span class="summary-name">ID_PREVF</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_NEXTF"></a><span class="summary-name">ID_NEXTF</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_UNZOOM"></a><span class="summary-name">ID_UNZOOM</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_ENGRID"></a><span class="summary-name">ID_ENGRID</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_ABOUT"></a><span class="summary-name">ID_ABOUT</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_EXIT"></a><span class="summary-name">ID_EXIT</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_SAVEDATA"></a><span class="summary-name">ID_SAVEDATA</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_SAVESP"></a><span class="summary-name">ID_SAVESP</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_SAVEP"></a><span class="summary-name">ID_SAVEP</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_CLOSE"></a><span class="summary-name">ID_CLOSE</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_OPENX"></a><span class="summary-name">ID_OPENX</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="ID_OPEN"></a><span class="summary-name">ID_OPEN</span>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="app"></a><span class="summary-name">app</span> = <code title="wx.PySimpleApp()">wx.PySimpleApp()</code>
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <a name="frame"></a><span class="summary-name">frame</span> = <code title="MainFrame(None,-1, "SILAC validator v. 0.2")">MainFrame(None,-1, "SILAC validator v. 0.2")</code>
+ </td>
+ </tr>
+</table>
+<!-- ==================== FUNCTION DETAILS ==================== -->
+<a name="section-FunctionDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Function Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-FunctionDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="get_flist_xml"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">get_flist_xml</span>(<span class="sig-arg">dirname</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#get_flist_xml">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>get all .xml file names from dirname, not recursive return only the
+ file name, not the path</p>
+ <p>Needed by the OnPrevFile and OnNextFile functions but called by
+ <XMLOpen> to set the self.filelist list of xml files from the
+ current folder.</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="ReadFromFileArray"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">ReadFromFileArray</span>(<span class="sig-arg">file</span>,
+ <span class="sig-arg">skip</span>=<span class="sig-default">0</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#ReadFromFileArray">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Obtain floats from a tab delimited file into a numarray array The
+ <skip> parameter indicate the number of lines not read.</p>
+ <p>This function is only used to directly open a complete spectrum or a
+ text delimited file with two columns - mz and intensity</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== VARIABLES DETAILS ==================== -->
+<a name="section-VariablesDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Variables Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-VariablesDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="msg"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <h3 class="epydoc">msg</h3>
+
+ <dl class="fields">
+ </dl>
+ <dl class="fields">
+ <dt>Value:</dt>
+ <dd><table><tr><td><pre class="variable">
+"""This program requires the Numeric or numarray
+ module to function - in fact is a requirement for the
+ wx.lib.plot module. Please install either Numeric or
+ numarray.
+ """
+</pre></td></tr></table>
+</dd>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
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+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
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+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
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+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
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+ <td align="left" class="footer">
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+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
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+
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+ <!--
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+</html>
diff --git a/docs/silacvalidator-pysrc.html b/docs/silacvalidator-pysrc.html
new file mode 100644
index 0000000000000000000000000000000000000000..b36d1ace53b4d406819366d357ffc548ef1c7010
--- /dev/null
+++ b/docs/silacvalidator-pysrc.html
@@ -0,0 +1,1267 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>silacvalidator</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
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+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
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+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
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+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ Module silacvalidator
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<h1 class="epydoc">Source Code for <a href="silacvalidator-module.html">Module silacvalidator</a></h1>
+<pre class="py-src">
+<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env pythonw</tt> </tt>
+<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""</tt> </tt>
+<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">SILAC validator v. 0.2, silacvalidator.py</tt> </tt>
+<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">requires Python (2.5 or higher), wxPython and numpy (Numeric or numarray)</tt> </tt>
+<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">(ElementTree is now included in Python 2.5)</tt> </tt>
+<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">INSTRUCTIONS:</tt> </tt>
+<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">This application recognizes XML files, as generated by lilamsXML. These files are</tt> </tt>
+<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">obtained from a spectrum (in text format) and a MsFit3.2 results file (in html for-</tt> </tt>
+<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">mat). Only the first entry in the file is quantified and generates an xml file.</tt> </tt>
+<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">After opening an XML file, the first peptide-associated spectrum is displayed in </tt> </tt>
+<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">the interactive plot window. You can zoom by drawing a rectangle with the left</tt> </tt>
+<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">mouse click and unzoom with the menu >Plot>Full Unzoom. When clicking anywhere</tt> </tt>
+<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">on the plot, the m/z value and intensity are shown in the status bar.</tt> </tt>
+<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">To associate a local background to a spectrum double-click on the maximum and</tt> </tt>
+<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">minimum of the peak considered as background. The difference of the two values</tt> </tt>
+<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">is shown in the status bar. By clicking on the <Set Bgrnd.> button the last va-</tt> </tt>
+<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">lue of the local background is inserted in the peptide table and the corrected</tt> </tt>
+<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">ratio is automatically calculated. To validate the peptide quantification click</tt> </tt>
+<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">on the <Validate> button.</tt> </tt>
+<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">Clicking on the column titles allows sorting of the peptide list by any criteria.</tt> </tt>
+<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">A visualisation program for XML files generated by lilamsxml. Allows validation</tt> </tt>
+<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">of SILAC experiments, peptide by peptide.</tt> </tt>
+<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">Written using wxPython, numarray, ElementTree et al., in Python, September 2004.</tt> </tt>
+<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring">Modified in January 2008, to be able to save in text format individual spectra</tt> </tt>
+<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">regions. Several ergonomy amelioration also done and debugged the Next/Previous</tt> </tt>
+<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">commands. THIS PROGRAM CONTAINS BUGS, SOME OF THEM IN THE UPSTREAM LIBRARIES!</tt> </tt>
+<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">Cosmin Saveanu in Alain Jacquier's laboratory, Institut Pasteur, CNRS-URA2171.</tt> </tt>
+<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring">Many thanks to all the people contributing to the development of tools like wxPython,</tt> </tt>
+<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">Python itself, ElementTree, and wx.lib.plot and the wonderful examples to get</tt> </tt>
+<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring">inspiration (and sometimes copy/paste) from.</tt> </tt>
+<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
+<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring">This program may be freely distributed as long as correct references to it are</tt> </tt>
+<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring">provided, with this included note.</tt> </tt>
+<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
+<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">wx</tt> </tt>
+<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">string</tt> </tt>
+<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
+<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-comment">#the required plot module to draw spectra</tt> </tt>
+<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#from elementtree import ElementTree as ET</tt> </tt>
+<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#elementtree is an excellent package written by Fredrik Lundh (effbot.org)</tt> </tt>
+<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#to deal with simple XML structures.</tt> </tt>
+<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">etree</tt><tt class="py-op">.</tt><tt class="py-name">cElementTree</tt> <tt class="py-keyword">as</tt> <tt class="py-name">ET</tt> <tt class="py-comment">#latest version integrated in Python 2.5</tt> </tt>
+<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt>
+<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment">#Imports for the ListCtrl class, copied from the wxPython documentation</tt> </tt>
+<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt><tt class="py-op">.</tt><tt class="py-name">mixins</tt><tt class="py-op">.</tt><tt class="py-name">listctrl</tt> <tt class="py-keyword">as</tt> <tt class="py-name">listmix</tt> </tt>
+<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">wx</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ImageFromStream</tt><tt class="py-op">,</tt> <tt class="py-name">BitmapFromImage</tt> </tt>
+<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
+<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">cStringIO</tt> </tt>
+<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
+<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">Numeric</tt> </tt>
+<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">numarray</tt> <tt class="py-keyword">as</tt> <tt class="py-name">Numeric</tt> </tt>
+<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">Numeric</tt> </tt>
+<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Variable silacvalidator.msg=silacvalidator-module.html#msg"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-0', 'msg', 'link-0');">msg</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""This program requires the Numeric or numarray</tt> </tt>
+<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-string"> module to function - in fact is a requirement for the</tt> </tt>
+<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-string"> wx.lib.plot module. Please install either Numeric or</tt> </tt>
+<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-string"> numarray.</tt> </tt>
+<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-string"> """</tt> </tt>
+<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ImportError</tt><tt class="py-op">,</tt> <tt class="py-string">"Numeric, numpy or numarray not found.\n"</tt><tt class="py-op">+</tt><tt id="link-1" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-1', 'msg', 'link-0');">msg</a></tt> </tt>
+<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
+<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-comment">#first - define unique identifiers for the different graphical elements </tt> </tt>
+<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-op">[</tt><tt class="py-name">ID_OPEN</tt><tt class="py-op">,</tt> </tt>
+<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-name">ID_OPENX</tt><tt class="py-op">,</tt> </tt>
+<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-name">ID_CLOSE</tt><tt class="py-op">,</tt> </tt>
+<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-name">ID_SAVEP</tt><tt class="py-op">,</tt> </tt>
+<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-name">ID_SAVESP</tt><tt class="py-op">,</tt> </tt>
+<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-name">ID_SAVEDATA</tt><tt class="py-op">,</tt> </tt>
+<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> </tt>
+<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> </tt>
+<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-name">ID_ENGRID</tt><tt class="py-op">,</tt> </tt>
+<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-name">ID_UNZOOM</tt><tt class="py-op">,</tt> </tt>
+<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-name">ID_NEXTF</tt><tt class="py-op">,</tt> </tt>
+<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-name">ID_PREVF</tt><tt class="py-op">,</tt> </tt>
+<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-name">ID_BTN1</tt><tt class="py-op">,</tt> </tt>
+<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-name">ID_BTN2</tt><tt class="py-op">,</tt> </tt>
+<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-name">ID_BTN3</tt> </tt>
+<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">init_ctrls</tt><tt class="py-op">:</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">NewId</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">15</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
+<a name="get_flist_xml"></a><div id="get_flist_xml-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="get_flist_xml-toggle" onclick="return toggle('get_flist_xml');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#get_flist_xml">get_flist_xml</a><tt class="py-op">(</tt><tt class="py-param">dirname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="get_flist_xml-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="get_flist_xml-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-docstring">"""get all .xml file names from dirname, not recursive</tt> </tt>
+<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> return only the file name, not the path</tt> </tt>
+<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> Needed by the OnPrevFile and OnNextFile functions</tt> </tt>
+<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> but called by <XMLOpen> to set the self.filelist list</tt> </tt>
+<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> of xml files from the current folder. </tt> </tt>
+<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">outlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L100"></a><tt class="py-lineno"> 100</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">f</tt> </tt>
+<a name="L101"></a><tt class="py-lineno"> 101</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L102"></a><tt class="py-lineno"> 102</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L103"></a><tt class="py-lineno"> 103</tt> <tt class="py-line"> <tt class="py-comment">#we do nothing with the subfolders</tt> </tt>
+<a name="L104"></a><tt class="py-lineno"> 104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L105"></a><tt class="py-lineno"> 105</tt> <tt class="py-line"> <tt class="py-name">extension</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L106"></a><tt class="py-lineno"> 106</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">extension</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">".xml"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L107"></a><tt class="py-lineno"> 107</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L108"></a><tt class="py-lineno"> 108</tt> <tt class="py-line"> <tt class="py-name">outlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
+<a name="L109"></a><tt class="py-lineno"> 109</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L110"></a><tt class="py-lineno"> 110</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L111"></a><tt class="py-lineno"> 111</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">outlist</tt> </tt>
+</div><a name="L112"></a><tt class="py-lineno"> 112</tt> <tt class="py-line"> </tt>
+<a name="get_flist_txt"></a><div id="get_flist_txt-def"><a name="L113"></a><tt class="py-lineno"> 113</tt> <a class="py-toggle" href="#" id="get_flist_txt-toggle" onclick="return toggle('get_flist_txt');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#get_flist_txt">get_flist_txt</a><tt class="py-op">(</tt><tt class="py-param">dirname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="get_flist_txt-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="get_flist_txt-expanded"><a name="L114"></a><tt class="py-lineno"> 114</tt> <tt class="py-line"> <tt class="py-docstring">"""get all .txt file names from dirname, not recursive</tt> </tt>
+<a name="L115"></a><tt class="py-lineno"> 115</tt> <tt class="py-line"><tt class="py-docstring"> return only the file name, not the path</tt> </tt>
+<a name="L116"></a><tt class="py-lineno"> 116</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L117"></a><tt class="py-lineno"> 117</tt> <tt class="py-line"> <tt class="py-name">outlist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L118"></a><tt class="py-lineno"> 118</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L119"></a><tt class="py-lineno"> 119</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">f</tt> </tt>
+<a name="L120"></a><tt class="py-lineno"> 120</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isdir</tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L121"></a><tt class="py-lineno"> 121</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L122"></a><tt class="py-lineno"> 122</tt> <tt class="py-line"> <tt class="py-comment">#we do nothing with the subfolders</tt> </tt>
+<a name="L123"></a><tt class="py-lineno"> 123</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L124"></a><tt class="py-lineno"> 124</tt> <tt class="py-line"> <tt class="py-name">extension</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+<a name="L125"></a><tt class="py-lineno"> 125</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">extension</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">".txt"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L126"></a><tt class="py-lineno"> 126</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L127"></a><tt class="py-lineno"> 127</tt> <tt class="py-line"> <tt class="py-name">outlist</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">)</tt> </tt>
+<a name="L128"></a><tt class="py-lineno"> 128</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L129"></a><tt class="py-lineno"> 129</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
+<a name="L130"></a><tt class="py-lineno"> 130</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">outlist</tt> </tt>
+</div><a name="L131"></a><tt class="py-lineno"> 131</tt> <tt class="py-line"> </tt>
+<a name="map_pos_inlist"></a><div id="map_pos_inlist-def"><a name="L132"></a><tt class="py-lineno"> 132</tt> <a class="py-toggle" href="#" id="map_pos_inlist-toggle" onclick="return toggle('map_pos_inlist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#map_pos_inlist">map_pos_inlist</a><tt class="py-op">(</tt><tt class="py-param">flist</tt><tt class="py-op">,</tt> <tt class="py-param">fname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="map_pos_inlist-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="map_pos_inlist-expanded"><a name="L133"></a><tt class="py-lineno"> 133</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L134"></a><tt class="py-lineno"> 134</tt> <tt class="py-line"><tt class="py-docstring"> Obtain the index of a file name in a file list</tt> </tt>
+<a name="L135"></a><tt class="py-lineno"> 135</tt> <tt class="py-line"><tt class="py-docstring"> If file name not found return 0 as the position</tt> </tt>
+<a name="L136"></a><tt class="py-lineno"> 136</tt> <tt class="py-line"><tt class="py-docstring"> Used in XMLOpen, generated a value for <self.where></tt> </tt>
+<a name="L137"></a><tt class="py-lineno"> 137</tt> <tt class="py-line"><tt class="py-docstring"> about the current position of a file in the file</tt> </tt>
+<a name="L138"></a><tt class="py-lineno"> 138</tt> <tt class="py-line"><tt class="py-docstring"> list obtained with <get_flist_xml>.</tt> </tt>
+<a name="L139"></a><tt class="py-lineno"> 139</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L140"></a><tt class="py-lineno"> 140</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">flist</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L141"></a><tt class="py-lineno"> 141</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">flist</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">fname</tt><tt class="py-op">:</tt> </tt>
+<a name="L142"></a><tt class="py-lineno"> 142</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">i</tt> </tt>
+<a name="L143"></a><tt class="py-lineno"> 143</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
+<a name="L144"></a><tt class="py-lineno"> 144</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L145"></a><tt class="py-lineno"> 145</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L146"></a><tt class="py-lineno"> 146</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
+</div><a name="L147"></a><tt class="py-lineno"> 147</tt> <tt class="py-line"> </tt>
+<a name="ReadFromFileArray"></a><div id="ReadFromFileArray-def"><a name="L148"></a><tt class="py-lineno"> 148</tt> <a class="py-toggle" href="#" id="ReadFromFileArray-toggle" onclick="return toggle('ReadFromFileArray');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#ReadFromFileArray">ReadFromFileArray</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt> <tt class="py-param">skip</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="ReadFromFileArray-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="ReadFromFileArray-expanded"><a name="L149"></a><tt class="py-lineno"> 149</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L150"></a><tt class="py-lineno"> 150</tt> <tt class="py-line"><tt class="py-docstring"> Obtain floats from a tab delimited file into a numarray array</tt> </tt>
+<a name="L151"></a><tt class="py-lineno"> 151</tt> <tt class="py-line"><tt class="py-docstring"> The <skip> parameter indicate the number of lines not</tt> </tt>
+<a name="L152"></a><tt class="py-lineno"> 152</tt> <tt class="py-line"><tt class="py-docstring"> read.</tt> </tt>
+<a name="L153"></a><tt class="py-lineno"> 153</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L154"></a><tt class="py-lineno"> 154</tt> <tt class="py-line"><tt class="py-docstring"> This function is only used to directly open a complete spectrum</tt> </tt>
+<a name="L155"></a><tt class="py-lineno"> 155</tt> <tt class="py-line"><tt class="py-docstring"> or a text delimited file with two columns - mz and intensity</tt> </tt>
+<a name="L156"></a><tt class="py-lineno"> 156</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L157"></a><tt class="py-lineno"> 157</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L158"></a><tt class="py-lineno"> 158</tt> <tt class="py-line"> <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L159"></a><tt class="py-lineno"> 159</tt> <tt class="py-line"> <tt class="py-name">errmsg</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
+<a name="L160"></a><tt class="py-lineno"> 160</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">=</tt><tt class="py-name">file</tt> </tt>
+<a name="L161"></a><tt class="py-lineno"> 161</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">skip</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L162"></a><tt class="py-lineno"> 162</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">readline</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L163"></a><tt class="py-lineno"> 163</tt> <tt class="py-line"> <tt class="py-comment">#simple test to see if the file look like a float coercible text file</tt> </tt>
+<a name="L164"></a><tt class="py-lineno"> 164</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L165"></a><tt class="py-lineno"> 165</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">f</tt><tt class="py-op">:</tt> </tt>
+<a name="L166"></a><tt class="py-lineno"> 166</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L167"></a><tt class="py-lineno"> 167</tt> <tt class="py-line"> <tt class="py-name">data_array</tt> <tt class="py-op">=</tt> <tt class="py-name">Numeric</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
+<a name="L168"></a><tt class="py-lineno"> 168</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
+<a name="L169"></a><tt class="py-lineno"> 169</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
+<a name="L170"></a><tt class="py-lineno"> 170</tt> <tt class="py-line"> <tt class="py-name">data_array</tt> <tt class="py-op">=</tt> <tt class="py-name">Numeric</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
+<a name="L171"></a><tt class="py-lineno"> 171</tt> <tt class="py-line"> <tt class="py-name">err</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
+<a name="L172"></a><tt class="py-lineno"> 172</tt> <tt class="py-line"> <tt class="py-name">errmsg</tt> <tt class="py-op">=</tt> <tt class="py-string">"The file you are trying to open does not look like a tab delimited one"</tt> </tt>
+<a name="L173"></a><tt class="py-lineno"> 173</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">data_array</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">,</tt> <tt class="py-name">errmsg</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L174"></a><tt class="py-lineno"> 174</tt> <tt class="py-line"> <tt class="py-comment">#the returned data is a tuple with an array of floats, error and errmsg</tt> </tt>
+<a name="L175"></a><tt class="py-lineno"> 175</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L176"></a><tt class="py-lineno"> 176</tt> <tt class="py-line"> </tt>
+<a name="L177"></a><tt class="py-lineno"> 177</tt> <tt class="py-line"><tt class="py-comment">############################################</tt> </tt>
+<a name="L178"></a><tt class="py-lineno"> 178</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># INTERFACE ############################</tt> </tt>
+<a name="L179"></a><tt class="py-lineno"> 179</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">############################################</tt> </tt>
+<a name="MainFrame"></a><div id="MainFrame-def"><a name="L180"></a><tt class="py-lineno"> 180</tt> <a class="py-toggle" href="#" id="MainFrame-toggle" onclick="return toggle('MainFrame');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html">MainFrame</a><tt class="py-op">(</tt><tt class="py-base-class">wx</tt><tt class="py-op">.</tt><tt class="py-base-class">Frame</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="MainFrame-expanded"><a name="L181"></a><tt class="py-lineno"> 181</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L182"></a><tt class="py-lineno"> 182</tt> <tt class="py-line"><tt class="py-docstring"> The application main frame. Contains the following</tt> </tt>
+<a name="L183"></a><tt class="py-lineno"> 183</tt> <tt class="py-line"><tt class="py-docstring"> graphic elements:</tt> </tt>
+<a name="L184"></a><tt class="py-lineno"> 184</tt> <tt class="py-line"><tt class="py-docstring"> self.panel |---- self.lb - the text list control</tt> </tt>
+<a name="L185"></a><tt class="py-lineno"> 185</tt> <tt class="py-line"><tt class="py-docstring"> |---- self.btnpanel1 - the panel containing</tt> </tt>
+<a name="L186"></a><tt class="py-lineno"> 186</tt> <tt class="py-line"><tt class="py-docstring"> three buttons (Validate, Invalidate</tt> </tt>
+<a name="L187"></a><tt class="py-lineno"> 187</tt> <tt class="py-line"><tt class="py-docstring"> and LocalBackground</tt> </tt>
+<a name="L188"></a><tt class="py-lineno"> 188</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L189"></a><tt class="py-lineno"> 189</tt> <tt class="py-line"><tt class="py-docstring"> self.panelplot - containing self.plotcanvas</tt> </tt>
+<a name="L190"></a><tt class="py-lineno"> 190</tt> <tt class="py-line"><tt class="py-docstring"> to allow drawing of spectra files</tt> </tt>
+<a name="L191"></a><tt class="py-lineno"> 191</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L192"></a><tt class="py-lineno"> 192</tt> <tt class="py-line"><tt class="py-docstring"> self.log - a TextCtrl panel with information</tt> </tt>
+<a name="L193"></a><tt class="py-lineno"> 193</tt> <tt class="py-line"><tt class="py-docstring"> on the analysed xml file</tt> </tt>
+<a name="L194"></a><tt class="py-lineno"> 194</tt> <tt class="py-line"><tt class="py-docstring"> ______________________ </tt> </tt>
+<a name="L195"></a><tt class="py-lineno"> 195</tt> <tt class="py-line"><tt class="py-docstring"> --------------- ------</tt> </tt>
+<a name="L196"></a><tt class="py-lineno"> 196</tt> <tt class="py-line"><tt class="py-docstring"> | || | self.lb and self.btnpanel1</tt> </tt>
+<a name="L197"></a><tt class="py-lineno"> 197</tt> <tt class="py-line"><tt class="py-docstring"> -----------------------</tt> </tt>
+<a name="L198"></a><tt class="py-lineno"> 198</tt> <tt class="py-line"><tt class="py-docstring"> | | </tt> </tt>
+<a name="L199"></a><tt class="py-lineno"> 199</tt> <tt class="py-line"><tt class="py-docstring"> | | self.panelplot with self.plotcanvas</tt> </tt>
+<a name="L200"></a><tt class="py-lineno"> 200</tt> <tt class="py-line"><tt class="py-docstring"> | |</tt> </tt>
+<a name="L201"></a><tt class="py-lineno"> 201</tt> <tt class="py-line"><tt class="py-docstring"> -----------------------</tt> </tt>
+<a name="L202"></a><tt class="py-lineno"> 202</tt> <tt class="py-line"><tt class="py-docstring"> | | self.log</tt> </tt>
+<a name="L203"></a><tt class="py-lineno"> 203</tt> <tt class="py-line"><tt class="py-docstring"> -----------------------</tt> </tt>
+<a name="L204"></a><tt class="py-lineno"> 204</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="MainFrame.__init__"></a><div id="MainFrame.__init__-def"><a name="L205"></a><tt class="py-lineno"> 205</tt> <a class="py-toggle" href="#" id="MainFrame.__init__-toggle" onclick="return toggle('MainFrame.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><a name="L206"></a><tt class="py-lineno"> 206</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Frame</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Collect_SILAC_XML.Usage.__init__()=Collect_SILAC_XML.Usage-class.html#__init__,Method MSFit_to_txt.MainFrame.__init__()=MSFit_to_txt.MainFrame-class.html#__init__,Method lilamslaunchGUI.MainFrame.__init__()=lilamslaunchGUI.MainFrame-class.html#__init__,Method lilamsxml.DataIntObj.__init__()=lilamsxml.DataIntObj-class.html#__init__,Method lilamsxml.Usage.__init__()=lilamsxml.Usage-class.html#__init__,Method silacvalidator.MainFrame.__init__()=silacvalidator.MainFrame-class.html#__init__,Method silacvalidator.PepListCtrl.__init__()=silacvalidator.PepListCtrl-class.html#__init__,Method silacvalidator.PepListCtrlPanel.__init__()=silacvalidator.PepListCtrlPanel-class.html#__init__"><a title="Collect_SILAC_XML.Usage.__init__
+MSFit_to_txt.MainFrame.__init__
+lilamslaunchGUI.MainFrame.__init__
+lilamsxml.DataIntObj.__init__
+lilamsxml.Usage.__init__
+silacvalidator.MainFrame.__init__
+silacvalidator.PepListCtrl.__init__
+silacvalidator.PepListCtrlPanel.__init__" class="py-name" href="#" onclick="return doclink('link-2', '__init__', 'link-2');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt class="py-name">id</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">,</tt> </tt>
+<a name="L207"></a><tt class="py-lineno"> 207</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultPosition</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">800</tt><tt class="py-op">,</tt> <tt class="py-number">700</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L208"></a><tt class="py-lineno"> 208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-string">"."</tt> </tt>
+<a name="L209"></a><tt class="py-lineno"> 209</tt> <tt class="py-line"> <tt class="py-comment">#default directory for opening files, will be modified after first open</tt> </tt>
+<a name="L210"></a><tt class="py-lineno"> 210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L211"></a><tt class="py-lineno"> 211</tt> <tt class="py-line"> <tt class="py-comment">#list with all the xml files in a folder</tt> </tt>
+<a name="L212"></a><tt class="py-lineno"> 212</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L213"></a><tt class="py-lineno"> 213</tt> <tt class="py-line"> <tt class="py-comment">#position in the list of files</tt> </tt>
+<a name="L214"></a><tt class="py-lineno"> 214</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">previousclick_y</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L215"></a><tt class="py-lineno"> 215</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">actualclick_y</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L216"></a><tt class="py-lineno"> 216</tt> <tt class="py-line"> <tt class="py-comment">#local background is calculated by substracting</tt> </tt>
+<a name="L217"></a><tt class="py-lineno"> 217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.previousclick_y from self.actualclick_y</tt> </tt>
+<a name="L218"></a><tt class="py-lineno"> 218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#absolute value is returned anyway</tt> </tt>
+<a name="L219"></a><tt class="py-lineno"> 219</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">localbg</tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
+<a name="L220"></a><tt class="py-lineno"> 220</tt> <tt class="py-line"> </tt>
+<a name="L221"></a><tt class="py-lineno"> 221</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Variable Collect_SILAC_XML.XMLdict=Collect_SILAC_XML-module.html#XMLdict"><a title="Collect_SILAC_XML.XMLdict" class="py-name" href="#" onclick="return doclink('link-3', 'XMLdict', 'link-3');">XMLdict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">:</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'mzh'</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">'leucines'</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> </tt>
+<a name="L222"></a><tt class="py-lineno"> 222</tt> <tt class="py-line"> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> </tt>
+<a name="L223"></a><tt class="py-lineno"> 223</tt> <tt class="py-line"> <tt class="py-string">'ratio'</tt><tt class="py-op">:</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-string">'validated'</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">,</tt> </tt>
+<a name="L224"></a><tt class="py-lineno"> 224</tt> <tt class="py-line"> <tt class="py-string">'local_bg'</tt><tt class="py-op">:</tt><tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">:</tt><tt class="py-number">9</tt><tt class="py-op">}</tt> </tt>
+<a name="L225"></a><tt class="py-lineno"> 225</tt> <tt class="py-line"> <tt class="py-comment">#the mapping of tags to numbers to allow easy orientation in the ElementTree</tt> </tt>
+<a name="L226"></a><tt class="py-lineno"> 226</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Element object obtained by parsing a SILAC XML file. If the lilams XML format</tt> </tt>
+<a name="L227"></a><tt class="py-lineno"> 227</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#changes you should change accordingly these numbers</tt> </tt>
+<a name="L228"></a><tt class="py-lineno"> 228</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt> </tt>
+<a name="L229"></a><tt class="py-lineno"> 229</tt> <tt class="py-line"> <tt class="py-comment">#in the XML tree the pepdata values are in this position</tt> </tt>
+<a name="L230"></a><tt class="py-lineno"> 230</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L231"></a><tt class="py-lineno"> 231</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L232"></a><tt class="py-lineno"> 232</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Create the menu bar and items</tt> </tt>
+<a name="L233"></a><tt class="py-lineno"> 233</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MenuBar</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L234"></a><tt class="py-lineno"> 234</tt> <tt class="py-line"> </tt>
+<a name="L235"></a><tt class="py-lineno"> 235</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L236"></a><tt class="py-lineno"> 236</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_OPENX</tt><tt class="py-op">,</tt> <tt class="py-string">'&Open XML SILAC file...\tCtrl+O'</tt><tt class="py-op">,</tt> <tt class="py-string">'Open XML file with SILAC data'</tt><tt class="py-op">)</tt> </tt>
+<a name="L237"></a><tt class="py-lineno"> 237</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEDATA</tt><tt class="py-op">,</tt> <tt class="py-string">'Save XML &modifications\tCtrl+S'</tt><tt class="py-op">,</tt> <tt class="py-string">'Save modifications with (validation/local background)'</tt><tt class="py-op">)</tt> </tt>
+<a name="L238"></a><tt class="py-lineno"> 238</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L239"></a><tt class="py-lineno"> 239</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_OPEN</tt><tt class="py-op">,</tt> <tt class="py-string">'O&pen text file...\tCtrl+T'</tt><tt class="py-op">,</tt> <tt class="py-string">'Open tab delimited file for plotting'</tt><tt class="py-op">)</tt> </tt>
+<a name="L240"></a><tt class="py-lineno"> 240</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_CLOSE</tt><tt class="py-op">,</tt> <tt class="py-string">'&Close text file\tCtrl+W'</tt><tt class="py-op">,</tt> <tt class="py-string">'Close text file'</tt><tt class="py-op">)</tt> </tt>
+<a name="L241"></a><tt class="py-lineno"> 241</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L242"></a><tt class="py-lineno"> 242</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEP</tt><tt class="py-op">,</tt> <tt class="py-string">'&Save plot image\tCtrl+I'</tt><tt class="py-op">,</tt> <tt class="py-string">'Save plot image in a bmp, png or jpg format'</tt><tt class="py-op">)</tt> </tt>
+<a name="L243"></a><tt class="py-lineno"> 243</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L244"></a><tt class="py-lineno"> 244</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVESP</tt><tt class="py-op">,</tt> <tt class="py-string">'Sa&ve plot data\tCtrl+D'</tt><tt class="py-op">,</tt> <tt class="py-string">'Save the data corresponding to the plotted spectrum in text format'</tt><tt class="py-op">)</tt> </tt>
+<a name="L245"></a><tt class="py-lineno"> 245</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L246"></a><tt class="py-lineno"> 246</tt> <tt class="py-line"> <tt class="py-name">filemenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> <tt class="py-string">'&Quit\tCtrl+Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'Exit program'</tt><tt class="py-op">)</tt> </tt>
+<a name="L247"></a><tt class="py-lineno"> 247</tt> <tt class="py-line"> </tt>
+<a name="L248"></a><tt class="py-lineno"> 248</tt> <tt class="py-line"> <tt class="py-name">navmenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L249"></a><tt class="py-lineno"> 249</tt> <tt class="py-line"> <tt class="py-name">navmenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_NEXTF</tt><tt class="py-op">,</tt> <tt class="py-string">'&Next XML file\tCtrl+N'</tt><tt class="py-op">,</tt> <tt class="py-string">'Open next xml file in the current folder'</tt><tt class="py-op">)</tt> </tt>
+<a name="L250"></a><tt class="py-lineno"> 250</tt> <tt class="py-line"> <tt class="py-name">navmenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_PREVF</tt><tt class="py-op">,</tt> <tt class="py-string">'&Previous XML file\tCtrl+P'</tt><tt class="py-op">,</tt> <tt class="py-string">'Open previous xml file in the current folder'</tt><tt class="py-op">)</tt> </tt>
+<a name="L251"></a><tt class="py-lineno"> 251</tt> <tt class="py-line"> </tt>
+<a name="L252"></a><tt class="py-lineno"> 252</tt> <tt class="py-line"> <tt class="py-name">plotmenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L253"></a><tt class="py-lineno"> 253</tt> <tt class="py-line"> <tt class="py-name">plotmenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_UNZOOM</tt><tt class="py-op">,</tt> <tt class="py-string">'Full &Unzoom\tCtrl+U'</tt><tt class="py-op">,</tt> <tt class="py-string">'Full unzoom for the current plot'</tt><tt class="py-op">)</tt> </tt>
+<a name="L254"></a><tt class="py-lineno"> 254</tt> <tt class="py-line"> <tt class="py-name">plotmenu</tt><tt class="py-op">.</tt><tt class="py-name">AppendSeparator</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L255"></a><tt class="py-lineno"> 255</tt> <tt class="py-line"> <tt class="py-name">plotmenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_ENGRID</tt><tt class="py-op">,</tt> <tt class="py-string">'Grid &enabled'</tt><tt class="py-op">,</tt> <tt class="py-string">'Enable or disable grid when drawing'</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ITEM_CHECK</tt><tt class="py-op">)</tt> </tt>
+<a name="L256"></a><tt class="py-lineno"> 256</tt> <tt class="py-line"> </tt>
+<a name="L257"></a><tt class="py-lineno"> 257</tt> <tt class="py-line"> <tt class="py-name">helpmenu</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Menu</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L258"></a><tt class="py-lineno"> 258</tt> <tt class="py-line"> <tt class="py-name">helpmenu</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> <tt class="py-string">'&About...\tCtrl+E'</tt><tt class="py-op">,</tt> <tt class="py-string">'About this program'</tt><tt class="py-op">)</tt> </tt>
+<a name="L259"></a><tt class="py-lineno"> 259</tt> <tt class="py-line"> </tt>
+<a name="L260"></a><tt class="py-lineno"> 260</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L261"></a><tt class="py-lineno"> 261</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Bind the events to methods </tt> </tt>
+<a name="L262"></a><tt class="py-lineno"> 262</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_OPENX</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method silacvalidator.MainFrame.OnXMLOpen()=silacvalidator.MainFrame-class.html#OnXMLOpen"><a title="silacvalidator.MainFrame.OnXMLOpen" class="py-name" href="#" onclick="return doclink('link-4', 'OnXMLOpen', 'link-4');">OnXMLOpen</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L263"></a><tt class="py-lineno"> 263</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_SAVEDATA</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method silacvalidator.MainFrame.OnXMLSave()=silacvalidator.MainFrame-class.html#OnXMLSave"><a title="silacvalidator.MainFrame.OnXMLSave" class="py-name" href="#" onclick="return doclink('link-5', 'OnXMLSave', 'link-5');">OnXMLSave</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L264"></a><tt class="py-lineno"> 264</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_OPEN</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method silacvalidator.MainFrame.OnFileOpen()=silacvalidator.MainFrame-class.html#OnFileOpen"><a title="silacvalidator.MainFrame.OnFileOpen" class="py-name" href="#" onclick="return doclink('link-6', 'OnFileOpen', 'link-6');">OnFileOpen</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L265"></a><tt class="py-lineno"> 265</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_CLOSE</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method silacvalidator.MainFrame.OnFileClose()=silacvalidator.MainFrame-class.html#OnFileClose"><a title="silacvalidator.MainFrame.OnFileClose" class="py-name" href="#" onclick="return doclink('link-7', 'OnFileClose', 'link-7');">OnFileClose</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L266"></a><tt class="py-lineno"> 266</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_SAVEP</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method silacvalidator.MainFrame.OnSaveImage()=silacvalidator.MainFrame-class.html#OnSaveImage"><a title="silacvalidator.MainFrame.OnSaveImage" class="py-name" href="#" onclick="return doclink('link-8', 'OnSaveImage', 'link-8');">OnSaveImage</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L267"></a><tt class="py-lineno"> 267</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_SAVESP</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method silacvalidator.MainFrame.OnSpectrumSave()=silacvalidator.MainFrame-class.html#OnSpectrumSave"><a title="silacvalidator.MainFrame.OnSpectrumSave" class="py-name" href="#" onclick="return doclink('link-9', 'OnSpectrumSave', 'link-9');">OnSpectrumSave</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L268"></a><tt class="py-lineno"> 268</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_EXIT</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnFileExit()=MSFit_to_txt.MainFrame-class.html#OnFileExit,Method lilamslaunchGUI.MainFrame.OnFileExit()=lilamslaunchGUI.MainFrame-class.html#OnFileExit,Method silacvalidator.MainFrame.OnFileExit()=silacvalidator.MainFrame-class.html#OnFileExit"><a title="MSFit_to_txt.MainFrame.OnFileExit
+lilamslaunchGUI.MainFrame.OnFileExit
+silacvalidator.MainFrame.OnFileExit" class="py-name" href="#" onclick="return doclink('link-10', 'OnFileExit', 'link-10');">OnFileExit</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L269"></a><tt class="py-lineno"> 269</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_NEXTF</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method silacvalidator.MainFrame.OnNextFile()=silacvalidator.MainFrame-class.html#OnNextFile"><a title="silacvalidator.MainFrame.OnNextFile" class="py-name" href="#" onclick="return doclink('link-11', 'OnNextFile', 'link-11');">OnNextFile</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L270"></a><tt class="py-lineno"> 270</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_PREVF</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method silacvalidator.MainFrame.OnPrevFile()=silacvalidator.MainFrame-class.html#OnPrevFile"><a title="silacvalidator.MainFrame.OnPrevFile" class="py-name" href="#" onclick="return doclink('link-12', 'OnPrevFile', 'link-12');">OnPrevFile</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L271"></a><tt class="py-lineno"> 271</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_ENGRID</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method silacvalidator.MainFrame.OnEnableGrid()=silacvalidator.MainFrame-class.html#OnEnableGrid"><a title="silacvalidator.MainFrame.OnEnableGrid" class="py-name" href="#" onclick="return doclink('link-13', 'OnEnableGrid', 'link-13');">OnEnableGrid</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L272"></a><tt class="py-lineno"> 272</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_UNZOOM</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method silacvalidator.MainFrame.OnFullUnzoom()=silacvalidator.MainFrame-class.html#OnFullUnzoom"><a title="silacvalidator.MainFrame.OnFullUnzoom" class="py-name" href="#" onclick="return doclink('link-14', 'OnFullUnzoom', 'link-14');">OnFullUnzoom</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L273"></a><tt class="py-lineno"> 273</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_MENU</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_ABOUT</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method MSFit_to_txt.MainFrame.OnHelpAbout()=MSFit_to_txt.MainFrame-class.html#OnHelpAbout,Method lilamslaunchGUI.MainFrame.OnHelpAbout()=lilamslaunchGUI.MainFrame-class.html#OnHelpAbout,Method silacvalidator.MainFrame.OnHelpAbout()=silacvalidator.MainFrame-class.html#OnHelpAbout"><a title="MSFit_to_txt.MainFrame.OnHelpAbout
+lilamslaunchGUI.MainFrame.OnHelpAbout
+silacvalidator.MainFrame.OnHelpAbout" class="py-name" href="#" onclick="return doclink('link-15', 'OnHelpAbout', 'link-15');">OnHelpAbout</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L274"></a><tt class="py-lineno"> 274</tt> <tt class="py-line"> </tt>
+<a name="L275"></a><tt class="py-lineno"> 275</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L276"></a><tt class="py-lineno"> 276</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Attach menus to the menubar</tt> </tt>
+<a name="L277"></a><tt class="py-lineno"> 277</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">filemenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&File'</tt><tt class="py-op">)</tt> </tt>
+<a name="L278"></a><tt class="py-lineno"> 278</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">navmenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&Next/Previous'</tt><tt class="py-op">)</tt> </tt>
+<a name="L279"></a><tt class="py-lineno"> 279</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">plotmenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&Plot'</tt><tt class="py-op">)</tt> </tt>
+<a name="L280"></a><tt class="py-lineno"> 280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Append</tt><tt class="py-op">(</tt><tt class="py-name">helpmenu</tt><tt class="py-op">,</tt> <tt class="py-string">'&Help'</tt><tt class="py-op">)</tt> </tt>
+<a name="L281"></a><tt class="py-lineno"> 281</tt> <tt class="py-line"> </tt>
+<a name="L282"></a><tt class="py-lineno"> 282</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">SetMenuBar</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">)</tt> </tt>
+<a name="L283"></a><tt class="py-lineno"> 283</tt> <tt class="py-line"> </tt>
+<a name="L284"></a><tt class="py-lineno"> 284</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L285"></a><tt class="py-lineno"> 285</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Disable by default some menus and buttons</tt> </tt>
+<a name="L286"></a><tt class="py-lineno"> 286</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_NEXTF</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L287"></a><tt class="py-lineno"> 287</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_PREVF</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L288"></a><tt class="py-lineno"> 288</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_UNZOOM</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L289"></a><tt class="py-lineno"> 289</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEP</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L290"></a><tt class="py-lineno"> 290</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVESP</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L291"></a><tt class="py-lineno"> 291</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEDATA</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L292"></a><tt class="py-lineno"> 292</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_CLOSE</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L293"></a><tt class="py-lineno"> 293</tt> <tt class="py-line"> </tt>
+<a name="L294"></a><tt class="py-lineno"> 294</tt> <tt class="py-line"> <tt class="py-comment"># A status bar to tell people what's happening</tt> </tt>
+<a name="L295"></a><tt class="py-lineno"> 295</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">CreateStatusBar</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L296"></a><tt class="py-lineno"> 296</tt> <tt class="py-line"> </tt>
+<a name="L297"></a><tt class="py-lineno"> 297</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">SetAutoLayout</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
+<a name="L298"></a><tt class="py-lineno"> 298</tt> <tt class="py-line"> </tt>
+<a name="L299"></a><tt class="py-lineno"> 299</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L300"></a><tt class="py-lineno"> 300</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Panel</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">SIMPLE_BORDER</tt><tt class="py-op">)</tt> </tt>
+<a name="L301"></a><tt class="py-lineno"> 301</tt> <tt class="py-line"> <tt class="py-comment">#in this case and all the others we use layout constraints</tt> </tt>
+<a name="L302"></a><tt class="py-lineno"> 302</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#I couldn't understand easily the sizers, while layout constraints seem</tt> </tt>
+<a name="L303"></a><tt class="py-lineno"> 303</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#quite easy to set up and they work very well.</tt> </tt>
+<a name="L304"></a><tt class="py-lineno"> 304</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.panel will contain the listctrl and button panel</tt> </tt>
+<a name="L305"></a><tt class="py-lineno"> 305</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L306"></a><tt class="py-lineno"> 306</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L307"></a><tt class="py-lineno"> 307</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Top</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L308"></a><tt class="py-lineno"> 308</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">right</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L309"></a><tt class="py-lineno"> 309</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">left</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Left</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L310"></a><tt class="py-lineno"> 310</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">PercentOf</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">30</tt><tt class="py-op">)</tt> </tt>
+<a name="L311"></a><tt class="py-lineno"> 311</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L312"></a><tt class="py-lineno"> 312</tt> <tt class="py-line"> </tt>
+<a name="L313"></a><tt class="py-lineno"> 313</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L314"></a><tt class="py-lineno"> 314</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#the peplistctrlpanel - with the list of peptides and interesting data</tt> </tt>
+<a name="L315"></a><tt class="py-lineno"> 315</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">smalldict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-string">"pepseq"</tt><tt class="py-op">,</tt> <tt class="py-string">"0"</tt><tt class="py-op">,</tt> <tt class="py-string">"mzh"</tt><tt class="py-op">,</tt> <tt class="py-string">"mzhcalc"</tt><tt class="py-op">,</tt> <tt class="py-string">"mono"</tt><tt class="py-op">,</tt> <tt class="py-string">"deuter"</tt><tt class="py-op">,</tt> <tt class="py-string">"ratio"</tt><tt class="py-op">,</tt> <tt class="py-string">"corr"</tt><tt class="py-op">,</tt> </tt>
+<a name="L316"></a><tt class="py-lineno"> 316</tt> <tt class="py-line"> <tt class="py-string">"localbg"</tt><tt class="py-op">,</tt> <tt class="py-string">"valid"</tt><tt class="py-op">)</tt><tt class="py-op">}</tt> </tt>
+<a name="L317"></a><tt class="py-lineno"> 317</tt> <tt class="py-line"> <tt class="py-comment">#we need this to fill up the listctrl at program initialization</tt> </tt>
+<a name="L318"></a><tt class="py-lineno"> 318</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Class silacvalidator.PepListCtrlPanel=silacvalidator.PepListCtrlPanel-class.html"><a title="silacvalidator.PepListCtrlPanel" class="py-name" href="#" onclick="return doclink('link-16', 'PepListCtrlPanel', 'link-16');">PepListCtrlPanel</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">dictwithdata</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">smalldict</tt><tt class="py-op">)</tt> </tt>
+<a name="L319"></a><tt class="py-lineno"> 319</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L320"></a><tt class="py-lineno"> 320</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Top</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L321"></a><tt class="py-lineno"> 321</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">right</tt><tt class="py-op">.</tt><tt class="py-name">PercentOf</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">80</tt><tt class="py-op">)</tt> <tt class="py-comment">#it will take up 80% of the panel</tt> </tt>
+<a name="L322"></a><tt class="py-lineno"> 322</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">left</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Left</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L323"></a><tt class="py-lineno"> 323</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L324"></a><tt class="py-lineno"> 324</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L325"></a><tt class="py-lineno"> 325</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L326"></a><tt class="py-lineno"> 326</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Bind</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_LIST_ITEM_SELECTED</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method silacvalidator.MainFrame.OnItemSelected()=silacvalidator.MainFrame-class.html#OnItemSelected,Method silacvalidator.PepListCtrlPanel.OnItemSelected()=silacvalidator.PepListCtrlPanel-class.html#OnItemSelected"><a title="silacvalidator.MainFrame.OnItemSelected
+silacvalidator.PepListCtrlPanel.OnItemSelected" class="py-name" href="#" onclick="return doclink('link-17', 'OnItemSelected', 'link-17');">OnItemSelected</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">)</tt> </tt>
+<a name="L327"></a><tt class="py-lineno"> 327</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L328"></a><tt class="py-lineno"> 328</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#the panel to hold the three buttons</tt> </tt>
+<a name="L329"></a><tt class="py-lineno"> 329</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Panel</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">SIMPLE_BORDER</tt><tt class="py-op">)</tt> </tt>
+<a name="L330"></a><tt class="py-lineno"> 330</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L331"></a><tt class="py-lineno"> 331</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Top</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L332"></a><tt class="py-lineno"> 332</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">right</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L333"></a><tt class="py-lineno"> 333</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">left</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L334"></a><tt class="py-lineno"> 334</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L335"></a><tt class="py-lineno"> 335</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L336"></a><tt class="py-lineno"> 336</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L337"></a><tt class="py-lineno"> 337</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#set up the buttons and bind to the corresponding functions</tt> </tt>
+<a name="L338"></a><tt class="py-lineno"> 338</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn1</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Button</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">,</tt> <tt class="py-name">ID_BTN1</tt><tt class="py-op">,</tt> <tt class="py-string">" Validate "</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultPosition</tt><tt class="py-op">)</tt> </tt>
+<a name="L339"></a><tt class="py-lineno"> 339</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn2</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Button</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">,</tt> <tt class="py-name">ID_BTN2</tt><tt class="py-op">,</tt> <tt class="py-string">"INvalidate"</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultPosition</tt><tt class="py-op">)</tt> </tt>
+<a name="L340"></a><tt class="py-lineno"> 340</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn3</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Button</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">,</tt> <tt class="py-name">ID_BTN3</tt><tt class="py-op">,</tt> <tt class="py-string">"Set Bgrnd."</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultPosition</tt><tt class="py-op">)</tt> </tt>
+<a name="L341"></a><tt class="py-lineno"> 341</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_BUTTON</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_BTN1</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method silacvalidator.MainFrame.OnValidate()=silacvalidator.MainFrame-class.html#OnValidate"><a title="silacvalidator.MainFrame.OnValidate" class="py-name" href="#" onclick="return doclink('link-18', 'OnValidate', 'link-18');">OnValidate</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L342"></a><tt class="py-lineno"> 342</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_BUTTON</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_BTN2</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method silacvalidator.MainFrame.OnInvalidate()=silacvalidator.MainFrame-class.html#OnInvalidate"><a title="silacvalidator.MainFrame.OnInvalidate" class="py-name" href="#" onclick="return doclink('link-19', 'OnInvalidate', 'link-19');">OnInvalidate</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L343"></a><tt class="py-lineno"> 343</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_BUTTON</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">ID_BTN3</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method silacvalidator.MainFrame.OnSetLocalBg()=silacvalidator.MainFrame-class.html#OnSetLocalBg"><a title="silacvalidator.MainFrame.OnSetLocalBg" class="py-name" href="#" onclick="return doclink('link-20', 'OnSetLocalBg', 'link-20');">OnSetLocalBg</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L344"></a><tt class="py-lineno"> 344</tt> <tt class="py-line"> </tt>
+<a name="L345"></a><tt class="py-lineno"> 345</tt> <tt class="py-line"> <tt class="py-comment">#Disable by default the three buttons</tt> </tt>
+<a name="L346"></a><tt class="py-lineno"> 346</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn1</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
+<a name="L347"></a><tt class="py-lineno"> 347</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn2</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
+<a name="L348"></a><tt class="py-lineno"> 348</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn3</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
+<a name="L349"></a><tt class="py-lineno"> 349</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L350"></a><tt class="py-lineno"> 350</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#layout the buttons on the btnpanel1</tt> </tt>
+<a name="L351"></a><tt class="py-lineno"> 351</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L352"></a><tt class="py-lineno"> 352</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">centreX</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">CentreX</tt><tt class="py-op">)</tt> </tt>
+<a name="L353"></a><tt class="py-lineno"> 353</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Top</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L354"></a><tt class="py-lineno"> 354</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">width</tt><tt class="py-op">.</tt><tt class="py-name">AsIs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L355"></a><tt class="py-lineno"> 355</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">height</tt><tt class="py-op">.</tt><tt class="py-name">AsIs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L356"></a><tt class="py-lineno"> 356</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn1</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L357"></a><tt class="py-lineno"> 357</tt> <tt class="py-line"> </tt>
+<a name="L358"></a><tt class="py-lineno"> 358</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L359"></a><tt class="py-lineno"> 359</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">centreX</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn1</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">CentreX</tt><tt class="py-op">)</tt> </tt>
+<a name="L360"></a><tt class="py-lineno"> 360</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">centreY</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">CentreY</tt><tt class="py-op">)</tt> </tt>
+<a name="L361"></a><tt class="py-lineno"> 361</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">width</tt><tt class="py-op">.</tt><tt class="py-name">AsIs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L362"></a><tt class="py-lineno"> 362</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">height</tt><tt class="py-op">.</tt><tt class="py-name">AsIs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L363"></a><tt class="py-lineno"> 363</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn2</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L364"></a><tt class="py-lineno"> 364</tt> <tt class="py-line"> </tt>
+<a name="L365"></a><tt class="py-lineno"> 365</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L366"></a><tt class="py-lineno"> 366</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">centreX</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn1</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">CentreX</tt><tt class="py-op">)</tt> </tt>
+<a name="L367"></a><tt class="py-lineno"> 367</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btnpanel1</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L368"></a><tt class="py-lineno"> 368</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">width</tt><tt class="py-op">.</tt><tt class="py-name">AsIs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L369"></a><tt class="py-lineno"> 369</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">height</tt><tt class="py-op">.</tt><tt class="py-name">AsIs</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L370"></a><tt class="py-lineno"> 370</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn3</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L371"></a><tt class="py-lineno"> 371</tt> <tt class="py-line"> </tt>
+<a name="L372"></a><tt class="py-lineno"> 372</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L373"></a><tt class="py-lineno"> 373</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#A black panel to give contrast to the plot</tt> </tt>
+<a name="L374"></a><tt class="py-lineno"> 374</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Window</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L375"></a><tt class="py-lineno"> 375</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">.</tt><tt class="py-name">SetBackgroundColour</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">BLACK</tt><tt class="py-op">)</tt> </tt>
+<a name="L376"></a><tt class="py-lineno"> 376</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L377"></a><tt class="py-lineno"> 377</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">Below</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panel</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L378"></a><tt class="py-lineno"> 378</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">left</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Left</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L379"></a><tt class="py-lineno"> 379</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">PercentOf</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">85</tt><tt class="py-op">)</tt> </tt>
+<a name="L380"></a><tt class="py-lineno"> 380</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">right</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L381"></a><tt class="py-lineno"> 381</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L382"></a><tt class="py-lineno"> 382</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L383"></a><tt class="py-lineno"> 383</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#The plot itself in self.panelplot</tt> </tt>
+<a name="L384"></a><tt class="py-lineno"> 384</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt> <tt class="py-op">=</tt> <tt class="py-name">PlotCanvas</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L385"></a><tt class="py-lineno"> 385</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L386"></a><tt class="py-lineno"> 386</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Top</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L387"></a><tt class="py-lineno"> 387</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">left</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Left</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L388"></a><tt class="py-lineno"> 388</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L389"></a><tt class="py-lineno"> 389</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">right</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L390"></a><tt class="py-lineno"> 390</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L391"></a><tt class="py-lineno"> 391</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L392"></a><tt class="py-lineno"> 392</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#A panel to hold the TextCtrl called self.log</tt> </tt>
+<a name="L393"></a><tt class="py-lineno"> 393</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logpanel</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Window</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L394"></a><tt class="py-lineno"> 394</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L395"></a><tt class="py-lineno"> 395</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">Below</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">panelplot</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L396"></a><tt class="py-lineno"> 396</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">left</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Left</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L397"></a><tt class="py-lineno"> 397</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L398"></a><tt class="py-lineno"> 398</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">right</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L399"></a><tt class="py-lineno"> 399</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logpanel</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L400"></a><tt class="py-lineno"> 400</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L401"></a><tt class="py-lineno"> 401</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#The text control that will hold informations on the protein and file used</tt> </tt>
+<a name="L402"></a><tt class="py-lineno"> 402</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">TextCtrl</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logpanel</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
+<a name="L403"></a><tt class="py-lineno"> 403</tt> <tt class="py-line"> <tt class="py-name">style</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">TE_MULTILINE</tt><tt class="py-op">|</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">TE_READONLY</tt><tt class="py-op">|</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">HSCROLL</tt><tt class="py-op">)</tt> </tt>
+<a name="L404"></a><tt class="py-lineno"> 404</tt> <tt class="py-line"> <tt class="py-name">lc</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LayoutConstraints</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L405"></a><tt class="py-lineno"> 405</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">top</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logpanel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Top</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L406"></a><tt class="py-lineno"> 406</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">left</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logpanel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Left</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L407"></a><tt class="py-lineno"> 407</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">bottom</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logpanel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Bottom</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L408"></a><tt class="py-lineno"> 408</tt> <tt class="py-line"> <tt class="py-name">lc</tt><tt class="py-op">.</tt><tt class="py-name">right</tt><tt class="py-op">.</tt><tt class="py-name">SameAs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">logpanel</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Right</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L409"></a><tt class="py-lineno"> 409</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">SetConstraints</tt><tt class="py-op">(</tt><tt class="py-name">lc</tt><tt class="py-op">)</tt> </tt>
+<a name="L410"></a><tt class="py-lineno"> 410</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">AppendText</tt><tt class="py-op">(</tt><tt class="py-string">"> Hello. Load a LILAMS XML file from the File> menu (or Cmd+O)."</tt><tt class="py-op">)</tt> </tt>
+<a name="L411"></a><tt class="py-lineno"> 411</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L412"></a><tt class="py-lineno"> 412</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Create mouse event for showing cursor coords in status bar</tt> </tt>
+<a name="L413"></a><tt class="py-lineno"> 413</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">Bind</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_LEFT_DOWN</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method silacvalidator.MainFrame.OnMLeftDown()=silacvalidator.MainFrame-class.html#OnMLeftDown"><a title="silacvalidator.MainFrame.OnMLeftDown" class="py-name" href="#" onclick="return doclink('link-21', 'OnMLeftDown', 'link-21');">OnMLeftDown</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L414"></a><tt class="py-lineno"> 414</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">Bind</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_LEFT_DCLICK</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method silacvalidator.MainFrame.OnMDoubleClick()=silacvalidator.MainFrame-class.html#OnMDoubleClick"><a title="silacvalidator.MainFrame.OnMDoubleClick" class="py-name" href="#" onclick="return doclink('link-22', 'OnMDoubleClick', 'link-22');">OnMDoubleClick</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L415"></a><tt class="py-lineno"> 415</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetEnableZoom</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-comment">#to ensure zoom by default</tt> </tt>
+<a name="L416"></a><tt class="py-lineno"> 416</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">SetCursor</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">StockCursor</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">CURSOR_CROSS</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment">#by default it is a "loupe"</tt> </tt>
+<a name="L417"></a><tt class="py-lineno"> 417</tt> <tt class="py-line"> </tt>
+<a name="L418"></a><tt class="py-lineno"> 418</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Show</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L419"></a><tt class="py-lineno"> 419</tt> <tt class="py-line"> </tt>
+<a name="L420"></a><tt class="py-lineno"> 420</tt> <tt class="py-line"> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L421"></a><tt class="py-lineno"> 421</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">## Main Frame function definitions ################################</tt> </tt>
+<a name="L422"></a><tt class="py-lineno"> 422</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">###################################################################</tt> </tt>
+<a name="L423"></a><tt class="py-lineno"> 423</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="MainFrame.OnXMLOpen"></a><div id="MainFrame.OnXMLOpen-def"><a name="L424"></a><tt class="py-lineno"> 424</tt> <a class="py-toggle" href="#" id="MainFrame.OnXMLOpen-toggle" onclick="return toggle('MainFrame.OnXMLOpen');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnXMLOpen">OnXMLOpen</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnXMLOpen-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnXMLOpen-expanded"><a name="L425"></a><tt class="py-lineno"> 425</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L426"></a><tt class="py-lineno"> 426</tt> <tt class="py-line"><tt class="py-docstring"> Opens a XML file with SILAC data and generates</tt> </tt>
+<a name="L427"></a><tt class="py-lineno"> 427</tt> <tt class="py-line"><tt class="py-docstring"> an ElementTree instance containing the data</tt> </tt>
+<a name="L428"></a><tt class="py-lineno"> 428</tt> <tt class="py-line"><tt class="py-docstring"> in the variable self.data</tt> </tt>
+<a name="L429"></a><tt class="py-lineno"> 429</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L430"></a><tt class="py-lineno"> 430</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method silacvalidator.MainFrame.resetDefaults()=silacvalidator.MainFrame-class.html#resetDefaults"><a title="silacvalidator.MainFrame.resetDefaults" class="py-name" href="#" onclick="return doclink('link-23', 'resetDefaults', 'link-23');">resetDefaults</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L431"></a><tt class="py-lineno"> 431</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"XML file (*.xml)|*.xml|"</tt>\ </tt>
+<a name="L432"></a><tt class="py-lineno"> 432</tt> <tt class="py-line"> <tt class="py-string">"All files (*.*)|*.*"</tt> </tt>
+<a name="L433"></a><tt class="py-lineno"> 433</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Choose a SILAC XML file:"</tt><tt class="py-op">,</tt> </tt>
+<a name="L434"></a><tt class="py-lineno"> 434</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OPEN</tt><tt class="py-op">)</tt> </tt>
+<a name="L435"></a><tt class="py-lineno"> 435</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L436"></a><tt class="py-lineno"> 436</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetFilename</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L437"></a><tt class="py-lineno"> 437</tt> <tt class="py-line"> <tt class="py-name">dirname</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetDirectory</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L438"></a><tt class="py-lineno"> 438</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L439"></a><tt class="py-lineno"> 439</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method silacvalidator.MainFrame.XMLOpen()=silacvalidator.MainFrame-class.html#XMLOpen"><a title="silacvalidator.MainFrame.XMLOpen" class="py-name" href="#" onclick="return doclink('link-24', 'XMLOpen', 'link-24');">XMLOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L440"></a><tt class="py-lineno"> 440</tt> <tt class="py-line"> <tt id="link-25" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-25', 'msg', 'link-0');">msg</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"""</tt> </tt>
+<a name="L441"></a><tt class="py-lineno"> 441</tt> <tt class="py-line"><tt class="py-string"> The file you wanted to open does not</tt> </tt>
+<a name="L442"></a><tt class="py-lineno"> 442</tt> <tt class="py-line"><tt class="py-string"> contain valid SILAC XML data. Try opening it with</tt> </tt>
+<a name="L443"></a><tt class="py-lineno"> 443</tt> <tt class="py-line"><tt class="py-string"> a text editor to see what is the problem."""</tt> </tt>
+<a name="L444"></a><tt class="py-lineno"> 444</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-26', 'msg', 'link-0');">msg</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Problem opening file'</tt><tt class="py-op">,</tt> </tt>
+<a name="L445"></a><tt class="py-lineno"> 445</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OK</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_INFORMATION</tt><tt class="py-op">)</tt> </tt>
+<a name="L446"></a><tt class="py-lineno"> 446</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L447"></a><tt class="py-lineno"> 447</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L448"></a><tt class="py-lineno"> 448</tt> <tt class="py-line"> <tt class="py-keyword">finally</tt><tt class="py-op">:</tt> </tt>
+<a name="L449"></a><tt class="py-lineno"> 449</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L450"></a><tt class="py-lineno"> 450</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.XMLOpen"></a><div id="MainFrame.XMLOpen-def"><a name="L451"></a><tt class="py-lineno"> 451</tt> <a class="py-toggle" href="#" id="MainFrame.XMLOpen-toggle" onclick="return toggle('MainFrame.XMLOpen');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#XMLOpen">XMLOpen</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dirname</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.XMLOpen-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.XMLOpen-expanded"><a name="L452"></a><tt class="py-lineno"> 452</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L453"></a><tt class="py-lineno"> 453</tt> <tt class="py-line"><tt class="py-docstring"> Will allow calls for XMLOpen from Previous</tt> </tt>
+<a name="L454"></a><tt class="py-lineno"> 454</tt> <tt class="py-line"><tt class="py-docstring"> and Next calls. Returns True if everything OK.</tt> </tt>
+<a name="L455"></a><tt class="py-lineno"> 455</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L456"></a><tt class="py-lineno"> 456</tt> <tt class="py-line"><tt class="py-docstring"> -uses get_flist_xml to set up the file list</tt> </tt>
+<a name="L457"></a><tt class="py-lineno"> 457</tt> <tt class="py-line"><tt class="py-docstring"> -uses map_pos_inlist to set up self.where</tt> </tt>
+<a name="L458"></a><tt class="py-lineno"> 458</tt> <tt class="py-line"><tt class="py-docstring"> -uses self.PlotSpectrumXML to plot the first peptide</tt> </tt>
+<a name="L459"></a><tt class="py-lineno"> 459</tt> <tt class="py-line"><tt class="py-docstring"> in file</tt> </tt>
+<a name="L460"></a><tt class="py-lineno"> 460</tt> <tt class="py-line"><tt class="py-docstring"> -uses self.PopulateList to populate the self.lb list</tt> </tt>
+<a name="L461"></a><tt class="py-lineno"> 461</tt> <tt class="py-line"><tt class="py-docstring"> control with data</tt> </tt>
+<a name="L462"></a><tt class="py-lineno"> 462</tt> <tt class="py-line"><tt class="py-docstring"> -uses self.GenerateListDict to generate the dictionary</tt> </tt>
+<a name="L463"></a><tt class="py-lineno"> 463</tt> <tt class="py-line"><tt class="py-docstring"> used to describe the data in the self.lb control</tt> </tt>
+<a name="L464"></a><tt class="py-lineno"> 464</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L465"></a><tt class="py-lineno"> 465</tt> <tt class="py-line"> <tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">filename</tt> </tt>
+<a name="L466"></a><tt class="py-lineno"> 466</tt> <tt class="py-line"> <tt class="py-name">dirname</tt><tt class="py-op">=</tt><tt class="py-name">dirname</tt> </tt>
+<a name="L467"></a><tt class="py-lineno"> 467</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-name">dirname</tt> </tt>
+<a name="L468"></a><tt class="py-lineno"> 468</tt> <tt class="py-line"> <tt class="py-name">fname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L469"></a><tt class="py-lineno"> 469</tt> <tt class="py-line"> <tt class="py-comment">#self.fnameout = fname+"x"</tt> </tt>
+<a name="L470"></a><tt class="py-lineno"> 470</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#we write in the same xml file, overwriting previous file</tt> </tt>
+<a name="L471"></a><tt class="py-lineno"> 471</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fnameout</tt> <tt class="py-op">=</tt> <tt class="py-name">fname</tt> </tt>
+<a name="L472"></a><tt class="py-lineno"> 472</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name" targets="Function silacvalidator.get_flist_xml()=silacvalidator-module.html#get_flist_xml"><a title="silacvalidator.get_flist_xml" class="py-name" href="#" onclick="return doclink('link-27', 'get_flist_xml', 'link-27');">get_flist_xml</a></tt><tt class="py-op">(</tt><tt class="py-name">dirname</tt><tt class="py-op">)</tt> </tt>
+<a name="L473"></a><tt class="py-lineno"> 473</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name" targets="Function silacvalidator.map_pos_inlist()=silacvalidator-module.html#map_pos_inlist"><a title="silacvalidator.map_pos_inlist" class="py-name" href="#" onclick="return doclink('link-28', 'map_pos_inlist', 'link-28');">map_pos_inlist</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L474"></a><tt class="py-lineno"> 474</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L475"></a><tt class="py-lineno"> 475</tt> <tt class="py-line"> <tt class="py-name">tree</tt> <tt class="py-op">=</tt> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">parse</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">)</tt> </tt>
+<a name="L476"></a><tt class="py-lineno"> 476</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">tree</tt><tt class="py-op">.</tt><tt class="py-name">getroot</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L477"></a><tt class="py-lineno"> 477</tt> <tt class="py-line"> <tt class="py-comment">#the root is a <protdata> entry</tt> </tt>
+<a name="L478"></a><tt class="py-lineno"> 478</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method silacvalidator.MainFrame.PlotSpectrumXML()=silacvalidator.MainFrame-class.html#PlotSpectrumXML"><a title="silacvalidator.MainFrame.PlotSpectrumXML" class="py-name" href="#" onclick="return doclink('link-29', 'PlotSpectrumXML', 'link-29');">PlotSpectrumXML</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">"peptide 1"</tt><tt class="py-op">)</tt> </tt>
+<a name="L479"></a><tt class="py-lineno"> 479</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method silacvalidator.MainFrame.PopulateList()=silacvalidator.MainFrame-class.html#PopulateList,Method silacvalidator.PepListCtrlPanel.PopulateList()=silacvalidator.PepListCtrlPanel-class.html#PopulateList"><a title="silacvalidator.MainFrame.PopulateList
+silacvalidator.PepListCtrlPanel.PopulateList" class="py-name" href="#" onclick="return doclink('link-30', 'PopulateList', 'link-30');">PopulateList</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Function Collect_SILAC_XML.GenerateListDict()=Collect_SILAC_XML-module.html#GenerateListDict,Method silacvalidator.MainFrame.GenerateListDict()=silacvalidator.MainFrame-class.html#GenerateListDict"><a title="Collect_SILAC_XML.GenerateListDict
+silacvalidator.MainFrame.GenerateListDict" class="py-name" href="#" onclick="return doclink('link-31', 'GenerateListDict', 'link-31');">GenerateListDict</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L480"></a><tt class="py-lineno"> 480</tt> <tt class="py-line"> <tt class="py-comment">#Clear the log, write text to it about the opened file</tt> </tt>
+<a name="L481"></a><tt class="py-lineno"> 481</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">Remove</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">GetLastPosition</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L482"></a><tt class="py-lineno"> 482</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">AppendText</tt><tt class="py-op">(</tt><tt class="py-string">"\n> Opened %s xml file.\n"</tt><tt class="py-op">%</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L483"></a><tt class="py-lineno"> 483</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">AppendText</tt><tt class="py-op">(</tt><tt class="py-string">"> Mowse score: %s, database: %s, ppm tolerance: %s.\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> </tt>
+<a name="L484"></a><tt class="py-lineno"> 484</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L485"></a><tt class="py-lineno"> 485</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">AppendText</tt><tt class="py-op">(</tt><tt class="py-string">"> Spot identification: %s.\n"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
+<a name="L486"></a><tt class="py-lineno"> 486</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">AppendText</tt><tt class="py-op">(</tt><tt class="py-string">"> Identified protein: %s, accesion number: %s.\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L487"></a><tt class="py-lineno"> 487</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">log</tt><tt class="py-op">.</tt><tt class="py-name">AppendText</tt><tt class="py-op">(</tt><tt class="py-string">"> Peptide coverage: %s percent, matched peptides: %s.\n"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L488"></a><tt class="py-lineno"> 488</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_NEXTF</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L489"></a><tt class="py-lineno"> 489</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_PREVF</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L490"></a><tt class="py-lineno"> 490</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEP</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L491"></a><tt class="py-lineno"> 491</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn1</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
+<a name="L492"></a><tt class="py-lineno"> 492</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn2</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
+<a name="L493"></a><tt class="py-lineno"> 493</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">btn3</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
+<a name="L494"></a><tt class="py-lineno"> 494</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_UNZOOM</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L495"></a><tt class="py-lineno"> 495</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVESP</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L496"></a><tt class="py-lineno"> 496</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
+<a name="L497"></a><tt class="py-lineno"> 497</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
+<a name="L498"></a><tt class="py-lineno"> 498</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
+</div><a name="L499"></a><tt class="py-lineno"> 499</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.PlotSpectrumXML"></a><div id="MainFrame.PlotSpectrumXML-def"><a name="L500"></a><tt class="py-lineno"> 500</tt> <a class="py-toggle" href="#" id="MainFrame.PlotSpectrumXML-toggle" onclick="return toggle('MainFrame.PlotSpectrumXML');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#PlotSpectrumXML">PlotSpectrumXML</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.PlotSpectrumXML-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.PlotSpectrumXML-expanded"><a name="L501"></a><tt class="py-lineno"> 501</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L502"></a><tt class="py-lineno"> 502</tt> <tt class="py-line"><tt class="py-docstring"> Recover and plot data for the record that has <index></tt> </tt>
+<a name="L503"></a><tt class="py-lineno"> 503</tt> <tt class="py-line"><tt class="py-docstring"> It is found in self.data[5] - that is pepdata,</tt> </tt>
+<a name="L504"></a><tt class="py-lineno"> 504</tt> <tt class="py-line"><tt class="py-docstring"> the subnode is 10 for <spectrum> and 0, 1 for </tt> </tt>
+<a name="L505"></a><tt class="py-lineno"> 505</tt> <tt class="py-line"><tt class="py-docstring"> the two lists mz and int. "5 "is contained in self.pdatapos</tt> </tt>
+<a name="L506"></a><tt class="py-lineno"> 506</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L507"></a><tt class="py-lineno"> 507</tt> <tt class="py-line"><tt class="py-docstring"> -uses self.PlotArray - a function to do the plotting</tt> </tt>
+<a name="L508"></a><tt class="py-lineno"> 508</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L509"></a><tt class="py-lineno"> 509</tt> <tt class="py-line"> <tt class="py-name">mzdata</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L510"></a><tt class="py-lineno"> 510</tt> <tt class="py-line"> <tt class="py-name">intdata</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L511"></a><tt class="py-lineno"> 511</tt> <tt class="py-line"> <tt class="py-name">dataforarray</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L512"></a><tt class="py-lineno"> 512</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">mzdata</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L513"></a><tt class="py-lineno"> 513</tt> <tt class="py-line"> <tt class="py-name">dataforarray</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">mzdata</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">intdata</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L514"></a><tt class="py-lineno"> 514</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method silacvalidator.MainFrame.PlotArray()=silacvalidator.MainFrame-class.html#PlotArray"><a title="silacvalidator.MainFrame.PlotArray" class="py-name" href="#" onclick="return doclink('link-32', 'PlotArray', 'link-32');">PlotArray</a></tt><tt class="py-op">(</tt><tt class="py-name">dataforarray</tt><tt class="py-op">,</tt> <tt class="py-string">"blue"</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L515"></a><tt class="py-lineno"> 515</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.PlotArray"></a><div id="MainFrame.PlotArray-def"><a name="L516"></a><tt class="py-lineno"> 516</tt> <a class="py-toggle" href="#" id="MainFrame.PlotArray-toggle" onclick="return toggle('MainFrame.PlotArray');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#PlotArray">PlotArray</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data_array</tt><tt class="py-op">,</tt> <tt class="py-param">color</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.PlotArray-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.PlotArray-expanded"><a name="L517"></a><tt class="py-lineno"> 517</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L518"></a><tt class="py-lineno"> 518</tt> <tt class="py-line"><tt class="py-docstring"> Used to plot on the plotcanvas the points of a data_array</tt> </tt>
+<a name="L519"></a><tt class="py-lineno"> 519</tt> <tt class="py-line"><tt class="py-docstring"> Default is autoscale, used by PlotSpectrumXML</tt> </tt>
+<a name="L520"></a><tt class="py-lineno"> 520</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L521"></a><tt class="py-lineno"> 521</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">PolyLine</tt><tt class="py-op">(</tt><tt class="py-name">data_array</tt><tt class="py-op">,</tt> <tt class="py-name">colour</tt> <tt class="py-op">=</tt> <tt class="py-name">color</tt><tt class="py-op">)</tt> </tt>
+<a name="L522"></a><tt class="py-lineno"> 522</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">Draw</tt><tt class="py-op">(</tt><tt class="py-name">PlotGraphics</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">line</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt><tt class="py-op">,</tt> <tt class="py-string">"m/z"</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L523"></a><tt class="py-lineno"> 523</tt> <tt class="py-line"> <tt class="py-comment">#self.plotcanvas.Redraw()</tt> </tt>
+<a name="L524"></a><tt class="py-lineno"> 524</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="MainFrame.GenerateListDict"></a><div id="MainFrame.GenerateListDict-def"><a name="L525"></a><tt class="py-lineno"> 525</tt> <a class="py-toggle" href="#" id="MainFrame.GenerateListDict-toggle" onclick="return toggle('MainFrame.GenerateListDict');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#GenerateListDict">GenerateListDict</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">xmldata</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.GenerateListDict-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.GenerateListDict-expanded"><a name="L526"></a><tt class="py-lineno"> 526</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L527"></a><tt class="py-lineno"> 527</tt> <tt class="py-line"><tt class="py-docstring"> forms a dictionary {1:["a", "b", "c"], 2:...}</tt> </tt>
+<a name="L528"></a><tt class="py-lineno"> 528</tt> <tt class="py-line"><tt class="py-docstring"> for the PepListCtrlPanel widget - to populate</tt> </tt>
+<a name="L529"></a><tt class="py-lineno"> 529</tt> <tt class="py-line"><tt class="py-docstring"> with XML data</tt> </tt>
+<a name="L530"></a><tt class="py-lineno"> 530</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L531"></a><tt class="py-lineno"> 531</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entriesdict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
+<a name="L532"></a><tt class="py-lineno"> 532</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xmldata</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L533"></a><tt class="py-lineno"> 533</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entriesdict</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Function Collect_SILAC_XML.GetValXML()=Collect_SILAC_XML-module.html#GetValXML,Method silacvalidator.MainFrame.GetValXML()=silacvalidator.MainFrame-class.html#GetValXML"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-33', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'pepseq'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L534"></a><tt class="py-lineno"> 534</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-34', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'leucines'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L535"></a><tt class="py-lineno"> 535</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-35', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'mzh'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L536"></a><tt class="py-lineno"> 536</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-36', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'calc_mzh'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L537"></a><tt class="py-lineno"> 537</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-37', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L538"></a><tt class="py-lineno"> 538</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-38', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L539"></a><tt class="py-lineno"> 539</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-39', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'ratio'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L540"></a><tt class="py-lineno"> 540</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-40', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'corrected_ratio'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L541"></a><tt class="py-lineno"> 541</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-41', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'local_bg'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
+<a name="L542"></a><tt class="py-lineno"> 542</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-42', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-string">'validated'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L543"></a><tt class="py-lineno"> 543</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">entriesdict</tt> </tt>
+</div><a name="L544"></a><tt class="py-lineno"> 544</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.PopulateList"></a><div id="MainFrame.PopulateList-def"><a name="L545"></a><tt class="py-lineno"> 545</tt> <a class="py-toggle" href="#" id="MainFrame.PopulateList-toggle" onclick="return toggle('MainFrame.PopulateList');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#PopulateList">PopulateList</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">externaldict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.PopulateList-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.PopulateList-expanded"><a name="L546"></a><tt class="py-lineno"> 546</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L547"></a><tt class="py-lineno"> 547</tt> <tt class="py-line"><tt class="py-docstring"> a wrapper to the function with the same name in self.lb</tt> </tt>
+<a name="L548"></a><tt class="py-lineno"> 548</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L549"></a><tt class="py-lineno"> 549</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="silacvalidator.MainFrame.PopulateList
+silacvalidator.PepListCtrlPanel.PopulateList" class="py-name" href="#" onclick="return doclink('link-43', 'PopulateList', 'link-30');">PopulateList</a></tt><tt class="py-op">(</tt><tt class="py-name">externaldict</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L550"></a><tt class="py-lineno"> 550</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnItemSelected"></a><div id="MainFrame.OnItemSelected-def"><a name="L551"></a><tt class="py-lineno"> 551</tt> <a class="py-toggle" href="#" id="MainFrame.OnItemSelected-toggle" onclick="return toggle('MainFrame.OnItemSelected');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnItemSelected">OnItemSelected</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnItemSelected-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnItemSelected-expanded"><a name="L552"></a><tt class="py-lineno"> 552</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L553"></a><tt class="py-lineno"> 553</tt> <tt class="py-line"><tt class="py-docstring"> Activated when one item in the self.lb list control</tt> </tt>
+<a name="L554"></a><tt class="py-lineno"> 554</tt> <tt class="py-line"><tt class="py-docstring"> is selected. Determines the generation of a unique key</tt> </tt>
+<a name="L555"></a><tt class="py-lineno"> 555</tt> <tt class="py-line"><tt class="py-docstring"> that will allow a correspondence between the list </tt> </tt>
+<a name="L556"></a><tt class="py-lineno"> 556</tt> <tt class="py-line"><tt class="py-docstring"> elements and the underlying ElementTree Element</tt> </tt>
+<a name="L557"></a><tt class="py-lineno"> 557</tt> <tt class="py-line"><tt class="py-docstring"> - uses MapUniqueKey function </tt> </tt>
+<a name="L558"></a><tt class="py-lineno"> 558</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L559"></a><tt class="py-lineno"> 559</tt> <tt class="py-line"> <tt class="py-comment">#print event.GetItem().GetTextColour()</tt> </tt>
+<a name="L560"></a><tt class="py-lineno"> 560</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt> <tt class="py-op">=</tt> <tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">m_itemIndex</tt> </tt>
+<a name="L561"></a><tt class="py-lineno"> 561</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">uniquekey</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItemText</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method silacvalidator.PepListCtrlPanel.getColumnText()=silacvalidator.PepListCtrlPanel-class.html#getColumnText"><a title="silacvalidator.PepListCtrlPanel.getColumnText" class="py-name" href="#" onclick="return doclink('link-44', 'getColumnText', 'link-44');">getColumnText</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
+<a name="L562"></a><tt class="py-lineno"> 562</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method silacvalidator.MainFrame.MapUniqueKey()=silacvalidator.MainFrame-class.html#MapUniqueKey"><a title="silacvalidator.MainFrame.MapUniqueKey" class="py-name" href="#" onclick="return doclink('link-45', 'MapUniqueKey', 'link-45');">MapUniqueKey</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">uniquekey</tt><tt class="py-op">)</tt> </tt>
+<a name="L563"></a><tt class="py-lineno"> 563</tt> <tt class="py-line"> <tt class="py-comment">#print self.index, "self.index"</tt> </tt>
+<a name="L564"></a><tt class="py-lineno"> 564</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="silacvalidator.MainFrame.PlotSpectrumXML" class="py-name" href="#" onclick="return doclink('link-46', 'PlotSpectrumXML', 'link-29');">PlotSpectrumXML</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-name">title</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-47', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-string">'pepseq'</tt><tt class="py-op">)</tt><tt class="py-op">+</tt>\ </tt>
+<a name="L565"></a><tt class="py-lineno"> 565</tt> <tt class="py-line"> <tt class="py-string">" / "</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-48', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-string">'mzh'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L566"></a><tt class="py-lineno"> 566</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEDATA</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L567"></a><tt class="py-lineno"> 567</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVESP</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L568"></a><tt class="py-lineno"> 568</tt> <tt class="py-line"> <tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">Skip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L569"></a><tt class="py-lineno"> 569</tt> <tt class="py-line"> <tt class="py-comment">#the self.index variable allows us to recover and change the data if validation occurs</tt> </tt>
+<a name="L570"></a><tt class="py-lineno"> 570</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="MainFrame.MapUniqueKey"></a><div id="MainFrame.MapUniqueKey-def"><a name="L571"></a><tt class="py-lineno"> 571</tt> <a class="py-toggle" href="#" id="MainFrame.MapUniqueKey-toggle" onclick="return toggle('MainFrame.MapUniqueKey');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#MapUniqueKey">MapUniqueKey</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uniquekey</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.MapUniqueKey-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.MapUniqueKey-expanded"><a name="L572"></a><tt class="py-lineno"> 572</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L573"></a><tt class="py-lineno"> 573</tt> <tt class="py-line"><tt class="py-docstring"> Used by <OnItemSelected> to allow a correspondence between</tt> </tt>
+<a name="L574"></a><tt class="py-lineno"> 574</tt> <tt class="py-line"><tt class="py-docstring"> self.currentItem - in the list and self.index in the ElementTree</tt> </tt>
+<a name="L575"></a><tt class="py-lineno"> 575</tt> <tt class="py-line"><tt class="py-docstring"> Element representing data read from the XML SILAC file</tt> </tt>
+<a name="L576"></a><tt class="py-lineno"> 576</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L577"></a><tt class="py-lineno"> 577</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L578"></a><tt class="py-lineno"> 578</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L579"></a><tt class="py-lineno"> 579</tt> <tt class="py-line"> <tt class="py-comment">#testing [0] is peptide sequence [1] is submitted m/z+h mass</tt> </tt>
+<a name="L580"></a><tt class="py-lineno"> 580</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">uniquekey</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">+</tt>\ </tt>
+<a name="L581"></a><tt class="py-lineno"> 581</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">:</tt> </tt>
+<a name="L582"></a><tt class="py-lineno"> 582</tt> <tt class="py-line"> <tt class="py-comment">#the index of the correspoinding key was found</tt> </tt>
+<a name="L583"></a><tt class="py-lineno"> 583</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">i</tt> </tt>
+<a name="L584"></a><tt class="py-lineno"> 584</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
+<a name="L585"></a><tt class="py-lineno"> 585</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
+</div><a name="L586"></a><tt class="py-lineno"> 586</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnValidate"></a><div id="MainFrame.OnValidate-def"><a name="L587"></a><tt class="py-lineno"> 587</tt> <a class="py-toggle" href="#" id="MainFrame.OnValidate-toggle" onclick="return toggle('MainFrame.OnValidate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnValidate">OnValidate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnValidate-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnValidate-expanded"><a name="L588"></a><tt class="py-lineno"> 588</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L589"></a><tt class="py-lineno"> 589</tt> <tt class="py-line"><tt class="py-docstring"> changes both the entry in the list control</tt> </tt>
+<a name="L590"></a><tt class="py-lineno"> 590</tt> <tt class="py-line"><tt class="py-docstring"> -- see SetValidated function --- and the</tt> </tt>
+<a name="L591"></a><tt class="py-lineno"> 591</tt> <tt class="py-line"><tt class="py-docstring"> same entry in the self.data (to be written)</tt> </tt>
+<a name="L592"></a><tt class="py-lineno"> 592</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L593"></a><tt class="py-lineno"> 593</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method silacvalidator.PepListCtrlPanel.SetValidated()=silacvalidator.PepListCtrlPanel-class.html#SetValidated"><a title="silacvalidator.PepListCtrlPanel.SetValidated" class="py-name" href="#" onclick="return doclink('link-49', 'SetValidated', 'link-49');">SetValidated</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt><tt class="py-op">,</tt> <tt class="py-string">"YES"</tt><tt class="py-op">)</tt> </tt>
+<a name="L594"></a><tt class="py-lineno"> 594</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method silacvalidator.MainFrame.SetXMLValidated()=silacvalidator.MainFrame-class.html#SetXMLValidated"><a title="silacvalidator.MainFrame.SetXMLValidated" class="py-name" href="#" onclick="return doclink('link-50', 'SetXMLValidated', 'link-50');">SetXMLValidated</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-string">"YES"</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L595"></a><tt class="py-lineno"> 595</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnInvalidate"></a><div id="MainFrame.OnInvalidate-def"><a name="L596"></a><tt class="py-lineno"> 596</tt> <a class="py-toggle" href="#" id="MainFrame.OnInvalidate-toggle" onclick="return toggle('MainFrame.OnInvalidate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnInvalidate">OnInvalidate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnInvalidate-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnInvalidate-expanded"><a name="L597"></a><tt class="py-lineno"> 597</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L598"></a><tt class="py-lineno"> 598</tt> <tt class="py-line"><tt class="py-docstring"> changes both the entry in the list control</tt> </tt>
+<a name="L599"></a><tt class="py-lineno"> 599</tt> <tt class="py-line"><tt class="py-docstring"> -- see SetValidated function --- and the</tt> </tt>
+<a name="L600"></a><tt class="py-lineno"> 600</tt> <tt class="py-line"><tt class="py-docstring"> same entry in the self.data (to be written)</tt> </tt>
+<a name="L601"></a><tt class="py-lineno"> 601</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L602"></a><tt class="py-lineno"> 602</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="silacvalidator.PepListCtrlPanel.SetValidated" class="py-name" href="#" onclick="return doclink('link-51', 'SetValidated', 'link-49');">SetValidated</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt><tt class="py-op">,</tt> <tt class="py-string">"NO"</tt><tt class="py-op">)</tt> </tt>
+<a name="L603"></a><tt class="py-lineno"> 603</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="silacvalidator.MainFrame.SetXMLValidated" class="py-name" href="#" onclick="return doclink('link-52', 'SetXMLValidated', 'link-50');">SetXMLValidated</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-string">"NO"</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L604"></a><tt class="py-lineno"> 604</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.SetXMLValidated"></a><div id="MainFrame.SetXMLValidated-def"><a name="L605"></a><tt class="py-lineno"> 605</tt> <a class="py-toggle" href="#" id="MainFrame.SetXMLValidated-toggle" onclick="return toggle('MainFrame.SetXMLValidated');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#SetXMLValidated">SetXMLValidated</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">,</tt> <tt class="py-param">what</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.SetXMLValidated-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.SetXMLValidated-expanded"><a name="L606"></a><tt class="py-lineno"> 606</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L607"></a><tt class="py-lineno"> 607</tt> <tt class="py-line"><tt class="py-docstring"> 7 is the actual position of the <validated> field</tt> </tt>
+<a name="L608"></a><tt class="py-lineno"> 608</tt> <tt class="py-line"><tt class="py-docstring"> in the self.data - coming from the SILAC XML tree</tt> </tt>
+<a name="L609"></a><tt class="py-lineno"> 609</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L610"></a><tt class="py-lineno"> 610</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-name">what</tt> </tt>
+</div><a name="L611"></a><tt class="py-lineno"> 611</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.GetValXML"></a><div id="MainFrame.GetValXML-def"><a name="L612"></a><tt class="py-lineno"> 612</tt> <a class="py-toggle" href="#" id="MainFrame.GetValXML-toggle" onclick="return toggle('MainFrame.GetValXML');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#GetValXML">GetValXML</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">what</tt><tt class="py-op">=</tt><tt class="py-string">'pepseq'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.GetValXML-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.GetValXML-expanded"><a name="L613"></a><tt class="py-lineno"> 613</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L614"></a><tt class="py-lineno"> 614</tt> <tt class="py-line"><tt class="py-docstring"> Returns the text attribute of an entry in an Element</tt> </tt>
+<a name="L615"></a><tt class="py-lineno"> 615</tt> <tt class="py-line"><tt class="py-docstring"> object based on the self.XMLdict dictionary that maps</tt> </tt>
+<a name="L616"></a><tt class="py-lineno"> 616</tt> <tt class="py-line"><tt class="py-docstring"> numbers to tags - definition in the init of the main</tt> </tt>
+<a name="L617"></a><tt class="py-lineno"> 617</tt> <tt class="py-line"><tt class="py-docstring"> frame. By default it returns the peptide sequence of </tt> </tt>
+<a name="L618"></a><tt class="py-lineno"> 618</tt> <tt class="py-line"><tt class="py-docstring"> the first record.</tt> </tt>
+<a name="L619"></a><tt class="py-lineno"> 619</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
+<a name="L620"></a><tt class="py-lineno"> 620</tt> <tt class="py-line"><tt class="py-docstring"> self.pdatapos - indicates the position of the <pepdata> in</tt> </tt>
+<a name="L621"></a><tt class="py-lineno"> 621</tt> <tt class="py-line"><tt class="py-docstring"> the root of the pepdata xml entry</tt> </tt>
+<a name="L622"></a><tt class="py-lineno"> 622</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L623"></a><tt class="py-lineno"> 623</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Collect_SILAC_XML.XMLdict" class="py-name" href="#" onclick="return doclink('link-53', 'XMLdict', 'link-3');">XMLdict</a></tt><tt class="py-op">[</tt><tt class="py-name">what</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> </tt>
+</div><a name="L624"></a><tt class="py-lineno"> 624</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnXMLSave"></a><div id="MainFrame.OnXMLSave-def"><a name="L625"></a><tt class="py-lineno"> 625</tt> <a class="py-toggle" href="#" id="MainFrame.OnXMLSave-toggle" onclick="return toggle('MainFrame.OnXMLSave');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnXMLSave">OnXMLSave</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnXMLSave-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnXMLSave-expanded"><a name="L626"></a><tt class="py-lineno"> 626</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L627"></a><tt class="py-lineno"> 627</tt> <tt class="py-line"><tt class="py-docstring"> Writes the contents of self.data to the self.fnameout</tt> </tt>
+<a name="L628"></a><tt class="py-lineno"> 628</tt> <tt class="py-line"><tt class="py-docstring"> (established when the actual file was opened)</tt> </tt>
+<a name="L629"></a><tt class="py-lineno"> 629</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L630"></a><tt class="py-lineno"> 630</tt> <tt class="py-line"> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">ElementTree</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fnameout</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L631"></a><tt class="py-lineno"> 631</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnSpectrumSave"></a><div id="MainFrame.OnSpectrumSave-def"><a name="L632"></a><tt class="py-lineno"> 632</tt> <a class="py-toggle" href="#" id="MainFrame.OnSpectrumSave-toggle" onclick="return toggle('MainFrame.OnSpectrumSave');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnSpectrumSave">OnSpectrumSave</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnSpectrumSave-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnSpectrumSave-expanded"><a name="L633"></a><tt class="py-lineno"> 633</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method silacvalidator.MainFrame.SpectrumSave()=silacvalidator.MainFrame-class.html#SpectrumSave"><a title="silacvalidator.MainFrame.SpectrumSave" class="py-name" href="#" onclick="return doclink('link-54', 'SpectrumSave', 'link-54');">SpectrumSave</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L634"></a><tt class="py-lineno"> 634</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.SpectrumSave"></a><div id="MainFrame.SpectrumSave-def"><a name="L635"></a><tt class="py-lineno"> 635</tt> <a class="py-toggle" href="#" id="MainFrame.SpectrumSave-toggle" onclick="return toggle('MainFrame.SpectrumSave');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#SpectrumSave">SpectrumSave</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.SpectrumSave-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.SpectrumSave-expanded"><a name="L636"></a><tt class="py-lineno"> 636</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L637"></a><tt class="py-lineno"> 637</tt> <tt class="py-line"><tt class="py-docstring"> Writes the contents of the actual selected spectrum</tt> </tt>
+<a name="L638"></a><tt class="py-lineno"> 638</tt> <tt class="py-line"><tt class="py-docstring"> to a given file name, in tab delimited format</tt> </tt>
+<a name="L639"></a><tt class="py-lineno"> 639</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L640"></a><tt class="py-lineno"> 640</tt> <tt class="py-line"> <tt class="py-name">mzdata</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L641"></a><tt class="py-lineno"> 641</tt> <tt class="py-line"> <tt class="py-name">intdata</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L642"></a><tt class="py-lineno"> 642</tt> <tt class="py-line"> <tt class="py-name">dataforarray</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
+<a name="L643"></a><tt class="py-lineno"> 643</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">mzdata</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L644"></a><tt class="py-lineno"> 644</tt> <tt class="py-line"> <tt class="py-name">dataforarray</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">mzdata</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">intdata</tt><tt class="py-op">[</tt><tt class="py-name">i</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L645"></a><tt class="py-lineno"> 645</tt> <tt class="py-line"> </tt>
+<a name="L646"></a><tt class="py-lineno"> 646</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"Tab delimited text file (*.txt)|*.txt|"</tt>\ </tt>
+<a name="L647"></a><tt class="py-lineno"> 647</tt> <tt class="py-line"> <tt class="py-string">"All files (*.*)|*.*"</tt> </tt>
+<a name="L648"></a><tt class="py-lineno"> 648</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt> </tt>
+<a name="L649"></a><tt class="py-lineno"> 649</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">message</tt><tt class="py-op">=</tt><tt class="py-string">"Save plot data to ..."</tt><tt class="py-op">,</tt> <tt class="py-name">defaultDir</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> </tt>
+<a name="L650"></a><tt class="py-lineno"> 650</tt> <tt class="py-line"> <tt class="py-name">defaultFile</tt><tt class="py-op">=</tt><tt class="py-string">"pepspecdata.txt"</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">=</tt><tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">SAVE</tt> </tt>
+<a name="L651"></a><tt class="py-lineno"> 651</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
+<a name="L652"></a><tt class="py-lineno"> 652</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">SetFilterIndex</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L653"></a><tt class="py-lineno"> 653</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L654"></a><tt class="py-lineno"> 654</tt> <tt class="py-line"> <tt class="py-name">path</tt> <tt class="py-op">=</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetPath</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L655"></a><tt class="py-lineno"> 655</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
+<a name="L656"></a><tt class="py-lineno"> 656</tt> <tt class="py-line"> <tt class="py-name">fout</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">,</tt> <tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
+<a name="L657"></a><tt class="py-lineno"> 657</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dataforarray</tt><tt class="py-op">:</tt> </tt>
+<a name="L658"></a><tt class="py-lineno"> 658</tt> <tt class="py-line"> <tt class="py-name">fout</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-string">'%.3f\t%d\n'</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L659"></a><tt class="py-lineno"> 659</tt> <tt class="py-line"> <tt class="py-name">fout</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L660"></a><tt class="py-lineno"> 660</tt> <tt class="py-line"> </tt>
+<a name="L661"></a><tt class="py-lineno"> 661</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">SetStatusText</tt><tt class="py-op">(</tt><tt class="py-string">"Data saved to file %s"</tt><tt class="py-op">%</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt>
+<a name="L662"></a><tt class="py-lineno"> 662</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> </tt>
+<a name="L663"></a><tt class="py-lineno"> 663</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Error. Maybe the output file is in use..."</tt><tt class="py-op">,</tt> <tt class="py-string">'Problem saving data'</tt><tt class="py-op">,</tt> </tt>
+<a name="L664"></a><tt class="py-lineno"> 664</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OK</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_INFORMATION</tt><tt class="py-op">)</tt> </tt>
+<a name="L665"></a><tt class="py-lineno"> 665</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L666"></a><tt class="py-lineno"> 666</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L667"></a><tt class="py-lineno"> 667</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L668"></a><tt class="py-lineno"> 668</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnNextFile"></a><div id="MainFrame.OnNextFile-def"><a name="L669"></a><tt class="py-lineno"> 669</tt> <a class="py-toggle" href="#" id="MainFrame.OnNextFile-toggle" onclick="return toggle('MainFrame.OnNextFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnNextFile">OnNextFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnNextFile-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnNextFile-expanded"><a name="L670"></a><tt class="py-lineno"> 670</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L671"></a><tt class="py-lineno"> 671</tt> <tt class="py-line"><tt class="py-docstring"> Allows navigation between the xml files</tt> </tt>
+<a name="L672"></a><tt class="py-lineno"> 672</tt> <tt class="py-line"><tt class="py-docstring"> in a folder. Calls the self.XMLOpen function</tt> </tt>
+<a name="L673"></a><tt class="py-lineno"> 673</tt> <tt class="py-line"><tt class="py-docstring"> exactly like the self.OnXMLOpen.</tt> </tt>
+<a name="L674"></a><tt class="py-lineno"> 674</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L675"></a><tt class="py-lineno"> 675</tt> <tt class="py-line"> <tt id="link-55" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-55', 'msg', 'link-0');">msg</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Save changes to the actual file ?"</tt> </tt>
+<a name="L676"></a><tt class="py-lineno"> 676</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-56" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-56', 'msg', 'link-0');">msg</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Save changes...'</tt><tt class="py-op">,</tt> </tt>
+<a name="L677"></a><tt class="py-lineno"> 677</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">YES_NO</tt><tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_QUESTION</tt><tt class="py-op">)</tt> </tt>
+<a name="L678"></a><tt class="py-lineno"> 678</tt> <tt class="py-line"> <tt class="py-name">response</tt> <tt class="py-op">=</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L679"></a><tt class="py-lineno"> 679</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L680"></a><tt class="py-lineno"> 680</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">response</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_YES</tt><tt class="py-op">:</tt> </tt>
+<a name="L681"></a><tt class="py-lineno"> 681</tt> <tt class="py-line"> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">ElementTree</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fnameout</tt><tt class="py-op">)</tt> </tt>
+<a name="L682"></a><tt class="py-lineno"> 682</tt> <tt class="py-line"> </tt>
+<a name="L683"></a><tt class="py-lineno"> 683</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L684"></a><tt class="py-lineno"> 684</tt> <tt class="py-line"> <tt class="py-comment">#print self.filelist</tt> </tt>
+<a name="L685"></a><tt class="py-lineno"> 685</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print self.where</tt> </tt>
+<a name="L686"></a><tt class="py-lineno"> 686</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
+<a name="L687"></a><tt class="py-lineno"> 687</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="silacvalidator.MainFrame.XMLOpen" class="py-name" href="#" onclick="return doclink('link-57', 'XMLOpen', 'link-24');">XMLOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L688"></a><tt class="py-lineno"> 688</tt> <tt class="py-line"> <tt class="py-comment">#self.where += 1 there is a risk in using global variables</tt> </tt>
+<a name="L689"></a><tt class="py-lineno"> 689</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#this one is already modified by XMLOpen to the correct value</tt> </tt>
+<a name="L690"></a><tt class="py-lineno"> 690</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L691"></a><tt class="py-lineno"> 691</tt> <tt class="py-line"> <tt class="py-comment">#we are at the end of the list, going on from the beginning</tt> </tt>
+<a name="L692"></a><tt class="py-lineno"> 692</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L693"></a><tt class="py-lineno"> 693</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="silacvalidator.MainFrame.XMLOpen" class="py-name" href="#" onclick="return doclink('link-58', 'XMLOpen', 'link-24');">XMLOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L694"></a><tt class="py-lineno"> 694</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnPrevFile"></a><div id="MainFrame.OnPrevFile-def"><a name="L695"></a><tt class="py-lineno"> 695</tt> <a class="py-toggle" href="#" id="MainFrame.OnPrevFile-toggle" onclick="return toggle('MainFrame.OnPrevFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnPrevFile">OnPrevFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnPrevFile-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnPrevFile-expanded"><a name="L696"></a><tt class="py-lineno"> 696</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L697"></a><tt class="py-lineno"> 697</tt> <tt class="py-line"><tt class="py-docstring"> Allows navigation between the xml files</tt> </tt>
+<a name="L698"></a><tt class="py-lineno"> 698</tt> <tt class="py-line"><tt class="py-docstring"> in a folder. Calls the self.XMLOpen function</tt> </tt>
+<a name="L699"></a><tt class="py-lineno"> 699</tt> <tt class="py-line"><tt class="py-docstring"> exactly like the self.OnXMLOpen.</tt> </tt>
+<a name="L700"></a><tt class="py-lineno"> 700</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L701"></a><tt class="py-lineno"> 701</tt> <tt class="py-line"> <tt id="link-59" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-59', 'msg', 'link-0');">msg</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Save changes to the actual file ?"</tt> </tt>
+<a name="L702"></a><tt class="py-lineno"> 702</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-60" class="py-name"><a title="silacvalidator.msg" class="py-name" href="#" onclick="return doclink('link-60', 'msg', 'link-0');">msg</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Save changes...'</tt><tt class="py-op">,</tt> </tt>
+<a name="L703"></a><tt class="py-lineno"> 703</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">YES_NO</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_QUESTION</tt><tt class="py-op">)</tt> </tt>
+<a name="L704"></a><tt class="py-lineno"> 704</tt> <tt class="py-line"> <tt class="py-name">response</tt> <tt class="py-op">=</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L705"></a><tt class="py-lineno"> 705</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L706"></a><tt class="py-lineno"> 706</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">response</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_YES</tt><tt class="py-op">:</tt> </tt>
+<a name="L707"></a><tt class="py-lineno"> 707</tt> <tt class="py-line"> <tt class="py-name">ET</tt><tt class="py-op">.</tt><tt class="py-name">ElementTree</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">write</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fnameout</tt><tt class="py-op">)</tt> </tt>
+<a name="L708"></a><tt class="py-lineno"> 708</tt> <tt class="py-line"> </tt>
+<a name="L709"></a><tt class="py-lineno"> 709</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L710"></a><tt class="py-lineno"> 710</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L711"></a><tt class="py-lineno"> 711</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="silacvalidator.MainFrame.XMLOpen" class="py-name" href="#" onclick="return doclink('link-61', 'XMLOpen', 'link-24');">XMLOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L712"></a><tt class="py-lineno"> 712</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L713"></a><tt class="py-lineno"> 713</tt> <tt class="py-line"> <tt class="py-comment">#we are at the beginning of the list</tt> </tt>
+<a name="L714"></a><tt class="py-lineno"> 714</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
+<a name="L715"></a><tt class="py-lineno"> 715</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="silacvalidator.MainFrame.XMLOpen" class="py-name" href="#" onclick="return doclink('link-62', 'XMLOpen', 'link-24');">XMLOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L716"></a><tt class="py-lineno"> 716</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFullUnzoom"></a><div id="MainFrame.OnFullUnzoom-def"><a name="L717"></a><tt class="py-lineno"> 717</tt> <a class="py-toggle" href="#" id="MainFrame.OnFullUnzoom-toggle" onclick="return toggle('MainFrame.OnFullUnzoom');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnFullUnzoom">OnFullUnzoom</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnFullUnzoom-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnFullUnzoom-expanded"><a name="L718"></a><tt class="py-lineno"> 718</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">Reset</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L719"></a><tt class="py-lineno"> 719</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFileOpen"></a><div id="MainFrame.OnFileOpen-def"><a name="L720"></a><tt class="py-lineno"> 720</tt> <a class="py-toggle" href="#" id="MainFrame.OnFileOpen-toggle" onclick="return toggle('MainFrame.OnFileOpen');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnFileOpen">OnFileOpen</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><a name="L721"></a><tt class="py-lineno"> 721</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L722"></a><tt class="py-lineno"> 722</tt> <tt class="py-line"><tt class="py-docstring"> Opens and plots a tab delimited text file</tt> </tt>
+<a name="L723"></a><tt class="py-lineno"> 723</tt> <tt class="py-line"><tt class="py-docstring"> If not a recognized file, a message is displayed</tt> </tt>
+<a name="L724"></a><tt class="py-lineno"> 724</tt> <tt class="py-line"><tt class="py-docstring"> Sets also the actual directory name: self.defaultdirname</tt> </tt>
+<a name="L725"></a><tt class="py-lineno"> 725</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L726"></a><tt class="py-lineno"> 726</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="silacvalidator.MainFrame.resetDefaults" class="py-name" href="#" onclick="return doclink('link-63', 'resetDefaults', 'link-23');">resetDefaults</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L727"></a><tt class="py-lineno"> 727</tt> <tt class="py-line"> <tt class="py-name">wildcard</tt> <tt class="py-op">=</tt> <tt class="py-string">"Tab delimited text file (*.txt)|*.txt|"</tt>\ </tt>
+<a name="L728"></a><tt class="py-lineno"> 728</tt> <tt class="py-line"> <tt class="py-string">"All files (*.*)|*.*"</tt> </tt>
+<a name="L729"></a><tt class="py-lineno"> 729</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">FileDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"Choose a tab delimited text file"</tt><tt class="py-op">,</tt> </tt>
+<a name="L730"></a><tt class="py-lineno"> 730</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt><tt class="py-op">,</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">wildcard</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OPEN</tt><tt class="py-op">)</tt> </tt>
+<a name="L731"></a><tt class="py-lineno"> 731</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ID_OK</tt><tt class="py-op">:</tt> </tt>
+<a name="L732"></a><tt class="py-lineno"> 732</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetFilename</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L733"></a><tt class="py-lineno"> 733</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">=</tt><tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">GetDirectory</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L734"></a><tt class="py-lineno"> 734</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">defaultdirname</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt> </tt>
+<a name="L735"></a><tt class="py-lineno"> 735</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filelist</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name" targets="Function silacvalidator.get_flist_txt()=silacvalidator-module.html#get_flist_txt"><a title="silacvalidator.get_flist_txt" class="py-name" href="#" onclick="return doclink('link-64', 'get_flist_txt', 'link-64');">get_flist_txt</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">)</tt> </tt>
+<a name="L736"></a><tt class="py-lineno"> 736</tt> <tt class="py-line"> <tt class="py-name">fname</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">dirname</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L737"></a><tt class="py-lineno"> 737</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
+<a name="L738"></a><tt class="py-lineno"> 738</tt> <tt class="py-line"> <tt class="py-name">readed</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name" targets="Function silacvalidator.ReadFromFileArray()=silacvalidator-module.html#ReadFromFileArray"><a title="silacvalidator.ReadFromFileArray" class="py-name" href="#" onclick="return doclink('link-65', 'ReadFromFileArray', 'link-65');">ReadFromFileArray</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L739"></a><tt class="py-lineno"> 739</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L740"></a><tt class="py-lineno"> 740</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">array</tt> <tt class="py-op">=</tt> <tt class="py-name">readed</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L741"></a><tt class="py-lineno"> 741</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L742"></a><tt class="py-lineno"> 742</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">readed</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-comment">#error</tt> </tt>
+<a name="L743"></a><tt class="py-lineno"> 743</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">readed</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'Problem opening file'</tt><tt class="py-op">,</tt> </tt>
+<a name="L744"></a><tt class="py-lineno"> 744</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OK</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_INFORMATION</tt><tt class="py-op">)</tt> </tt>
+<a name="L745"></a><tt class="py-lineno"> 745</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L746"></a><tt class="py-lineno"> 746</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L747"></a><tt class="py-lineno"> 747</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L748"></a><tt class="py-lineno"> 748</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="silacvalidator.MainFrame.PlotArray" class="py-name" href="#" onclick="return doclink('link-66', 'PlotArray', 'link-32');">PlotArray</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-string">"blue"</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
+<a name="L749"></a><tt class="py-lineno"> 749</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_NEXTF</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L750"></a><tt class="py-lineno"> 750</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_PREVF</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L751"></a><tt class="py-lineno"> 751</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_UNZOOM</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L752"></a><tt class="py-lineno"> 752</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEP</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L753"></a><tt class="py-lineno"> 753</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_SAVEDATA</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L754"></a><tt class="py-lineno"> 754</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_CLOSE</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L755"></a><tt class="py-lineno"> 755</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.PlotFile"></a><div id="MainFrame.PlotFile-def"><a name="L756"></a><tt class="py-lineno"> 756</tt> <a class="py-toggle" href="#" id="MainFrame.PlotFile-toggle" onclick="return toggle('MainFrame.PlotFile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#PlotFile">PlotFile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">fname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.PlotFile-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.PlotFile-expanded"><a name="L757"></a><tt class="py-lineno"> 757</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">,</tt> <tt class="py-string">"r"</tt><tt class="py-op">)</tt> </tt>
+<a name="L758"></a><tt class="py-lineno"> 758</tt> <tt class="py-line"> <tt class="py-name">readed</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="silacvalidator.ReadFromFileArray" class="py-name" href="#" onclick="return doclink('link-67', 'ReadFromFileArray', 'link-65');">ReadFromFileArray</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
+<a name="L759"></a><tt class="py-lineno"> 759</tt> <tt class="py-line"> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt class="py-name">close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L760"></a><tt class="py-lineno"> 760</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">array</tt> <tt class="py-op">=</tt> <tt class="py-name">readed</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
+<a name="L761"></a><tt class="py-lineno"> 761</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">readed</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> <tt class="py-comment">#error</tt> </tt>
+<a name="L762"></a><tt class="py-lineno"> 762</tt> <tt class="py-line"> <tt class="py-name">dlg</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">MessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">readed</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'Problem opening file'</tt><tt class="py-op">,</tt> </tt>
+<a name="L763"></a><tt class="py-lineno"> 763</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">OK</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ICON_INFORMATION</tt><tt class="py-op">)</tt> </tt>
+<a name="L764"></a><tt class="py-lineno"> 764</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L765"></a><tt class="py-lineno"> 765</tt> <tt class="py-line"> <tt class="py-name">dlg</tt><tt class="py-op">.</tt><tt class="py-name">Destroy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L766"></a><tt class="py-lineno"> 766</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L767"></a><tt class="py-lineno"> 767</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="silacvalidator.MainFrame.PlotArray" class="py-name" href="#" onclick="return doclink('link-68', 'PlotArray', 'link-32');">PlotArray</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">,</tt> <tt class="py-string">"blue"</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L768"></a><tt class="py-lineno"> 768</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFileClose"></a><div id="MainFrame.OnFileClose-def"><a name="L769"></a><tt class="py-lineno"> 769</tt> <a class="py-toggle" href="#" id="MainFrame.OnFileClose-toggle" onclick="return toggle('MainFrame.OnFileClose');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnFileClose">OnFileClose</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnFileClose-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnFileClose-expanded"><a name="L770"></a><tt class="py-lineno"> 770</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">Clear</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L771"></a><tt class="py-lineno"> 771</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_NEXTF</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+<a name="L772"></a><tt class="py-lineno"> 772</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">menubar</tt><tt class="py-op">.</tt><tt class="py-name">Enable</tt><tt class="py-op">(</tt><tt class="py-name">ID_PREVF</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L773"></a><tt class="py-lineno"> 773</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnMLeftDown"></a><div id="MainFrame.OnMLeftDown-def"><a name="L774"></a><tt class="py-lineno"> 774</tt> <a class="py-toggle" href="#" id="MainFrame.OnMLeftDown-toggle" onclick="return toggle('MainFrame.OnMLeftDown');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnMLeftDown">OnMLeftDown</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnMLeftDown-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnMLeftDown-expanded"><a name="L775"></a><tt class="py-lineno"> 775</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">localbg</tt> <tt class="py-op">=</tt> <tt class="py-name">abs</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">actualclick_y</tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">previousclick_y</tt><tt class="py-op">)</tt> </tt>
+<a name="L776"></a><tt class="py-lineno"> 776</tt> <tt class="py-line"> <tt class="py-comment">#self.position = event.GetPosition()</tt> </tt>
+<a name="L777"></a><tt class="py-lineno"> 777</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print self.position</tt> </tt>
+<a name="L778"></a><tt class="py-lineno"> 778</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">s</tt><tt class="py-op">=</tt> <tt class="py-string">"(m/z : %.2f, Intensity : %.2f)"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">GetXY</tt><tt class="py-op">(</tt><tt class="py-name">event</tt><tt class="py-op">)</tt><tt class="py-op">+</tt>\ </tt>
+<a name="L779"></a><tt class="py-lineno"> 779</tt> <tt class="py-line"> <tt class="py-string">" Local background : %.0f"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">localbg</tt> </tt>
+<a name="L780"></a><tt class="py-lineno"> 780</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">SetStatusText</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
+<a name="L781"></a><tt class="py-lineno"> 781</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">SetCursor</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">StockCursor</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">CURSOR_CROSS</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L782"></a><tt class="py-lineno"> 782</tt> <tt class="py-line"> <tt class="py-comment">#we have to update the cursor form, otherwise it gets reset to "lens"</tt> </tt>
+<a name="L783"></a><tt class="py-lineno"> 783</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L784"></a><tt class="py-lineno"> 784</tt> <tt class="py-line"> <tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">Skip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L785"></a><tt class="py-lineno"> 785</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnMDoubleClick"></a><div id="MainFrame.OnMDoubleClick-def"><a name="L786"></a><tt class="py-lineno"> 786</tt> <a class="py-toggle" href="#" id="MainFrame.OnMDoubleClick-toggle" onclick="return toggle('MainFrame.OnMDoubleClick');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnMDoubleClick">OnMDoubleClick</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnMDoubleClick-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnMDoubleClick-expanded"><a name="L787"></a><tt class="py-lineno"> 787</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">previousclick_y</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">actualclick_y</tt> </tt>
+<a name="L788"></a><tt class="py-lineno"> 788</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">actualclick_y</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">GetXY</tt><tt class="py-op">(</tt><tt class="py-name">event</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
+</div><a name="L789"></a><tt class="py-lineno"> 789</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnSetLocalBg"></a><div id="MainFrame.OnSetLocalBg-def"><a name="L790"></a><tt class="py-lineno"> 790</tt> <a class="py-toggle" href="#" id="MainFrame.OnSetLocalBg-toggle" onclick="return toggle('MainFrame.OnSetLocalBg');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnSetLocalBg">OnSetLocalBg</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnSetLocalBg-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnSetLocalBg-expanded"><a name="L791"></a><tt class="py-lineno"> 791</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L792"></a><tt class="py-lineno"> 792</tt> <tt class="py-line"><tt class="py-docstring"> Updates the local background data both in the shown list</tt> </tt>
+<a name="L793"></a><tt class="py-lineno"> 793</tt> <tt class="py-line"><tt class="py-docstring"> and in self.data. Recalculated the corrected ratio</tt> </tt>
+<a name="L794"></a><tt class="py-lineno"> 794</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L795"></a><tt class="py-lineno"> 795</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">8</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%0.f"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">localbg</tt> </tt>
+<a name="L796"></a><tt class="py-lineno"> 796</tt> <tt class="py-line"> <tt class="py-name">deut</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-69', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-string">'deuterated_intensity'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">localbg</tt> </tt>
+<a name="L797"></a><tt class="py-lineno"> 797</tt> <tt class="py-line"> <tt class="py-name">monoiso</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Collect_SILAC_XML.GetValXML
+silacvalidator.MainFrame.GetValXML" class="py-name" href="#" onclick="return doclink('link-70', 'GetValXML', 'link-33');">GetValXML</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-string">'mono_iso_int'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">localbg</tt> </tt>
+<a name="L798"></a><tt class="py-lineno"> 798</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdatapos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">index</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">text</tt> <tt class="py-op">=</tt> <tt class="py-string">"%.2f"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt class="py-name">deut</tt><tt class="py-op">/</tt><tt class="py-name">monoiso</tt><tt class="py-op">)</tt> </tt>
+<a name="L799"></a><tt class="py-lineno"> 799</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lb</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Method silacvalidator.PepListCtrlPanel.SetBg()=silacvalidator.PepListCtrlPanel-class.html#SetBg"><a title="silacvalidator.PepListCtrlPanel.SetBg" class="py-name" href="#" onclick="return doclink('link-71', 'SetBg', 'link-71');">SetBg</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">localbg</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">deut</tt><tt class="py-op">/</tt><tt class="py-name">monoiso</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L800"></a><tt class="py-lineno"> 800</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnSaveImage"></a><div id="MainFrame.OnSaveImage-def"><a name="L801"></a><tt class="py-lineno"> 801</tt> <a class="py-toggle" href="#" id="MainFrame.OnSaveImage-toggle" onclick="return toggle('MainFrame.OnSaveImage');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnSaveImage">OnSaveImage</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnSaveImage-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnSaveImage-expanded"><a name="L802"></a><tt class="py-lineno"> 802</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SaveFile</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L803"></a><tt class="py-lineno"> 803</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnFileExit"></a><div id="MainFrame.OnFileExit-def"><a name="L804"></a><tt class="py-lineno"> 804</tt> <a class="py-toggle" href="#" id="MainFrame.OnFileExit-toggle" onclick="return toggle('MainFrame.OnFileExit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnFileExit">OnFileExit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnFileExit-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnFileExit-expanded"><a name="L805"></a><tt class="py-lineno"> 805</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Close</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L806"></a><tt class="py-lineno"> 806</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnPlotRedraw"></a><div id="MainFrame.OnPlotRedraw-def"><a name="L807"></a><tt class="py-lineno"> 807</tt> <a class="py-toggle" href="#" id="MainFrame.OnPlotRedraw-toggle" onclick="return toggle('MainFrame.OnPlotRedraw');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnPlotRedraw">OnPlotRedraw</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnPlotRedraw-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnPlotRedraw-expanded"><a name="L808"></a><tt class="py-lineno"> 808</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">Redraw</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L809"></a><tt class="py-lineno"> 809</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnPlotClear"></a><div id="MainFrame.OnPlotClear-def"><a name="L810"></a><tt class="py-lineno"> 810</tt> <a class="py-toggle" href="#" id="MainFrame.OnPlotClear-toggle" onclick="return toggle('MainFrame.OnPlotClear');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnPlotClear">OnPlotClear</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnPlotClear-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnPlotClear-expanded"><a name="L811"></a><tt class="py-lineno"> 811</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">Clear</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L812"></a><tt class="py-lineno"> 812</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnPlotScale"></a><div id="MainFrame.OnPlotScale-def"><a name="L813"></a><tt class="py-lineno"> 813</tt> <a class="py-toggle" href="#" id="MainFrame.OnPlotScale-toggle" onclick="return toggle('MainFrame.OnPlotScale');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnPlotScale">OnPlotScale</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnPlotScale-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnPlotScale-expanded"><a name="L814"></a><tt class="py-lineno"> 814</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">last_draw</tt> <tt class="py-op">!=</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
+<a name="L815"></a><tt class="py-lineno"> 815</tt> <tt class="py-line"> <tt class="py-name">graphics</tt><tt class="py-op">,</tt> <tt class="py-name">xAxis</tt><tt class="py-op">,</tt> <tt class="py-name">yAxis</tt><tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">last_draw</tt> </tt>
+<a name="L816"></a><tt class="py-lineno"> 816</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">Draw</tt><tt class="py-op">(</tt><tt class="py-name">graphics</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">3.05</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L817"></a><tt class="py-lineno"> 817</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnEnableZoom"></a><div id="MainFrame.OnEnableZoom-def"><a name="L818"></a><tt class="py-lineno"> 818</tt> <a class="py-toggle" href="#" id="MainFrame.OnEnableZoom-toggle" onclick="return toggle('MainFrame.OnEnableZoom');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnEnableZoom">OnEnableZoom</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnEnableZoom-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnEnableZoom-expanded"><a name="L819"></a><tt class="py-lineno"> 819</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetEnableZoom</tt><tt class="py-op">(</tt><tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">IsChecked</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L820"></a><tt class="py-lineno"> 820</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnEnableGrid"></a><div id="MainFrame.OnEnableGrid-def"><a name="L821"></a><tt class="py-lineno"> 821</tt> <a class="py-toggle" href="#" id="MainFrame.OnEnableGrid-toggle" onclick="return toggle('MainFrame.OnEnableGrid');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnEnableGrid">OnEnableGrid</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnEnableGrid-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnEnableGrid-expanded"><a name="L822"></a><tt class="py-lineno"> 822</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetEnableGrid</tt><tt class="py-op">(</tt><tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">IsChecked</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L823"></a><tt class="py-lineno"> 823</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnEnableLegend"></a><div id="MainFrame.OnEnableLegend-def"><a name="L824"></a><tt class="py-lineno"> 824</tt> <a class="py-toggle" href="#" id="MainFrame.OnEnableLegend-toggle" onclick="return toggle('MainFrame.OnEnableLegend');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnEnableLegend">OnEnableLegend</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnEnableLegend-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnEnableLegend-expanded"><a name="L825"></a><tt class="py-lineno"> 825</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetEnableLegend</tt><tt class="py-op">(</tt><tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">IsChecked</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="MainFrame.OnReset"></a><div id="MainFrame.OnReset-def"><a name="L826"></a><tt class="py-lineno"> 826</tt> <a class="py-toggle" href="#" id="MainFrame.OnReset-toggle" onclick="return toggle('MainFrame.OnReset');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnReset">OnReset</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnReset-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnReset-expanded"><a name="L827"></a><tt class="py-lineno"> 827</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">Reset</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L828"></a><tt class="py-lineno"> 828</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.OnHelpAbout"></a><div id="MainFrame.OnHelpAbout-def"><a name="L829"></a><tt class="py-lineno"> 829</tt> <a class="py-toggle" href="#" id="MainFrame.OnHelpAbout-toggle" onclick="return toggle('MainFrame.OnHelpAbout');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#OnHelpAbout">OnHelpAbout</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.OnHelpAbout-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.OnHelpAbout-expanded"><a name="L830"></a><tt class="py-lineno"> 830</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt><tt class="py-op">.</tt><tt class="py-name">dialogs</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ScrolledMessageDialog</tt> </tt>
+<a name="L831"></a><tt class="py-lineno"> 831</tt> <tt class="py-line"> <tt class="py-name">about</tt> <tt class="py-op">=</tt> <tt class="py-name">ScrolledMessageDialog</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">__doc__</tt><tt class="py-op">,</tt> <tt class="py-string">"About..."</tt><tt class="py-op">,</tt> <tt class="py-name">size</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-number">600</tt><tt class="py-op">,</tt> <tt class="py-number">400</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L832"></a><tt class="py-lineno"> 832</tt> <tt class="py-line"> <tt class="py-name">about</tt><tt class="py-op">.</tt><tt class="py-name">ShowModal</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L833"></a><tt class="py-lineno"> 833</tt> <tt class="py-line"> </tt>
+<a name="MainFrame.resetDefaults"></a><div id="MainFrame.resetDefaults-def"><a name="L834"></a><tt class="py-lineno"> 834</tt> <a class="py-toggle" href="#" id="MainFrame.resetDefaults-toggle" onclick="return toggle('MainFrame.resetDefaults');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.MainFrame-class.html#resetDefaults">resetDefaults</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="MainFrame.resetDefaults-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="MainFrame.resetDefaults-expanded"><a name="L835"></a><tt class="py-lineno"> 835</tt> <tt class="py-line"> <tt class="py-docstring">"""Just to reset the fonts back to the PlotCanvas defaults"""</tt> </tt>
+<a name="L836"></a><tt class="py-lineno"> 836</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetFont</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Font</tt><tt class="py-op">(</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">SWISS</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">NORMAL</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">NORMAL</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L837"></a><tt class="py-lineno"> 837</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetFontSizeAxis</tt><tt class="py-op">(</tt><tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L838"></a><tt class="py-lineno"> 838</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetFontSizeLegend</tt><tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">)</tt> </tt>
+<a name="L839"></a><tt class="py-lineno"> 839</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetXSpec</tt><tt class="py-op">(</tt><tt class="py-string">'auto'</tt><tt class="py-op">)</tt> </tt>
+<a name="L840"></a><tt class="py-lineno"> 840</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetYSpec</tt><tt class="py-op">(</tt><tt class="py-string">'auto'</tt><tt class="py-op">)</tt> </tt>
+<a name="L841"></a><tt class="py-lineno"> 841</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">plotcanvas</tt><tt class="py-op">.</tt><tt class="py-name">SetEnableZoom</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+</div></div><a name="L842"></a><tt class="py-lineno"> 842</tt> <tt class="py-line"> </tt>
+<a name="L843"></a><tt class="py-lineno"> 843</tt> <tt class="py-line"><tt class="py-comment">#######################################################</tt> </tt>
+<a name="L844"></a><tt class="py-lineno"> 844</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#######################################################</tt> </tt>
+<a name="L845"></a><tt class="py-lineno"> 845</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">################ PepListCtrlPanel ###############</tt> </tt>
+<a name="L846"></a><tt class="py-lineno"> 846</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">################ and PepListCtrl classes###############</tt> </tt>
+<a name="L847"></a><tt class="py-lineno"> 847</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#######################################################</tt> </tt>
+<a name="L848"></a><tt class="py-lineno"> 848</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#######################################################</tt> </tt>
+<a name="L849"></a><tt class="py-lineno"> 849</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#######################################################</tt> </tt>
+<a name="L850"></a><tt class="py-lineno"> 850</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#----------------------------------------------------------------------------</tt> </tt>
+<a name="L851"></a><tt class="py-lineno"> 851</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Name: ListCtrl.py</tt> </tt>
+<a name="L852"></a><tt class="py-lineno"> 852</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Purpose: Testing lots of stuff, controls, window types, etc.</tt> </tt>
+<a name="L853"></a><tt class="py-lineno"> 853</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
+<a name="L854"></a><tt class="py-lineno"> 854</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Author: Robin Dunn & Gary Dumer</tt> </tt>
+<a name="L855"></a><tt class="py-lineno"> 855</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
+<a name="L856"></a><tt class="py-lineno"> 856</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Created:</tt> </tt>
+<a name="L857"></a><tt class="py-lineno"> 857</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># RCS-ID: $Id: ListCtrl.py,v 1.3 2004/03/05 00:06:32 RD Exp $</tt> </tt>
+<a name="L858"></a><tt class="py-lineno"> 858</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright: (c) 1998 by Total Control Software</tt> </tt>
+<a name="L859"></a><tt class="py-lineno"> 859</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Licence: wxWindows license</tt> </tt>
+<a name="L860"></a><tt class="py-lineno"> 860</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
+<a name="L861"></a><tt class="py-lineno"> 861</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Modified by Cosmin Saveanu, IP, September 2004</tt> </tt>
+<a name="L862"></a><tt class="py-lineno"> 862</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># to be able to deal with peptide entries for SILAC</tt> </tt>
+<a name="L863"></a><tt class="py-lineno"> 863</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#----------------------------------------------------------------------------</tt> </tt>
+<a name="getSmallUpArrowData"></a><div id="getSmallUpArrowData-def"><a name="L864"></a><tt class="py-lineno"> 864</tt> <a class="py-toggle" href="#" id="getSmallUpArrowData-toggle" onclick="return toggle('getSmallUpArrowData');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#getSmallUpArrowData">getSmallUpArrowData</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="getSmallUpArrowData-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getSmallUpArrowData-expanded"><a name="L865"></a><tt class="py-lineno"> 865</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> \ </tt>
+<a name="L866"></a><tt class="py-lineno"> 866</tt> <tt class="py-line"><tt class="py-string">'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\</tt> </tt>
+<a name="L867"></a><tt class="py-lineno"> 867</tt> <tt class="py-line"><tt class="py-string">\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\</tt> </tt>
+<a name="L868"></a><tt class="py-lineno"> 868</tt> <tt class="py-line"><tt class="py-string">\x00\x00<IDATx\x9ccddbf\xa0\x040Q\xa4{h\x18\xf0\xff\xdf\xdf\xffd\x1b\x00\xd3\</tt> </tt>
+<a name="L869"></a><tt class="py-lineno"> 869</tt> <tt class="py-line"><tt class="py-string">\x8c\xcf\x10\x9c\x06\xa0k\xc2e\x08m\xc2\x00\x97m\xd8\xc41\x0c \x14h\xe8\xf2\</tt> </tt>
+<a name="L870"></a><tt class="py-lineno"> 870</tt> <tt class="py-line"><tt class="py-string">\x8c\xa3)q\x10\x18\x00\x00R\xd8#\xec\x95{\xc4\x11\x00\x00\x00\x00IEND\xaeB`\</tt> </tt>
+<a name="L871"></a><tt class="py-lineno"> 871</tt> <tt class="py-line"><tt class="py-string">\x82'</tt> </tt>
+</div><a name="L872"></a><tt class="py-lineno"> 872</tt> <tt class="py-line"> </tt>
+<a name="getSmallUpArrowBitmap"></a><div id="getSmallUpArrowBitmap-def"><a name="L873"></a><tt class="py-lineno"> 873</tt> <a class="py-toggle" href="#" id="getSmallUpArrowBitmap-toggle" onclick="return toggle('getSmallUpArrowBitmap');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#getSmallUpArrowBitmap">getSmallUpArrowBitmap</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="getSmallUpArrowBitmap-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getSmallUpArrowBitmap-expanded"><a name="L874"></a><tt class="py-lineno"> 874</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">BitmapFromImage</tt><tt class="py-op">(</tt><tt id="link-72" class="py-name" targets="Function silacvalidator.getSmallUpArrowImage()=silacvalidator-module.html#getSmallUpArrowImage"><a title="silacvalidator.getSmallUpArrowImage" class="py-name" href="#" onclick="return doclink('link-72', 'getSmallUpArrowImage', 'link-72');">getSmallUpArrowImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="getSmallUpArrowImage"></a><div id="getSmallUpArrowImage-def"><a name="L875"></a><tt class="py-lineno"> 875</tt> <a class="py-toggle" href="#" id="getSmallUpArrowImage-toggle" onclick="return toggle('getSmallUpArrowImage');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#getSmallUpArrowImage">getSmallUpArrowImage</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="getSmallUpArrowImage-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getSmallUpArrowImage-expanded"><a name="L876"></a><tt class="py-lineno"> 876</tt> <tt class="py-line"> <tt class="py-name">stream</tt> <tt class="py-op">=</tt> <tt class="py-name">cStringIO</tt><tt class="py-op">.</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-73" class="py-name" targets="Function silacvalidator.getSmallUpArrowData()=silacvalidator-module.html#getSmallUpArrowData"><a title="silacvalidator.getSmallUpArrowData" class="py-name" href="#" onclick="return doclink('link-73', 'getSmallUpArrowData', 'link-73');">getSmallUpArrowData</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L877"></a><tt class="py-lineno"> 877</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ImageFromStream</tt><tt class="py-op">(</tt><tt class="py-name">stream</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L878"></a><tt class="py-lineno"> 878</tt> <tt class="py-line"><tt class="py-comment">#----------------------------------------------------------------------</tt> </tt>
+<a name="L879"></a><tt class="py-lineno"> 879</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="getSmallDnArrowData"></a><div id="getSmallDnArrowData-def"><a name="L880"></a><tt class="py-lineno"> 880</tt> <a class="py-toggle" href="#" id="getSmallDnArrowData-toggle" onclick="return toggle('getSmallDnArrowData');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#getSmallDnArrowData">getSmallDnArrowData</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="getSmallDnArrowData-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getSmallDnArrowData-expanded"><a name="L881"></a><tt class="py-lineno"> 881</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> \ </tt>
+<a name="L882"></a><tt class="py-lineno"> 882</tt> <tt class="py-line"><tt class="py-string">"\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\</tt> </tt>
+<a name="L883"></a><tt class="py-lineno"> 883</tt> <tt class="py-line"><tt class="py-string">\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\</tt> </tt>
+<a name="L884"></a><tt class="py-lineno"> 884</tt> <tt class="py-line"><tt class="py-string">\x00\x00HIDATx\x9ccddbf\xa0\x040Q\xa4{\xd4\x00\x06\x06\x06\x06\x06\x16t\x81\</tt> </tt>
+<a name="L885"></a><tt class="py-lineno"> 885</tt> <tt class="py-line"><tt class="py-string">\xff\xff\xfe\xfe'\xa4\x89\x91\x89\x99\x11\xa7\x0b\x90%\ti\xc6j\x00>C\xb0\x89\</tt> </tt>
+<a name="L886"></a><tt class="py-lineno"> 886</tt> <tt class="py-line"><tt class="py-string">\xd3.\x10\xd1m\xc3\xe5*\xbc.\x80i\xc2\x17.\x8c\xa3y\x81\x01\x00\xa1\x0e\x04e\</tt> </tt>
+<a name="L887"></a><tt class="py-lineno"> 887</tt> <tt class="py-line"><tt class="py-string">\x1d\xc4;\xb7\x00\x00\x00\x00IEND\xaeB`\x82"</tt> </tt>
+</div><a name="getSmallDnArrowBitmap"></a><div id="getSmallDnArrowBitmap-def"><a name="L888"></a><tt class="py-lineno"> 888</tt> <a class="py-toggle" href="#" id="getSmallDnArrowBitmap-toggle" onclick="return toggle('getSmallDnArrowBitmap');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#getSmallDnArrowBitmap">getSmallDnArrowBitmap</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="getSmallDnArrowBitmap-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getSmallDnArrowBitmap-expanded"><a name="L889"></a><tt class="py-lineno"> 889</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">BitmapFromImage</tt><tt class="py-op">(</tt><tt id="link-74" class="py-name" targets="Function silacvalidator.getSmallDnArrowImage()=silacvalidator-module.html#getSmallDnArrowImage"><a title="silacvalidator.getSmallDnArrowImage" class="py-name" href="#" onclick="return doclink('link-74', 'getSmallDnArrowImage', 'link-74');">getSmallDnArrowImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L890"></a><tt class="py-lineno"> 890</tt> <tt class="py-line"> </tt>
+<a name="getSmallDnArrowImage"></a><div id="getSmallDnArrowImage-def"><a name="L891"></a><tt class="py-lineno"> 891</tt> <a class="py-toggle" href="#" id="getSmallDnArrowImage-toggle" onclick="return toggle('getSmallDnArrowImage');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator-module.html#getSmallDnArrowImage">getSmallDnArrowImage</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="getSmallDnArrowImage-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="getSmallDnArrowImage-expanded"><a name="L892"></a><tt class="py-lineno"> 892</tt> <tt class="py-line"> <tt class="py-name">stream</tt> <tt class="py-op">=</tt> <tt class="py-name">cStringIO</tt><tt class="py-op">.</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-75" class="py-name" targets="Function silacvalidator.getSmallDnArrowData()=silacvalidator-module.html#getSmallDnArrowData"><a title="silacvalidator.getSmallDnArrowData" class="py-name" href="#" onclick="return doclink('link-75', 'getSmallDnArrowData', 'link-75');">getSmallDnArrowData</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L893"></a><tt class="py-lineno"> 893</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">ImageFromStream</tt><tt class="py-op">(</tt><tt class="py-name">stream</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L894"></a><tt class="py-lineno"> 894</tt> <tt class="py-line"><tt class="py-comment">#----------------------------------------------------------------------</tt> </tt>
+<a name="PepListCtrl"></a><div id="PepListCtrl-def"><a name="L895"></a><tt class="py-lineno"> 895</tt> <a class="py-toggle" href="#" id="PepListCtrl-toggle" onclick="return toggle('PepListCtrl');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="silacvalidator.PepListCtrl-class.html">PepListCtrl</a><tt class="py-op">(</tt><tt class="py-base-class">wx</tt><tt class="py-op">.</tt><tt class="py-base-class">ListCtrl</tt><tt class="py-op">,</tt> <tt class="py-base-class">listmix</tt><tt class="py-op">.</tt><tt class="py-base-class">ListCtrlAutoWidthMixin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrl-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="PepListCtrl-expanded"><a name="L896"></a><tt class="py-lineno"> 896</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrl.__init__"></a><div id="PepListCtrl.__init__-def"><a name="L897"></a><tt class="py-lineno"> 897</tt> <a class="py-toggle" href="#" id="PepListCtrl.__init__-toggle" onclick="return toggle('PepListCtrl.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrl-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">,</tt> <tt class="py-param">ID</tt><tt class="py-op">,</tt> <tt class="py-param">pos</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultPosition</tt><tt class="py-op">,</tt> </tt>
+<a name="L898"></a><tt class="py-lineno"> 898</tt> <tt class="py-line"> <tt class="py-param">size</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">DefaultSize</tt><tt class="py-op">,</tt> <tt class="py-param">style</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrl.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrl.__init__-expanded"><a name="L899"></a><tt class="py-lineno"> 899</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ListCtrl</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Collect_SILAC_XML.Usage.__init__
+MSFit_to_txt.MainFrame.__init__
+lilamslaunchGUI.MainFrame.__init__
+lilamsxml.DataIntObj.__init__
+lilamsxml.Usage.__init__
+silacvalidator.MainFrame.__init__
+silacvalidator.PepListCtrl.__init__
+silacvalidator.PepListCtrlPanel.__init__" class="py-name" href="#" onclick="return doclink('link-76', '__init__', 'link-2');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt class="py-name">ID</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">size</tt><tt class="py-op">,</tt> <tt class="py-name">style</tt><tt class="py-op">)</tt> </tt>
+<a name="L900"></a><tt class="py-lineno"> 900</tt> <tt class="py-line"> <tt class="py-name">listmix</tt><tt class="py-op">.</tt><tt class="py-name">ListCtrlAutoWidthMixin</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Collect_SILAC_XML.Usage.__init__
+MSFit_to_txt.MainFrame.__init__
+lilamslaunchGUI.MainFrame.__init__
+lilamsxml.DataIntObj.__init__
+lilamsxml.Usage.__init__
+silacvalidator.MainFrame.__init__
+silacvalidator.PepListCtrl.__init__
+silacvalidator.PepListCtrlPanel.__init__" class="py-name" href="#" onclick="return doclink('link-77', '__init__', 'link-2');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
+</div></div><a name="L901"></a><tt class="py-lineno"> 901</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel"></a><div id="PepListCtrlPanel-def"><a name="L902"></a><tt class="py-lineno"> 902</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel-toggle" onclick="return toggle('PepListCtrlPanel');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html">PepListCtrlPanel</a><tt class="py-op">(</tt><tt class="py-base-class">wx</tt><tt class="py-op">.</tt><tt class="py-base-class">Panel</tt><tt class="py-op">,</tt> <tt class="py-base-class">listmix</tt><tt class="py-op">.</tt><tt class="py-base-class">ColumnSorterMixin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel-collapsed" style="display:none;" pad="++++" indent="++++"></div><div id="PepListCtrlPanel-expanded"><a name="L903"></a><tt class="py-lineno"> 903</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.__init__"></a><div id="PepListCtrlPanel.__init__-def"><a name="L904"></a><tt class="py-lineno"> 904</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.__init__-toggle" onclick="return toggle('PepListCtrlPanel.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">parent</tt><tt class="py-op">,</tt> <tt class="py-param">dictwithdata</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.__init__-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.__init__-expanded"><a name="L905"></a><tt class="py-lineno"> 905</tt> <tt class="py-line"> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">Panel</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Collect_SILAC_XML.Usage.__init__
+MSFit_to_txt.MainFrame.__init__
+lilamslaunchGUI.MainFrame.__init__
+lilamsxml.DataIntObj.__init__
+lilamsxml.Usage.__init__
+silacvalidator.MainFrame.__init__
+silacvalidator.PepListCtrl.__init__
+silacvalidator.PepListCtrlPanel.__init__" class="py-name" href="#" onclick="return doclink('link-78', '__init__', 'link-2');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">parent</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">WANTS_CHARS</tt><tt class="py-op">)</tt> </tt>
+<a name="L906"></a><tt class="py-lineno"> 906</tt> <tt class="py-line"> <tt class="py-name">tID</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">NewId</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L907"></a><tt class="py-lineno"> 907</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">il</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ImageList</tt><tt class="py-op">(</tt><tt class="py-number">16</tt><tt class="py-op">,</tt> <tt class="py-number">16</tt><tt class="py-op">)</tt> </tt>
+<a name="L908"></a><tt class="py-lineno"> 908</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sm_up</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">il</tt><tt class="py-op">.</tt><tt class="py-name">Add</tt><tt class="py-op">(</tt><tt id="link-79" class="py-name" targets="Function silacvalidator.getSmallUpArrowBitmap()=silacvalidator-module.html#getSmallUpArrowBitmap"><a title="silacvalidator.getSmallUpArrowBitmap" class="py-name" href="#" onclick="return doclink('link-79', 'getSmallUpArrowBitmap', 'link-79');">getSmallUpArrowBitmap</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L909"></a><tt class="py-lineno"> 909</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sm_dn</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">il</tt><tt class="py-op">.</tt><tt class="py-name">Add</tt><tt class="py-op">(</tt><tt id="link-80" class="py-name" targets="Function silacvalidator.getSmallDnArrowBitmap()=silacvalidator-module.html#getSmallDnArrowBitmap"><a title="silacvalidator.getSmallDnArrowBitmap" class="py-name" href="#" onclick="return doclink('link-80', 'getSmallDnArrowBitmap', 'link-80');">getSmallDnArrowBitmap</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
+<a name="L910"></a><tt class="py-lineno"> 910</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name" targets="Class silacvalidator.PepListCtrl=silacvalidator.PepListCtrl-class.html"><a title="silacvalidator.PepListCtrl" class="py-name" href="#" onclick="return doclink('link-81', 'PepListCtrl', 'link-81');">PepListCtrl</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">tID</tt><tt class="py-op">,</tt> </tt>
+<a name="L911"></a><tt class="py-lineno"> 911</tt> <tt class="py-line"> <tt class="py-name">style</tt><tt class="py-op">=</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LC_REPORT</tt> </tt>
+<a name="L912"></a><tt class="py-lineno"> 912</tt> <tt class="py-line"> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">SUNKEN_BORDER</tt> </tt>
+<a name="L913"></a><tt class="py-lineno"> 913</tt> <tt class="py-line"> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LC_SINGLE_SEL</tt> </tt>
+<a name="L914"></a><tt class="py-lineno"> 914</tt> <tt class="py-line"> <tt class="py-comment">#| wx.LC_HRULES</tt> </tt>
+<a name="L915"></a><tt class="py-lineno"> 915</tt> <tt class="py-line"> <tt class="py-comment">#| wx.LC_EDIT_LABELS</tt> </tt>
+<a name="L916"></a><tt class="py-lineno"> 916</tt> <tt class="py-line"> <tt class="py-comment">#| wxLC_NO_HEADER</tt> </tt>
+<a name="L917"></a><tt class="py-lineno"> 917</tt> <tt class="py-line"> <tt class="py-comment">#| wxLC_VRULES </tt> </tt>
+<a name="L918"></a><tt class="py-lineno"> 918</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
+<a name="L919"></a><tt class="py-lineno"> 919</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetImageList</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">il</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">IMAGE_LIST_SMALL</tt><tt class="py-op">)</tt> </tt>
+<a name="L920"></a><tt class="py-lineno"> 920</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="silacvalidator.MainFrame.PopulateList
+silacvalidator.PepListCtrlPanel.PopulateList" class="py-name" href="#" onclick="return doclink('link-82', 'PopulateList', 'link-30');">PopulateList</a></tt><tt class="py-op">(</tt><tt class="py-name">dictwithdata</tt><tt class="py-op">)</tt> </tt>
+<a name="L921"></a><tt class="py-lineno"> 921</tt> <tt class="py-line"> <tt class="py-comment"># Now that the list exists we can init the other base class,</tt> </tt>
+<a name="L922"></a><tt class="py-lineno"> 922</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># see wxPython/lib/mixins/listctrl.py</tt> </tt>
+<a name="L923"></a><tt class="py-lineno"> 923</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
+<a name="L924"></a><tt class="py-lineno"> 924</tt> <tt class="py-line"> <tt class="py-name">listmix</tt><tt class="py-op">.</tt><tt class="py-name">ColumnSorterMixin</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Collect_SILAC_XML.Usage.__init__
+MSFit_to_txt.MainFrame.__init__
+lilamslaunchGUI.MainFrame.__init__
+lilamsxml.DataIntObj.__init__
+lilamsxml.Usage.__init__
+silacvalidator.MainFrame.__init__
+silacvalidator.PepListCtrl.__init__
+silacvalidator.PepListCtrlPanel.__init__" class="py-name" href="#" onclick="return doclink('link-83', '__init__', 'link-2');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
+<a name="L925"></a><tt class="py-lineno"> 925</tt> <tt class="py-line"> <tt class="py-comment">#self.SortListItems(0, True)</tt> </tt>
+<a name="L926"></a><tt class="py-lineno"> 926</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Bind</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_SIZE</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name" targets="Method silacvalidator.PepListCtrlPanel.OnSize()=silacvalidator.PepListCtrlPanel-class.html#OnSize"><a title="silacvalidator.PepListCtrlPanel.OnSize" class="py-name" href="#" onclick="return doclink('link-84', 'OnSize', 'link-84');">OnSize</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L927"></a><tt class="py-lineno"> 927</tt> <tt class="py-line"> <tt class="py-comment">#self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.list)</tt> </tt>
+<a name="L928"></a><tt class="py-lineno"> 928</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">Bind</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">EVT_LIST_COL_CLICK</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Method silacvalidator.PepListCtrlPanel.OnColClick()=silacvalidator.PepListCtrlPanel-class.html#OnColClick"><a title="silacvalidator.PepListCtrlPanel.OnColClick" class="py-name" href="#" onclick="return doclink('link-85', 'OnColClick', 'link-85');">OnColClick</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L929"></a><tt class="py-lineno"> 929</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.PopulateList"></a><div id="PepListCtrlPanel.PopulateList-def"><a name="L930"></a><tt class="py-lineno"> 930</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.PopulateList-toggle" onclick="return toggle('PepListCtrlPanel.PopulateList');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#PopulateList">PopulateList</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">externaldict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.PopulateList-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.PopulateList-expanded"><a name="L931"></a><tt class="py-lineno"> 931</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L932"></a><tt class="py-lineno"> 932</tt> <tt class="py-line"><tt class="py-docstring"> Constructs the headings of the list control</tt> </tt>
+<a name="L933"></a><tt class="py-lineno"> 933</tt> <tt class="py-line"><tt class="py-docstring"> and populates it with data</tt> </tt>
+<a name="L934"></a><tt class="py-lineno"> 934</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L935"></a><tt class="py-lineno"> 935</tt> <tt class="py-line"> </tt>
+<a name="L936"></a><tt class="py-lineno"> 936</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">itemDataMap</tt> <tt class="py-op">=</tt> <tt class="py-name">externaldict</tt> </tt>
+<a name="L937"></a><tt class="py-lineno"> 937</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">ClearAll</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L938"></a><tt class="py-lineno"> 938</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
+<a name="L939"></a><tt class="py-lineno"> 939</tt> <tt class="py-line"> <tt class="py-comment"># for normal, simple columns, you can add them like this:</tt> </tt>
+<a name="L940"></a><tt class="py-lineno"> 940</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumn</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"Peptide"</tt><tt class="py-op">)</tt> </tt>
+<a name="L941"></a><tt class="py-lineno"> 941</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumn</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"Leucines"</tt><tt class="py-op">,</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LIST_FORMAT_RIGHT</tt><tt class="py-op">)</tt> </tt>
+<a name="L942"></a><tt class="py-lineno"> 942</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumn</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">"m/z measured"</tt><tt class="py-op">)</tt> </tt>
+<a name="L943"></a><tt class="py-lineno"> 943</tt> <tt class="py-line"> <tt class="py-comment">#etc...</tt> </tt>
+<a name="L944"></a><tt class="py-lineno"> 944</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
+<a name="L945"></a><tt class="py-lineno"> 945</tt> <tt class="py-line"> <tt class="py-comment"># but since we want images on the column header we have to do it the hard way:</tt> </tt>
+<a name="L946"></a><tt class="py-lineno"> 946</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">ListItem</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L947"></a><tt class="py-lineno"> 947</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_mask</tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LIST_MASK_TEXT</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LIST_MASK_IMAGE</tt> <tt class="py-op">|</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LIST_MASK_FORMAT</tt> </tt>
+<a name="L948"></a><tt class="py-lineno"> 948</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_image</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
+<a name="L949"></a><tt class="py-lineno"> 949</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L950"></a><tt class="py-lineno"> 950</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Peptide"</tt> </tt>
+<a name="L951"></a><tt class="py-lineno"> 951</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L952"></a><tt class="py-lineno"> 952</tt> <tt class="py-line"> <tt class="py-comment">#info.m_format = wx.LIST_FORMAT_RIGHT</tt> </tt>
+<a name="L953"></a><tt class="py-lineno"> 953</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L954"></a><tt class="py-lineno"> 954</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Leucines"</tt> </tt>
+<a name="L955"></a><tt class="py-lineno"> 955</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L956"></a><tt class="py-lineno"> 956</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L957"></a><tt class="py-lineno"> 957</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"m/z meas."</tt> </tt>
+<a name="L958"></a><tt class="py-lineno"> 958</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L959"></a><tt class="py-lineno"> 959</tt> <tt class="py-line"> </tt>
+<a name="L960"></a><tt class="py-lineno"> 960</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L961"></a><tt class="py-lineno"> 961</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"m/z calc."</tt> </tt>
+<a name="L962"></a><tt class="py-lineno"> 962</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L963"></a><tt class="py-lineno"> 963</tt> <tt class="py-line"> </tt>
+<a name="L964"></a><tt class="py-lineno"> 964</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L965"></a><tt class="py-lineno"> 965</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Base_int."</tt> </tt>
+<a name="L966"></a><tt class="py-lineno"> 966</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L967"></a><tt class="py-lineno"> 967</tt> <tt class="py-line"> </tt>
+<a name="L968"></a><tt class="py-lineno"> 968</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L969"></a><tt class="py-lineno"> 969</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Deut_int."</tt> </tt>
+<a name="L970"></a><tt class="py-lineno"> 970</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L971"></a><tt class="py-lineno"> 971</tt> <tt class="py-line"> </tt>
+<a name="L972"></a><tt class="py-lineno"> 972</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L973"></a><tt class="py-lineno"> 973</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Ratio"</tt> </tt>
+<a name="L974"></a><tt class="py-lineno"> 974</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L975"></a><tt class="py-lineno"> 975</tt> <tt class="py-line"> </tt>
+<a name="L976"></a><tt class="py-lineno"> 976</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L977"></a><tt class="py-lineno"> 977</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Corr_ratio"</tt> </tt>
+<a name="L978"></a><tt class="py-lineno"> 978</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L979"></a><tt class="py-lineno"> 979</tt> <tt class="py-line"> </tt>
+<a name="L980"></a><tt class="py-lineno"> 980</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L981"></a><tt class="py-lineno"> 981</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Local_bg"</tt> </tt>
+<a name="L982"></a><tt class="py-lineno"> 982</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L983"></a><tt class="py-lineno"> 983</tt> <tt class="py-line"> </tt>
+<a name="L984"></a><tt class="py-lineno"> 984</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_format</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+<a name="L985"></a><tt class="py-lineno"> 985</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">.</tt><tt class="py-name">m_text</tt> <tt class="py-op">=</tt> <tt class="py-string">"Valid."</tt> </tt>
+<a name="L986"></a><tt class="py-lineno"> 986</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertColumnInfo</tt><tt class="py-op">(</tt><tt class="py-number">9</tt><tt class="py-op">,</tt> <tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
+<a name="L987"></a><tt class="py-lineno"> 987</tt> <tt class="py-line"> <tt class="py-comment">#Now put inside the data from the dictionary </tt> </tt>
+<a name="L988"></a><tt class="py-lineno"> 988</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">items</tt> <tt class="py-op">=</tt> <tt class="py-name">externaldict</tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L989"></a><tt class="py-lineno"> 989</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">items</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L990"></a><tt class="py-lineno"> 990</tt> <tt class="py-line"> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">items</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">]</tt> </tt>
+<a name="L991"></a><tt class="py-lineno"> 991</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">InsertStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L992"></a><tt class="py-lineno"> 992</tt> <tt class="py-line"> <tt class="py-comment">#self.list.InsertImageStringItem(x, data[0], self.sm_up)</tt> </tt>
+<a name="L993"></a><tt class="py-lineno"> 993</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L994"></a><tt class="py-lineno"> 994</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L995"></a><tt class="py-lineno"> 995</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L996"></a><tt class="py-lineno"> 996</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L997"></a><tt class="py-lineno"> 997</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L998"></a><tt class="py-lineno"> 998</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L999"></a><tt class="py-lineno"> 999</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">7</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L1000"></a><tt class="py-lineno">1000</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">8</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L1001"></a><tt class="py-lineno">1001</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-number">9</tt><tt class="py-op">,</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
+<a name="L1002"></a><tt class="py-lineno">1002</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetItemData</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt> <tt class="py-name">key</tt><tt class="py-op">)</tt> <tt class="py-comment">#why is that necessary ?</tt> </tt>
+<a name="L1003"></a><tt class="py-lineno">1003</tt> <tt class="py-line"> <tt class="py-comment">#Set colors for the adnotation - is light grey if</tt> </tt>
+<a name="L1004"></a><tt class="py-lineno">1004</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#no leucine exists in the peptide sequence</tt> </tt>
+<a name="L1005"></a><tt class="py-lineno">1005</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"YES"</tt><tt class="py-op">:</tt> </tt>
+<a name="L1006"></a><tt class="py-lineno">1006</tt> <tt class="py-line"> <tt class="py-name">item</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
+<a name="L1007"></a><tt class="py-lineno">1007</tt> <tt class="py-line"> <tt class="py-name">item</tt><tt class="py-op">.</tt><tt class="py-name">SetTextColour</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">BLUE</tt><tt class="py-op">)</tt> </tt>
+<a name="L1008"></a><tt class="py-lineno">1008</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetItem</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt> </tt>
+<a name="L1009"></a><tt class="py-lineno">1009</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"NO"</tt><tt class="py-op">:</tt> </tt>
+<a name="L1010"></a><tt class="py-lineno">1010</tt> <tt class="py-line"> <tt class="py-name">item</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
+<a name="L1011"></a><tt class="py-lineno">1011</tt> <tt class="py-line"> <tt class="py-name">item</tt><tt class="py-op">.</tt><tt class="py-name">SetTextColour</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">RED</tt><tt class="py-op">)</tt> </tt>
+<a name="L1012"></a><tt class="py-lineno">1012</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetItem</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt> </tt>
+<a name="L1013"></a><tt class="py-lineno">1013</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"0"</tt><tt class="py-op">:</tt> </tt>
+<a name="L1014"></a><tt class="py-lineno">1014</tt> <tt class="py-line"> <tt class="py-name">item</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItem</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
+<a name="L1015"></a><tt class="py-lineno">1015</tt> <tt class="py-line"> <tt class="py-name">item</tt><tt class="py-op">.</tt><tt class="py-name">SetTextColour</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">LIGHT_GREY</tt><tt class="py-op">)</tt> </tt>
+<a name="L1016"></a><tt class="py-lineno">1016</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetItem</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt> </tt>
+<a name="L1017"></a><tt class="py-lineno">1017</tt> <tt class="py-line"> </tt>
+<a name="L1018"></a><tt class="py-lineno">1018</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">9</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+<a name="L1019"></a><tt class="py-lineno">1019</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetColumnWidth</tt><tt class="py-op">(</tt><tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-number">60</tt><tt class="py-op">)</tt> </tt>
+<a name="L1020"></a><tt class="py-lineno">1020</tt> <tt class="py-line"> <tt class="py-comment">#self.list.SetColumnWidth(i, wx.LIST_AUTOSIZE)</tt> </tt>
+<a name="L1021"></a><tt class="py-lineno">1021</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetColumnWidth</tt><tt class="py-op">(</tt><tt class="py-number">9</tt><tt class="py-op">,</tt> <tt class="py-number">100</tt><tt class="py-op">)</tt> </tt>
+<a name="L1022"></a><tt class="py-lineno">1022</tt> <tt class="py-line"> <tt class="py-comment"># show how to select an item</tt> </tt>
+<a name="L1023"></a><tt class="py-lineno">1023</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.list.SetItemState(5, wx.LIST_STATE_SELECTED, wx.LIST_STATE_SELECTED)</tt> </tt>
+<a name="L1024"></a><tt class="py-lineno">1024</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
+</div><a name="L1025"></a><tt class="py-lineno">1025</tt> <tt class="py-line"> </tt>
+<a name="L1026"></a><tt class="py-lineno">1026</tt> <tt class="py-line"> <tt class="py-comment"># Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py</tt> </tt>
+<a name="PepListCtrlPanel.GetListCtrl"></a><div id="PepListCtrlPanel.GetListCtrl-def"><a name="L1027"></a><tt class="py-lineno">1027</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.GetListCtrl-toggle" onclick="return toggle('PepListCtrlPanel.GetListCtrl');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#GetListCtrl">GetListCtrl</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.GetListCtrl-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.GetListCtrl-expanded"><a name="L1028"></a><tt class="py-lineno">1028</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt> </tt>
+</div><a name="L1029"></a><tt class="py-lineno">1029</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.SetValidated"></a><div id="PepListCtrlPanel.SetValidated-def"><a name="L1030"></a><tt class="py-lineno">1030</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.SetValidated-toggle" onclick="return toggle('PepListCtrlPanel.SetValidated');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#SetValidated">SetValidated</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">where</tt><tt class="py-op">,</tt> <tt class="py-param">what</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.SetValidated-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.SetValidated-expanded"><a name="L1031"></a><tt class="py-lineno">1031</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L1032"></a><tt class="py-lineno">1032</tt> <tt class="py-line"><tt class="py-docstring"> Called when the OnValidate or OnInvalidate are activated</tt> </tt>
+<a name="L1033"></a><tt class="py-lineno">1033</tt> <tt class="py-line"><tt class="py-docstring"> Changes the 9th element in the current list item to "YES"</tt> </tt>
+<a name="L1034"></a><tt class="py-lineno">1034</tt> <tt class="py-line"><tt class="py-docstring"> or "NO"</tt> </tt>
+<a name="L1035"></a><tt class="py-lineno">1035</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L1036"></a><tt class="py-lineno">1036</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">where</tt><tt class="py-op">,</tt> <tt class="py-number">9</tt><tt class="py-op">,</tt> <tt class="py-name">what</tt><tt class="py-op">)</tt> </tt>
+<a name="L1037"></a><tt class="py-lineno">1037</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">what</tt> <tt class="py-op">==</tt> <tt class="py-string">"YES"</tt><tt class="py-op">:</tt> </tt>
+<a name="L1038"></a><tt class="py-lineno">1038</tt> <tt class="py-line"> <tt class="py-name">item</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItem</tt><tt class="py-op">(</tt><tt class="py-name">where</tt><tt class="py-op">)</tt> </tt>
+<a name="L1039"></a><tt class="py-lineno">1039</tt> <tt class="py-line"> <tt class="py-name">item</tt><tt class="py-op">.</tt><tt class="py-name">SetTextColour</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">BLUE</tt><tt class="py-op">)</tt> </tt>
+<a name="L1040"></a><tt class="py-lineno">1040</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetItem</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt> </tt>
+<a name="L1041"></a><tt class="py-lineno">1041</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">what</tt> <tt class="py-op">==</tt> <tt class="py-string">"NO"</tt><tt class="py-op">:</tt> </tt>
+<a name="L1042"></a><tt class="py-lineno">1042</tt> <tt class="py-line"> <tt class="py-name">item</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItem</tt><tt class="py-op">(</tt><tt class="py-name">where</tt><tt class="py-op">)</tt> </tt>
+<a name="L1043"></a><tt class="py-lineno">1043</tt> <tt class="py-line"> <tt class="py-name">item</tt><tt class="py-op">.</tt><tt class="py-name">SetTextColour</tt><tt class="py-op">(</tt><tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">RED</tt><tt class="py-op">)</tt> </tt>
+<a name="L1044"></a><tt class="py-lineno">1044</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetItem</tt><tt class="py-op">(</tt><tt class="py-name">item</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L1045"></a><tt class="py-lineno">1045</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.SetBg"></a><div id="PepListCtrlPanel.SetBg-def"><a name="L1046"></a><tt class="py-lineno">1046</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.SetBg-toggle" onclick="return toggle('PepListCtrlPanel.SetBg');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#SetBg">SetBg</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">where</tt><tt class="py-op">,</tt> <tt class="py-param">bg</tt><tt class="py-op">,</tt> <tt class="py-param">ratio</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.SetBg-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.SetBg-expanded"><a name="L1047"></a><tt class="py-lineno">1047</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L1048"></a><tt class="py-lineno">1048</tt> <tt class="py-line"><tt class="py-docstring"> Shows local background value in the list and</tt> </tt>
+<a name="L1049"></a><tt class="py-lineno">1049</tt> <tt class="py-line"><tt class="py-docstring"> the updated value of corrected ratio</tt> </tt>
+<a name="L1050"></a><tt class="py-lineno">1050</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L1051"></a><tt class="py-lineno">1051</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">where</tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-string">"%.0f"</tt><tt class="py-op">%</tt><tt class="py-name">bg</tt><tt class="py-op">)</tt> </tt>
+<a name="L1052"></a><tt class="py-lineno">1052</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetStringItem</tt><tt class="py-op">(</tt><tt class="py-name">where</tt><tt class="py-op">,</tt> <tt class="py-number">7</tt><tt class="py-op">,</tt> <tt class="py-string">"%.2f"</tt><tt class="py-op">%</tt><tt class="py-name">ratio</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L1053"></a><tt class="py-lineno">1053</tt> <tt class="py-line"> </tt>
+<a name="L1054"></a><tt class="py-lineno">1054</tt> <tt class="py-line"> <tt class="py-comment"># Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py</tt> </tt>
+<a name="PepListCtrlPanel.GetSortImages"></a><div id="PepListCtrlPanel.GetSortImages-def"><a name="L1055"></a><tt class="py-lineno">1055</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.GetSortImages-toggle" onclick="return toggle('PepListCtrlPanel.GetSortImages');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#GetSortImages">GetSortImages</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.GetSortImages-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.GetSortImages-expanded"><a name="L1056"></a><tt class="py-lineno">1056</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sm_dn</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sm_up</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L1057"></a><tt class="py-lineno">1057</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.getColumnText"></a><div id="PepListCtrlPanel.getColumnText-def"><a name="L1058"></a><tt class="py-lineno">1058</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.getColumnText-toggle" onclick="return toggle('PepListCtrlPanel.getColumnText');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#getColumnText">getColumnText</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">,</tt> <tt class="py-param">col</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.getColumnText-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.getColumnText-expanded"><a name="L1059"></a><tt class="py-lineno">1059</tt> <tt class="py-line"> <tt class="py-name">item</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItem</tt><tt class="py-op">(</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-name">col</tt><tt class="py-op">)</tt> </tt>
+<a name="L1060"></a><tt class="py-lineno">1060</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">item</tt><tt class="py-op">.</tt><tt class="py-name">GetText</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L1061"></a><tt class="py-lineno">1061</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.OnItemSelected"></a><div id="PepListCtrlPanel.OnItemSelected-def"><a name="L1062"></a><tt class="py-lineno">1062</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.OnItemSelected-toggle" onclick="return toggle('PepListCtrlPanel.OnItemSelected');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#OnItemSelected">OnItemSelected</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.OnItemSelected-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.OnItemSelected-expanded"><a name="L1063"></a><tt class="py-lineno">1063</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
+<a name="L1064"></a><tt class="py-lineno">1064</tt> <tt class="py-line"><tt class="py-docstring"> Overwritten by its equivalent in MainFrame</tt> </tt>
+<a name="L1065"></a><tt class="py-lineno">1065</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
+<a name="L1066"></a><tt class="py-lineno">1066</tt> <tt class="py-line"> <tt class="py-comment">##print event.GetItem().GetTextColour()</tt> </tt>
+<a name="L1067"></a><tt class="py-lineno">1067</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt> <tt class="py-op">=</tt> <tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">m_itemIndex</tt> </tt>
+<a name="L1068"></a><tt class="py-lineno">1068</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">uniquekey</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">GetItemText</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt><tt class="py-op">)</tt><tt class="py-op">+</tt>\ </tt>
+<a name="L1069"></a><tt class="py-lineno">1069</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="silacvalidator.PepListCtrlPanel.getColumnText" class="py-name" href="#" onclick="return doclink('link-86', 'getColumnText', 'link-44');">getColumnText</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">currentItem</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
+<a name="L1070"></a><tt class="py-lineno">1070</tt> <tt class="py-line"> <tt class="py-comment">#print self.uniquekey</tt> </tt>
+<a name="L1071"></a><tt class="py-lineno">1071</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">Skip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L1072"></a><tt class="py-lineno">1072</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.OnColClick"></a><div id="PepListCtrlPanel.OnColClick-def"><a name="L1073"></a><tt class="py-lineno">1073</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.OnColClick-toggle" onclick="return toggle('PepListCtrlPanel.OnColClick');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#OnColClick">OnColClick</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.OnColClick-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.OnColClick-expanded"><a name="L1074"></a><tt class="py-lineno">1074</tt> <tt class="py-line"> <tt class="py-comment">#print ("OnColClick: %d\n" % event.GetColumn())</tt> </tt>
+<a name="L1075"></a><tt class="py-lineno">1075</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">event</tt><tt class="py-op">.</tt><tt class="py-name">Skip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+</div><a name="L1076"></a><tt class="py-lineno">1076</tt> <tt class="py-line"> </tt>
+<a name="PepListCtrlPanel.OnSize"></a><div id="PepListCtrlPanel.OnSize-def"><a name="L1077"></a><tt class="py-lineno">1077</tt> <a class="py-toggle" href="#" id="PepListCtrlPanel.OnSize-toggle" onclick="return toggle('PepListCtrlPanel.OnSize');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="silacvalidator.PepListCtrlPanel-class.html#OnSize">OnSize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">event</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
+</div><div id="PepListCtrlPanel.OnSize-collapsed" style="display:none;" pad="++++" indent="++++++++"></div><div id="PepListCtrlPanel.OnSize-expanded"><a name="L1078"></a><tt class="py-lineno">1078</tt> <tt class="py-line"> <tt class="py-name">w</tt><tt class="py-op">,</tt> <tt class="py-name">h</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">GetClientSizeTuple</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L1079"></a><tt class="py-lineno">1079</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">list</tt><tt class="py-op">.</tt><tt class="py-name">SetDimensions</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">w</tt><tt class="py-op">,</tt> <tt class="py-name">h</tt><tt class="py-op">)</tt> </tt>
+</div></div><a name="L1080"></a><tt class="py-lineno">1080</tt> <tt class="py-line"> </tt>
+<a name="L1081"></a><tt class="py-lineno">1081</tt> <tt class="py-line"><tt class="py-comment">#######################################################</tt> </tt>
+<a name="L1082"></a><tt class="py-lineno">1082</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#the equivalent of a main function.</tt> </tt>
+<a name="L1083"></a><tt class="py-lineno">1083</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-87" class="py-name" targets="Variable MSFit_to_txt.app=MSFit_to_txt-module.html#app,Variable lilamslaunchGUI.app=lilamslaunchGUI-module.html#app,Variable silacvalidator.app=silacvalidator-module.html#app"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-87', 'app', 'link-87');">app</a></tt> <tt class="py-op">=</tt> <tt class="py-name">wx</tt><tt class="py-op">.</tt><tt class="py-name">PySimpleApp</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L1084"></a><tt class="py-lineno">1084</tt> <tt class="py-line"><tt id="link-88" class="py-name" targets="Variable MSFit_to_txt.frame=MSFit_to_txt-module.html#frame,Variable lilamslaunchGUI.frame=lilamslaunchGUI-module.html#frame,Variable silacvalidator.frame=silacvalidator-module.html#frame"><a title="MSFit_to_txt.frame
+lilamslaunchGUI.frame
+silacvalidator.frame" class="py-name" href="#" onclick="return doclink('link-88', 'frame', 'link-88');">frame</a></tt> <tt class="py-op">=</tt> <tt id="link-89" class="py-name" targets="Class MSFit_to_txt.MainFrame=MSFit_to_txt.MainFrame-class.html,Class lilamslaunchGUI.MainFrame=lilamslaunchGUI.MainFrame-class.html,Class silacvalidator.MainFrame=silacvalidator.MainFrame-class.html"><a title="MSFit_to_txt.MainFrame
+lilamslaunchGUI.MainFrame
+silacvalidator.MainFrame" class="py-name" href="#" onclick="return doclink('link-89', 'MainFrame', 'link-89');">MainFrame</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">"SILAC validator v. 0.2"</tt><tt class="py-op">)</tt> </tt>
+<a name="L1085"></a><tt class="py-lineno">1085</tt> <tt class="py-line"><tt id="link-90" class="py-name"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-90', 'app', 'link-87');">app</a></tt><tt class="py-op">.</tt><tt class="py-name">SetTopWindow</tt><tt class="py-op">(</tt><tt id="link-91" class="py-name"><a title="MSFit_to_txt.frame
+lilamslaunchGUI.frame
+silacvalidator.frame" class="py-name" href="#" onclick="return doclink('link-91', 'frame', 'link-88');">frame</a></tt><tt class="py-op">)</tt> </tt>
+<a name="L1086"></a><tt class="py-lineno">1086</tt> <tt class="py-line"><tt id="link-92" class="py-name"><a title="MSFit_to_txt.app
+lilamslaunchGUI.app
+silacvalidator.app" class="py-name" href="#" onclick="return doclink('link-92', 'app', 'link-87');">app</a></tt><tt class="py-op">.</tt><tt class="py-name">MainLoop</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
+<a name="L1087"></a><tt class="py-lineno">1087</tt> <tt class="py-line"><tt class="py-comment">#######################################################</tt> </tt>
+<a name="L1088"></a><tt class="py-lineno">1088</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt><script type="text/javascript">
+<!--
+expandto(location.href);
+// -->
+</script>
+</pre>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:24 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/silacvalidator.MainFrame-class.html b/docs/silacvalidator.MainFrame-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..adabacd0ca2dacd7f341477164b59604e49dbb98
--- /dev/null
+++ b/docs/silacvalidator.MainFrame-class.html
@@ -0,0 +1,1045 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>silacvalidator.MainFrame</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="silacvalidator-module.html">Module silacvalidator</a> ::
+ Class MainFrame
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class MainFrame</h1><p class="nomargin-top"><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame">source code</a></span></p>
+<pre class="base-tree">
+wx.lib.plot.wx.Frame --+
+ |
+ <strong class="uidshort">MainFrame</strong>
+</pre>
+
+<hr />
+<pre class="literalblock">
+
+The application main frame. Contains the following
+graphic elements:
+self.panel |---- self.lb - the text list control
+ |---- self.btnpanel1 - the panel containing
+ three buttons (Validate, Invalidate
+ and LocalBackground
+
+self.panelplot - containing self.plotcanvas
+ to allow drawing of spectra files
+
+self.log - a TextCtrl panel with information
+ on the analysed xml file
+ ______________________
+ --------------- ------
+ | || | self.lb and self.btnpanel1
+ -----------------------
+ | |
+ | | self.panelplot with self.plotcanvas
+ | |
+ -----------------------
+ | | self.log
+ -----------------------
+
+</pre>
+
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">parent</span>,
+ <span class="summary-sig-arg">id</span>,
+ <span class="summary-sig-arg">title</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnXMLOpen"></a><span class="summary-sig-name">OnXMLOpen</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Opens a XML file with SILAC data and generates an ElementTree
+ instance containing the data in the variable self.data</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnXMLOpen">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#XMLOpen" class="summary-sig-name">XMLOpen</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">dirname</span>,
+ <span class="summary-sig-arg">filename</span>)</span><br />
+ Will allow calls for XMLOpen from Previous and Next calls.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.XMLOpen">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#PlotSpectrumXML" class="summary-sig-name">PlotSpectrumXML</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">index</span>=<span class="summary-sig-default">0</span>,
+ <span class="summary-sig-arg">title</span>=<span class="summary-sig-default">""</span>)</span><br />
+ Recover and plot data for the record that has <index> It is
+ found in self.data[5] - that is pepdata, the subnode is 10 for
+ <spectrum> and 0, 1 for the two lists mz and int.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.PlotSpectrumXML">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="PlotArray"></a><span class="summary-sig-name">PlotArray</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">data_array</span>,
+ <span class="summary-sig-arg">color</span>,
+ <span class="summary-sig-arg">title</span>)</span><br />
+ Used to plot on the plotcanvas the points of a data_array Default is
+ autoscale, used by PlotSpectrumXML</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.PlotArray">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#GenerateListDict" class="summary-sig-name">GenerateListDict</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">xmldata</span>)</span><br />
+ forms a dictionary {1:["a", "b", "c"],
+ 2:...</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.GenerateListDict">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="PopulateList"></a><span class="summary-sig-name">PopulateList</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">externaldict</span>)</span><br />
+ a wrapper to the function with the same name in self.lb</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.PopulateList">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#OnItemSelected" class="summary-sig-name">OnItemSelected</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Activated when one item in the self.lb list control
+is selected.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnItemSelected">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="MapUniqueKey"></a><span class="summary-sig-name">MapUniqueKey</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">uniquekey</span>)</span><br />
+ Used by <OnItemSelected> to allow a correspondence between
+ self.currentItem - in the list and self.index in the ElementTree
+ Element representing data read from the XML SILAC file</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.MapUniqueKey">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnValidate"></a><span class="summary-sig-name">OnValidate</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ changes both the entry in the list control -- see SetValidated
+ function --- and the same entry in the self.data (to be written)</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnValidate">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnInvalidate"></a><span class="summary-sig-name">OnInvalidate</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ changes both the entry in the list control -- see SetValidated
+ function --- and the same entry in the self.data (to be written)</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnInvalidate">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="SetXMLValidated"></a><span class="summary-sig-name">SetXMLValidated</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">index</span>,
+ <span class="summary-sig-arg">what</span>)</span><br />
+ 7 is the actual position of the <validated> field in the
+ self.data - coming from the SILAC XML tree</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.SetXMLValidated">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#GetValXML" class="summary-sig-name">GetValXML</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">index</span>=<span class="summary-sig-default">0</span>,
+ <span class="summary-sig-arg">what</span>=<span class="summary-sig-default">'pepseq'</span>)</span><br />
+ Returns the text attribute of an entry in an Element object based on
+ the self.XMLdict dictionary that maps numbers to tags - definition in
+ the init of the main frame.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.GetValXML">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnXMLSave"></a><span class="summary-sig-name">OnXMLSave</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Writes the contents of self.data to the self.fnameout (established
+ when the actual file was opened)</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnXMLSave">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnSpectrumSave"></a><span class="summary-sig-name">OnSpectrumSave</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnSpectrumSave">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#SpectrumSave" class="summary-sig-name">SpectrumSave</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">index</span>=<span class="summary-sig-default">0</span>)</span><br />
+ Writes the contents of the actual selected spectrum...</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.SpectrumSave">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#OnNextFile" class="summary-sig-name">OnNextFile</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Allows navigation between the xml files in a folder.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnNextFile">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#OnPrevFile" class="summary-sig-name">OnPrevFile</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Allows navigation between the xml files in a folder.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnPrevFile">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFullUnzoom"></a><span class="summary-sig-name">OnFullUnzoom</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnFullUnzoom">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFileOpen"></a><span class="summary-sig-name">OnFileOpen</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Opens and plots a tab delimited text file If not a recognized file, a
+ message is displayed Sets also the actual directory name:
+ self.defaultdirname</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnFileOpen">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="PlotFile"></a><span class="summary-sig-name">PlotFile</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">fname</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.PlotFile">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFileClose"></a><span class="summary-sig-name">OnFileClose</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnFileClose">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnMLeftDown"></a><span class="summary-sig-name">OnMLeftDown</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnMLeftDown">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnMDoubleClick"></a><span class="summary-sig-name">OnMDoubleClick</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnMDoubleClick">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.MainFrame-class.html#OnSetLocalBg" class="summary-sig-name">OnSetLocalBg</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Updates the local background data both in the shown list and in
+ self.data.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnSetLocalBg">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnSaveImage"></a><span class="summary-sig-name">OnSaveImage</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnSaveImage">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnFileExit"></a><span class="summary-sig-name">OnFileExit</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnFileExit">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnPlotRedraw"></a><span class="summary-sig-name">OnPlotRedraw</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnPlotRedraw">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnPlotClear"></a><span class="summary-sig-name">OnPlotClear</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnPlotClear">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnPlotScale"></a><span class="summary-sig-name">OnPlotScale</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnPlotScale">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnEnableZoom"></a><span class="summary-sig-name">OnEnableZoom</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnEnableZoom">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnEnableGrid"></a><span class="summary-sig-name">OnEnableGrid</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnEnableGrid">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnEnableLegend"></a><span class="summary-sig-name">OnEnableLegend</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnEnableLegend">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnReset"></a><span class="summary-sig-name">OnReset</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnReset">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnHelpAbout"></a><span class="summary-sig-name">OnHelpAbout</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnHelpAbout">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="resetDefaults"></a><span class="summary-sig-name">resetDefaults</span>(<span class="summary-sig-arg">self</span>)</span><br />
+ Just to reset the fonts back to the PlotCanvas defaults</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.resetDefaults">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+</table>
+<!-- ==================== METHOD DETAILS ==================== -->
+<a name="section-MethodDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Method Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-MethodDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="XMLOpen"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">XMLOpen</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">dirname</span>,
+ <span class="sig-arg">filename</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.XMLOpen">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Will allow calls for XMLOpen from Previous and Next calls. Returns
+ True if everything OK.</p>
+ <p>-uses get_flist_xml to set up the file list -uses map_pos_inlist to
+ set up self.where -uses self.PlotSpectrumXML to plot the first peptide in
+ file -uses self.PopulateList to populate the self.lb list control with
+ data -uses self.GenerateListDict to generate the dictionary used to
+ describe the data in the self.lb control</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="PlotSpectrumXML"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">PlotSpectrumXML</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">index</span>=<span class="sig-default">0</span>,
+ <span class="sig-arg">title</span>=<span class="sig-default">""</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.PlotSpectrumXML">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Recover and plot data for the record that has <index> It is
+ found in self.data[5] - that is pepdata, the subnode is 10 for
+ <spectrum> and 0, 1 for the two lists mz and int. "5 "is
+ contained in self.pdatapos</p>
+ <p>-uses self.PlotArray - a function to do the plotting</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="GenerateListDict"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GenerateListDict</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">xmldata</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.GenerateListDict">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>forms a dictionary {1:["a", "b", "c"],
+ 2:...} for the PepListCtrlPanel widget - to populate with XML data</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="OnItemSelected"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">OnItemSelected</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">event</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnItemSelected">source code</a></span>
+ </td>
+ </tr></table>
+
+ <pre class="literalblock">
+
+Activated when one item in the self.lb list control
+is selected. Determines the generation of a unique key
+that will allow a correspondence between the list
+elements and the underlying ElementTree Element
+- uses MapUniqueKey function
+
+</pre>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="GetValXML"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GetValXML</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">index</span>=<span class="sig-default">0</span>,
+ <span class="sig-arg">what</span>=<span class="sig-default">'pepseq'</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.GetValXML">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns the text attribute of an entry in an Element object based on
+ the self.XMLdict dictionary that maps numbers to tags - definition in the
+ init of the main frame. By default it returns the peptide sequence of the
+ first record.</p>
+ <p>self.pdatapos - indicates the position of the <pepdata> in the
+ root of the pepdata xml entry</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="SpectrumSave"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">SpectrumSave</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">index</span>=<span class="sig-default">0</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.SpectrumSave">source code</a></span>
+ </td>
+ </tr></table>
+
+ <pre class="literalblock">
+
+Writes the contents of the actual selected spectrum
+ to a given file name, in tab delimited format
+
+</pre>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="OnNextFile"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">OnNextFile</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">event</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnNextFile">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Allows navigation between the xml files in a folder. Calls the
+ self.XMLOpen function exactly like the self.OnXMLOpen.</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="OnPrevFile"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">OnPrevFile</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">event</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnPrevFile">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Allows navigation between the xml files in a folder. Calls the
+ self.XMLOpen function exactly like the self.OnXMLOpen.</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<a name="OnSetLocalBg"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">OnSetLocalBg</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">event</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#MainFrame.OnSetLocalBg">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Updates the local background data both in the shown list and in
+ self.data. Recalculated the corrected ratio</p>
+ <dl class="fields">
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
+ </td>
+ </tr>
+</table>
+
+<script type="text/javascript">
+ <!--
+ // Private objects are initially displayed (because if
+ // javascript is turned off then we want them to be
+ // visible); but by default, we want to hide them. So hide
+ // them unless we have a cookie that says to show them.
+ checkCookie();
+ // -->
+</script>
+</body>
+</html>
diff --git a/docs/silacvalidator.PepListCtrl-class.html b/docs/silacvalidator.PepListCtrl-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..1fc03ccb3a124e9fd9852e9a981941e9f3939ba0
--- /dev/null
+++ b/docs/silacvalidator.PepListCtrl-class.html
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>silacvalidator.PepListCtrl</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="silacvalidator-module.html">Module silacvalidator</a> ::
+ Class PepListCtrl
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class PepListCtrl</h1><p class="nomargin-top"><span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrl">source code</a></span></p>
+<pre class="base-tree">
+ wx.lib.plot.wx.ListCtrl --+
+ |
+wx.lib.mixins.listctrl.ListCtrlAutoWidthMixin --+
+ |
+ <strong class="uidshort">PepListCtrl</strong>
+</pre>
+
+<hr />
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.PepListCtrl-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">parent</span>,
+ <span class="summary-sig-arg">ID</span>,
+ <span class="summary-sig-arg">pos</span>=<span class="summary-sig-default">wx.DefaultPosition</span>,
+ <span class="summary-sig-arg">size</span>=<span class="summary-sig-default">wx.DefaultSize</span>,
+ <span class="summary-sig-arg">style</span>=<span class="summary-sig-default">0</span>)</span><br />
+ Standard initialiser.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrl.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>wx.lib.mixins.listctrl.ListCtrlAutoWidthMixin</code></b>:
+ <code>resizeColumn</code>,
+ <code>resizeLastColumn</code>,
+ <code>setResizeColumn</code>
+ </p>
+ <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>wx.lib.mixins.listctrl.ListCtrlAutoWidthMixin</code></b> (private):
+ <code>_doResize</code>,
+ <code>_onResize</code>
+ </p></div>
+ </td>
+ </tr>
+</table>
+<!-- ==================== METHOD DETAILS ==================== -->
+<a name="section-MethodDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Method Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-MethodDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="__init__"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">parent</span>,
+ <span class="sig-arg">ID</span>,
+ <span class="sig-arg">pos</span>=<span class="sig-default">wx.DefaultPosition</span>,
+ <span class="sig-arg">size</span>=<span class="sig-default">wx.DefaultSize</span>,
+ <span class="sig-arg">style</span>=<span class="sig-default">0</span>)</span>
+ <br /><em class="fname">(Constructor)</em>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrl.__init__">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Standard initialiser.</p>
+ <dl class="fields">
+ <dt>Overrides:
+ wx.lib.mixins.listctrl.ListCtrlAutoWidthMixin.__init__
+ <dd><em class="note">(inherited documentation)</em></dd>
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
+ <a target="mainFrame" href="http://epydoc.sourceforge.net"
+ >http://epydoc.sourceforge.net</a>
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+
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+ <!--
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diff --git a/docs/silacvalidator.PepListCtrlPanel-class.html b/docs/silacvalidator.PepListCtrlPanel-class.html
new file mode 100644
index 0000000000000000000000000000000000000000..752a27246d67bd54d08d3418ae5ebc0831a92653
--- /dev/null
+++ b/docs/silacvalidator.PepListCtrlPanel-class.html
@@ -0,0 +1,396 @@
+<?xml version="1.0" encoding="ascii"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>silacvalidator.PepListCtrlPanel</title>
+ <link rel="stylesheet" href="epydoc.css" type="text/css" />
+ <script type="text/javascript" src="epydoc.js"></script>
+</head>
+
+<body bgcolor="white" text="black" link="blue" vlink="#204080"
+ alink="#204080">
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table width="100%" cellpadding="0" cellspacing="0">
+ <tr valign="top">
+ <td width="100%">
+ <span class="breadcrumbs">
+ <a href="silacvalidator-module.html">Module silacvalidator</a> ::
+ Class PepListCtrlPanel
+ </span>
+ </td>
+ <td>
+ <table cellpadding="0" cellspacing="0">
+ <!-- hide/show private -->
+ <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
+ onclick="toggle_private();">hide private</a>]</span></td></tr>
+ </table>
+ </td>
+ </tr>
+</table>
+<!-- ==================== CLASS DESCRIPTION ==================== -->
+<h1 class="epydoc">Class PepListCtrlPanel</h1><p class="nomargin-top"><span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel">source code</a></span></p>
+<pre class="base-tree">
+ wx.lib.plot.wx.Panel --+
+ |
+wx.lib.mixins.listctrl.ColumnSorterMixin --+
+ |
+ <strong class="uidshort">PepListCtrlPanel</strong>
+</pre>
+
+<hr />
+<!-- ==================== INSTANCE METHODS ==================== -->
+<a name="section-InstanceMethods"></a>
+<table class="summary" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Instance Methods</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-InstanceMethods"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.PepListCtrlPanel-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">parent</span>,
+ <span class="summary-sig-arg">dictwithdata</span>=<span class="summary-sig-default">{}</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.__init__">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="PopulateList"></a><span class="summary-sig-name">PopulateList</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">externaldict</span>)</span><br />
+ Constructs the headings of the list control and populates it with
+ data</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.PopulateList">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="GetListCtrl"></a><span class="summary-sig-name">GetListCtrl</span>(<span class="summary-sig-arg">self</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.GetListCtrl">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="SetValidated"></a><span class="summary-sig-name">SetValidated</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">where</span>,
+ <span class="summary-sig-arg">what</span>)</span><br />
+ Called when the OnValidate or OnInvalidate are activated Changes the
+ 9th element in the current list item to "YES" or
+ "NO"</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.SetValidated">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="SetBg"></a><span class="summary-sig-name">SetBg</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">where</span>,
+ <span class="summary-sig-arg">bg</span>,
+ <span class="summary-sig-arg">ratio</span>)</span><br />
+ Shows local background value in the list and the updated value of
+ corrected ratio</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.SetBg">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a href="silacvalidator.PepListCtrlPanel-class.html#GetSortImages" class="summary-sig-name">GetSortImages</a>(<span class="summary-sig-arg">self</span>)</span><br />
+ Returns a tuple of image list indexesthe indexes in the image list
+ for an image to be put on the column header when sorting in
+ descending order.</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.GetSortImages">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="getColumnText"></a><span class="summary-sig-name">getColumnText</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">index</span>,
+ <span class="summary-sig-arg">col</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.getColumnText">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnItemSelected"></a><span class="summary-sig-name">OnItemSelected</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span><br />
+ Overwritten by its equivalent in MainFrame</td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.OnItemSelected">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnColClick"></a><span class="summary-sig-name">OnColClick</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.OnColClick">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+<tr>
+ <td width="15%" align="right" valign="top" class="summary">
+ <span class="summary-type"> </span>
+ </td><td class="summary">
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr>
+ <td><span class="summary-sig"><a name="OnSize"></a><span class="summary-sig-name">OnSize</span>(<span class="summary-sig-arg">self</span>,
+ <span class="summary-sig-arg">event</span>)</span></td>
+ <td align="right" valign="top">
+ <span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.OnSize">source code</a></span>
+
+ </td>
+ </tr>
+ </table>
+
+ </td>
+ </tr>
+ <tr>
+ <td colspan="2" class="summary">
+ <p class="indent-wrapped-lines"><b>Inherited from <code>wx.lib.mixins.listctrl.ColumnSorterMixin</code></b>:
+ <code>GetColumnSorter</code>,
+ <code>GetColumnWidths</code>,
+ <code>GetSecondarySortValues</code>,
+ <code>OnSortOrderChanged</code>,
+ <code>SetColumnCount</code>,
+ <code>SortListItems</code>
+ </p>
+ </td>
+ </tr>
+</table>
+<!-- ==================== METHOD DETAILS ==================== -->
+<a name="section-MethodDetails"></a>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr bgcolor="#70b0f0" class="table-header">
+ <td colspan="2" class="table-header">
+ <table border="0" cellpadding="0" cellspacing="0" width="100%">
+ <tr valign="top">
+ <td align="left"><span class="table-header">Method Details</span></td>
+ <td align="right" valign="top"
+ ><span class="options">[<a href="#section-MethodDetails"
+ class="privatelink" onclick="toggle_private();"
+ >hide private</a>]</span></td>
+ </tr>
+ </table>
+ </td>
+</tr>
+</table>
+<a name="__init__"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
+ <span class="sig-arg">parent</span>,
+ <span class="sig-arg">dictwithdata</span>=<span class="sig-default">{}</span>)</span>
+ <br /><em class="fname">(Constructor)</em>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.__init__">source code</a></span>
+ </td>
+ </tr></table>
+
+
+ <dl class="fields">
+ <dt>Overrides:
+ wx.lib.mixins.listctrl.ColumnSorterMixin.__init__
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<a name="GetSortImages"></a>
+<div>
+<table class="details" border="1" cellpadding="3"
+ cellspacing="0" width="100%" bgcolor="white">
+<tr><td>
+ <table width="100%" cellpadding="0" cellspacing="0" border="0">
+ <tr valign="top"><td>
+ <h3 class="epydoc"><span class="sig"><span class="sig-name">GetSortImages</span>(<span class="sig-arg">self</span>)</span>
+ </h3>
+ </td><td align="right" valign="top"
+ ><span class="codelink"><a href="silacvalidator-pysrc.html#PepListCtrlPanel.GetSortImages">source code</a></span>
+ </td>
+ </tr></table>
+
+ <p>Returns a tuple of image list indexesthe indexes in the image list for
+ an image to be put on the column header when sorting in descending
+ order.</p>
+ <dl class="fields">
+ <dt>Overrides:
+ wx.lib.mixins.listctrl.ColumnSorterMixin.GetSortImages
+ <dd><em class="note">(inherited documentation)</em></dd>
+ </dt>
+ </dl>
+</td></tr></table>
+</div>
+<br />
+<!-- ==================== NAVIGATION BAR ==================== -->
+<table class="navbar" border="0" width="100%" cellpadding="0"
+ bgcolor="#a0c0ff" cellspacing="0">
+ <tr valign="middle">
+
+ <!-- Tree link -->
+ <th> <a
+ href="module-tree.html">Trees</a> </th>
+
+ <!-- Index link -->
+ <th> <a
+ href="identifier-index.html">Indices</a> </th>
+
+ <!-- Help link -->
+ <th> <a
+ href="help.html">Help</a> </th>
+
+ <!-- Project homepage -->
+ <th class="navbar" align="right" width="100%">
+ <table border="0" cellpadding="0" cellspacing="0">
+ <tr><th class="navbar" align="center"
+ ><a class="navbar" target="_top" href="http://www.pasteur.fr/recherche/unites/Gim/Suppl_Lebreton08/lilams/lilamsdoc.html">Lilams docs</a></th>
+ </tr></table></th>
+ </tr>
+</table>
+<table border="0" cellpadding="0" cellspacing="0" width="100%%">
+ <tr>
+ <td align="left" class="footer">
+ Generated by Epydoc 3.0.1 on Tue Apr 29 19:05:23 2008
+ </td>
+ <td align="right" class="footer">
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+ >http://epydoc.sourceforge.net</a>
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+</html>
diff --git a/ipc-1.1/.DS_Store b/ipc-1.1/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..bec0df08827c376fd0d90aa5b319d3f6ac88d5c2
Binary files /dev/null and b/ipc-1.1/.DS_Store differ
diff --git a/ipc-1.1/ADDING_ELEMENTS b/ipc-1.1/ADDING_ELEMENTS
new file mode 100644
index 0000000000000000000000000000000000000000..7f02b75f09918a230551b139728de30e76a8d1ed
--- /dev/null
+++ b/ipc-1.1/ADDING_ELEMENTS
@@ -0,0 +1,23 @@
+I was too lazy to put in all known elements, but I made it
+easy to add the missing.
+
+Every time ipc is called it reads a file called elemente which
+contains for every element its chemical symbol its isotopes and
+their probabilities.
+
+The entries in the file have the following form:
+
+<chemical symbol>
+<mass 1st isotope> <probability of 1st isotope>
+ . .
+ . .
+ . .
+<mass last isotope > probability last isotpe>
+
+If an element you need is not present in this file you can
+add this element by adding an entry like shown above. Next time
+you start ipc the parser will recognize the added element with the
+<chemical symbol> you put in.
+
+The chemical symbol must start with an upper case letter.
+It is highly recommended to give the isotopes in ascending order.
diff --git a/ipc-1.1/AUTHORS b/ipc-1.1/AUTHORS
new file mode 100644
index 0000000000000000000000000000000000000000..81a9208d001e23755507f6faf11cfc19728f7d2d
--- /dev/null
+++ b/ipc-1.1/AUTHORS
@@ -0,0 +1,7 @@
+Dipl. chem. Dirk Nolting
+Inst. f. physikalische und Elektrochemie I
+Universit�tsstr. 1
+40225 D�sseldorf
+
+email: nolting@uni-duesseldorf.de
+
diff --git a/ipc-1.1/COPYING b/ipc-1.1/COPYING
new file mode 100644
index 0000000000000000000000000000000000000000..d60c31a97a544b53039088d14fe9114583c0efc3
--- /dev/null
+++ b/ipc-1.1/COPYING
@@ -0,0 +1,340 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of such a program, whether
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+you have. You must make sure that they, too, receive or can get the
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+rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
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+
+ Also, for each author's protection and ours, we want to make certain
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+
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+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
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+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three
+ years, to give any third party, for a charge no more than your
+ cost of physically performing source distribution, a complete
+ machine-readable copy of the corresponding source code, to be
+ distributed under the terms of Sections 1 and 2 above on a medium
+ customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer
+ to distribute corresponding source code. (This alternative is
+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable. However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+ 5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+ 6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+ 7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all. For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded. In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+ 9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
diff --git a/ipc-1.1/ChangeLog b/ipc-1.1/ChangeLog
new file mode 100644
index 0000000000000000000000000000000000000000..814a4b4979af3a7449bf7ce6ed7d03d77e33a67c
--- /dev/null
+++ b/ipc-1.1/ChangeLog
@@ -0,0 +1,4 @@
+- V 1.0: First public version
+- V 1.1: Added Elements P and Si
+ Added "Covered Intensity" Display for FastCalc
+ Fixed error in the sum formula of glutamic acid (thnx to Frederic)
\ No newline at end of file
diff --git a/ipc-1.1/INSTALL b/ipc-1.1/INSTALL
new file mode 100644
index 0000000000000000000000000000000000000000..4a039574e8b0fc9b29022d3c1b0c31d0f388487b
--- /dev/null
+++ b/ipc-1.1/INSTALL
@@ -0,0 +1,49 @@
+The easy way:
+-------------
+
+turn into root and place the sources into /usr/local/ipc-1.1
+
+$ cd ipc-1.1
+$ ./configure
+$ make all
+$ make install
+
+
+The not so easy way:
+--------------------
+
+When installing ipc there are two points to take care of:
+
+1: The file "elemente":
+----------------------
+
+ipc expects its sources to be placed in /usr/local/ipc-1.1 and this is
+where it exepects the file elemete too.
+
+When installing into an other directory you must give configure the
+directory via --prefix otherwise ipc won�t find this file and therefore not
+recognize any chemical symbol.
+After the installation all files may be removed except the file "elemente"
+
+So if you want ipc in your home directory you should do something like:
+
+$ cd ~
+$ tar -xzf ipc-1.1.tar.gz"
+$ cd ipc-1.1
+$ ./configure --prefix=/home/<your_username>
+$ make
+
+This will produce an executable ipc in the directory
+/home/<username>/ipc-1.1 which will need the file
+/home/<your_username>/ipc-1.1/elemente
+in order to work.
+
+2: ipc and GNUPlot
+------------------
+
+ipc can produce output which is suitable for GNUPlot. When producing gnuplot
+output GNUPlot is also called to show the data.
+If you don�t like this or if gnuplot is not available on your system you
+can give configure --enable-NO_GNUPLOT
+The -g optin will still work but ipc will not try to call GNUPLot afterwards.
+Try ./configure --help for details on configure
\ No newline at end of file
diff --git a/ipc-1.1/Makefile b/ipc-1.1/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..12849541710539fa7bf7b9d4a647f3f5414b9bf4
--- /dev/null
+++ b/ipc-1.1/Makefile
@@ -0,0 +1,357 @@
+# Generated automatically from Makefile.in by configure.
+# Makefile.in generated automatically by automake 1.4 from Makefile.am
+
+# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+SHELL = /bin/sh
+
+srcdir = .
+top_srcdir = .
+prefix = /Volumes/Moomoo/Cosmin/Programmation/
+exec_prefix = ${prefix}
+
+bindir = ${exec_prefix}/bin
+sbindir = ${exec_prefix}/sbin
+libexecdir = ${exec_prefix}/libexec
+datadir = ${prefix}/share
+sysconfdir = ${prefix}/etc
+sharedstatedir = ${prefix}/com
+localstatedir = ${prefix}/var
+libdir = ${exec_prefix}/lib
+infodir = ${prefix}/info
+mandir = ${prefix}/man
+includedir = ${prefix}/include
+oldincludedir = /usr/include
+
+DESTDIR =
+
+pkgdatadir = $(datadir)/ipc
+pkglibdir = $(libdir)/ipc
+pkgincludedir = $(includedir)/ipc
+
+top_builddir = .
+
+ACLOCAL = aclocal
+AUTOCONF = autoconf
+AUTOMAKE = automake
+AUTOHEADER = autoheader
+
+INSTALL = /usr/bin/install -c
+INSTALL_PROGRAM = ${INSTALL} $(AM_INSTALL_PROGRAM_FLAGS)
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_SCRIPT = ${INSTALL_PROGRAM}
+transform = s,x,x,
+
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+CC = gcc
+LN_S = ln -s
+MAKEINFO = makeinfo
+PACKAGE = ipc
+VERSION = 1.1
+
+bin_PROGRAMS = ipc
+ipc_SOURCES = ipc.c element.c pars.c gp_out.c element.h gp_out.h ipc.h global.h pars.h
+
+DEFS = -DHAVE_CONFIG_H -I. -I$(srcdir) -I. -DPREFIX=\"$(prefix)/$(distdir)\"
+
+EXTRA_DIST = elemente ADDING_ELEMENTS
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = config.h
+CONFIG_CLEAN_FILES =
+PROGRAMS = $(bin_PROGRAMS)
+
+CPPFLAGS =
+LDFLAGS =
+LIBS = -lm
+ipc_OBJECTS = ipc.o element.o pars.o gp_out.o
+ipc_LDADD = $(LDADD)
+ipc_DEPENDENCIES =
+ipc_LDFLAGS =
+CFLAGS = -g -O2
+COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
+DIST_COMMON = README ./stamp-h.in AUTHORS COPYING ChangeLog INSTALL \
+Makefile.am Makefile.in NEWS acconfig.h aclocal.m4 config.h.in \
+configure configure.in install-sh missing mkinstalldirs
+
+
+DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
+
+TAR = tar
+GZIP_ENV = --best
+SOURCES = $(ipc_SOURCES)
+OBJECTS = $(ipc_OBJECTS)
+
+all: all-redirect
+.SUFFIXES:
+.SUFFIXES: .S .c .o .s
+$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
+ cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps Makefile
+
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ cd $(top_builddir) \
+ && CONFIG_FILES=$@ CONFIG_HEADERS= $(SHELL) ./config.status
+
+$(ACLOCAL_M4): configure.in
+ cd $(srcdir) && $(ACLOCAL)
+
+config.status: $(srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ $(SHELL) ./config.status --recheck
+$(srcdir)/configure: $(srcdir)/configure.in $(ACLOCAL_M4) $(CONFIGURE_DEPENDENCIES)
+ cd $(srcdir) && $(AUTOCONF)
+
+config.h: stamp-h
+ @if test ! -f $@; then \
+ rm -f stamp-h; \
+ $(MAKE) stamp-h; \
+ else :; fi
+stamp-h: $(srcdir)/config.h.in $(top_builddir)/config.status
+ cd $(top_builddir) \
+ && CONFIG_FILES= CONFIG_HEADERS=config.h \
+ $(SHELL) ./config.status
+ @echo timestamp > stamp-h 2> /dev/null
+$(srcdir)/config.h.in: $(srcdir)/stamp-h.in
+ @if test ! -f $@; then \
+ rm -f $(srcdir)/stamp-h.in; \
+ $(MAKE) $(srcdir)/stamp-h.in; \
+ else :; fi
+$(srcdir)/stamp-h.in: $(top_srcdir)/configure.in $(ACLOCAL_M4) acconfig.h
+ cd $(top_srcdir) && $(AUTOHEADER)
+ @echo timestamp > $(srcdir)/stamp-h.in 2> /dev/null
+
+mostlyclean-hdr:
+
+clean-hdr:
+
+distclean-hdr:
+ -rm -f config.h
+
+maintainer-clean-hdr:
+
+mostlyclean-binPROGRAMS:
+
+clean-binPROGRAMS:
+ -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
+distclean-binPROGRAMS:
+
+maintainer-clean-binPROGRAMS:
+
+install-binPROGRAMS: $(bin_PROGRAMS)
+ @$(NORMAL_INSTALL)
+ $(mkinstalldirs) $(DESTDIR)$(bindir)
+ @list='$(bin_PROGRAMS)'; for p in $$list; do \
+ if test -f $$p; then \
+ echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
+ $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
+ else :; fi; \
+ done
+
+uninstall-binPROGRAMS:
+ @$(NORMAL_UNINSTALL)
+ list='$(bin_PROGRAMS)'; for p in $$list; do \
+ rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
+ done
+
+.c.o:
+ $(COMPILE) -c $<
+
+.s.o:
+ $(COMPILE) -c $<
+
+.S.o:
+ $(COMPILE) -c $<
+
+mostlyclean-compile:
+ -rm -f *.o core *.core
+
+clean-compile:
+
+distclean-compile:
+ -rm -f *.tab.c
+
+maintainer-clean-compile:
+
+ipc: $(ipc_OBJECTS) $(ipc_DEPENDENCIES)
+ @rm -f ipc
+ $(LINK) $(ipc_LDFLAGS) $(ipc_OBJECTS) $(ipc_LDADD) $(LIBS)
+
+tags: TAGS
+
+ID: $(HEADERS) $(SOURCES) $(LISP)
+ list='$(SOURCES) $(HEADERS)'; \
+ unique=`for i in $$list; do echo $$i; done | \
+ awk ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ here=`pwd` && cd $(srcdir) \
+ && mkid -f$$here/ID $$unique $(LISP)
+
+TAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS)'; \
+ unique=`for i in $$list; do echo $$i; done | \
+ awk ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ test -z "$(ETAGS_ARGS)config.h.in$$unique$(LISP)$$tags" \
+ || (cd $(srcdir) && etags $(ETAGS_ARGS) $$tags config.h.in $$unique $(LISP) -o $$here/TAGS)
+
+mostlyclean-tags:
+
+clean-tags:
+
+distclean-tags:
+ -rm -f TAGS ID
+
+maintainer-clean-tags:
+
+distdir = $(PACKAGE)-$(VERSION)
+top_distdir = $(distdir)
+
+# This target untars the dist file and tries a VPATH configuration. Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+ -rm -rf $(distdir)
+ GZIP=$(GZIP_ENV) $(TAR) zxf $(distdir).tar.gz
+ mkdir $(distdir)/=build
+ mkdir $(distdir)/=inst
+ dc_install_base=`cd $(distdir)/=inst && pwd`; \
+ cd $(distdir)/=build \
+ && ../configure --srcdir=.. --prefix=$$dc_install_base \
+ && $(MAKE) $(AM_MAKEFLAGS) \
+ && $(MAKE) $(AM_MAKEFLAGS) dvi \
+ && $(MAKE) $(AM_MAKEFLAGS) check \
+ && $(MAKE) $(AM_MAKEFLAGS) install \
+ && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+ && $(MAKE) $(AM_MAKEFLAGS) dist
+ -rm -rf $(distdir)
+ @banner="$(distdir).tar.gz is ready for distribution"; \
+ dashes=`echo "$$banner" | sed s/./=/g`; \
+ echo "$$dashes"; \
+ echo "$$banner"; \
+ echo "$$dashes"
+dist: distdir
+ -chmod -R a+r $(distdir)
+ GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+ -rm -rf $(distdir)
+dist-all: distdir
+ -chmod -R a+r $(distdir)
+ GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+ -rm -rf $(distdir)
+distdir: $(DISTFILES)
+ -rm -rf $(distdir)
+ mkdir $(distdir)
+ -chmod 777 $(distdir)
+ @for file in $(DISTFILES); do \
+ d=$(srcdir); \
+ if test -d $$d/$$file; then \
+ cp -pr $$d/$$file $(distdir)/$$file; \
+ else \
+ test -f $(distdir)/$$file \
+ || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
+ || cp -p $$d/$$file $(distdir)/$$file || :; \
+ fi; \
+ done
+element.o: element.c global.h config.h element.h
+gp_out.o: gp_out.c global.h config.h gp_out.h
+ipc.o: ipc.c global.h config.h ipc.h pars.h element.h gp_out.h
+pars.o: pars.c global.h config.h pars.h element.h
+
+info-am:
+info: info-am
+dvi-am:
+dvi: dvi-am
+check-am: all-am
+check: check-am
+installcheck-am:
+installcheck: installcheck-am
+all-recursive-am: config.h
+ $(MAKE) $(AM_MAKEFLAGS) all-recursive
+
+install-exec-am: install-binPROGRAMS
+install-exec: install-exec-am
+
+install-data-am:
+install-data: install-data-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+install: install-am
+uninstall-am: uninstall-binPROGRAMS
+uninstall: uninstall-am
+all-am: Makefile $(PROGRAMS) config.h
+all-redirect: all-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
+installdirs:
+ $(mkinstalldirs) $(DESTDIR)$(bindir)
+
+
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -rm -f Makefile $(CONFIG_CLEAN_FILES)
+ -rm -f config.cache config.log stamp-h stamp-h[0-9]*
+
+maintainer-clean-generic:
+mostlyclean-am: mostlyclean-hdr mostlyclean-binPROGRAMS \
+ mostlyclean-compile mostlyclean-tags \
+ mostlyclean-generic
+
+mostlyclean: mostlyclean-am
+
+clean-am: clean-hdr clean-binPROGRAMS clean-compile clean-tags \
+ clean-generic mostlyclean-am
+
+clean: clean-am
+
+distclean-am: distclean-hdr distclean-binPROGRAMS distclean-compile \
+ distclean-tags distclean-generic clean-am
+
+distclean: distclean-am
+ -rm -f config.status
+
+maintainer-clean-am: maintainer-clean-hdr maintainer-clean-binPROGRAMS \
+ maintainer-clean-compile maintainer-clean-tags \
+ maintainer-clean-generic distclean-am
+ @echo "This command is intended for maintainers to use;"
+ @echo "it deletes files that may require special tools to rebuild."
+
+maintainer-clean: maintainer-clean-am
+ -rm -f config.status
+
+.PHONY: mostlyclean-hdr distclean-hdr clean-hdr maintainer-clean-hdr \
+mostlyclean-binPROGRAMS distclean-binPROGRAMS clean-binPROGRAMS \
+maintainer-clean-binPROGRAMS uninstall-binPROGRAMS install-binPROGRAMS \
+mostlyclean-compile distclean-compile clean-compile \
+maintainer-clean-compile tags mostlyclean-tags distclean-tags \
+clean-tags maintainer-clean-tags distdir info-am info dvi-am dvi check \
+check-am installcheck-am installcheck all-recursive-am install-exec-am \
+install-exec install-data-am install-data install-am install \
+uninstall-am uninstall all-redirect all-am all installdirs \
+mostlyclean-generic distclean-generic clean-generic \
+maintainer-clean-generic clean mostlyclean distclean maintainer-clean
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/ipc-1.1/Makefile.am b/ipc-1.1/Makefile.am
new file mode 100644
index 0000000000000000000000000000000000000000..5f93b6e291cdcb660df6e5be05a33e3959d38bfa
--- /dev/null
+++ b/ipc-1.1/Makefile.am
@@ -0,0 +1,6 @@
+bin_PROGRAMS = ipc
+ipc_SOURCES = ipc.c element.c pars.c gp_out.c element.h gp_out.h ipc.h global.h pars.h
+
+DEFS = @DEFS@ -I. -I$(srcdir) -I. -DPREFIX=\"$(prefix)/$(distdir)\"
+
+EXTRA_DIST = elemente ADDING_ELEMENTS
\ No newline at end of file
diff --git a/ipc-1.1/Makefile.in b/ipc-1.1/Makefile.in
new file mode 100644
index 0000000000000000000000000000000000000000..76fde9c926c2b8722fabe54f8783eed67c85c9ff
--- /dev/null
+++ b/ipc-1.1/Makefile.in
@@ -0,0 +1,357 @@
+# Makefile.in generated automatically by automake 1.4 from Makefile.am
+
+# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+SHELL = @SHELL@
+
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+prefix = @prefix@
+exec_prefix = @exec_prefix@
+
+bindir = @bindir@
+sbindir = @sbindir@
+libexecdir = @libexecdir@
+datadir = @datadir@
+sysconfdir = @sysconfdir@
+sharedstatedir = @sharedstatedir@
+localstatedir = @localstatedir@
+libdir = @libdir@
+infodir = @infodir@
+mandir = @mandir@
+includedir = @includedir@
+oldincludedir = /usr/include
+
+DESTDIR =
+
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+
+top_builddir = .
+
+ACLOCAL = @ACLOCAL@
+AUTOCONF = @AUTOCONF@
+AUTOMAKE = @AUTOMAKE@
+AUTOHEADER = @AUTOHEADER@
+
+INSTALL = @INSTALL@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+transform = @program_transform_name@
+
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+CC = @CC@
+LN_S = @LN_S@
+MAKEINFO = @MAKEINFO@
+PACKAGE = @PACKAGE@
+VERSION = @VERSION@
+
+bin_PROGRAMS = ipc
+ipc_SOURCES = ipc.c element.c pars.c gp_out.c element.h gp_out.h ipc.h global.h pars.h
+
+DEFS = @DEFS@ -I. -I$(srcdir) -I. -DPREFIX=\"$(prefix)/$(distdir)\"
+
+EXTRA_DIST = elemente ADDING_ELEMENTS
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_HEADER = config.h
+CONFIG_CLEAN_FILES =
+PROGRAMS = $(bin_PROGRAMS)
+
+CPPFLAGS = @CPPFLAGS@
+LDFLAGS = @LDFLAGS@
+LIBS = @LIBS@
+ipc_OBJECTS = ipc.o element.o pars.o gp_out.o
+ipc_LDADD = $(LDADD)
+ipc_DEPENDENCIES =
+ipc_LDFLAGS =
+CFLAGS = @CFLAGS@
+COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
+DIST_COMMON = README ./stamp-h.in AUTHORS COPYING ChangeLog INSTALL \
+Makefile.am Makefile.in NEWS acconfig.h aclocal.m4 config.h.in \
+configure configure.in install-sh missing mkinstalldirs
+
+
+DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
+
+TAR = tar
+GZIP_ENV = --best
+SOURCES = $(ipc_SOURCES)
+OBJECTS = $(ipc_OBJECTS)
+
+all: all-redirect
+.SUFFIXES:
+.SUFFIXES: .S .c .o .s
+$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4)
+ cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps Makefile
+
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ cd $(top_builddir) \
+ && CONFIG_FILES=$@ CONFIG_HEADERS= $(SHELL) ./config.status
+
+$(ACLOCAL_M4): configure.in
+ cd $(srcdir) && $(ACLOCAL)
+
+config.status: $(srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+ $(SHELL) ./config.status --recheck
+$(srcdir)/configure: $(srcdir)/configure.in $(ACLOCAL_M4) $(CONFIGURE_DEPENDENCIES)
+ cd $(srcdir) && $(AUTOCONF)
+
+config.h: stamp-h
+ @if test ! -f $@; then \
+ rm -f stamp-h; \
+ $(MAKE) stamp-h; \
+ else :; fi
+stamp-h: $(srcdir)/config.h.in $(top_builddir)/config.status
+ cd $(top_builddir) \
+ && CONFIG_FILES= CONFIG_HEADERS=config.h \
+ $(SHELL) ./config.status
+ @echo timestamp > stamp-h 2> /dev/null
+$(srcdir)/config.h.in: $(srcdir)/stamp-h.in
+ @if test ! -f $@; then \
+ rm -f $(srcdir)/stamp-h.in; \
+ $(MAKE) $(srcdir)/stamp-h.in; \
+ else :; fi
+$(srcdir)/stamp-h.in: $(top_srcdir)/configure.in $(ACLOCAL_M4) acconfig.h
+ cd $(top_srcdir) && $(AUTOHEADER)
+ @echo timestamp > $(srcdir)/stamp-h.in 2> /dev/null
+
+mostlyclean-hdr:
+
+clean-hdr:
+
+distclean-hdr:
+ -rm -f config.h
+
+maintainer-clean-hdr:
+
+mostlyclean-binPROGRAMS:
+
+clean-binPROGRAMS:
+ -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+
+distclean-binPROGRAMS:
+
+maintainer-clean-binPROGRAMS:
+
+install-binPROGRAMS: $(bin_PROGRAMS)
+ @$(NORMAL_INSTALL)
+ $(mkinstalldirs) $(DESTDIR)$(bindir)
+ @list='$(bin_PROGRAMS)'; for p in $$list; do \
+ if test -f $$p; then \
+ echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
+ $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
+ else :; fi; \
+ done
+
+uninstall-binPROGRAMS:
+ @$(NORMAL_UNINSTALL)
+ list='$(bin_PROGRAMS)'; for p in $$list; do \
+ rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
+ done
+
+.c.o:
+ $(COMPILE) -c $<
+
+.s.o:
+ $(COMPILE) -c $<
+
+.S.o:
+ $(COMPILE) -c $<
+
+mostlyclean-compile:
+ -rm -f *.o core *.core
+
+clean-compile:
+
+distclean-compile:
+ -rm -f *.tab.c
+
+maintainer-clean-compile:
+
+ipc: $(ipc_OBJECTS) $(ipc_DEPENDENCIES)
+ @rm -f ipc
+ $(LINK) $(ipc_LDFLAGS) $(ipc_OBJECTS) $(ipc_LDADD) $(LIBS)
+
+tags: TAGS
+
+ID: $(HEADERS) $(SOURCES) $(LISP)
+ list='$(SOURCES) $(HEADERS)'; \
+ unique=`for i in $$list; do echo $$i; done | \
+ awk ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ here=`pwd` && cd $(srcdir) \
+ && mkid -f$$here/ID $$unique $(LISP)
+
+TAGS: $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) $(LISP)
+ tags=; \
+ here=`pwd`; \
+ list='$(SOURCES) $(HEADERS)'; \
+ unique=`for i in $$list; do echo $$i; done | \
+ awk ' { files[$$0] = 1; } \
+ END { for (i in files) print i; }'`; \
+ test -z "$(ETAGS_ARGS)config.h.in$$unique$(LISP)$$tags" \
+ || (cd $(srcdir) && etags $(ETAGS_ARGS) $$tags config.h.in $$unique $(LISP) -o $$here/TAGS)
+
+mostlyclean-tags:
+
+clean-tags:
+
+distclean-tags:
+ -rm -f TAGS ID
+
+maintainer-clean-tags:
+
+distdir = $(PACKAGE)-$(VERSION)
+top_distdir = $(distdir)
+
+# This target untars the dist file and tries a VPATH configuration. Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+ -rm -rf $(distdir)
+ GZIP=$(GZIP_ENV) $(TAR) zxf $(distdir).tar.gz
+ mkdir $(distdir)/=build
+ mkdir $(distdir)/=inst
+ dc_install_base=`cd $(distdir)/=inst && pwd`; \
+ cd $(distdir)/=build \
+ && ../configure --srcdir=.. --prefix=$$dc_install_base \
+ && $(MAKE) $(AM_MAKEFLAGS) \
+ && $(MAKE) $(AM_MAKEFLAGS) dvi \
+ && $(MAKE) $(AM_MAKEFLAGS) check \
+ && $(MAKE) $(AM_MAKEFLAGS) install \
+ && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+ && $(MAKE) $(AM_MAKEFLAGS) dist
+ -rm -rf $(distdir)
+ @banner="$(distdir).tar.gz is ready for distribution"; \
+ dashes=`echo "$$banner" | sed s/./=/g`; \
+ echo "$$dashes"; \
+ echo "$$banner"; \
+ echo "$$dashes"
+dist: distdir
+ -chmod -R a+r $(distdir)
+ GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+ -rm -rf $(distdir)
+dist-all: distdir
+ -chmod -R a+r $(distdir)
+ GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+ -rm -rf $(distdir)
+distdir: $(DISTFILES)
+ -rm -rf $(distdir)
+ mkdir $(distdir)
+ -chmod 777 $(distdir)
+ @for file in $(DISTFILES); do \
+ d=$(srcdir); \
+ if test -d $$d/$$file; then \
+ cp -pr $$d/$$file $(distdir)/$$file; \
+ else \
+ test -f $(distdir)/$$file \
+ || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
+ || cp -p $$d/$$file $(distdir)/$$file || :; \
+ fi; \
+ done
+element.o: element.c global.h config.h element.h
+gp_out.o: gp_out.c global.h config.h gp_out.h
+ipc.o: ipc.c global.h config.h ipc.h pars.h element.h gp_out.h
+pars.o: pars.c global.h config.h pars.h element.h
+
+info-am:
+info: info-am
+dvi-am:
+dvi: dvi-am
+check-am: all-am
+check: check-am
+installcheck-am:
+installcheck: installcheck-am
+all-recursive-am: config.h
+ $(MAKE) $(AM_MAKEFLAGS) all-recursive
+
+install-exec-am: install-binPROGRAMS
+install-exec: install-exec-am
+
+install-data-am:
+install-data: install-data-am
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+install: install-am
+uninstall-am: uninstall-binPROGRAMS
+uninstall: uninstall-am
+all-am: Makefile $(PROGRAMS) config.h
+all-redirect: all-am
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
+installdirs:
+ $(mkinstalldirs) $(DESTDIR)$(bindir)
+
+
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -rm -f Makefile $(CONFIG_CLEAN_FILES)
+ -rm -f config.cache config.log stamp-h stamp-h[0-9]*
+
+maintainer-clean-generic:
+mostlyclean-am: mostlyclean-hdr mostlyclean-binPROGRAMS \
+ mostlyclean-compile mostlyclean-tags \
+ mostlyclean-generic
+
+mostlyclean: mostlyclean-am
+
+clean-am: clean-hdr clean-binPROGRAMS clean-compile clean-tags \
+ clean-generic mostlyclean-am
+
+clean: clean-am
+
+distclean-am: distclean-hdr distclean-binPROGRAMS distclean-compile \
+ distclean-tags distclean-generic clean-am
+
+distclean: distclean-am
+ -rm -f config.status
+
+maintainer-clean-am: maintainer-clean-hdr maintainer-clean-binPROGRAMS \
+ maintainer-clean-compile maintainer-clean-tags \
+ maintainer-clean-generic distclean-am
+ @echo "This command is intended for maintainers to use;"
+ @echo "it deletes files that may require special tools to rebuild."
+
+maintainer-clean: maintainer-clean-am
+ -rm -f config.status
+
+.PHONY: mostlyclean-hdr distclean-hdr clean-hdr maintainer-clean-hdr \
+mostlyclean-binPROGRAMS distclean-binPROGRAMS clean-binPROGRAMS \
+maintainer-clean-binPROGRAMS uninstall-binPROGRAMS install-binPROGRAMS \
+mostlyclean-compile distclean-compile clean-compile \
+maintainer-clean-compile tags mostlyclean-tags distclean-tags \
+clean-tags maintainer-clean-tags distdir info-am info dvi-am dvi check \
+check-am installcheck-am installcheck all-recursive-am install-exec-am \
+install-exec install-data-am install-data install-am install \
+uninstall-am uninstall all-redirect all-am all installdirs \
+mostlyclean-generic distclean-generic clean-generic \
+maintainer-clean-generic clean mostlyclean distclean maintainer-clean
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/ipc-1.1/NEWS b/ipc-1.1/NEWS
new file mode 100644
index 0000000000000000000000000000000000000000..d90136ad413d27fca10cada8726c961dde17a5af
--- /dev/null
+++ b/ipc-1.1/NEWS
@@ -0,0 +1,2 @@
+no NEWS
+
\ No newline at end of file
diff --git a/ipc-1.1/README b/ipc-1.1/README
new file mode 100644
index 0000000000000000000000000000000000000000..f0188548e23d3f6fc879bb53f820dcda71c616ef
--- /dev/null
+++ b/ipc-1.1/README
@@ -0,0 +1,117 @@
+IPC Isotopic Pattern Generator
+
+What is IPC?
+------------
+IPC is a program that calculates the isotopic distribution
+of a given chemical formula. It gives the rel. intensities
+and the propability of the masses belonging to a molecule
+ion, fragment or whatever is represented by the given
+chemical formula. Furthernmore it can use GNUPlot to
+visualize the result. Only masses with a rel. Intensity
+bigger then 0.009% are shown. Additionaly ipc prints the
+overall number of peaks and the needed computation time.
+
+INVOKING IPC
+------------
+
+ipc understands two types of input: chemical sum formulas and
+peptide sequences given in one letter notation.
+
+-c <chemical formula> passes a chemical formula to the parser.
+ The parser is a very basic one so no brackets are understood.
+
+ example: ipc -c CCl4
+
+ This results in the isotopic distribution of Tetra.
+
+ Atoms given with -c are taken additional to those given with
+ -a or -p (see below). Until now the parser doesn�t understand all
+ element symbols. But adding new ones is simple, see file
+ ADDING_ELEMENTS for this.
+
+-a As I�m working on oligopeptides ipc accepts also peptides and
+ peptide sequences given in one letter notation. Peptides given
+ this way are additional to atoms given via -c
+
+ example: ipc -a GW
+
+ would give the distribution for the dipeptide Glycine-Tryptophane.
+ As -a and -c are cumulative, ipc -a GW -c H would give the distribution
+ for the protonated dipeptide Gly-Trp.
+
+
+
+OPTIONS
+-------
+
+-f <int> The -f option is a bit special. Normally ipc calculates the exact
+ distribution. As the possible permutations grow exponential with
+ the amount of atoms this is very time and memory consumpting.
+ The -f (fast) option is the only one which leads to an approximation
+ during the calculation of the peak masses.
+
+ -f tries to calculate only the first <int> permutations resulting from
+ each element. If <int> was choosen too small some rel. Int. might be
+ wrong or some of the more intensive peaks might be missing.
+ If <int> was choosen properly computation time is reduced dramatically
+ and the shown peaks are exact.
+
+ example for comparison : ipc -a GWW, ipc -a GWW -f 10, ipc -a GWW -f 100,
+ ipc -a GWW -f 1000
+
+ I propose to start with small <int> and increase the value until no
+ change is observed in the result.
+ When using -f the overall number of peaks is no longer shown, as it
+ would be <int>. Instead the sum of the probabilities of the computed
+ peaks is given in %.
+
+-g <name> This tells ipc to prepare GNUPlot output. ipc will create two
+ files: <name> and <name>.gnu in your pwd. The file <name> contains
+ data which can be plotted as standard x,y-graph. <name>.gnu contains
+ some commands for GNUPlot for displaying the data in the file <name>.
+ Per default ipc then calls gnuplot <name>.gnu to display the calculated
+ pattern.
+
+ If there are problems when trying to invoke GNUPlot automaticly
+ read INSTALL on details how to turn this off.
+
+-d <int> ipc calculates the masses of the peaks to the 5th place after the
+ decimal point and displays them with all decimal places.
+ With -d the result is rounded to the <int>th position after the decimal
+ point. Peaks which end up with the same mass are combined. This has no
+ influence on the calculation and changes only the way of displaying
+ the results.
+
+ example for comparison: ipc -a GW, ipc -a GW -d 1
+
+-z <int> This tells ipc to calculate a mass/charge (m/z) ratio which is used
+ in mass spectrometry. Thus you can give with -z the <int> charges on your
+ ion.
+
+ example: ipc -c SO4 -z 2
+
+ would show the m/z pattern of the double negativly charged molecule ion of
+ sulfate
+
+-p <name> ipc reads the peptide sequence given in the file <name>.
+ The file must only contain the peptide sequence and there must
+ be a terminating new line at the end of each line.
+ -p is cumumlative with -a and -c
+
+-s before printig the isotopic pattern print the sum formula. When
+ giving peptide sequences to ipc it might be informative what
+ sum formula is hidden behind it.
+
+ example: ipc -a GW -c H -s
+
+ would print the isotopic distribution of the protonated dipeptide
+ GW and the sum formula of the dipeptide
+
+-x prevents the calculation of the isotopic distribution. Useful when
+ you just want the sum formula of a large peptide.
+
+ example:ipc -a GW -c H -s -x
+
+ This would only print the sum formula of the protonated dipeptide GW
+
+-h shows a small help text
\ No newline at end of file
diff --git a/ipc-1.1/acconfig.h b/ipc-1.1/acconfig.h
new file mode 100644
index 0000000000000000000000000000000000000000..dc695f9e2bf6039aa505ccc1c6407f9726bfb66e
--- /dev/null
+++ b/ipc-1.1/acconfig.h
@@ -0,0 +1,2 @@
+/* Set when gnuplot should be run automaticaly */
+# define NOT_RUN_GNUPLOT 1
diff --git a/ipc-1.1/aclocal.m4 b/ipc-1.1/aclocal.m4
new file mode 100644
index 0000000000000000000000000000000000000000..bd4779c714aed5b2b454684c922ec5b3005012df
--- /dev/null
+++ b/ipc-1.1/aclocal.m4
@@ -0,0 +1,127 @@
+dnl aclocal.m4 generated automatically by aclocal 1.4
+
+dnl Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+dnl This file is free software; the Free Software Foundation
+dnl gives unlimited permission to copy and/or distribute it,
+dnl with or without modifications, as long as this notice is preserved.
+
+dnl This program is distributed in the hope that it will be useful,
+dnl but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+dnl even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+dnl PARTICULAR PURPOSE.
+
+# Like AC_CONFIG_HEADER, but automatically create stamp file.
+
+AC_DEFUN(AM_CONFIG_HEADER,
+[AC_PREREQ([2.12])
+AC_CONFIG_HEADER([$1])
+dnl When config.status generates a header, we must update the stamp-h file.
+dnl This file resides in the same directory as the config header
+dnl that is generated. We must strip everything past the first ":",
+dnl and everything past the last "/".
+AC_OUTPUT_COMMANDS(changequote(<<,>>)dnl
+ifelse(patsubst(<<$1>>, <<[^ ]>>, <<>>), <<>>,
+<<test -z "<<$>>CONFIG_HEADERS" || echo timestamp > patsubst(<<$1>>, <<^\([^:]*/\)?.*>>, <<\1>>)stamp-h<<>>dnl>>,
+<<am_indx=1
+for am_file in <<$1>>; do
+ case " <<$>>CONFIG_HEADERS " in
+ *" <<$>>am_file "*<<)>>
+ echo timestamp > `echo <<$>>am_file | sed -e 's%:.*%%' -e 's%[^/]*$%%'`stamp-h$am_indx
+ ;;
+ esac
+ am_indx=`expr "<<$>>am_indx" + 1`
+done<<>>dnl>>)
+changequote([,]))])
+
+# Do all the work for Automake. This macro actually does too much --
+# some checks are only needed if your package does certain things.
+# But this isn't really a big deal.
+
+# serial 1
+
+dnl Usage:
+dnl AM_INIT_AUTOMAKE(package,version, [no-define])
+
+AC_DEFUN(AM_INIT_AUTOMAKE,
+[AC_REQUIRE([AC_PROG_INSTALL])
+PACKAGE=[$1]
+AC_SUBST(PACKAGE)
+VERSION=[$2]
+AC_SUBST(VERSION)
+dnl test to see if srcdir already configured
+if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
+ AC_MSG_ERROR([source directory already configured; run "make distclean" there first])
+fi
+ifelse([$3],,
+AC_DEFINE_UNQUOTED(PACKAGE, "$PACKAGE", [Name of package])
+AC_DEFINE_UNQUOTED(VERSION, "$VERSION", [Version number of package]))
+AC_REQUIRE([AM_SANITY_CHECK])
+AC_REQUIRE([AC_ARG_PROGRAM])
+dnl FIXME This is truly gross.
+missing_dir=`cd $ac_aux_dir && pwd`
+AM_MISSING_PROG(ACLOCAL, aclocal, $missing_dir)
+AM_MISSING_PROG(AUTOCONF, autoconf, $missing_dir)
+AM_MISSING_PROG(AUTOMAKE, automake, $missing_dir)
+AM_MISSING_PROG(AUTOHEADER, autoheader, $missing_dir)
+AM_MISSING_PROG(MAKEINFO, makeinfo, $missing_dir)
+AC_REQUIRE([AC_PROG_MAKE_SET])])
+
+#
+# Check to make sure that the build environment is sane.
+#
+
+AC_DEFUN(AM_SANITY_CHECK,
+[AC_MSG_CHECKING([whether build environment is sane])
+# Just in case
+sleep 1
+echo timestamp > conftestfile
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt $srcdir/configure conftestfile 2> /dev/null`
+ if test "[$]*" = "X"; then
+ # -L didn't work.
+ set X `ls -t $srcdir/configure conftestfile`
+ fi
+ if test "[$]*" != "X $srcdir/configure conftestfile" \
+ && test "[$]*" != "X conftestfile $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ AC_MSG_ERROR([ls -t appears to fail. Make sure there is not a broken
+alias in your environment])
+ fi
+
+ test "[$]2" = conftestfile
+ )
+then
+ # Ok.
+ :
+else
+ AC_MSG_ERROR([newly created file is older than distributed files!
+Check your system clock])
+fi
+rm -f conftest*
+AC_MSG_RESULT(yes)])
+
+dnl AM_MISSING_PROG(NAME, PROGRAM, DIRECTORY)
+dnl The program must properly implement --version.
+AC_DEFUN(AM_MISSING_PROG,
+[AC_MSG_CHECKING(for working $2)
+# Run test in a subshell; some versions of sh will print an error if
+# an executable is not found, even if stderr is redirected.
+# Redirect stdin to placate older versions of autoconf. Sigh.
+if ($2 --version) < /dev/null > /dev/null 2>&1; then
+ $1=$2
+ AC_MSG_RESULT(found)
+else
+ $1="$3/missing $2"
+ AC_MSG_RESULT(missing)
+fi
+AC_SUBST($1)])
+
diff --git a/ipc-1.1/config.cache b/ipc-1.1/config.cache
new file mode 100644
index 0000000000000000000000000000000000000000..b612b1fde06896894f0cc9b257798703ae639e46
--- /dev/null
+++ b/ipc-1.1/config.cache
@@ -0,0 +1,36 @@
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs. It is not useful on other systems.
+# If it contains results you don't want to keep, you may remove or edit it.
+#
+# By default, configure uses ./config.cache as the cache file,
+# creating it if it does not exist already. You can give configure
+# the --cache-file=FILE option to use a different cache file; that is
+# what configure does when it calls configure scripts in
+# subdirectories, so they share the cache.
+# Giving --cache-file=/dev/null disables caching, for debugging configure.
+# config.status only pays attention to the cache file if you give it the
+# --recheck option to rerun configure.
+#
+ac_cv_func_getcwd=${ac_cv_func_getcwd=yes}
+ac_cv_func_signal=${ac_cv_func_signal=yes}
+ac_cv_func_strdup=${ac_cv_func_strdup=yes}
+ac_cv_func_strtol=${ac_cv_func_strtol=yes}
+ac_cv_func_system=${ac_cv_func_system=yes}
+ac_cv_func_time=${ac_cv_func_time=yes}
+ac_cv_header_math_h=${ac_cv_header_math_h=yes}
+ac_cv_header_signal_h=${ac_cv_header_signal_h=yes}
+ac_cv_header_stdc=${ac_cv_header_stdc=yes}
+ac_cv_header_time_h=${ac_cv_header_time_h=yes}
+ac_cv_header_unistd_h=${ac_cv_header_unistd_h=yes}
+ac_cv_lib_m_rint=${ac_cv_lib_m_rint=yes}
+ac_cv_path_install=${ac_cv_path_install='/usr/bin/install -c'}
+ac_cv_prog_CC=${ac_cv_prog_CC=gcc}
+ac_cv_prog_CPP=${ac_cv_prog_CPP='gcc -E -traditional-cpp'}
+ac_cv_prog_LN_S=${ac_cv_prog_LN_S='ln -s'}
+ac_cv_prog_cc_cross=${ac_cv_prog_cc_cross=no}
+ac_cv_prog_cc_g=${ac_cv_prog_cc_g=yes}
+ac_cv_prog_cc_works=${ac_cv_prog_cc_works=yes}
+ac_cv_prog_gcc=${ac_cv_prog_gcc=yes}
+ac_cv_prog_make_make_set=${ac_cv_prog_make_make_set=yes}
+ac_cv_type_signal=${ac_cv_type_signal=void}
diff --git a/ipc-1.1/config.h b/ipc-1.1/config.h
new file mode 100644
index 0000000000000000000000000000000000000000..bac2b40ade603c3df41fdce7d6a2f17afc32dbae
--- /dev/null
+++ b/ipc-1.1/config.h
@@ -0,0 +1,51 @@
+/* config.h. Generated automatically by configure. */
+/* config.h.in. Generated automatically from configure.in by autoheader. */
+
+/* Define as the return type of signal handlers (int or void). */
+#define RETSIGTYPE void
+
+/* Define if you have the ANSI C header files. */
+#define STDC_HEADERS 1
+
+/* Set when gnuplot should be run automaticaly */
+# define NOT_RUN_GNUPLOT 0
+
+/* Define if you have the getcwd function. */
+#define HAVE_GETCWD 1
+
+/* Define if you have the signal function. */
+#define HAVE_SIGNAL 1
+
+/* Define if you have the strdup function. */
+#define HAVE_STRDUP 1
+
+/* Define if you have the strtol function. */
+#define HAVE_STRTOL 1
+
+/* Define if you have the system function. */
+#define HAVE_SYSTEM 1
+
+/* Define if you have the time function. */
+#define HAVE_TIME 1
+
+/* Define if you have the <math.h> header file. */
+#define HAVE_MATH_H 1
+
+/* Define if you have the <signal.h> header file. */
+#define HAVE_SIGNAL_H 1
+
+/* Define if you have the <time.h> header file. */
+#define HAVE_TIME_H 1
+
+/* Define if you have the <unistd.h> header file. */
+#define HAVE_UNISTD_H 1
+
+/* Define if you have the m library (-lm). */
+#define HAVE_LIBM 1
+
+/* Name of package */
+#define PACKAGE "ipc"
+
+/* Version number of package */
+#define VERSION "1.1"
+
diff --git a/ipc-1.1/config.h.in b/ipc-1.1/config.h.in
new file mode 100644
index 0000000000000000000000000000000000000000..7b3a117a14cfb4f3d55a18c4a6ec03fb3d887235
--- /dev/null
+++ b/ipc-1.1/config.h.in
@@ -0,0 +1,50 @@
+/* config.h.in. Generated automatically from configure.in by autoheader. */
+
+/* Define as the return type of signal handlers (int or void). */
+#undef RETSIGTYPE
+
+/* Define if you have the ANSI C header files. */
+#undef STDC_HEADERS
+
+/* Set when gnuplot should be run automaticaly */
+# define NOT_RUN_GNUPLOT 1
+
+/* Define if you have the getcwd function. */
+#undef HAVE_GETCWD
+
+/* Define if you have the signal function. */
+#undef HAVE_SIGNAL
+
+/* Define if you have the strdup function. */
+#undef HAVE_STRDUP
+
+/* Define if you have the strtol function. */
+#undef HAVE_STRTOL
+
+/* Define if you have the system function. */
+#undef HAVE_SYSTEM
+
+/* Define if you have the time function. */
+#undef HAVE_TIME
+
+/* Define if you have the <math.h> header file. */
+#undef HAVE_MATH_H
+
+/* Define if you have the <signal.h> header file. */
+#undef HAVE_SIGNAL_H
+
+/* Define if you have the <time.h> header file. */
+#undef HAVE_TIME_H
+
+/* Define if you have the <unistd.h> header file. */
+#undef HAVE_UNISTD_H
+
+/* Define if you have the m library (-lm). */
+#undef HAVE_LIBM
+
+/* Name of package */
+#undef PACKAGE
+
+/* Version number of package */
+#undef VERSION
+
diff --git a/ipc-1.1/config.log b/ipc-1.1/config.log
new file mode 100644
index 0000000000000000000000000000000000000000..8de71c5ba076b4d39c0f3099956e2930f7db2b2b
--- /dev/null
+++ b/ipc-1.1/config.log
@@ -0,0 +1,33 @@
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+configure:561: checking for a BSD compatible install
+configure:614: checking whether build environment is sane
+configure:671: checking whether make sets ${MAKE}
+configure:717: checking for working aclocal
+configure:730: checking for working autoconf
+configure:743: checking for working automake
+configure:756: checking for working autoheader
+configure:769: checking for working makeinfo
+configure:795: checking for a BSD compatible install
+configure:848: checking whether ln -s works
+configure:871: checking for gcc
+configure:984: checking whether the C compiler (gcc ) works
+configure:1000: gcc -o conftest conftest.c 1>&5
+configure:1026: checking whether the C compiler (gcc ) is a cross-compiler
+configure:1031: checking whether we are using GNU C
+configure:1059: checking whether gcc accepts -g
+configure:1092: checking for rint in -lm
+configure:1141: checking how to run the C preprocessor
+configure:1221: checking for ANSI C header files
+configure:1328: checking for math.h
+configure:1328: checking for time.h
+configure:1328: checking for signal.h
+configure:1328: checking for unistd.h
+configure:1367: checking return type of signal handlers
+configure:1410: checking for strdup
+configure:1410: checking for strtol
+configure:1410: checking for getcwd
+configure:1466: checking for system
+configure:1466: checking for signal
+configure:1466: checking for time
diff --git a/ipc-1.1/config.status b/ipc-1.1/config.status
new file mode 100644
index 0000000000000000000000000000000000000000..9fac7b1c1e00d60f126fe9d99340470b42c14648
--- /dev/null
+++ b/ipc-1.1/config.status
@@ -0,0 +1,305 @@
+#! /bin/sh
+# Generated automatically by configure.
+# Run this file to recreate the current configuration.
+# This directory was configured as follows,
+# on host moomoo.gim.pasteur.fr:
+#
+# ./configure --prefix=/Volumes/Moomoo/Cosmin/Programmation/
+#
+# Compiler output produced by configure, useful for debugging
+# configure, is in ./config.log if it exists.
+
+ac_cs_usage="Usage: ./config.status [--recheck] [--version] [--help]"
+for ac_option
+do
+ case "$ac_option" in
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ echo "running ${CONFIG_SHELL-/bin/sh} ./configure --prefix=/Volumes/Moomoo/Cosmin/Programmation/ --no-create --no-recursion"
+ exec ${CONFIG_SHELL-/bin/sh} ./configure --prefix=/Volumes/Moomoo/Cosmin/Programmation/ --no-create --no-recursion ;;
+ -version | --version | --versio | --versi | --vers | --ver | --ve | --v)
+ echo "./config.status generated by autoconf version 2.13"
+ exit 0 ;;
+ -help | --help | --hel | --he | --h)
+ echo "$ac_cs_usage"; exit 0 ;;
+ *) echo "$ac_cs_usage"; exit 1 ;;
+ esac
+done
+
+ac_given_srcdir=.
+ac_given_INSTALL="/usr/bin/install -c"
+
+trap 'rm -fr Makefile config.h conftest*; exit 1' 1 2 15
+
+# Protect against being on the right side of a sed subst in config.status.
+sed 's/%@/@@/; s/@%/@@/; s/%g$/@g/; /@g$/s/[\\&%]/\\&/g;
+ s/@@/%@/; s/@@/@%/; s/@g$/%g/' > conftest.subs <<\CEOF
+/^[ ]*VPATH[ ]*=[^:]*$/d
+
+s%@SHELL@%/bin/sh%g
+s%@CFLAGS@%-g -O2%g
+s%@CPPFLAGS@%%g
+s%@CXXFLAGS@%%g
+s%@FFLAGS@%%g
+s%@DEFS@%-DHAVE_CONFIG_H%g
+s%@LDFLAGS@%%g
+s%@LIBS@%-lm %g
+s%@exec_prefix@%${prefix}%g
+s%@prefix@%/Volumes/Moomoo/Cosmin/Programmation/%g
+s%@program_transform_name@%s,x,x,%g
+s%@bindir@%${exec_prefix}/bin%g
+s%@sbindir@%${exec_prefix}/sbin%g
+s%@libexecdir@%${exec_prefix}/libexec%g
+s%@datadir@%${prefix}/share%g
+s%@sysconfdir@%${prefix}/etc%g
+s%@sharedstatedir@%${prefix}/com%g
+s%@localstatedir@%${prefix}/var%g
+s%@libdir@%${exec_prefix}/lib%g
+s%@includedir@%${prefix}/include%g
+s%@oldincludedir@%/usr/include%g
+s%@infodir@%${prefix}/info%g
+s%@mandir@%${prefix}/man%g
+s%@INSTALL_PROGRAM@%${INSTALL}%g
+s%@INSTALL_SCRIPT@%${INSTALL_PROGRAM}%g
+s%@INSTALL_DATA@%${INSTALL} -m 644%g
+s%@PACKAGE@%ipc%g
+s%@VERSION@%1.1%g
+s%@ACLOCAL@%aclocal%g
+s%@AUTOCONF@%autoconf%g
+s%@AUTOMAKE@%automake%g
+s%@AUTOHEADER@%autoheader%g
+s%@MAKEINFO@%makeinfo%g
+s%@SET_MAKE@%%g
+s%@LN_S@%ln -s%g
+s%@CC@%gcc%g
+s%@CPP@%gcc -E -traditional-cpp%g
+
+CEOF
+
+# Split the substitutions into bite-sized pieces for seds with
+# small command number limits, like on Digital OSF/1 and HP-UX.
+ac_max_sed_cmds=90 # Maximum number of lines to put in a sed script.
+ac_file=1 # Number of current file.
+ac_beg=1 # First line for current file.
+ac_end=$ac_max_sed_cmds # Line after last line for current file.
+ac_more_lines=:
+ac_sed_cmds=""
+while $ac_more_lines; do
+ if test $ac_beg -gt 1; then
+ sed "1,${ac_beg}d; ${ac_end}q" conftest.subs > conftest.s$ac_file
+ else
+ sed "${ac_end}q" conftest.subs > conftest.s$ac_file
+ fi
+ if test ! -s conftest.s$ac_file; then
+ ac_more_lines=false
+ rm -f conftest.s$ac_file
+ else
+ if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds="sed -f conftest.s$ac_file"
+ else
+ ac_sed_cmds="$ac_sed_cmds | sed -f conftest.s$ac_file"
+ fi
+ ac_file=`expr $ac_file + 1`
+ ac_beg=$ac_end
+ ac_end=`expr $ac_end + $ac_max_sed_cmds`
+ fi
+done
+if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds=cat
+fi
+
+CONFIG_FILES=${CONFIG_FILES-"Makefile"}
+for ac_file in .. $CONFIG_FILES; do if test "x$ac_file" != x..; then
+ # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+ case "$ac_file" in
+ *:*) ac_file_in=`echo "$ac_file"|sed 's%[^:]*:%%'`
+ ac_file=`echo "$ac_file"|sed 's%:.*%%'` ;;
+ *) ac_file_in="${ac_file}.in" ;;
+ esac
+
+ # Adjust a relative srcdir, top_srcdir, and INSTALL for subdirectories.
+
+ # Remove last slash and all that follows it. Not all systems have dirname.
+ ac_dir=`echo $ac_file|sed 's%/[^/][^/]*$%%'`
+ if test "$ac_dir" != "$ac_file" && test "$ac_dir" != .; then
+ # The file is in a subdirectory.
+ test ! -d "$ac_dir" && mkdir "$ac_dir"
+ ac_dir_suffix="/`echo $ac_dir|sed 's%^\./%%'`"
+ # A "../" for each directory in $ac_dir_suffix.
+ ac_dots=`echo $ac_dir_suffix|sed 's%/[^/]*%../%g'`
+ else
+ ac_dir_suffix= ac_dots=
+ fi
+
+ case "$ac_given_srcdir" in
+ .) srcdir=.
+ if test -z "$ac_dots"; then top_srcdir=.
+ else top_srcdir=`echo $ac_dots|sed 's%/$%%'`; fi ;;
+ /*) srcdir="$ac_given_srcdir$ac_dir_suffix"; top_srcdir="$ac_given_srcdir" ;;
+ *) # Relative path.
+ srcdir="$ac_dots$ac_given_srcdir$ac_dir_suffix"
+ top_srcdir="$ac_dots$ac_given_srcdir" ;;
+ esac
+
+ case "$ac_given_INSTALL" in
+ [/$]*) INSTALL="$ac_given_INSTALL" ;;
+ *) INSTALL="$ac_dots$ac_given_INSTALL" ;;
+ esac
+
+ echo creating "$ac_file"
+ rm -f "$ac_file"
+ configure_input="Generated automatically from `echo $ac_file_in|sed 's%.*/%%'` by configure."
+ case "$ac_file" in
+ *Makefile*) ac_comsub="1i\\
+# $configure_input" ;;
+ *) ac_comsub= ;;
+ esac
+
+ ac_file_inputs=`echo $ac_file_in|sed -e "s%^%$ac_given_srcdir/%" -e "s%:% $ac_given_srcdir/%g"`
+ sed -e "$ac_comsub
+s%@configure_input@%$configure_input%g
+s%@srcdir@%$srcdir%g
+s%@top_srcdir@%$top_srcdir%g
+s%@INSTALL@%$INSTALL%g
+" $ac_file_inputs | (eval "$ac_sed_cmds") > $ac_file
+fi; done
+rm -f conftest.s*
+
+# These sed commands are passed to sed as "A NAME B NAME C VALUE D", where
+# NAME is the cpp macro being defined and VALUE is the value it is being given.
+#
+# ac_d sets the value in "#define NAME VALUE" lines.
+ac_dA='s%^\([ ]*\)#\([ ]*define[ ][ ]*\)'
+ac_dB='\([ ][ ]*\)[^ ]*%\1#\2'
+ac_dC='\3'
+ac_dD='%g'
+# ac_u turns "#undef NAME" with trailing blanks into "#define NAME VALUE".
+ac_uA='s%^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)'
+ac_uB='\([ ]\)%\1#\2define\3'
+ac_uC=' '
+ac_uD='\4%g'
+# ac_e turns "#undef NAME" without trailing blanks into "#define NAME VALUE".
+ac_eA='s%^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)'
+ac_eB='$%\1#\2define\3'
+ac_eC=' '
+ac_eD='%g'
+
+if test "${CONFIG_HEADERS+set}" != set; then
+ CONFIG_HEADERS="config.h"
+fi
+for ac_file in .. $CONFIG_HEADERS; do if test "x$ac_file" != x..; then
+ # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+ case "$ac_file" in
+ *:*) ac_file_in=`echo "$ac_file"|sed 's%[^:]*:%%'`
+ ac_file=`echo "$ac_file"|sed 's%:.*%%'` ;;
+ *) ac_file_in="${ac_file}.in" ;;
+ esac
+
+ echo creating $ac_file
+
+ rm -f conftest.frag conftest.in conftest.out
+ ac_file_inputs=`echo $ac_file_in|sed -e "s%^%$ac_given_srcdir/%" -e "s%:% $ac_given_srcdir/%g"`
+ cat $ac_file_inputs > conftest.in
+
+ cat > conftest.frag <<CEOF
+${ac_dA}PACKAGE${ac_dB}PACKAGE${ac_dC}"ipc"${ac_dD}
+${ac_uA}PACKAGE${ac_uB}PACKAGE${ac_uC}"ipc"${ac_uD}
+${ac_eA}PACKAGE${ac_eB}PACKAGE${ac_eC}"ipc"${ac_eD}
+${ac_dA}VERSION${ac_dB}VERSION${ac_dC}"1.1"${ac_dD}
+${ac_uA}VERSION${ac_uB}VERSION${ac_uC}"1.1"${ac_uD}
+${ac_eA}VERSION${ac_eB}VERSION${ac_eC}"1.1"${ac_eD}
+${ac_dA}HAVE_LIBM${ac_dB}HAVE_LIBM${ac_dC}1${ac_dD}
+${ac_uA}HAVE_LIBM${ac_uB}HAVE_LIBM${ac_uC}1${ac_uD}
+${ac_eA}HAVE_LIBM${ac_eB}HAVE_LIBM${ac_eC}1${ac_eD}
+${ac_dA}STDC_HEADERS${ac_dB}STDC_HEADERS${ac_dC}1${ac_dD}
+${ac_uA}STDC_HEADERS${ac_uB}STDC_HEADERS${ac_uC}1${ac_uD}
+${ac_eA}STDC_HEADERS${ac_eB}STDC_HEADERS${ac_eC}1${ac_eD}
+CEOF
+ sed -f conftest.frag conftest.in > conftest.out
+ rm -f conftest.in
+ mv conftest.out conftest.in
+
+ cat > conftest.frag <<CEOF
+${ac_dA}HAVE_MATH_H${ac_dB}HAVE_MATH_H${ac_dC}1${ac_dD}
+${ac_uA}HAVE_MATH_H${ac_uB}HAVE_MATH_H${ac_uC}1${ac_uD}
+${ac_eA}HAVE_MATH_H${ac_eB}HAVE_MATH_H${ac_eC}1${ac_eD}
+${ac_dA}HAVE_TIME_H${ac_dB}HAVE_TIME_H${ac_dC}1${ac_dD}
+${ac_uA}HAVE_TIME_H${ac_uB}HAVE_TIME_H${ac_uC}1${ac_uD}
+${ac_eA}HAVE_TIME_H${ac_eB}HAVE_TIME_H${ac_eC}1${ac_eD}
+${ac_dA}HAVE_SIGNAL_H${ac_dB}HAVE_SIGNAL_H${ac_dC}1${ac_dD}
+${ac_uA}HAVE_SIGNAL_H${ac_uB}HAVE_SIGNAL_H${ac_uC}1${ac_uD}
+${ac_eA}HAVE_SIGNAL_H${ac_eB}HAVE_SIGNAL_H${ac_eC}1${ac_eD}
+${ac_dA}HAVE_UNISTD_H${ac_dB}HAVE_UNISTD_H${ac_dC}1${ac_dD}
+${ac_uA}HAVE_UNISTD_H${ac_uB}HAVE_UNISTD_H${ac_uC}1${ac_uD}
+${ac_eA}HAVE_UNISTD_H${ac_eB}HAVE_UNISTD_H${ac_eC}1${ac_eD}
+CEOF
+ sed -f conftest.frag conftest.in > conftest.out
+ rm -f conftest.in
+ mv conftest.out conftest.in
+
+ cat > conftest.frag <<CEOF
+${ac_dA}RETSIGTYPE${ac_dB}RETSIGTYPE${ac_dC}void${ac_dD}
+${ac_uA}RETSIGTYPE${ac_uB}RETSIGTYPE${ac_uC}void${ac_uD}
+${ac_eA}RETSIGTYPE${ac_eB}RETSIGTYPE${ac_eC}void${ac_eD}
+${ac_dA}HAVE_STRDUP${ac_dB}HAVE_STRDUP${ac_dC}1${ac_dD}
+${ac_uA}HAVE_STRDUP${ac_uB}HAVE_STRDUP${ac_uC}1${ac_uD}
+${ac_eA}HAVE_STRDUP${ac_eB}HAVE_STRDUP${ac_eC}1${ac_eD}
+${ac_dA}HAVE_STRTOL${ac_dB}HAVE_STRTOL${ac_dC}1${ac_dD}
+${ac_uA}HAVE_STRTOL${ac_uB}HAVE_STRTOL${ac_uC}1${ac_uD}
+${ac_eA}HAVE_STRTOL${ac_eB}HAVE_STRTOL${ac_eC}1${ac_eD}
+${ac_dA}HAVE_GETCWD${ac_dB}HAVE_GETCWD${ac_dC}1${ac_dD}
+${ac_uA}HAVE_GETCWD${ac_uB}HAVE_GETCWD${ac_uC}1${ac_uD}
+${ac_eA}HAVE_GETCWD${ac_eB}HAVE_GETCWD${ac_eC}1${ac_eD}
+CEOF
+ sed -f conftest.frag conftest.in > conftest.out
+ rm -f conftest.in
+ mv conftest.out conftest.in
+
+ cat > conftest.frag <<CEOF
+${ac_dA}HAVE_SYSTEM${ac_dB}HAVE_SYSTEM${ac_dC}1${ac_dD}
+${ac_uA}HAVE_SYSTEM${ac_uB}HAVE_SYSTEM${ac_uC}1${ac_uD}
+${ac_eA}HAVE_SYSTEM${ac_eB}HAVE_SYSTEM${ac_eC}1${ac_eD}
+${ac_dA}HAVE_SIGNAL${ac_dB}HAVE_SIGNAL${ac_dC}1${ac_dD}
+${ac_uA}HAVE_SIGNAL${ac_uB}HAVE_SIGNAL${ac_uC}1${ac_uD}
+${ac_eA}HAVE_SIGNAL${ac_eB}HAVE_SIGNAL${ac_eC}1${ac_eD}
+${ac_dA}HAVE_TIME${ac_dB}HAVE_TIME${ac_dC}1${ac_dD}
+${ac_uA}HAVE_TIME${ac_uB}HAVE_TIME${ac_uC}1${ac_uD}
+${ac_eA}HAVE_TIME${ac_eB}HAVE_TIME${ac_eC}1${ac_eD}
+${ac_dA}NOT_RUN_GNUPLOT${ac_dB}NOT_RUN_GNUPLOT${ac_dC}0${ac_dD}
+${ac_uA}NOT_RUN_GNUPLOT${ac_uB}NOT_RUN_GNUPLOT${ac_uC}0${ac_uD}
+${ac_eA}NOT_RUN_GNUPLOT${ac_eB}NOT_RUN_GNUPLOT${ac_eC}0${ac_eD}
+CEOF
+ sed -f conftest.frag conftest.in > conftest.out
+ rm -f conftest.in
+ mv conftest.out conftest.in
+
+ cat > conftest.frag <<CEOF
+s%^[ ]*#[ ]*undef[ ][ ]*[a-zA-Z_][a-zA-Z_0-9]*%/* & */%
+CEOF
+ sed -f conftest.frag conftest.in > conftest.out
+ rm -f conftest.in
+ mv conftest.out conftest.in
+
+ rm -f conftest.frag conftest.h
+ echo "/* $ac_file. Generated automatically by configure. */" > conftest.h
+ cat conftest.in >> conftest.h
+ rm -f conftest.in
+ if cmp -s $ac_file conftest.h 2>/dev/null; then
+ echo "$ac_file is unchanged"
+ rm -f conftest.h
+ else
+ # Remove last slash and all that follows it. Not all systems have dirname.
+ ac_dir=`echo $ac_file|sed 's%/[^/][^/]*$%%'`
+ if test "$ac_dir" != "$ac_file" && test "$ac_dir" != .; then
+ # The file is in a subdirectory.
+ test ! -d "$ac_dir" && mkdir "$ac_dir"
+ fi
+ rm -f $ac_file
+ mv conftest.h $ac_file
+ fi
+fi; done
+
+
+
+test -z "$CONFIG_HEADERS" || echo timestamp > stamp-h
+
+exit 0
diff --git a/ipc-1.1/configure b/ipc-1.1/configure
new file mode 100644
index 0000000000000000000000000000000000000000..9c261ac3376204eaee5e387b8d7e07ad59b8de78
--- /dev/null
+++ b/ipc-1.1/configure
@@ -0,0 +1,1901 @@
+#! /bin/sh
+
+# Guess values for system-dependent variables and create Makefiles.
+# Generated automatically using autoconf version 2.13
+# Copyright (C) 1992, 93, 94, 95, 96 Free Software Foundation, Inc.
+#
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+
+# Defaults:
+ac_help=
+ac_default_prefix=/usr/local
+# Any additions from configure.in:
+ac_help="$ac_help
+NO_GNUPLOT : IPC should not run GNU Plot when invoking -g option"
+
+# Initialize some variables set by options.
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+build=NONE
+cache_file=./config.cache
+exec_prefix=NONE
+host=NONE
+no_create=
+nonopt=NONE
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+target=NONE
+verbose=
+x_includes=NONE
+x_libraries=NONE
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datadir='${prefix}/share'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+libdir='${exec_prefix}/lib'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+infodir='${prefix}/info'
+mandir='${prefix}/man'
+
+# Initialize some other variables.
+subdirs=
+MFLAGS= MAKEFLAGS=
+SHELL=${CONFIG_SHELL-/bin/sh}
+# Maximum number of lines to put in a shell here document.
+ac_max_here_lines=12
+
+ac_prev=
+for ac_option
+do
+
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval "$ac_prev=\$ac_option"
+ ac_prev=
+ continue
+ fi
+
+ case "$ac_option" in
+ -*=*) ac_optarg=`echo "$ac_option" | sed 's/[-_a-zA-Z0-9]*=//'` ;;
+ *) ac_optarg= ;;
+ esac
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case "$ac_option" in
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir="$ac_optarg" ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build="$ac_optarg" ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file="$ac_optarg" ;;
+
+ -datadir | --datadir | --datadi | --datad | --data | --dat | --da)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=* | --data=* | --dat=* \
+ | --da=*)
+ datadir="$ac_optarg" ;;
+
+ -disable-* | --disable-*)
+ ac_feature=`echo $ac_option|sed -e 's/-*disable-//'`
+ # Reject names that are not valid shell variable names.
+ if test -n "`echo $ac_feature| sed 's/[-a-zA-Z0-9_]//g'`"; then
+ { echo "configure: error: $ac_feature: invalid feature name" 1>&2; exit 1; }
+ fi
+ ac_feature=`echo $ac_feature| sed 's/-/_/g'`
+ eval "enable_${ac_feature}=no" ;;
+
+ -enable-* | --enable-*)
+ ac_feature=`echo $ac_option|sed -e 's/-*enable-//' -e 's/=.*//'`
+ # Reject names that are not valid shell variable names.
+ if test -n "`echo $ac_feature| sed 's/[-_a-zA-Z0-9]//g'`"; then
+ { echo "configure: error: $ac_feature: invalid feature name" 1>&2; exit 1; }
+ fi
+ ac_feature=`echo $ac_feature| sed 's/-/_/g'`
+ case "$ac_option" in
+ *=*) ;;
+ *) ac_optarg=yes ;;
+ esac
+ eval "enable_${ac_feature}='$ac_optarg'" ;;
+
+ -exec-prefix | --exec_prefix | --exec-prefix | --exec-prefi \
+ | --exec-pref | --exec-pre | --exec-pr | --exec-p | --exec- \
+ | --exec | --exe | --ex)
+ ac_prev=exec_prefix ;;
+ -exec-prefix=* | --exec_prefix=* | --exec-prefix=* | --exec-prefi=* \
+ | --exec-pref=* | --exec-pre=* | --exec-pr=* | --exec-p=* | --exec-=* \
+ | --exec=* | --exe=* | --ex=*)
+ exec_prefix="$ac_optarg" ;;
+
+ -gas | --gas | --ga | --g)
+ # Obsolete; use --with-gas.
+ with_gas=yes ;;
+
+ -help | --help | --hel | --he)
+ # Omit some internal or obsolete options to make the list less imposing.
+ # This message is too long to be a string in the A/UX 3.1 sh.
+ cat << EOF
+Usage: configure [options] [host]
+Options: [defaults in brackets after descriptions]
+Configuration:
+ --cache-file=FILE cache test results in FILE
+ --help print this message
+ --no-create do not create output files
+ --quiet, --silent do not print \`checking...' messages
+ --version print the version of autoconf that created configure
+Directory and file names:
+ --prefix=PREFIX install architecture-independent files in PREFIX
+ [$ac_default_prefix]
+ --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
+ [same as prefix]
+ --bindir=DIR user executables in DIR [EPREFIX/bin]
+ --sbindir=DIR system admin executables in DIR [EPREFIX/sbin]
+ --libexecdir=DIR program executables in DIR [EPREFIX/libexec]
+ --datadir=DIR read-only architecture-independent data in DIR
+ [PREFIX/share]
+ --sysconfdir=DIR read-only single-machine data in DIR [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data in DIR
+ [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data in DIR [PREFIX/var]
+ --libdir=DIR object code libraries in DIR [EPREFIX/lib]
+ --includedir=DIR C header files in DIR [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc in DIR [/usr/include]
+ --infodir=DIR info documentation in DIR [PREFIX/info]
+ --mandir=DIR man documentation in DIR [PREFIX/man]
+ --srcdir=DIR find the sources in DIR [configure dir or ..]
+ --program-prefix=PREFIX prepend PREFIX to installed program names
+ --program-suffix=SUFFIX append SUFFIX to installed program names
+ --program-transform-name=PROGRAM
+ run sed PROGRAM on installed program names
+EOF
+ cat << EOF
+Host type:
+ --build=BUILD configure for building on BUILD [BUILD=HOST]
+ --host=HOST configure for HOST [guessed]
+ --target=TARGET configure for TARGET [TARGET=HOST]
+Features and packages:
+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
+ --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
+ --x-includes=DIR X include files are in DIR
+ --x-libraries=DIR X library files are in DIR
+EOF
+ if test -n "$ac_help"; then
+ echo "--enable and --with options recognized:$ac_help"
+ fi
+ exit 0 ;;
+
+ -host | --host | --hos | --ho)
+ ac_prev=host ;;
+ -host=* | --host=* | --hos=* | --ho=*)
+ host="$ac_optarg" ;;
+
+ -includedir | --includedir | --includedi | --included | --include \
+ | --includ | --inclu | --incl | --inc)
+ ac_prev=includedir ;;
+ -includedir=* | --includedir=* | --includedi=* | --included=* | --include=* \
+ | --includ=* | --inclu=* | --incl=* | --inc=*)
+ includedir="$ac_optarg" ;;
+
+ -infodir | --infodir | --infodi | --infod | --info | --inf)
+ ac_prev=infodir ;;
+ -infodir=* | --infodir=* | --infodi=* | --infod=* | --info=* | --inf=*)
+ infodir="$ac_optarg" ;;
+
+ -libdir | --libdir | --libdi | --libd)
+ ac_prev=libdir ;;
+ -libdir=* | --libdir=* | --libdi=* | --libd=*)
+ libdir="$ac_optarg" ;;
+
+ -libexecdir | --libexecdir | --libexecdi | --libexecd | --libexec \
+ | --libexe | --libex | --libe)
+ ac_prev=libexecdir ;;
+ -libexecdir=* | --libexecdir=* | --libexecdi=* | --libexecd=* | --libexec=* \
+ | --libexe=* | --libex=* | --libe=*)
+ libexecdir="$ac_optarg" ;;
+
+ -localstatedir | --localstatedir | --localstatedi | --localstated \
+ | --localstate | --localstat | --localsta | --localst \
+ | --locals | --local | --loca | --loc | --lo)
+ ac_prev=localstatedir ;;
+ -localstatedir=* | --localstatedir=* | --localstatedi=* | --localstated=* \
+ | --localstate=* | --localstat=* | --localsta=* | --localst=* \
+ | --locals=* | --local=* | --loca=* | --loc=* | --lo=*)
+ localstatedir="$ac_optarg" ;;
+
+ -mandir | --mandir | --mandi | --mand | --man | --ma | --m)
+ ac_prev=mandir ;;
+ -mandir=* | --mandir=* | --mandi=* | --mand=* | --man=* | --ma=* | --m=*)
+ mandir="$ac_optarg" ;;
+
+ -nfp | --nfp | --nf)
+ # Obsolete; use --without-fp.
+ with_fp=no ;;
+
+ -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+ | --no-cr | --no-c)
+ no_create=yes ;;
+
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r)
+ no_recursion=yes ;;
+
+ -oldincludedir | --oldincludedir | --oldincludedi | --oldincluded \
+ | --oldinclude | --oldinclud | --oldinclu | --oldincl | --oldinc \
+ | --oldin | --oldi | --old | --ol | --o)
+ ac_prev=oldincludedir ;;
+ -oldincludedir=* | --oldincludedir=* | --oldincludedi=* | --oldincluded=* \
+ | --oldinclude=* | --oldinclud=* | --oldinclu=* | --oldincl=* | --oldinc=* \
+ | --oldin=* | --oldi=* | --old=* | --ol=* | --o=*)
+ oldincludedir="$ac_optarg" ;;
+
+ -prefix | --prefix | --prefi | --pref | --pre | --pr | --p)
+ ac_prev=prefix ;;
+ -prefix=* | --prefix=* | --prefi=* | --pref=* | --pre=* | --pr=* | --p=*)
+ prefix="$ac_optarg" ;;
+
+ -program-prefix | --program-prefix | --program-prefi | --program-pref \
+ | --program-pre | --program-pr | --program-p)
+ ac_prev=program_prefix ;;
+ -program-prefix=* | --program-prefix=* | --program-prefi=* \
+ | --program-pref=* | --program-pre=* | --program-pr=* | --program-p=*)
+ program_prefix="$ac_optarg" ;;
+
+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
+ | --program-suf | --program-su | --program-s)
+ ac_prev=program_suffix ;;
+ -program-suffix=* | --program-suffix=* | --program-suffi=* \
+ | --program-suff=* | --program-suf=* | --program-su=* | --program-s=*)
+ program_suffix="$ac_optarg" ;;
+
+ -program-transform-name | --program-transform-name \
+ | --program-transform-nam | --program-transform-na \
+ | --program-transform-n | --program-transform- \
+ | --program-transform | --program-transfor \
+ | --program-transfo | --program-transf \
+ | --program-trans | --program-tran \
+ | --progr-tra | --program-tr | --program-t)
+ ac_prev=program_transform_name ;;
+ -program-transform-name=* | --program-transform-name=* \
+ | --program-transform-nam=* | --program-transform-na=* \
+ | --program-transform-n=* | --program-transform-=* \
+ | --program-transform=* | --program-transfor=* \
+ | --program-transfo=* | --program-transf=* \
+ | --program-trans=* | --program-tran=* \
+ | --progr-tra=* | --program-tr=* | --program-t=*)
+ program_transform_name="$ac_optarg" ;;
+
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ silent=yes ;;
+
+ -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
+ ac_prev=sbindir ;;
+ -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
+ | --sbi=* | --sb=*)
+ sbindir="$ac_optarg" ;;
+
+ -sharedstatedir | --sharedstatedir | --sharedstatedi \
+ | --sharedstated | --sharedstate | --sharedstat | --sharedsta \
+ | --sharedst | --shareds | --shared | --share | --shar \
+ | --sha | --sh)
+ ac_prev=sharedstatedir ;;
+ -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
+ | --sharedstated=* | --sharedstate=* | --sharedstat=* | --sharedsta=* \
+ | --sharedst=* | --shareds=* | --shared=* | --share=* | --shar=* \
+ | --sha=* | --sh=*)
+ sharedstatedir="$ac_optarg" ;;
+
+ -site | --site | --sit)
+ ac_prev=site ;;
+ -site=* | --site=* | --sit=*)
+ site="$ac_optarg" ;;
+
+ -srcdir | --srcdir | --srcdi | --srcd | --src | --sr)
+ ac_prev=srcdir ;;
+ -srcdir=* | --srcdir=* | --srcdi=* | --srcd=* | --src=* | --sr=*)
+ srcdir="$ac_optarg" ;;
+
+ -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
+ | --syscon | --sysco | --sysc | --sys | --sy)
+ ac_prev=sysconfdir ;;
+ -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
+ | --syscon=* | --sysco=* | --sysc=* | --sys=* | --sy=*)
+ sysconfdir="$ac_optarg" ;;
+
+ -target | --target | --targe | --targ | --tar | --ta | --t)
+ ac_prev=target ;;
+ -target=* | --target=* | --targe=* | --targ=* | --tar=* | --ta=* | --t=*)
+ target="$ac_optarg" ;;
+
+ -v | -verbose | --verbose | --verbos | --verbo | --verb)
+ verbose=yes ;;
+
+ -version | --version | --versio | --versi | --vers)
+ echo "configure generated by autoconf version 2.13"
+ exit 0 ;;
+
+ -with-* | --with-*)
+ ac_package=`echo $ac_option|sed -e 's/-*with-//' -e 's/=.*//'`
+ # Reject names that are not valid shell variable names.
+ if test -n "`echo $ac_package| sed 's/[-_a-zA-Z0-9]//g'`"; then
+ { echo "configure: error: $ac_package: invalid package name" 1>&2; exit 1; }
+ fi
+ ac_package=`echo $ac_package| sed 's/-/_/g'`
+ case "$ac_option" in
+ *=*) ;;
+ *) ac_optarg=yes ;;
+ esac
+ eval "with_${ac_package}='$ac_optarg'" ;;
+
+ -without-* | --without-*)
+ ac_package=`echo $ac_option|sed -e 's/-*without-//'`
+ # Reject names that are not valid shell variable names.
+ if test -n "`echo $ac_package| sed 's/[-a-zA-Z0-9_]//g'`"; then
+ { echo "configure: error: $ac_package: invalid package name" 1>&2; exit 1; }
+ fi
+ ac_package=`echo $ac_package| sed 's/-/_/g'`
+ eval "with_${ac_package}=no" ;;
+
+ --x)
+ # Obsolete; use --with-x.
+ with_x=yes ;;
+
+ -x-includes | --x-includes | --x-include | --x-includ | --x-inclu \
+ | --x-incl | --x-inc | --x-in | --x-i)
+ ac_prev=x_includes ;;
+ -x-includes=* | --x-includes=* | --x-include=* | --x-includ=* | --x-inclu=* \
+ | --x-incl=* | --x-inc=* | --x-in=* | --x-i=*)
+ x_includes="$ac_optarg" ;;
+
+ -x-libraries | --x-libraries | --x-librarie | --x-librari \
+ | --x-librar | --x-libra | --x-libr | --x-lib | --x-li | --x-l)
+ ac_prev=x_libraries ;;
+ -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
+ | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*)
+ x_libraries="$ac_optarg" ;;
+
+ -*) { echo "configure: error: $ac_option: invalid option; use --help to show usage" 1>&2; exit 1; }
+ ;;
+
+ *)
+ if test -n "`echo $ac_option| sed 's/[-a-z0-9.]//g'`"; then
+ echo "configure: warning: $ac_option: invalid host type" 1>&2
+ fi
+ if test "x$nonopt" != xNONE; then
+ { echo "configure: error: can only configure for one host and one target at a time" 1>&2; exit 1; }
+ fi
+ nonopt="$ac_option"
+ ;;
+
+ esac
+done
+
+if test -n "$ac_prev"; then
+ { echo "configure: error: missing argument to --`echo $ac_prev | sed 's/_/-/g'`" 1>&2; exit 1; }
+fi
+
+trap 'rm -fr conftest* confdefs* core core.* *.core $ac_clean_files; exit 1' 1 2 15
+
+# File descriptor usage:
+# 0 standard input
+# 1 file creation
+# 2 errors and warnings
+# 3 some systems may open it to /dev/tty
+# 4 used on the Kubota Titan
+# 6 checking for... messages and results
+# 5 compiler messages saved in config.log
+if test "$silent" = yes; then
+ exec 6>/dev/null
+else
+ exec 6>&1
+fi
+exec 5>./config.log
+
+echo "\
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+" 1>&5
+
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Also quote any args containing shell metacharacters.
+ac_configure_args=
+for ac_arg
+do
+ case "$ac_arg" in
+ -no-create | --no-create | --no-creat | --no-crea | --no-cre \
+ | --no-cr | --no-c) ;;
+ -no-recursion | --no-recursion | --no-recursio | --no-recursi \
+ | --no-recurs | --no-recur | --no-recu | --no-rec | --no-re | --no-r) ;;
+ *" "*|*" "*|*[\[\]\~\#\$\^\&\*\(\)\{\}\\\|\;\<\>\?]*)
+ ac_configure_args="$ac_configure_args '$ac_arg'" ;;
+ *) ac_configure_args="$ac_configure_args $ac_arg" ;;
+ esac
+done
+
+# NLS nuisances.
+# Only set these to C if already set. These must not be set unconditionally
+# because not all systems understand e.g. LANG=C (notably SCO).
+# Fixing LC_MESSAGES prevents Solaris sh from translating var values in `set'!
+# Non-C LC_CTYPE values break the ctype check.
+if test "${LANG+set}" = set; then LANG=C; export LANG; fi
+if test "${LC_ALL+set}" = set; then LC_ALL=C; export LC_ALL; fi
+if test "${LC_MESSAGES+set}" = set; then LC_MESSAGES=C; export LC_MESSAGES; fi
+if test "${LC_CTYPE+set}" = set; then LC_CTYPE=C; export LC_CTYPE; fi
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
+rm -rf conftest* confdefs.h
+# AIX cpp loses on an empty file, so make sure it contains at least a newline.
+echo > confdefs.h
+
+# A filename unique to this package, relative to the directory that
+# configure is in, which we can look for to find out if srcdir is correct.
+ac_unique_file=element.c
+
+# Find the source files, if location was not specified.
+if test -z "$srcdir"; then
+ ac_srcdir_defaulted=yes
+ # Try the directory containing this script, then its parent.
+ ac_prog=$0
+ ac_confdir=`echo $ac_prog|sed 's%/[^/][^/]*$%%'`
+ test "x$ac_confdir" = "x$ac_prog" && ac_confdir=.
+ srcdir=$ac_confdir
+ if test ! -r $srcdir/$ac_unique_file; then
+ srcdir=..
+ fi
+else
+ ac_srcdir_defaulted=no
+fi
+if test ! -r $srcdir/$ac_unique_file; then
+ if test "$ac_srcdir_defaulted" = yes; then
+ { echo "configure: error: can not find sources in $ac_confdir or .." 1>&2; exit 1; }
+ else
+ { echo "configure: error: can not find sources in $srcdir" 1>&2; exit 1; }
+ fi
+fi
+srcdir=`echo "${srcdir}" | sed 's%\([^/]\)/*$%\1%'`
+
+# Prefer explicitly selected file to automatically selected ones.
+if test -z "$CONFIG_SITE"; then
+ if test "x$prefix" != xNONE; then
+ CONFIG_SITE="$prefix/share/config.site $prefix/etc/config.site"
+ else
+ CONFIG_SITE="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site"
+ fi
+fi
+for ac_site_file in $CONFIG_SITE; do
+ if test -r "$ac_site_file"; then
+ echo "loading site script $ac_site_file"
+ . "$ac_site_file"
+ fi
+done
+
+if test -r "$cache_file"; then
+ echo "loading cache $cache_file"
+ . $cache_file
+else
+ echo "creating cache $cache_file"
+ > $cache_file
+fi
+
+ac_ext=c
+# CFLAGS is not in ac_cpp because -g, -O, etc. are not valid cpp options.
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='${CC-cc} -c $CFLAGS $CPPFLAGS conftest.$ac_ext 1>&5'
+ac_link='${CC-cc} -o conftest${ac_exeext} $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS 1>&5'
+cross_compiling=$ac_cv_prog_cc_cross
+
+ac_exeext=
+ac_objext=o
+if (echo "testing\c"; echo 1,2,3) | grep c >/dev/null; then
+ # Stardent Vistra SVR4 grep lacks -e, says ghazi@caip.rutgers.edu.
+ if (echo -n testing; echo 1,2,3) | sed s/-n/xn/ | grep xn >/dev/null; then
+ ac_n= ac_c='
+' ac_t=' '
+ else
+ ac_n=-n ac_c= ac_t=
+ fi
+else
+ ac_n= ac_c='\c' ac_t=
+fi
+
+
+
+
+
+ac_aux_dir=
+for ac_dir in $srcdir $srcdir/.. $srcdir/../..; do
+ if test -f $ac_dir/install-sh; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install-sh -c"
+ break
+ elif test -f $ac_dir/install.sh; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
+ break
+ fi
+done
+if test -z "$ac_aux_dir"; then
+ { echo "configure: error: can not find install-sh or install.sh in $srcdir $srcdir/.. $srcdir/../.." 1>&2; exit 1; }
+fi
+ac_config_guess=$ac_aux_dir/config.guess
+ac_config_sub=$ac_aux_dir/config.sub
+ac_configure=$ac_aux_dir/configure # This should be Cygnus configure.
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# ./install, which can be erroneously created by make from ./install.sh.
+echo $ac_n "checking for a BSD compatible install""... $ac_c" 1>&6
+echo "configure:561: checking for a BSD compatible install" >&5
+if test -z "$INSTALL"; then
+if eval "test \"`echo '$''{'ac_cv_path_install'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ IFS="${IFS= }"; ac_save_IFS="$IFS"; IFS=":"
+ for ac_dir in $PATH; do
+ # Account for people who put trailing slashes in PATH elements.
+ case "$ac_dir/" in
+ /|./|.//|/etc/*|/usr/sbin/*|/usr/etc/*|/sbin/*|/usr/afsws/bin/*|/usr/ucb/*) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ if test -f $ac_dir/$ac_prog; then
+ if test $ac_prog = install &&
+ grep dspmsg $ac_dir/$ac_prog >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ else
+ ac_cv_path_install="$ac_dir/$ac_prog -c"
+ break 2
+ fi
+ fi
+ done
+ ;;
+ esac
+ done
+ IFS="$ac_save_IFS"
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL="$ac_cv_path_install"
+ else
+ # As a last resort, use the slow shell script. We don't cache a
+ # path for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the path is relative.
+ INSTALL="$ac_install_sh"
+ fi
+fi
+echo "$ac_t""$INSTALL" 1>&6
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL_PROGRAM}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+echo $ac_n "checking whether build environment is sane""... $ac_c" 1>&6
+echo "configure:614: checking whether build environment is sane" >&5
+# Just in case
+sleep 1
+echo timestamp > conftestfile
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt $srcdir/configure conftestfile 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t $srcdir/configure conftestfile`
+ fi
+ if test "$*" != "X $srcdir/configure conftestfile" \
+ && test "$*" != "X conftestfile $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ { echo "configure: error: ls -t appears to fail. Make sure there is not a broken
+alias in your environment" 1>&2; exit 1; }
+ fi
+
+ test "$2" = conftestfile
+ )
+then
+ # Ok.
+ :
+else
+ { echo "configure: error: newly created file is older than distributed files!
+Check your system clock" 1>&2; exit 1; }
+fi
+rm -f conftest*
+echo "$ac_t""yes" 1>&6
+if test "$program_transform_name" = s,x,x,; then
+ program_transform_name=
+else
+ # Double any \ or $. echo might interpret backslashes.
+ cat <<\EOF_SED > conftestsed
+s,\\,\\\\,g; s,\$,$$,g
+EOF_SED
+ program_transform_name="`echo $program_transform_name|sed -f conftestsed`"
+ rm -f conftestsed
+fi
+test "$program_prefix" != NONE &&
+ program_transform_name="s,^,${program_prefix},; $program_transform_name"
+# Use a double $ so make ignores it.
+test "$program_suffix" != NONE &&
+ program_transform_name="s,\$\$,${program_suffix},; $program_transform_name"
+
+# sed with no file args requires a program.
+test "$program_transform_name" = "" && program_transform_name="s,x,x,"
+
+echo $ac_n "checking whether ${MAKE-make} sets \${MAKE}""... $ac_c" 1>&6
+echo "configure:671: checking whether ${MAKE-make} sets \${MAKE}" >&5
+set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y%./+-%__p_%'`
+if eval "test \"`echo '$''{'ac_cv_prog_make_${ac_make}_set'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ cat > conftestmake <<\EOF
+all:
+ @echo 'ac_maketemp="${MAKE}"'
+EOF
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+eval `${MAKE-make} -f conftestmake 2>/dev/null | grep temp=`
+if test -n "$ac_maketemp"; then
+ eval ac_cv_prog_make_${ac_make}_set=yes
+else
+ eval ac_cv_prog_make_${ac_make}_set=no
+fi
+rm -f conftestmake
+fi
+if eval "test \"`echo '$ac_cv_prog_make_'${ac_make}_set`\" = yes"; then
+ echo "$ac_t""yes" 1>&6
+ SET_MAKE=
+else
+ echo "$ac_t""no" 1>&6
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+
+PACKAGE=ipc
+
+VERSION=1.1
+
+if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
+ { echo "configure: error: source directory already configured; run "make distclean" there first" 1>&2; exit 1; }
+fi
+cat >> confdefs.h <<EOF
+#define PACKAGE "$PACKAGE"
+EOF
+
+cat >> confdefs.h <<EOF
+#define VERSION "$VERSION"
+EOF
+
+
+
+missing_dir=`cd $ac_aux_dir && pwd`
+echo $ac_n "checking for working aclocal""... $ac_c" 1>&6
+echo "configure:717: checking for working aclocal" >&5
+# Run test in a subshell; some versions of sh will print an error if
+# an executable is not found, even if stderr is redirected.
+# Redirect stdin to placate older versions of autoconf. Sigh.
+if (aclocal --version) < /dev/null > /dev/null 2>&1; then
+ ACLOCAL=aclocal
+ echo "$ac_t""found" 1>&6
+else
+ ACLOCAL="$missing_dir/missing aclocal"
+ echo "$ac_t""missing" 1>&6
+fi
+
+echo $ac_n "checking for working autoconf""... $ac_c" 1>&6
+echo "configure:730: checking for working autoconf" >&5
+# Run test in a subshell; some versions of sh will print an error if
+# an executable is not found, even if stderr is redirected.
+# Redirect stdin to placate older versions of autoconf. Sigh.
+if (autoconf --version) < /dev/null > /dev/null 2>&1; then
+ AUTOCONF=autoconf
+ echo "$ac_t""found" 1>&6
+else
+ AUTOCONF="$missing_dir/missing autoconf"
+ echo "$ac_t""missing" 1>&6
+fi
+
+echo $ac_n "checking for working automake""... $ac_c" 1>&6
+echo "configure:743: checking for working automake" >&5
+# Run test in a subshell; some versions of sh will print an error if
+# an executable is not found, even if stderr is redirected.
+# Redirect stdin to placate older versions of autoconf. Sigh.
+if (automake --version) < /dev/null > /dev/null 2>&1; then
+ AUTOMAKE=automake
+ echo "$ac_t""found" 1>&6
+else
+ AUTOMAKE="$missing_dir/missing automake"
+ echo "$ac_t""missing" 1>&6
+fi
+
+echo $ac_n "checking for working autoheader""... $ac_c" 1>&6
+echo "configure:756: checking for working autoheader" >&5
+# Run test in a subshell; some versions of sh will print an error if
+# an executable is not found, even if stderr is redirected.
+# Redirect stdin to placate older versions of autoconf. Sigh.
+if (autoheader --version) < /dev/null > /dev/null 2>&1; then
+ AUTOHEADER=autoheader
+ echo "$ac_t""found" 1>&6
+else
+ AUTOHEADER="$missing_dir/missing autoheader"
+ echo "$ac_t""missing" 1>&6
+fi
+
+echo $ac_n "checking for working makeinfo""... $ac_c" 1>&6
+echo "configure:769: checking for working makeinfo" >&5
+# Run test in a subshell; some versions of sh will print an error if
+# an executable is not found, even if stderr is redirected.
+# Redirect stdin to placate older versions of autoconf. Sigh.
+if (makeinfo --version) < /dev/null > /dev/null 2>&1; then
+ MAKEINFO=makeinfo
+ echo "$ac_t""found" 1>&6
+else
+ MAKEINFO="$missing_dir/missing makeinfo"
+ echo "$ac_t""missing" 1>&6
+fi
+
+
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# ./install, which can be erroneously created by make from ./install.sh.
+echo $ac_n "checking for a BSD compatible install""... $ac_c" 1>&6
+echo "configure:795: checking for a BSD compatible install" >&5
+if test -z "$INSTALL"; then
+if eval "test \"`echo '$''{'ac_cv_path_install'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ IFS="${IFS= }"; ac_save_IFS="$IFS"; IFS=":"
+ for ac_dir in $PATH; do
+ # Account for people who put trailing slashes in PATH elements.
+ case "$ac_dir/" in
+ /|./|.//|/etc/*|/usr/sbin/*|/usr/etc/*|/sbin/*|/usr/afsws/bin/*|/usr/ucb/*) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ if test -f $ac_dir/$ac_prog; then
+ if test $ac_prog = install &&
+ grep dspmsg $ac_dir/$ac_prog >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ else
+ ac_cv_path_install="$ac_dir/$ac_prog -c"
+ break 2
+ fi
+ fi
+ done
+ ;;
+ esac
+ done
+ IFS="$ac_save_IFS"
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL="$ac_cv_path_install"
+ else
+ # As a last resort, use the slow shell script. We don't cache a
+ # path for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the path is relative.
+ INSTALL="$ac_install_sh"
+ fi
+fi
+echo "$ac_t""$INSTALL" 1>&6
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL_PROGRAM}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+echo $ac_n "checking whether ln -s works""... $ac_c" 1>&6
+echo "configure:848: checking whether ln -s works" >&5
+if eval "test \"`echo '$''{'ac_cv_prog_LN_S'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ rm -f conftestdata
+if ln -s X conftestdata 2>/dev/null
+then
+ rm -f conftestdata
+ ac_cv_prog_LN_S="ln -s"
+else
+ ac_cv_prog_LN_S=ln
+fi
+fi
+LN_S="$ac_cv_prog_LN_S"
+if test "$ac_cv_prog_LN_S" = "ln -s"; then
+ echo "$ac_t""yes" 1>&6
+else
+ echo "$ac_t""no" 1>&6
+fi
+
+# Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
+echo "configure:871: checking for $ac_word" >&5
+if eval "test \"`echo '$''{'ac_cv_prog_CC'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ IFS="${IFS= }"; ac_save_ifs="$IFS"; IFS=":"
+ ac_dummy="$PATH"
+ for ac_dir in $ac_dummy; do
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/$ac_word; then
+ ac_cv_prog_CC="gcc"
+ break
+ fi
+ done
+ IFS="$ac_save_ifs"
+fi
+fi
+CC="$ac_cv_prog_CC"
+if test -n "$CC"; then
+ echo "$ac_t""$CC" 1>&6
+else
+ echo "$ac_t""no" 1>&6
+fi
+
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
+echo "configure:901: checking for $ac_word" >&5
+if eval "test \"`echo '$''{'ac_cv_prog_CC'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ IFS="${IFS= }"; ac_save_ifs="$IFS"; IFS=":"
+ ac_prog_rejected=no
+ ac_dummy="$PATH"
+ for ac_dir in $ac_dummy; do
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/$ac_word; then
+ if test "$ac_dir/$ac_word" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ break
+ fi
+ done
+ IFS="$ac_save_ifs"
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# -gt 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ set dummy "$ac_dir/$ac_word" "$@"
+ shift
+ ac_cv_prog_CC="$@"
+ fi
+fi
+fi
+fi
+CC="$ac_cv_prog_CC"
+if test -n "$CC"; then
+ echo "$ac_t""$CC" 1>&6
+else
+ echo "$ac_t""no" 1>&6
+fi
+
+ if test -z "$CC"; then
+ case "`uname -s`" in
+ *win32* | *WIN32*)
+ # Extract the first word of "cl", so it can be a program name with args.
+set dummy cl; ac_word=$2
+echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
+echo "configure:952: checking for $ac_word" >&5
+if eval "test \"`echo '$''{'ac_cv_prog_CC'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ IFS="${IFS= }"; ac_save_ifs="$IFS"; IFS=":"
+ ac_dummy="$PATH"
+ for ac_dir in $ac_dummy; do
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/$ac_word; then
+ ac_cv_prog_CC="cl"
+ break
+ fi
+ done
+ IFS="$ac_save_ifs"
+fi
+fi
+CC="$ac_cv_prog_CC"
+if test -n "$CC"; then
+ echo "$ac_t""$CC" 1>&6
+else
+ echo "$ac_t""no" 1>&6
+fi
+ ;;
+ esac
+ fi
+ test -z "$CC" && { echo "configure: error: no acceptable cc found in \$PATH" 1>&2; exit 1; }
+fi
+
+echo $ac_n "checking whether the C compiler ($CC $CFLAGS $LDFLAGS) works""... $ac_c" 1>&6
+echo "configure:984: checking whether the C compiler ($CC $CFLAGS $LDFLAGS) works" >&5
+
+ac_ext=c
+# CFLAGS is not in ac_cpp because -g, -O, etc. are not valid cpp options.
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='${CC-cc} -c $CFLAGS $CPPFLAGS conftest.$ac_ext 1>&5'
+ac_link='${CC-cc} -o conftest${ac_exeext} $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS 1>&5'
+cross_compiling=$ac_cv_prog_cc_cross
+
+cat > conftest.$ac_ext << EOF
+
+#line 995 "configure"
+#include "confdefs.h"
+
+main(){return(0);}
+EOF
+if { (eval echo configure:1000: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+ ac_cv_prog_cc_works=yes
+ # If we can't run a trivial program, we are probably using a cross compiler.
+ if (./conftest; exit) 2>/dev/null; then
+ ac_cv_prog_cc_cross=no
+ else
+ ac_cv_prog_cc_cross=yes
+ fi
+else
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ ac_cv_prog_cc_works=no
+fi
+rm -fr conftest*
+ac_ext=c
+# CFLAGS is not in ac_cpp because -g, -O, etc. are not valid cpp options.
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='${CC-cc} -c $CFLAGS $CPPFLAGS conftest.$ac_ext 1>&5'
+ac_link='${CC-cc} -o conftest${ac_exeext} $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS 1>&5'
+cross_compiling=$ac_cv_prog_cc_cross
+
+echo "$ac_t""$ac_cv_prog_cc_works" 1>&6
+if test $ac_cv_prog_cc_works = no; then
+ { echo "configure: error: installation or configuration problem: C compiler cannot create executables." 1>&2; exit 1; }
+fi
+echo $ac_n "checking whether the C compiler ($CC $CFLAGS $LDFLAGS) is a cross-compiler""... $ac_c" 1>&6
+echo "configure:1026: checking whether the C compiler ($CC $CFLAGS $LDFLAGS) is a cross-compiler" >&5
+echo "$ac_t""$ac_cv_prog_cc_cross" 1>&6
+cross_compiling=$ac_cv_prog_cc_cross
+
+echo $ac_n "checking whether we are using GNU C""... $ac_c" 1>&6
+echo "configure:1031: checking whether we are using GNU C" >&5
+if eval "test \"`echo '$''{'ac_cv_prog_gcc'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ cat > conftest.c <<EOF
+#ifdef __GNUC__
+ yes;
+#endif
+EOF
+if { ac_try='${CC-cc} -E conftest.c'; { (eval echo configure:1040: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; } | egrep yes >/dev/null 2>&1; then
+ ac_cv_prog_gcc=yes
+else
+ ac_cv_prog_gcc=no
+fi
+fi
+
+echo "$ac_t""$ac_cv_prog_gcc" 1>&6
+
+if test $ac_cv_prog_gcc = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+
+ac_test_CFLAGS="${CFLAGS+set}"
+ac_save_CFLAGS="$CFLAGS"
+CFLAGS=
+echo $ac_n "checking whether ${CC-cc} accepts -g""... $ac_c" 1>&6
+echo "configure:1059: checking whether ${CC-cc} accepts -g" >&5
+if eval "test \"`echo '$''{'ac_cv_prog_cc_g'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ echo 'void f(){}' > conftest.c
+if test -z "`${CC-cc} -g -c conftest.c 2>&1`"; then
+ ac_cv_prog_cc_g=yes
+else
+ ac_cv_prog_cc_g=no
+fi
+rm -f conftest*
+
+fi
+
+echo "$ac_t""$ac_cv_prog_cc_g" 1>&6
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS="$ac_save_CFLAGS"
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+
+
+echo $ac_n "checking for rint in -lm""... $ac_c" 1>&6
+echo "configure:1092: checking for rint in -lm" >&5
+ac_lib_var=`echo m'_'rint | sed 'y%./+-%__p_%'`
+if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ ac_save_LIBS="$LIBS"
+LIBS="-lm $LIBS"
+cat > conftest.$ac_ext <<EOF
+#line 1100 "configure"
+#include "confdefs.h"
+/* Override any gcc2 internal prototype to avoid an error. */
+/* We use char because int might match the return type of a gcc2
+ builtin and then its argument prototype would still apply. */
+char rint();
+
+int main() {
+rint()
+; return 0; }
+EOF
+if { (eval echo configure:1111: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+ rm -rf conftest*
+ eval "ac_cv_lib_$ac_lib_var=yes"
+else
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ eval "ac_cv_lib_$ac_lib_var=no"
+fi
+rm -f conftest*
+LIBS="$ac_save_LIBS"
+
+fi
+if eval "test \"`echo '$ac_cv_lib_'$ac_lib_var`\" = yes"; then
+ echo "$ac_t""yes" 1>&6
+ ac_tr_lib=HAVE_LIB`echo m | sed -e 's/[^a-zA-Z0-9_]/_/g' \
+ -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`
+ cat >> confdefs.h <<EOF
+#define $ac_tr_lib 1
+EOF
+
+ LIBS="-lm $LIBS"
+
+else
+ echo "$ac_t""no" 1>&6
+fi
+
+
+
+echo $ac_n "checking how to run the C preprocessor""... $ac_c" 1>&6
+echo "configure:1141: checking how to run the C preprocessor" >&5
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+if eval "test \"`echo '$''{'ac_cv_prog_CPP'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ # This must be in double quotes, not single quotes, because CPP may get
+ # substituted into the Makefile and "${CC-cc}" will confuse make.
+ CPP="${CC-cc} -E"
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp.
+ cat > conftest.$ac_ext <<EOF
+#line 1156 "configure"
+#include "confdefs.h"
+#include <assert.h>
+Syntax Error
+EOF
+ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+{ (eval echo configure:1162: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+if test -z "$ac_err"; then
+ :
+else
+ echo "$ac_err" >&5
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ CPP="${CC-cc} -E -traditional-cpp"
+ cat > conftest.$ac_ext <<EOF
+#line 1173 "configure"
+#include "confdefs.h"
+#include <assert.h>
+Syntax Error
+EOF
+ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+{ (eval echo configure:1179: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+if test -z "$ac_err"; then
+ :
+else
+ echo "$ac_err" >&5
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ CPP="${CC-cc} -nologo -E"
+ cat > conftest.$ac_ext <<EOF
+#line 1190 "configure"
+#include "confdefs.h"
+#include <assert.h>
+Syntax Error
+EOF
+ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+{ (eval echo configure:1196: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+if test -z "$ac_err"; then
+ :
+else
+ echo "$ac_err" >&5
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ CPP=/lib/cpp
+fi
+rm -f conftest*
+fi
+rm -f conftest*
+fi
+rm -f conftest*
+ ac_cv_prog_CPP="$CPP"
+fi
+ CPP="$ac_cv_prog_CPP"
+else
+ ac_cv_prog_CPP="$CPP"
+fi
+echo "$ac_t""$CPP" 1>&6
+
+echo $ac_n "checking for ANSI C header files""... $ac_c" 1>&6
+echo "configure:1221: checking for ANSI C header files" >&5
+if eval "test \"`echo '$''{'ac_cv_header_stdc'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ cat > conftest.$ac_ext <<EOF
+#line 1226 "configure"
+#include "confdefs.h"
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+EOF
+ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+{ (eval echo configure:1234: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+if test -z "$ac_err"; then
+ rm -rf conftest*
+ ac_cv_header_stdc=yes
+else
+ echo "$ac_err" >&5
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+cat > conftest.$ac_ext <<EOF
+#line 1251 "configure"
+#include "confdefs.h"
+#include <string.h>
+EOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ egrep "memchr" >/dev/null 2>&1; then
+ :
+else
+ rm -rf conftest*
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+cat > conftest.$ac_ext <<EOF
+#line 1269 "configure"
+#include "confdefs.h"
+#include <stdlib.h>
+EOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ egrep "free" >/dev/null 2>&1; then
+ :
+else
+ rm -rf conftest*
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+if test "$cross_compiling" = yes; then
+ :
+else
+ cat > conftest.$ac_ext <<EOF
+#line 1290 "configure"
+#include "confdefs.h"
+#include <ctype.h>
+#define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+#define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int main () { int i; for (i = 0; i < 256; i++)
+if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) exit(2);
+exit (0); }
+
+EOF
+if { (eval echo configure:1301: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext} && (./conftest; exit) 2>/dev/null
+then
+ :
+else
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -fr conftest*
+ ac_cv_header_stdc=no
+fi
+rm -fr conftest*
+fi
+
+fi
+fi
+
+echo "$ac_t""$ac_cv_header_stdc" 1>&6
+if test $ac_cv_header_stdc = yes; then
+ cat >> confdefs.h <<\EOF
+#define STDC_HEADERS 1
+EOF
+
+fi
+
+for ac_hdr in math.h time.h signal.h unistd.h
+do
+ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'`
+echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6
+echo "configure:1328: checking for $ac_hdr" >&5
+if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ cat > conftest.$ac_ext <<EOF
+#line 1333 "configure"
+#include "confdefs.h"
+#include <$ac_hdr>
+EOF
+ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+{ (eval echo configure:1338: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+if test -z "$ac_err"; then
+ rm -rf conftest*
+ eval "ac_cv_header_$ac_safe=yes"
+else
+ echo "$ac_err" >&5
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ eval "ac_cv_header_$ac_safe=no"
+fi
+rm -f conftest*
+fi
+if eval "test \"`echo '$ac_cv_header_'$ac_safe`\" = yes"; then
+ echo "$ac_t""yes" 1>&6
+ ac_tr_hdr=HAVE_`echo $ac_hdr | sed 'y%abcdefghijklmnopqrstuvwxyz./-%ABCDEFGHIJKLMNOPQRSTUVWXYZ___%'`
+ cat >> confdefs.h <<EOF
+#define $ac_tr_hdr 1
+EOF
+
+else
+ echo "$ac_t""no" 1>&6
+fi
+done
+
+
+
+echo $ac_n "checking return type of signal handlers""... $ac_c" 1>&6
+echo "configure:1367: checking return type of signal handlers" >&5
+if eval "test \"`echo '$''{'ac_cv_type_signal'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ cat > conftest.$ac_ext <<EOF
+#line 1372 "configure"
+#include "confdefs.h"
+#include <sys/types.h>
+#include <signal.h>
+#ifdef signal
+#undef signal
+#endif
+#ifdef __cplusplus
+extern "C" void (*signal (int, void (*)(int)))(int);
+#else
+void (*signal ()) ();
+#endif
+
+int main() {
+int i;
+; return 0; }
+EOF
+if { (eval echo configure:1389: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+ rm -rf conftest*
+ ac_cv_type_signal=void
+else
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ ac_cv_type_signal=int
+fi
+rm -f conftest*
+fi
+
+echo "$ac_t""$ac_cv_type_signal" 1>&6
+cat >> confdefs.h <<EOF
+#define RETSIGTYPE $ac_cv_type_signal
+EOF
+
+
+for ac_func in strdup strtol getcwd
+do
+echo $ac_n "checking for $ac_func""... $ac_c" 1>&6
+echo "configure:1410: checking for $ac_func" >&5
+if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ cat > conftest.$ac_ext <<EOF
+#line 1415 "configure"
+#include "confdefs.h"
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func(); below. */
+#include <assert.h>
+/* Override any gcc2 internal prototype to avoid an error. */
+/* We use char because int might match the return type of a gcc2
+ builtin and then its argument prototype would still apply. */
+char $ac_func();
+
+int main() {
+
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined (__stub_$ac_func) || defined (__stub___$ac_func)
+choke me
+#else
+$ac_func();
+#endif
+
+; return 0; }
+EOF
+if { (eval echo configure:1438: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+ rm -rf conftest*
+ eval "ac_cv_func_$ac_func=yes"
+else
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ eval "ac_cv_func_$ac_func=no"
+fi
+rm -f conftest*
+fi
+
+if eval "test \"`echo '$ac_cv_func_'$ac_func`\" = yes"; then
+ echo "$ac_t""yes" 1>&6
+ ac_tr_func=HAVE_`echo $ac_func | tr 'abcdefghijklmnopqrstuvwxyz' 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'`
+ cat >> confdefs.h <<EOF
+#define $ac_tr_func 1
+EOF
+
+else
+ echo "$ac_t""no" 1>&6
+{ echo "configure: error: necessary lib function not found" 1>&2; exit 1; }
+fi
+done
+
+for ac_func in system signal time
+do
+echo $ac_n "checking for $ac_func""... $ac_c" 1>&6
+echo "configure:1466: checking for $ac_func" >&5
+if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then
+ echo $ac_n "(cached) $ac_c" 1>&6
+else
+ cat > conftest.$ac_ext <<EOF
+#line 1471 "configure"
+#include "confdefs.h"
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func(); below. */
+#include <assert.h>
+/* Override any gcc2 internal prototype to avoid an error. */
+/* We use char because int might match the return type of a gcc2
+ builtin and then its argument prototype would still apply. */
+char $ac_func();
+
+int main() {
+
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined (__stub_$ac_func) || defined (__stub___$ac_func)
+choke me
+#else
+$ac_func();
+#endif
+
+; return 0; }
+EOF
+if { (eval echo configure:1494: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+ rm -rf conftest*
+ eval "ac_cv_func_$ac_func=yes"
+else
+ echo "configure: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ eval "ac_cv_func_$ac_func=no"
+fi
+rm -f conftest*
+fi
+
+if eval "test \"`echo '$ac_cv_func_'$ac_func`\" = yes"; then
+ echo "$ac_t""yes" 1>&6
+ ac_tr_func=HAVE_`echo $ac_func | tr 'abcdefghijklmnopqrstuvwxyz' 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'`
+ cat >> confdefs.h <<EOF
+#define $ac_tr_func 1
+EOF
+
+else
+ echo "$ac_t""no" 1>&6
+fi
+done
+
+
+# Check whether --enable-NO_GNUPLOT or --disable-NO_GNUPLOT was given.
+if test "${enable_NO_GNUPLOT+set}" = set; then
+ enableval="$enable_NO_GNUPLOT"
+ cat >> confdefs.h <<\EOF
+#define NOT_RUN_GNUPLOT 1
+EOF
+
+else
+ cat >> confdefs.h <<\EOF
+#define NOT_RUN_GNUPLOT 0
+EOF
+
+fi
+
+
+
+trap '' 1 2 15
+cat > confcache <<\EOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs. It is not useful on other systems.
+# If it contains results you don't want to keep, you may remove or edit it.
+#
+# By default, configure uses ./config.cache as the cache file,
+# creating it if it does not exist already. You can give configure
+# the --cache-file=FILE option to use a different cache file; that is
+# what configure does when it calls configure scripts in
+# subdirectories, so they share the cache.
+# Giving --cache-file=/dev/null disables caching, for debugging configure.
+# config.status only pays attention to the cache file if you give it the
+# --recheck option to rerun configure.
+#
+EOF
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, don't put newlines in cache variables' values.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(set) 2>&1 |
+ case `(ac_space=' '; set | grep ac_space) 2>&1` in
+ *ac_space=\ *)
+ # `set' does not quote correctly, so add quotes (double-quote substitution
+ # turns \\\\ into \\, and sed turns \\ into \).
+ sed -n \
+ -e "s/'/'\\\\''/g" \
+ -e "s/^\\([a-zA-Z0-9_]*_cv_[a-zA-Z0-9_]*\\)=\\(.*\\)/\\1=\${\\1='\\2'}/p"
+ ;;
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n -e 's/^\([a-zA-Z0-9_]*_cv_[a-zA-Z0-9_]*\)=\(.*\)/\1=${\1=\2}/p'
+ ;;
+ esac >> confcache
+if cmp -s $cache_file confcache; then
+ :
+else
+ if test -w $cache_file; then
+ echo "updating cache $cache_file"
+ cat confcache > $cache_file
+ else
+ echo "not updating unwritable cache $cache_file"
+ fi
+fi
+rm -f confcache
+
+trap 'rm -fr conftest* confdefs* core core.* *.core $ac_clean_files; exit 1' 1 2 15
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+# Any assignment to VPATH causes Sun make to only execute
+# the first set of double-colon rules, so remove it if not needed.
+# If there is a colon in the path, we need to keep it.
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=[^:]*$/d'
+fi
+
+trap 'rm -f $CONFIG_STATUS conftest*; exit 1' 1 2 15
+
+DEFS=-DHAVE_CONFIG_H
+
+# Without the "./", some shells look in PATH for config.status.
+: ${CONFIG_STATUS=./config.status}
+
+echo creating $CONFIG_STATUS
+rm -f $CONFIG_STATUS
+cat > $CONFIG_STATUS <<EOF
+#! /bin/sh
+# Generated automatically by configure.
+# Run this file to recreate the current configuration.
+# This directory was configured as follows,
+# on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+#
+# $0 $ac_configure_args
+#
+# Compiler output produced by configure, useful for debugging
+# configure, is in ./config.log if it exists.
+
+ac_cs_usage="Usage: $CONFIG_STATUS [--recheck] [--version] [--help]"
+for ac_option
+do
+ case "\$ac_option" in
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ echo "running \${CONFIG_SHELL-/bin/sh} $0 $ac_configure_args --no-create --no-recursion"
+ exec \${CONFIG_SHELL-/bin/sh} $0 $ac_configure_args --no-create --no-recursion ;;
+ -version | --version | --versio | --versi | --vers | --ver | --ve | --v)
+ echo "$CONFIG_STATUS generated by autoconf version 2.13"
+ exit 0 ;;
+ -help | --help | --hel | --he | --h)
+ echo "\$ac_cs_usage"; exit 0 ;;
+ *) echo "\$ac_cs_usage"; exit 1 ;;
+ esac
+done
+
+ac_given_srcdir=$srcdir
+ac_given_INSTALL="$INSTALL"
+
+trap 'rm -fr `echo "Makefile config.h" | sed "s/:[^ ]*//g"` conftest*; exit 1' 1 2 15
+EOF
+cat >> $CONFIG_STATUS <<EOF
+
+# Protect against being on the right side of a sed subst in config.status.
+sed 's/%@/@@/; s/@%/@@/; s/%g\$/@g/; /@g\$/s/[\\\\&%]/\\\\&/g;
+ s/@@/%@/; s/@@/@%/; s/@g\$/%g/' > conftest.subs <<\\CEOF
+$ac_vpsub
+$extrasub
+s%@SHELL@%$SHELL%g
+s%@CFLAGS@%$CFLAGS%g
+s%@CPPFLAGS@%$CPPFLAGS%g
+s%@CXXFLAGS@%$CXXFLAGS%g
+s%@FFLAGS@%$FFLAGS%g
+s%@DEFS@%$DEFS%g
+s%@LDFLAGS@%$LDFLAGS%g
+s%@LIBS@%$LIBS%g
+s%@exec_prefix@%$exec_prefix%g
+s%@prefix@%$prefix%g
+s%@program_transform_name@%$program_transform_name%g
+s%@bindir@%$bindir%g
+s%@sbindir@%$sbindir%g
+s%@libexecdir@%$libexecdir%g
+s%@datadir@%$datadir%g
+s%@sysconfdir@%$sysconfdir%g
+s%@sharedstatedir@%$sharedstatedir%g
+s%@localstatedir@%$localstatedir%g
+s%@libdir@%$libdir%g
+s%@includedir@%$includedir%g
+s%@oldincludedir@%$oldincludedir%g
+s%@infodir@%$infodir%g
+s%@mandir@%$mandir%g
+s%@INSTALL_PROGRAM@%$INSTALL_PROGRAM%g
+s%@INSTALL_SCRIPT@%$INSTALL_SCRIPT%g
+s%@INSTALL_DATA@%$INSTALL_DATA%g
+s%@PACKAGE@%$PACKAGE%g
+s%@VERSION@%$VERSION%g
+s%@ACLOCAL@%$ACLOCAL%g
+s%@AUTOCONF@%$AUTOCONF%g
+s%@AUTOMAKE@%$AUTOMAKE%g
+s%@AUTOHEADER@%$AUTOHEADER%g
+s%@MAKEINFO@%$MAKEINFO%g
+s%@SET_MAKE@%$SET_MAKE%g
+s%@LN_S@%$LN_S%g
+s%@CC@%$CC%g
+s%@CPP@%$CPP%g
+
+CEOF
+EOF
+
+cat >> $CONFIG_STATUS <<\EOF
+
+# Split the substitutions into bite-sized pieces for seds with
+# small command number limits, like on Digital OSF/1 and HP-UX.
+ac_max_sed_cmds=90 # Maximum number of lines to put in a sed script.
+ac_file=1 # Number of current file.
+ac_beg=1 # First line for current file.
+ac_end=$ac_max_sed_cmds # Line after last line for current file.
+ac_more_lines=:
+ac_sed_cmds=""
+while $ac_more_lines; do
+ if test $ac_beg -gt 1; then
+ sed "1,${ac_beg}d; ${ac_end}q" conftest.subs > conftest.s$ac_file
+ else
+ sed "${ac_end}q" conftest.subs > conftest.s$ac_file
+ fi
+ if test ! -s conftest.s$ac_file; then
+ ac_more_lines=false
+ rm -f conftest.s$ac_file
+ else
+ if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds="sed -f conftest.s$ac_file"
+ else
+ ac_sed_cmds="$ac_sed_cmds | sed -f conftest.s$ac_file"
+ fi
+ ac_file=`expr $ac_file + 1`
+ ac_beg=$ac_end
+ ac_end=`expr $ac_end + $ac_max_sed_cmds`
+ fi
+done
+if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds=cat
+fi
+EOF
+
+cat >> $CONFIG_STATUS <<EOF
+
+CONFIG_FILES=\${CONFIG_FILES-"Makefile"}
+EOF
+cat >> $CONFIG_STATUS <<\EOF
+for ac_file in .. $CONFIG_FILES; do if test "x$ac_file" != x..; then
+ # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+ case "$ac_file" in
+ *:*) ac_file_in=`echo "$ac_file"|sed 's%[^:]*:%%'`
+ ac_file=`echo "$ac_file"|sed 's%:.*%%'` ;;
+ *) ac_file_in="${ac_file}.in" ;;
+ esac
+
+ # Adjust a relative srcdir, top_srcdir, and INSTALL for subdirectories.
+
+ # Remove last slash and all that follows it. Not all systems have dirname.
+ ac_dir=`echo $ac_file|sed 's%/[^/][^/]*$%%'`
+ if test "$ac_dir" != "$ac_file" && test "$ac_dir" != .; then
+ # The file is in a subdirectory.
+ test ! -d "$ac_dir" && mkdir "$ac_dir"
+ ac_dir_suffix="/`echo $ac_dir|sed 's%^\./%%'`"
+ # A "../" for each directory in $ac_dir_suffix.
+ ac_dots=`echo $ac_dir_suffix|sed 's%/[^/]*%../%g'`
+ else
+ ac_dir_suffix= ac_dots=
+ fi
+
+ case "$ac_given_srcdir" in
+ .) srcdir=.
+ if test -z "$ac_dots"; then top_srcdir=.
+ else top_srcdir=`echo $ac_dots|sed 's%/$%%'`; fi ;;
+ /*) srcdir="$ac_given_srcdir$ac_dir_suffix"; top_srcdir="$ac_given_srcdir" ;;
+ *) # Relative path.
+ srcdir="$ac_dots$ac_given_srcdir$ac_dir_suffix"
+ top_srcdir="$ac_dots$ac_given_srcdir" ;;
+ esac
+
+ case "$ac_given_INSTALL" in
+ [/$]*) INSTALL="$ac_given_INSTALL" ;;
+ *) INSTALL="$ac_dots$ac_given_INSTALL" ;;
+ esac
+
+ echo creating "$ac_file"
+ rm -f "$ac_file"
+ configure_input="Generated automatically from `echo $ac_file_in|sed 's%.*/%%'` by configure."
+ case "$ac_file" in
+ *Makefile*) ac_comsub="1i\\
+# $configure_input" ;;
+ *) ac_comsub= ;;
+ esac
+
+ ac_file_inputs=`echo $ac_file_in|sed -e "s%^%$ac_given_srcdir/%" -e "s%:% $ac_given_srcdir/%g"`
+ sed -e "$ac_comsub
+s%@configure_input@%$configure_input%g
+s%@srcdir@%$srcdir%g
+s%@top_srcdir@%$top_srcdir%g
+s%@INSTALL@%$INSTALL%g
+" $ac_file_inputs | (eval "$ac_sed_cmds") > $ac_file
+fi; done
+rm -f conftest.s*
+
+# These sed commands are passed to sed as "A NAME B NAME C VALUE D", where
+# NAME is the cpp macro being defined and VALUE is the value it is being given.
+#
+# ac_d sets the value in "#define NAME VALUE" lines.
+ac_dA='s%^\([ ]*\)#\([ ]*define[ ][ ]*\)'
+ac_dB='\([ ][ ]*\)[^ ]*%\1#\2'
+ac_dC='\3'
+ac_dD='%g'
+# ac_u turns "#undef NAME" with trailing blanks into "#define NAME VALUE".
+ac_uA='s%^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)'
+ac_uB='\([ ]\)%\1#\2define\3'
+ac_uC=' '
+ac_uD='\4%g'
+# ac_e turns "#undef NAME" without trailing blanks into "#define NAME VALUE".
+ac_eA='s%^\([ ]*\)#\([ ]*\)undef\([ ][ ]*\)'
+ac_eB='$%\1#\2define\3'
+ac_eC=' '
+ac_eD='%g'
+
+if test "${CONFIG_HEADERS+set}" != set; then
+EOF
+cat >> $CONFIG_STATUS <<EOF
+ CONFIG_HEADERS="config.h"
+EOF
+cat >> $CONFIG_STATUS <<\EOF
+fi
+for ac_file in .. $CONFIG_HEADERS; do if test "x$ac_file" != x..; then
+ # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+ case "$ac_file" in
+ *:*) ac_file_in=`echo "$ac_file"|sed 's%[^:]*:%%'`
+ ac_file=`echo "$ac_file"|sed 's%:.*%%'` ;;
+ *) ac_file_in="${ac_file}.in" ;;
+ esac
+
+ echo creating $ac_file
+
+ rm -f conftest.frag conftest.in conftest.out
+ ac_file_inputs=`echo $ac_file_in|sed -e "s%^%$ac_given_srcdir/%" -e "s%:% $ac_given_srcdir/%g"`
+ cat $ac_file_inputs > conftest.in
+
+EOF
+
+# Transform confdefs.h into a sed script conftest.vals that substitutes
+# the proper values into config.h.in to produce config.h. And first:
+# Protect against being on the right side of a sed subst in config.status.
+# Protect against being in an unquoted here document in config.status.
+rm -f conftest.vals
+cat > conftest.hdr <<\EOF
+s/[\\&%]/\\&/g
+s%[\\$`]%\\&%g
+s%#define \([A-Za-z_][A-Za-z0-9_]*\) *\(.*\)%${ac_dA}\1${ac_dB}\1${ac_dC}\2${ac_dD}%gp
+s%ac_d%ac_u%gp
+s%ac_u%ac_e%gp
+EOF
+sed -n -f conftest.hdr confdefs.h > conftest.vals
+rm -f conftest.hdr
+
+# This sed command replaces #undef with comments. This is necessary, for
+# example, in the case of _POSIX_SOURCE, which is predefined and required
+# on some systems where configure will not decide to define it.
+cat >> conftest.vals <<\EOF
+s%^[ ]*#[ ]*undef[ ][ ]*[a-zA-Z_][a-zA-Z_0-9]*%/* & */%
+EOF
+
+# Break up conftest.vals because some shells have a limit on
+# the size of here documents, and old seds have small limits too.
+
+rm -f conftest.tail
+while :
+do
+ ac_lines=`grep -c . conftest.vals`
+ # grep -c gives empty output for an empty file on some AIX systems.
+ if test -z "$ac_lines" || test "$ac_lines" -eq 0; then break; fi
+ # Write a limited-size here document to conftest.frag.
+ echo ' cat > conftest.frag <<CEOF' >> $CONFIG_STATUS
+ sed ${ac_max_here_lines}q conftest.vals >> $CONFIG_STATUS
+ echo 'CEOF
+ sed -f conftest.frag conftest.in > conftest.out
+ rm -f conftest.in
+ mv conftest.out conftest.in
+' >> $CONFIG_STATUS
+ sed 1,${ac_max_here_lines}d conftest.vals > conftest.tail
+ rm -f conftest.vals
+ mv conftest.tail conftest.vals
+done
+rm -f conftest.vals
+
+cat >> $CONFIG_STATUS <<\EOF
+ rm -f conftest.frag conftest.h
+ echo "/* $ac_file. Generated automatically by configure. */" > conftest.h
+ cat conftest.in >> conftest.h
+ rm -f conftest.in
+ if cmp -s $ac_file conftest.h 2>/dev/null; then
+ echo "$ac_file is unchanged"
+ rm -f conftest.h
+ else
+ # Remove last slash and all that follows it. Not all systems have dirname.
+ ac_dir=`echo $ac_file|sed 's%/[^/][^/]*$%%'`
+ if test "$ac_dir" != "$ac_file" && test "$ac_dir" != .; then
+ # The file is in a subdirectory.
+ test ! -d "$ac_dir" && mkdir "$ac_dir"
+ fi
+ rm -f $ac_file
+ mv conftest.h $ac_file
+ fi
+fi; done
+
+EOF
+cat >> $CONFIG_STATUS <<EOF
+
+
+EOF
+cat >> $CONFIG_STATUS <<\EOF
+test -z "$CONFIG_HEADERS" || echo timestamp > stamp-h
+
+exit 0
+EOF
+chmod +x $CONFIG_STATUS
+rm -fr confdefs* $ac_clean_files
+test "$no_create" = yes || ${CONFIG_SHELL-/bin/sh} $CONFIG_STATUS || exit 1
+
diff --git a/ipc-1.1/configure.in b/ipc-1.1/configure.in
new file mode 100644
index 0000000000000000000000000000000000000000..05a0b5eb716da96990e37c4ed1490909190ed08e
--- /dev/null
+++ b/ipc-1.1/configure.in
@@ -0,0 +1,29 @@
+dnl Process this file with autoconf to produce a configure script.
+AC_INIT(element.c)
+AM_CONFIG_HEADER(config.h)
+AM_INIT_AUTOMAKE(ipc,1.1)
+
+dnl Checks for programs.
+AC_PROG_INSTALL
+AC_PROG_LN_S
+AC_PROG_CC
+
+dnl Checks for libraries.
+AC_CHECK_LIB(m,rint)
+
+
+dnl Checks for header files.
+AC_HEADER_STDC
+AC_CHECK_HEADERS(math.h time.h signal.h unistd.h)
+
+dnl Checks for typedefs, structures, and compiler characteristics.
+
+dnl Checks for library functions.
+AC_TYPE_SIGNAL
+AC_CHECK_FUNCS(strdup strtol getcwd,,AC_MSG_ERROR(necessary lib function not found))
+AC_CHECK_FUNCS(system signal time)
+
+AC_ARG_ENABLE(NO_GNUPLOT,NO_GNUPLOT : IPC should not run GNU Plot when invoking -g option,AC_DEFINE(NOT_RUN_GNUPLOT),AC_DEFINE(NOT_RUN_GNUPLOT,0))
+
+
+AC_OUTPUT(Makefile)
diff --git a/ipc-1.1/element.c b/ipc-1.1/element.c
new file mode 100644
index 0000000000000000000000000000000000000000..64b28ba853e8ae5c77ee607a9df26c94f6f82efd
--- /dev/null
+++ b/ipc-1.1/element.c
@@ -0,0 +1,141 @@
+/***************************************************************************
+ * file : element.c *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#include "global.h"
+#include "element.h"
+#include <unistd.h>
+
+element *elements=NULL;
+
+FILE *open_file(char *filename)
+{
+ FILE *datenfile;
+ char *pwd;
+
+ pwd=getcwd(NULL,0);
+
+ if( (chdir(PREFIX)) == -1 )
+ {
+ printf("Can't change to directory %s\n",PREFIX);
+ return 0;
+ }
+
+ if(!(datenfile=fopen(filename,"r")))
+ {
+ printf("Can't open file: %s.\n",filename);
+ return 0;
+ }
+ if( (chdir(pwd)) == -1 )
+ {
+ printf("Can't change to directory %s\n",pwd);
+ return 0;
+ }
+ return datenfile;
+}
+
+char *get_token(char *linebuffer)
+{
+ static char *buffer;
+ static char token[MAX_LINE];
+ int c=0;
+
+ if(linebuffer)
+ buffer=linebuffer;
+
+ while( (*buffer!=' ') && (*buffer!='\n') && (*buffer!='\r') )
+ {
+ token[c]=*buffer;
+ *buffer++;
+ c++;
+ }
+ token[c]='\0';
+ *buffer++;
+ return token;
+}
+
+void add_element(element *ce)
+{
+ element *cur;
+
+ if(!(elements))
+ {
+ elements=ce;
+ elements->previous=NULL;
+ return;
+ }
+
+ cur=elements;
+ while(cur->next)
+ cur=cur->next;
+
+ cur->next=ce;
+ ce->previous=cur;
+}
+
+void add_isotope(isotope *ci,element *ce)
+{
+ isotope *cur;
+
+ if(!(ce->isotopes))
+ {
+ ce->isotopes=ci;
+ ci->previous=NULL;
+ return;
+ }
+
+ cur=ce->isotopes;
+ while(cur->next)
+ cur=cur->next;
+ cur->next=ci;
+ ci->previous=cur;
+ return;
+}
+
+int init_elements()
+{
+ FILE *data;
+ char linebuffer[MAX_LINE];
+ element *ce=NULL;
+ isotope *ci=NULL;
+ char *par;
+
+ if(!(data=open_file(ELEMENTFILE)))
+ return 0;
+
+ while(fgets(linebuffer,MAX_LINE,data))
+ {
+ if(isalpha(*linebuffer))
+ {
+ ce=(element*)malloc(sizeof(element));
+ ce->symbol=strdup(get_token(linebuffer));
+ ce->next=NULL;
+ ce->isotopes=NULL;
+ add_element(ce);
+ }
+ if(isdigit(*linebuffer))
+ {
+ ci=(isotope *)malloc(sizeof(isotope));
+ par=strdup(get_token(linebuffer));
+ ci->mass=atof(par);
+ par=strdup(get_token(0));
+ ci->p=atof(par);
+ ci->next=NULL;
+ add_isotope(ci,ce);
+ }
+ }
+
+ fclose(data);
+ return 1;
+}
diff --git a/ipc-1.1/element.c.old b/ipc-1.1/element.c.old
new file mode 100644
index 0000000000000000000000000000000000000000..1707d54692306f1e6510bd5a2ed506cb1fd0c8cd
--- /dev/null
+++ b/ipc-1.1/element.c.old
@@ -0,0 +1,140 @@
+/***************************************************************************
+ * file : element.c *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#include "global.h"
+#include "element.h"
+#include <unistd.h>
+
+element *elements=NULL;
+
+FILE *open_file(char *filename)
+{
+ FILE *datenfile;
+ char *pwd;
+
+ pwd=getcwd(NULL,0);
+
+ if( (chdir(PREFIX)) == -1 )
+ {
+ printf("Can't change to directory %s\n",PREFIX);
+ return 0;
+ }
+
+ if(!(datenfile=fopen(filename,"r")))
+ {
+ printf("Can't open file: %s.\n",filename);
+ return 0;
+ }
+ if( (chdir(pwd)) == -1 )
+ {
+ printf("Can't change to directory %s\n",pwd);
+ return 0;
+ }
+ return datenfile;
+}
+
+char *get_token(char *linebuffer)
+{
+ static char *buffer;
+ static char token[MAX_LINE];
+ int c=0;
+
+ if(linebuffer)
+ buffer=linebuffer;
+
+ while( (*buffer!=' ') && (*buffer!='\n') && (*buffer!='\r') )
+ {
+ token[c]=*buffer;
+ *buffer++;
+ c++;
+ }
+ token[c]='\0';
+ *buffer++;
+ return token;
+}
+
+void add_element(element *ce)
+{
+ element *cur;
+
+ if(!(elements))
+ {
+ elements=ce;
+ elements->previous=NULL;
+ return;
+ }
+
+ cur=elements;
+ while(cur->next)
+ cur=cur->next;
+
+ cur->next=ce;
+ ce->previous=cur;
+}
+
+void add_isotope(isotope *ci,element *ce)
+{
+ isotope *cur;
+
+ if(!(ce->isotopes))
+ {
+ ce->isotopes=ci;
+ ci->previous=NULL;
+ return;
+ }
+
+ cur=ce->isotopes;
+ while(cur->next)
+ cur=cur->next;
+ cur->next=ci;
+ ci->previous=cur;
+ return;
+}
+
+int init_elements()
+{
+ FILE *data;
+ char linebuffer[MAX_LINE];
+ element *ce=NULL;
+ isotope *ci=NULL;
+ char *par;
+
+ if(!(data=open_file(ELEMENTFILE)))
+ return 0;
+
+ while(fgets(linebuffer,MAX_LINE,data))
+ {
+ if(isalpha(*linebuffer))
+ {
+ ce=(element*)malloc(sizeof(element));
+ ce->symbol=strdup(get_token(linebuffer));
+ ce->next=NULL;
+ add_element(ce);
+ }
+ if(isdigit(*linebuffer))
+ {
+ ci=(isotope *)malloc(sizeof(isotope));
+ par=strdup(get_token(linebuffer));
+ ci->mass=atof(par);
+ par=strdup(get_token(0));
+ ci->p=atof(par);
+ ci->next=NULL;
+ add_isotope(ci,ce);
+ }
+ }
+
+ fclose(data);
+ return 1;
+}
diff --git a/ipc-1.1/element.h b/ipc-1.1/element.h
new file mode 100644
index 0000000000000000000000000000000000000000..7736f423ae3c2b4674d152a65987cb622ae7c610
--- /dev/null
+++ b/ipc-1.1/element.h
@@ -0,0 +1,31 @@
+/***************************************************************************
+ * file : element.h *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#ifndef _ELEMENT_H_
+#define _ELEMENT_H_
+
+#include <string.h>
+#include <ctype.h>
+
+#define ELEMENTFILE "elemente"
+#define MAX_LINE 30
+
+int init_elements(void);
+FILE* open_file(char *filename);
+void add_element(element *ce);
+void add_isotope(isotope *ci,element *ce);
+char *get_token(char *linebuffer);
+
+#endif
diff --git a/ipc-1.1/element.o b/ipc-1.1/element.o
new file mode 100644
index 0000000000000000000000000000000000000000..b69c8074bb5096b438480fc677ed60dd1d506f91
Binary files /dev/null and b/ipc-1.1/element.o differ
diff --git a/ipc-1.1/elemente b/ipc-1.1/elemente
new file mode 100644
index 0000000000000000000000000000000000000000..bf9c1afd73be401704612a9da3b87e52f82357a1
--- /dev/null
+++ b/ipc-1.1/elemente
@@ -0,0 +1,54 @@
+H
+1.007825 0.9999
+2.014102 0.0001
+
+C
+12.000000 0.9889
+13.003354 0.0111
+
+N
+14.003074 0.9963
+15.000108 0.0037
+
+O
+15.994915 0.9976
+16.999133 0.0004
+17.999160 0.0020
+
+F
+18.998405 1
+
+Na
+22.989773 1
+
+Si
+27.976927 0.9221
+28.976491 0.0470
+29.973761 0.0309
+
+P
+30.973763 1
+
+Ni
+57.935342 0.6788
+59.930783 0.2623
+60.931049 0.0119
+61.928345 0.0366
+63.927959 0.0108
+
+S
+31.972074 0.9502
+32.971460 0.0076
+33.967864 0.0422
+35.967091 0.0001
+
+Cl
+34.968854 0.7553
+36.965896 0.2447
+
+Br
+78.918348 0.5054
+80.916344 0.4946
+
+I
+126.904352 1
diff --git a/ipc-1.1/global.h b/ipc-1.1/global.h
new file mode 100644
index 0000000000000000000000000000000000000000..b15956729e68342d08f6e689529c3d842bbcff44
--- /dev/null
+++ b/ipc-1.1/global.h
@@ -0,0 +1,49 @@
+/***************************************************************************
+ * file : global.h *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#ifndef _GLOBAL_H_
+#define _GLOBAL_H_
+
+#include "config.h"
+#include <stdio.h>
+#include <stdlib.h>
+
+#define USE_DIGITS 5
+
+typedef struct isotope{
+ struct isotope *next,*previous;
+ double p;
+ double mass;
+} isotope;
+
+typedef struct compound {
+ struct compound *next,*previous;
+ int amount;
+ struct isotope *isotopes;
+} compound;
+
+typedef struct element {
+ struct element *next,*previous;
+ char *symbol;
+ struct isotope *isotopes;
+} element;
+
+extern element *elements;
+extern compound *verbindung;
+extern isotope *peaks;
+
+extern int fast_calc;
+
+#endif
diff --git a/ipc-1.1/gp_out.c b/ipc-1.1/gp_out.c
new file mode 100644
index 0000000000000000000000000000000000000000..4b0ed8451d156f0455bba8eb9a82f581c774cd4e
--- /dev/null
+++ b/ipc-1.1/gp_out.c
@@ -0,0 +1,162 @@
+#include "global.h"
+#include "gp_out.h"
+#include <math.h>
+
+void free_spectrum(spec_points *spectrum)
+{
+ while(spectrum->next)
+ {
+ spectrum=spectrum->next;
+ free(spectrum->previous);
+ }
+ free(spectrum);
+}
+
+void print_spectrum(spec_points *spectrum, FILE *output)
+{
+ while(spectrum)
+ {
+ fprintf(output,"%f, %f\n", spectrum->x, spectrum->y);
+ spectrum=spectrum->next;
+ }
+}
+
+spec_points *add_new_point(spec_points *spectrum)
+{
+ spec_points *dummy;
+
+ if(!(dummy=malloc(sizeof(spec_points))))
+ {
+ printf("Out of memory\n");
+ return 0;
+ }
+ spectrum->next=dummy;
+ dummy->previous=spectrum;
+ dummy->next=NULL;
+ return dummy;
+}
+
+spec_points *calc_points()
+{
+ isotope *reiter;
+ spec_points *point, *reiter2;
+ double maxp=0;
+ int end;
+
+ for(reiter=peaks;reiter;reiter=reiter->next)
+ if(reiter->p > maxp)
+ maxp=reiter->p;
+
+ reiter=peaks;
+ point=malloc(sizeof(spec_points));
+ point->previous=NULL;
+ point->next=NULL;
+ point->x=floor(reiter->mass-1);
+ point->y=0;
+ reiter2=point;
+
+ while(reiter)
+ {
+ if( (reiter->p)*10000 > maxp )
+ {
+
+ if(!(reiter2=add_new_point(reiter2)))
+ return 0;
+
+ reiter2->y=0;
+ reiter2->x=reiter->mass;
+
+ if(!(reiter2=add_new_point(reiter2)))
+ return 0;
+ reiter2->y=(reiter->p / maxp) * 100;
+ reiter2->x=reiter->mass;
+
+ if(!(reiter2=add_new_point(reiter2)))
+ return 0;
+ reiter2->y=0;
+ reiter2->x=reiter->mass;
+ }
+ reiter=reiter->next;
+ }
+
+ end=1+reiter2->x;
+ if(!(reiter2=add_new_point(reiter2)))
+ return 0;
+ reiter2->x=end;
+ reiter2->y=0;
+
+ return point;
+}
+
+int make_gnuplot_output(char *gnuplotfile)
+{
+ char *data_file,*start_gp;
+ spec_points *spectrum, *reiter;
+ FILE *gp,*data;
+ float xmin,xmax;
+
+ data_file=(char *) strdup(gnuplotfile);
+ strcat(gnuplotfile,".gnu");
+
+ if(!(spectrum=calc_points())){
+ printf("Error in calc_points");
+ return 0;
+ }
+
+ if(!(data=fopen(data_file,"w")))
+ {
+ printf("Error while opening data file\n");
+ return 0;
+ }
+
+ print_spectrum(spectrum, data);
+
+ if(fclose(data))
+ {
+ printf("Error while closing data file\n");
+ return 0;
+ }
+
+ if(!(gp=fopen(gnuplotfile,"w")))
+ {
+ printf("Error while opening gnuplot file\n");
+ return 0;
+ }
+
+ xmin=spectrum->x;
+ reiter=spectrum;
+ while(reiter->next)
+ reiter=reiter->next;
+ xmax=reiter->x;
+
+ fprintf(gp,"set xrange[%f:%f]\n",xmin,xmax);
+ fprintf(gp,"set yrange[-1:101]\n");
+ fprintf(gp,"set tics out\n");
+ fprintf(gp,"set nox2tics\n");
+ fprintf(gp,"set noy2tics\n");
+ fprintf(gp,"set ylabel \"rel. Int.\"\n");
+ fprintf(gp,"set xlabel \"m/z\"\n");
+ fprintf(gp,"plot \"%s\" with lines\n",data_file);
+ fprintf(gp,"pause -1 \"Press Return\"\n");
+
+ if(fclose(gp))
+ {
+ printf("Error while closing gnuplot file\n");
+ return 0;
+ }
+
+
+ free_spectrum(spectrum);
+
+ start_gp=(char *) strdup("gnuplot ");
+ start_gp=(char *) strcat(start_gp,gnuplotfile);
+
+#ifdef HAVE_SYSTEM
+
+ if(!(NOT_RUN_GNUPLOT))
+ system(start_gp);
+
+#endif
+
+ return 1;
+}
diff --git a/ipc-1.1/gp_out.h b/ipc-1.1/gp_out.h
new file mode 100644
index 0000000000000000000000000000000000000000..ff906c6818f9674cef5cb897fde0fb1d93b2e40f
--- /dev/null
+++ b/ipc-1.1/gp_out.h
@@ -0,0 +1,30 @@
+/***************************************************************************
+ * file : gp_out.h *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#ifndef _GPOUT_H_
+#define _GPOUT_H_
+
+typedef struct spec_points {
+ struct spec_points *next, *previous;
+ float x,y;
+} spec_points;
+
+int make_gnuplot_output(char *gnuplotfile);
+spec_points *calc_points(void);
+spec_points *add_new_point(spec_points *spectrum);
+void print_spectrum(spec_points *spectrum, FILE *output);
+void free_spectrum(spec_points *spectrum);
+
+#endif
diff --git a/ipc-1.1/gp_out.o b/ipc-1.1/gp_out.o
new file mode 100644
index 0000000000000000000000000000000000000000..7992134d49cd235a0a689cd02252a304d1e8eb3e
Binary files /dev/null and b/ipc-1.1/gp_out.o differ
diff --git a/ipc-1.1/install-sh b/ipc-1.1/install-sh
new file mode 100644
index 0000000000000000000000000000000000000000..e9de23842dcd44d2953129c866b1ad25f7e1f1d9
--- /dev/null
+++ b/ipc-1.1/install-sh
@@ -0,0 +1,251 @@
+#!/bin/sh
+#
+# install - install a program, script, or datafile
+# This comes from X11R5 (mit/util/scripts/install.sh).
+#
+# Copyright 1991 by the Massachusetts Institute of Technology
+#
+# Permission to use, copy, modify, distribute, and sell this software and its
+# documentation for any purpose is hereby granted without fee, provided that
+# the above copyright notice appear in all copies and that both that
+# copyright notice and this permission notice appear in supporting
+# documentation, and that the name of M.I.T. not be used in advertising or
+# publicity pertaining to distribution of the software without specific,
+# written prior permission. M.I.T. makes no representations about the
+# suitability of this software for any purpose. It is provided "as is"
+# without express or implied warranty.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch. It can only install one file at a time, a restriction
+# shared with many OS's install programs.
+
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit="${DOITPROG-}"
+
+
+# put in absolute paths if you don't have them in your path; or use env. vars.
+
+mvprog="${MVPROG-mv}"
+cpprog="${CPPROG-cp}"
+chmodprog="${CHMODPROG-chmod}"
+chownprog="${CHOWNPROG-chown}"
+chgrpprog="${CHGRPPROG-chgrp}"
+stripprog="${STRIPPROG-strip}"
+rmprog="${RMPROG-rm}"
+mkdirprog="${MKDIRPROG-mkdir}"
+
+transformbasename=""
+transform_arg=""
+instcmd="$mvprog"
+chmodcmd="$chmodprog 0755"
+chowncmd=""
+chgrpcmd=""
+stripcmd=""
+rmcmd="$rmprog -f"
+mvcmd="$mvprog"
+src=""
+dst=""
+dir_arg=""
+
+while [ x"$1" != x ]; do
+ case $1 in
+ -c) instcmd="$cpprog"
+ shift
+ continue;;
+
+ -d) dir_arg=true
+ shift
+ continue;;
+
+ -m) chmodcmd="$chmodprog $2"
+ shift
+ shift
+ continue;;
+
+ -o) chowncmd="$chownprog $2"
+ shift
+ shift
+ continue;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift
+ shift
+ continue;;
+
+ -s) stripcmd="$stripprog"
+ shift
+ continue;;
+
+ -t=*) transformarg=`echo $1 | sed 's/-t=//'`
+ shift
+ continue;;
+
+ -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
+ shift
+ continue;;
+
+ *) if [ x"$src" = x ]
+ then
+ src=$1
+ else
+ # this colon is to work around a 386BSD /bin/sh bug
+ :
+ dst=$1
+ fi
+ shift
+ continue;;
+ esac
+done
+
+if [ x"$src" = x ]
+then
+ echo "install: no input file specified"
+ exit 1
+else
+ true
+fi
+
+if [ x"$dir_arg" != x ]; then
+ dst=$src
+ src=""
+
+ if [ -d $dst ]; then
+ instcmd=:
+ chmodcmd=""
+ else
+ instcmd=mkdir
+ fi
+else
+
+# Waiting for this to be detected by the "$instcmd $src $dsttmp" command
+# might cause directories to be created, which would be especially bad
+# if $src (and thus $dsttmp) contains '*'.
+
+ if [ -f $src -o -d $src ]
+ then
+ true
+ else
+ echo "install: $src does not exist"
+ exit 1
+ fi
+
+ if [ x"$dst" = x ]
+ then
+ echo "install: no destination specified"
+ exit 1
+ else
+ true
+ fi
+
+# If destination is a directory, append the input filename; if your system
+# does not like double slashes in filenames, you may need to add some logic
+
+ if [ -d $dst ]
+ then
+ dst="$dst"/`basename $src`
+ else
+ true
+ fi
+fi
+
+## this sed command emulates the dirname command
+dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
+
+# Make sure that the destination directory exists.
+# this part is taken from Noah Friedman's mkinstalldirs script
+
+# Skip lots of stat calls in the usual case.
+if [ ! -d "$dstdir" ]; then
+defaultIFS='
+'
+IFS="${IFS-${defaultIFS}}"
+
+oIFS="${IFS}"
+# Some sh's can't handle IFS=/ for some reason.
+IFS='%'
+set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'`
+IFS="${oIFS}"
+
+pathcomp=''
+
+while [ $# -ne 0 ] ; do
+ pathcomp="${pathcomp}${1}"
+ shift
+
+ if [ ! -d "${pathcomp}" ] ;
+ then
+ $mkdirprog "${pathcomp}"
+ else
+ true
+ fi
+
+ pathcomp="${pathcomp}/"
+done
+fi
+
+if [ x"$dir_arg" != x ]
+then
+ $doit $instcmd $dst &&
+
+ if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi &&
+ if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi &&
+ if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi &&
+ if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi
+else
+
+# If we're going to rename the final executable, determine the name now.
+
+ if [ x"$transformarg" = x ]
+ then
+ dstfile=`basename $dst`
+ else
+ dstfile=`basename $dst $transformbasename |
+ sed $transformarg`$transformbasename
+ fi
+
+# don't allow the sed command to completely eliminate the filename
+
+ if [ x"$dstfile" = x ]
+ then
+ dstfile=`basename $dst`
+ else
+ true
+ fi
+
+# Make a temp file name in the proper directory.
+
+ dsttmp=$dstdir/#inst.$$#
+
+# Move or copy the file name to the temp name
+
+ $doit $instcmd $src $dsttmp &&
+
+ trap "rm -f ${dsttmp}" 0 &&
+
+# and set any options; do chmod last to preserve setuid bits
+
+# If any of these fail, we abort the whole thing. If we want to
+# ignore errors from any of these, just make sure not to ignore
+# errors from the above "$doit $instcmd $src $dsttmp" command.
+
+ if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi &&
+ if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi &&
+ if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi &&
+ if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi &&
+
+# Now rename the file to the real destination.
+
+ $doit $rmcmd -f $dstdir/$dstfile &&
+ $doit $mvcmd $dsttmp $dstdir/$dstfile
+
+fi &&
+
+
+exit 0
diff --git a/ipc-1.1/ipc b/ipc-1.1/ipc
new file mode 100644
index 0000000000000000000000000000000000000000..8f3eb19b48a24ffea6114ff7fec034e4755a5ba3
Binary files /dev/null and b/ipc-1.1/ipc differ
diff --git a/ipc-1.1/ipc.c b/ipc-1.1/ipc.c
new file mode 100644
index 0000000000000000000000000000000000000000..6c42d21a729e998a90ad2cf6a94c0bc1d6a3c4ff
--- /dev/null
+++ b/ipc-1.1/ipc.c
@@ -0,0 +1,372 @@
+/***************************************************************************
+ * file : ipc.c *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#include "global.h"
+#include "ipc.h"
+#include "pars.h"
+#include "element.h"
+#include "gp_out.h"
+#include <time.h>
+#include <signal.h>
+#include <math.h>
+
+compound *verbindung=NULL;
+isotope *peaks;
+int fast_calc=0;
+
+void free_list(isotope *target)
+{
+ while(target->next)
+ {
+ target=target->next;
+ free(target->previous);
+ }
+ free(target);
+}
+
+void cut_peaks(isotope *spectrum)
+{
+ int dummy=1;
+
+ while( (spectrum->next) && (dummy<fast_calc) )
+ {
+ dummy++;
+ spectrum=spectrum->next;
+ }
+
+ if(spectrum->next)
+ {
+ free_list(spectrum->next);
+ spectrum->next=NULL;
+ }
+}
+
+void summarize_peaks()
+{ isotope *dummy,*d2;
+
+ for(dummy=peaks;dummy;dummy=dummy->next)
+ /* Differenz wegen Rundungsfehlern */
+ while( dummy->next && (dummy->next->mass - dummy->mass < 0.00000001) )
+ {
+ d2=dummy->next;
+ dummy->next=d2->next;
+ if(dummy->next)
+ dummy->next->previous=dummy;
+ dummy->p+=d2->p;
+ free(d2);
+ }
+}
+
+isotope *add_peak(isotope *base,isotope *peak)
+{
+ static isotope *reiter;
+
+ if(!(base->mass))
+ {
+ peak->next=NULL;
+ peak->previous=NULL;
+ reiter=peak;
+ return peak;
+ }
+
+ if( peak->mass >= reiter->mass )
+ while( (reiter->next) && (reiter->mass < peak->mass))
+ reiter=reiter->next;
+ else
+ {
+ while( (reiter->previous) && (reiter->mass > peak->mass) )
+ reiter=reiter->previous;
+ reiter=reiter->next;
+ }
+
+ if( (reiter->mass) >= (peak->mass) )
+ {
+ peak->next=reiter;
+ peak->previous=reiter->previous;
+ peak->previous->next=peak;
+ reiter->previous=peak;
+ return base;
+ }
+ else
+ {
+ reiter->next=peak;
+ peak->next=NULL;
+ peak->previous=reiter;
+ return base;
+ }
+ return 0;
+}
+
+int calculate_peaks(){
+ compound *c;
+ isotope *npeaks,*p,*i,*np1;
+ int anzahl;
+
+ if(!(peaks=malloc(sizeof(isotope))))
+ return 0;
+ peaks->mass=0;
+ peaks->p=1;
+ peaks->previous=NULL;
+ peaks->next=NULL;
+
+ for(c=verbindung;c;c=c->next){
+ for(anzahl=0;anzahl < c->amount;anzahl++){
+
+ if(!(npeaks=malloc(sizeof(isotope))))
+ return 0;
+ npeaks->mass=0;
+
+ for(p=peaks;p;p=p->next){
+ for(i=c->isotopes;i;i=i->next){
+
+ if(!(np1=malloc(sizeof(isotope))))
+ return 0;
+
+ np1->mass=p->mass + i->mass;
+ np1->p=p->p * i->p;
+ if( !(npeaks=add_peak(npeaks,np1)) )
+ return 0;
+ }
+ }
+ free_list(peaks);
+ peaks=npeaks;
+ summarize_peaks();
+ if(fast_calc)
+ cut_peaks(peaks);
+ }
+ }
+ return 1;
+}
+
+
+void print_result(int digits,int charge){
+ isotope *d;
+ double maxp=0,relint=0,sump=0;
+ int permutationen=0;
+
+ printf("\n");
+
+ for(d=peaks;d;d=d->next)
+ {
+ permutationen++;
+ sump+=d->p;
+ d->mass=d->mass / charge;
+ d->mass=(rint( d->mass * pow(10,digits) ) / pow(10,digits) );
+ }
+
+ summarize_peaks();
+ for(d=peaks;d;d=d->next)
+ if(d->p > maxp)
+ maxp=d->p;
+
+ for(d=peaks;d;d=d->next)
+ {
+ if( ( relint=(d->p/maxp)*100) > MIN_INT )
+ printf("M= %f, p= %e, rel. Int.= %f%%\n",
+ d->mass,d->p,relint);
+ }
+ if(!(fast_calc))
+ printf("\nNumber of permutations: %i\n",permutationen);
+ else
+ {
+ sump=(rint(sump*10000)/100);
+ printf("\nCovered Intensity: %2.2f%% \n",sump);
+ }
+}
+
+int main(int argc,char **argv){
+ long seconds;
+ int d=1,zeig_summenformel=0,calc_peaks=1,gnuplot=0,use_digits=USE_DIGITS,charge=1;
+ char *gnuplotfile=NULL;
+
+ if(!argv[d])
+ {
+ usage();
+ return 1;
+ }
+
+#ifdef HAVE_SIGNAL
+ signal(SIGHUP,SIG_IGN);
+#endif
+
+ if(!init_elements()){
+ printf("Error in init_elements\n");
+ return 1;
+ }
+ while(argv[d])
+ {
+ if(!strcmp(argv[d],"-f"))
+ {
+ d++;
+ if(!argv[d])
+ {
+ printf("Missing argument for -f\n");
+ return 1;
+ }
+ fast_calc=strtol(argv[d],NULL,10);
+ }
+
+ else if(!strcmp(argv[d],"-z"))
+ {
+ d++;
+ if(!argv[d])
+ {
+ printf("Missing argument for -z\n");
+ return 1;
+ }
+ charge=strtol(argv[d],NULL,10);
+ }
+
+ else if(!strcmp(argv[d],"-d"))
+ {
+ d++;
+ if(!argv[d])
+ {
+ printf("Missing argument for -d\n");
+ return 1;
+ }
+ use_digits=strtol(argv[d],NULL,10);
+ }
+
+ else if(!strcmp(argv[d],"-c")){
+ d++;
+ if(!argv[d])
+ {
+ printf("Missing argument for -c\n");
+ return 1;
+ }
+ if(!pars_chem_form(argv[d])){
+ printf("Parser error.\n");
+ return 1;
+ }
+ }
+
+ else if(!strcmp(argv[d],"-g")){
+ d++;
+ if(!argv[d]){
+ printf("Missing argument for -g\n");
+ return 1;
+ }
+ gnuplot=1;
+ if(!(gnuplotfile=strdup(argv[d]))){
+ printf("Not enough memory\n");
+ return 1;
+ }
+ }
+
+
+ else if(!strcmp(argv[d],"-p")){
+ d++;
+ if(!argv[d]){
+ printf("Missing argument for -p\n");
+ return 1;
+ }
+ if(!(pars_peptid(argv[d]))){
+ printf("Error in peptid parser.\n");
+ return 1;
+ }
+ }
+
+ else if(!strcmp(argv[d],"-a")){
+ d++;
+ if(!argv[d]){
+ printf("Missing argument for -a\n");
+ return 1;
+ }
+ if(!pars_amino_acid(argv[d])){
+ printf("Error in pars_amino_acid.\n");
+ return 1;
+ }
+ }
+
+ else if(!strcmp(argv[d],"-s"))
+ zeig_summenformel=1;
+
+ else if(!strcmp(argv[d],"-h"))
+ {
+ usage();
+ return 1;
+ }
+
+ else if(!strcmp(argv[d],"-x"))
+ calc_peaks=0;
+
+ else
+ {
+ printf("Unknown flag: %s\n",argv[d]);
+ usage();
+ return 1;
+ }
+ d++;
+ }
+
+ if(zeig_summenformel)
+ {
+ if(!print_sum())
+ {
+ printf("error while showing chemical formula.\n");
+ return 1;
+ }
+ }
+#ifdef HAVE_TIME
+ seconds=time(0);
+#endif
+
+ if(calc_peaks)
+ if(!calculate_peaks()){
+ printf("Error in calculate_peaks\n");
+ return 1;
+ }
+
+ print_result(use_digits,charge);
+
+#ifdef HAVE_TIME
+ seconds=time(0)-seconds;
+ printf("Computing time: %li seconds.\n",seconds);
+#endif
+
+ if(gnuplot)
+ if(!(make_gnuplot_output(gnuplotfile))){
+ printf("Error while generating gnuplot file\n");
+ return 1;
+ }
+
+ return 0;
+}
+
+
+void usage()
+{
+ printf("\nThis is IPC v %s\nCopyright Dirk Nolting 2001\n\n",VERSION);
+ printf("\nSynopsis:\n ipc -d <int> -z <int> -f <int> <-a <amino acid> -c <chemical formula> -p <File> -g <name> -s -x -h\n\n");
+
+ printf("-c <chemical formula> calculates the isotopic pattern of the \n");
+ printf(" given chemical formula. Additive with -p\n");
+
+ printf("-p <File> reads peptide sequenz (one letter notation) from the \n");
+ printf(" given file and calculates the isotopic pattern. Additive with -c\n");
+
+ printf("-a <amino acids> calculate isotopic pattern from given amino acids\n");
+ printf(" in one letter notation\n");
+
+ printf("-s gives the chemical formula. Usefull for -a or -p\n");
+ printf("-g creates gnuplot output and stores it in the file <name> and <name>.gnu\n");
+
+ printf("-x no calculation of the isotopic pattern. Usefull for -s\n");
+ printf("-f fast calc, calculates only first <int> peaks\n");
+ printf("-d <int> digits significant\n");
+ printf("-z assume <int> charges on ion \n");
+ printf("-h show this text\n\n");
+}
diff --git a/ipc-1.1/ipc.h b/ipc-1.1/ipc.h
new file mode 100644
index 0000000000000000000000000000000000000000..d8d50f48fbc620f3c608f26ffecee013f25a355f
--- /dev/null
+++ b/ipc-1.1/ipc.h
@@ -0,0 +1,31 @@
+/***************************************************************************
+ * file : ipc.h *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#ifndef _IPC_H
+#define _IPC_H
+
+#define MIN_DIF 0.0009
+#define MIN_INT 0.009
+
+int main(int argc,char **argv);
+int calculate_peaks(void);
+void print_result(int digits,int charge);
+void free_list(isotope *target);
+void summarize_peaks(void);
+isotope *add_peak(isotope *base,isotope *peak);
+void usage(void);
+void cut_peaks(isotope *spectrum);
+
+#endif
diff --git a/ipc-1.1/ipc.o b/ipc-1.1/ipc.o
new file mode 100644
index 0000000000000000000000000000000000000000..2e4eb2f6ee206b9b837d0c0dfda9ff3f04db7f73
Binary files /dev/null and b/ipc-1.1/ipc.o differ
diff --git a/ipc-1.1/missing b/ipc-1.1/missing
new file mode 100644
index 0000000000000000000000000000000000000000..7789652e877fbc83c770377691249820eebea1f2
--- /dev/null
+++ b/ipc-1.1/missing
@@ -0,0 +1,190 @@
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+# Copyright (C) 1996, 1997 Free Software Foundation, Inc.
+# Franc,ois Pinard <pinard@iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+case "$1" in
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]"
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing - GNU libit 0.0"
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+ aclocal)
+ echo 1>&2 "\
+WARNING: \`$1' is missing on your system. You should only need it if
+ you modified \`acinclude.m4' or \`configure.in'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf)
+ echo 1>&2 "\
+WARNING: \`$1' is missing on your system. You should only need it if
+ you modified \`configure.in'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader)
+ echo 1>&2 "\
+WARNING: \`$1' is missing on your system. You should only need it if
+ you modified \`acconfig.h' or \`configure.in'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' configure.in`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case "$f" in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake)
+ echo 1>&2 "\
+WARNING: \`$1' is missing on your system. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`configure.in'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ bison|yacc)
+ echo 1>&2 "\
+WARNING: \`$1' is missing on your system. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f y.tab.h ]; then
+ echo >y.tab.h
+ fi
+ if [ ! -f y.tab.c ]; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex|flex)
+ echo 1>&2 "\
+WARNING: \`$1' is missing on your system. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if [ $# -ne 1 ]; then
+ eval LASTARG="\${$#}"
+ case "$LASTARG" in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if [ -f "$SRCFILE" ]; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if [ ! -f lex.yy.c ]; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ makeinfo)
+ echo 1>&2 "\
+WARNING: \`$1' is missing on your system. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+ if test -z "$file"; then
+ file=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $file`
+ fi
+ touch $file
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and you do not seem to have it handy on your
+ system. You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequirements for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
diff --git a/ipc-1.1/mkinstalldirs b/ipc-1.1/mkinstalldirs
new file mode 100644
index 0000000000000000000000000000000000000000..4f58503ea4e09c65165aa1ecaeac7c2c688648f3
--- /dev/null
+++ b/ipc-1.1/mkinstalldirs
@@ -0,0 +1,40 @@
+#! /bin/sh
+# mkinstalldirs --- make directory hierarchy
+# Author: Noah Friedman <friedman@prep.ai.mit.edu>
+# Created: 1993-05-16
+# Public domain
+
+# $Id: mkinstalldirs,v 1.13 1999/01/05 03:18:55 bje Exp $
+
+errstatus=0
+
+for file
+do
+ set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'`
+ shift
+
+ pathcomp=
+ for d
+ do
+ pathcomp="$pathcomp$d"
+ case "$pathcomp" in
+ -* ) pathcomp=./$pathcomp ;;
+ esac
+
+ if test ! -d "$pathcomp"; then
+ echo "mkdir $pathcomp"
+
+ mkdir "$pathcomp" || lasterr=$?
+
+ if test ! -d "$pathcomp"; then
+ errstatus=$lasterr
+ fi
+ fi
+
+ pathcomp="$pathcomp/"
+ done
+done
+
+exit $errstatus
+
+# mkinstalldirs ends here
diff --git a/ipc-1.1/pars.c b/ipc-1.1/pars.c
new file mode 100644
index 0000000000000000000000000000000000000000..8937cd0487eff147784f39e000e1041b9be6c97e
--- /dev/null
+++ b/ipc-1.1/pars.c
@@ -0,0 +1,323 @@
+/***************************************************************************
+ * file : pars.c *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#include "global.h"
+#include "pars.h"
+#include "element.h"
+
+int is_symbol(char *probe)
+{
+ element *cur;
+
+ cur=elements;
+ while(cur)
+ {
+ if(!strcmp(probe,cur->symbol))
+ return 1;
+ cur=cur->next;
+ }
+ return 0;
+}
+
+int add_component(char *symbol,int number)
+{
+ element *el;
+ compound *newco=NULL,*co;
+
+ el=elements;
+ while(el)
+ {
+ if(!strcmp(symbol,el->symbol))
+ {
+ newco=(compound *)malloc(sizeof(compound));
+ newco->isotopes=el->isotopes;
+ newco->amount=number;
+ newco->next=NULL;
+ }
+ el=el->next;
+ }
+
+ if(!newco)
+ {
+ printf("Unknown element: %s. Check input or file elemente\n",symbol);
+ return 0;
+ }
+
+ co=verbindung;
+ if(!verbindung)
+ {
+ newco->previous=NULL;
+ verbindung=newco;
+ return 1;
+ }
+
+ while(co)
+ {
+ if( co->isotopes == newco->isotopes )
+ {
+ co->amount+=newco->amount;
+ free(newco);
+ return 1;
+ }
+ co=co->next;
+ }
+
+ co=verbindung;
+ while(co->next)
+ co=co->next;
+ co->next=newco;
+ newco->previous=co;
+ return 1;
+}
+
+int pars_chem_form(char *formel)
+{
+ char par[MAX_DIGITS],par1[MAX_DIGITS];
+ int m=0,number=0;
+
+ if(!formel) return 0;
+
+ while(*formel)
+ {
+ m=0;
+ while( isalpha(*formel) )
+ {
+ par[m]=*formel;
+ par[m+1]='\0';
+ m++;
+ *formel++;
+ /*Adding omiited 1, e.g. CCl4 ->C1Cl4 */
+ if(is_symbol(par) && isupper(*formel))
+ {
+ add_component(par,1);
+ m=0;
+ }
+ }
+ m=0;
+
+ while( isdigit(*formel))
+ {
+ par1[m]=*formel;
+ m++;
+ *formel++;
+ }
+ par1[m]='\0';
+ number=atoi(par1);
+ /* Adding omitted last 1, e.g. CH3Cl -> CH3Cl1 */
+ if(!number) number=1;
+ if(!add_component(par,number))
+ return 0;
+ }
+ return 1;
+}
+
+int add_amino_acid(char acid)
+{
+ switch(acid)
+ {
+ case 'A':
+ add_component("C",3);
+ add_component("H",5);
+ add_component("N",1);
+ add_component("O",1);
+ break;
+ case 'R':
+ add_component("C",6);
+ add_component("H",12);
+ add_component("N",4);
+ add_component("O",1);
+ break;
+ case 'N':
+ add_component("C",4);
+ add_component("H",6);
+ add_component("N",2);
+ add_component("O",2);
+ break;
+ case 'B':
+ case 'D':
+ add_component("C",4);
+ add_component("H",5);
+ add_component("N",1);
+ add_component("O",3);
+ break;
+ case 'C':
+ add_component("C",3);
+ add_component("H",5);
+ add_component("N",1);
+ add_component("O",1);
+ add_component("S",1);
+ break;
+ case 'E':
+ add_component("C",5);
+ add_component("H",7);
+ add_component("N",1);
+ add_component("O",3);
+ break;
+ case 'Z':
+ case 'Q':
+ add_component("C",5);
+ add_component("H",8);
+ add_component("N",2);
+ add_component("O",2);
+ break;
+ case 'X':
+ case 'G':
+ add_component("C",2);
+ add_component("H",3);
+ add_component("N",1);
+ add_component("O",1);
+ break;
+ case 'H':
+ add_component("C",6);
+ add_component("H",7);
+ add_component("N",3);
+ add_component("O",1);
+ break;
+ case 'I':
+ case 'L':
+ add_component("C",6);
+ add_component("H",11);
+ add_component("N",1);
+ add_component("O",1);
+ break;
+ case 'K':
+ add_component("C",6);
+ add_component("H",12);
+ add_component("N",2);
+ add_component("O",1);
+ break;
+ case 'M':
+ add_component("C",5);
+ add_component("H",9);
+ add_component("N",1);
+ add_component("O",1);
+ add_component("S",1);
+ break;
+ case 'F':
+ add_component("C",9);
+ add_component("H",9);
+ add_component("N",1);
+ add_component("O",1);
+ break;
+ case 'P':
+ add_component("C",5);
+ add_component("H",7);
+ add_component("N",1);
+ add_component("O",1);
+ break;
+ case 'S':
+ add_component("C",3);
+ add_component("H",5);
+ add_component("N",1);
+ add_component("O",2);
+ break;
+ case 'T':
+ add_component("C",4);
+ add_component("H",7);
+ add_component("N",1);
+ add_component("O",2);
+ break;
+ case 'W':
+ add_component("C",11);
+ add_component("H",10);
+ add_component("N",2);
+ add_component("O",1);
+ break;
+ case 'Y':
+ add_component("C",9);
+ add_component("H",9);
+ add_component("N",1);
+ add_component("O",2);
+ break;
+ case 'V':
+ add_component("C",5);
+ add_component("H",9);
+ add_component("N",1);
+ add_component("O",1);
+ break;
+ default:
+ printf("Unknown symbol: %c\n",acid);
+ return 0;
+ }
+ return 1;
+}
+
+int pars_amino_acid(char *formel)
+{
+ while(*formel)
+ {
+ if(!add_amino_acid(*formel))
+ return 0;
+ *formel++;
+ }
+ add_component("O",1);
+ add_component("H",2);
+
+ return 1;
+}
+
+int pars_peptid(char *formel)
+{
+ FILE *peptid_file;
+ char linebuffer[MAX_PEP_LINE];
+ int index=0;
+
+ if(!(peptid_file=fopen(formel,"r")))
+ {
+ printf("Can�t open file: %s\n",formel);
+ return 0;
+ }
+
+ while( fgets(linebuffer,MAX_PEP_LINE,peptid_file) )
+ {
+ while( linebuffer[index] != '\n' )
+ {
+ add_amino_acid(linebuffer[index]);
+ index++;
+ }
+ index=0;
+ }
+
+ add_component("O",1);
+ add_component("H",2);
+
+ fclose(peptid_file);
+
+ return 1;
+}
+
+
+int print_sum()
+{
+ element *el;
+ compound *co;
+
+ printf("\nChemical formula: ");
+ co=verbindung;
+
+ while(co)
+ {
+ el=elements;
+ while( el && ( co->isotopes != el->isotopes) )
+ el=el->next;
+
+ if(!el) return 0;
+ printf("%s%i ",el->symbol,co->amount);
+ co=co->next;
+ }
+
+ printf("\n");
+ return 1;
+}
diff --git a/ipc-1.1/pars.h b/ipc-1.1/pars.h
new file mode 100644
index 0000000000000000000000000000000000000000..3f7f3b1ad1545d41d39cdbc2e7f5dd467676672c
--- /dev/null
+++ b/ipc-1.1/pars.h
@@ -0,0 +1,33 @@
+/***************************************************************************
+ * file : pars.h *
+ * copyright : (C) 2001 by Dirk Nolting *
+ * email : nolting@uni-duesseldorf.de *
+ ***************************************************************************/
+
+/***************************************************************************
+ * *
+ * This program is free software; you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation; either version 2 of the License, or *
+ * (at your option) any later version. *
+ * *
+ ***************************************************************************/
+
+#ifndef _PARS_H_
+#define _PARS_H_
+
+#define MAX_DIGITS 10
+#define MAX_PEP_LINE 81
+
+#include <string.h>
+#include <ctype.h>
+
+int pars_peptid(char *formel);
+int pars_chem_form(char *formel);
+int is_symbol(char *probe);
+int add_component(char *symbol,int number);
+int pars_amino_acid(char *formel);
+int add_amino_acid(char acid);
+int print_sum(void);
+
+#endif
diff --git a/ipc-1.1/pars.o b/ipc-1.1/pars.o
new file mode 100644
index 0000000000000000000000000000000000000000..49eb74a5bc66086ccc54a8051941a46e1d731f60
Binary files /dev/null and b/ipc-1.1/pars.o differ
diff --git a/ipc-1.1/stamp-h b/ipc-1.1/stamp-h
new file mode 100644
index 0000000000000000000000000000000000000000..9788f70238c91894045d22366fa941580826c3c1
--- /dev/null
+++ b/ipc-1.1/stamp-h
@@ -0,0 +1 @@
+timestamp
diff --git a/ipc-1.1/stamp-h.in b/ipc-1.1/stamp-h.in
new file mode 100644
index 0000000000000000000000000000000000000000..9788f70238c91894045d22366fa941580826c3c1
--- /dev/null
+++ b/ipc-1.1/stamp-h.in
@@ -0,0 +1 @@
+timestamp
diff --git a/samples/.DS_Store b/samples/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..22197d36428968c206e2e9bb603bead3508627cd
Binary files /dev/null and b/samples/.DS_Store differ
diff --git a/samples/MS_Fit_files/.DS_Store b/samples/MS_Fit_files/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/samples/MS_Fit_files/.DS_Store differ
diff --git a/samples/MS_Fit_files/C25plst02.html b/samples/MS_Fit_files/C25plst02.html
new file mode 100644
index 0000000000000000000000000000000000000000..507325b6fabe672fc9b87df0b5a5dace21f96160
--- /dev/null
+++ b/samples/MS_Fit_files/C25plst02.html
@@ -0,0 +1,119 @@
+<TITLE></TITLE>
+<TITLE>MS-Fit Search Results</TITLE>
+<BODY BGCOLOR=DDFFDD TEXT=000000 LINK=4D4DFF VLINK=FF0000>
+<H2 ALIGN=center>MS-Fit Search Results</H2><HR>
+Press stop on your browser if you wish to abort this MS-Fit search prematurely.<BR>
+ <SCRIPT LANGUAGE="Javascript">msprodLink="/ucsfbin3.2/msprod.cgi?it=i&it=m&it=a&it=b&it=y&it=I&it=h&it=n&it=B&mass_type=monoisotopic&instrument_name=MALDI-TOF&user_aa_c=0&user_aa_h=0&user_aa_n=0&user_aa_o=0&user_aa_s=0&user_aa_p=0&msparams_dir=msparams3.2/&seqdb_dir=seqdb/&cys=carbamidomethylation&nterm=Hydrogen&cterm=Free+Acid&";
+msdigestLink="/ucsfbin3.2/msdigest.cgi?min_digest_fragment_mass=500.0&mod_AA=User+Defined+1&mod_AA=Oxidation+of+M&user1_name=Deuteration+of+L&database=PA.cosyeast200409&instrument_name=MALDI-TOF&enzyme=Trypsin&missed_cleavages=2&msparams_dir=msparams3.2/&seqdb_dir=seqdb/&cys=carbamidomethylation&nterm=Hydrogen&cterm=Free+Acid&";
+accessLink="../ucsfhtml3.2/instruct/servadmn.htm#update_acclinks?";
+</SCRIPT>
+
+<TABLE CELLSPACING=4><TR><TD>
+Sample ID (comment):<B> <!--comment-->C25plst.txt</B><BR>
+Database searched:<B> <!--database-->PA.cosyeast200409</B><BR>Molecular weight search (<B>25000 - 75000 Da</B>) selects <B>3317</B> entries.<BR>Full pI range: <B>6774</B> entries.<BR>Combined molecular weight and pI searches select <B>3317</B> entries.<BR>
+MS-Fit search selects <B>574</B> entries (results displayed for top <B>5</B> matches).<P>
+</TD>
+</TABLE>Considered modifications: | <B>Deuteration of L</B> | <B>Oxidation of M</B> | <BR>
+<TABLE CELLPADDING=4>
+<TR><TD ALIGN=center>Min. # Peptides<BR>to Match<BR><B><!--min_matches-->4</B><TD ALIGN=center>Peptide Mass<BR>Tolerance (+/-)<BR><B><!--parent_mass_tolerance-->30.000 <!--tolerance_units-->ppm</B><TD ALIGN=center>Peptide Masses<BR>are<BR><B>monoisotopic</B><TD ALIGN=center>Digest<BR>Used<BR><B><!--enzyme-->Trypsin</B><TD ALIGN=center>Max. # Missed<BR>Cleavages<BR><B><!--missed_cleavages-->1</B><TD ALIGN=center>Cysteines<BR>Modified by<BR><B><!--cys-->carbamidomethylation</B>
+<TD NOWRAP ALIGN=center>Peptide<BR>N terminus<BR><B>Hydrogen (H)</B><TD NOWRAP ALIGN=center>Peptide<BR>C terminus<BR><B>Free Acid (O H)</B><TD ALIGN=center>Input #<BR>Peptide Masses<BR><B>85</B>
+</TABLE>
+
+<H3 ALIGN=center>Result Summary</H3>
+
+<TABLE>
+<TR><TH>Rank<TH>MOWSE<BR>Score<TH># (%)<BR>Masses<BR>Matched <TH>Protein<BR>MW (Da)/pI<TH>Species<TH>PA.cosyeast200409<BR>Accession #<TH ALIGN=left>Protein Name
+<TR>
+<TR><TH><!--rank--><A HREF="#0">1</A><TH><!--mowse_score-->5.3e+004<TH NOWRAP>15/85 (17%)<TH NOWRAP><!--protein_mw--> 55488.9 / <!--protein_pI-->9.52<TD><!--species-->SACCHAROMYCES CEREVISIAE<TH><!--accession_number--><SCRIPT> document.writeln ( "<A HREF =\"" + accessLink + "YNR053C\"> YNR053C </A>" );</SCRIPT><TD><!--entry_name-->NOG2
+<TR><TH><!--rank--><A HREF="#1">2</A><TH><!--mowse_score-->666<TH NOWRAP>6/85 (7%)<TH NOWRAP><!--protein_mw--> 46681.7 / <!--protein_pI-->7.19<TD><!--species-->SACCHAROMYCES CEREVISIAE<TH><!--accession_number--><SCRIPT> document.writeln ( "<A HREF =\"" + accessLink + "YOL140W\"> YOL140W </A>" );</SCRIPT><TD><!--entry_name-->ARG8
+<TR><TH><!--rank--><A HREF="#2">3</A><TH><!--mowse_score-->602<TH NOWRAP>8/85 (9%)<TH NOWRAP><!--protein_mw--> 59518.9 / <!--protein_pI-->5.13<TD><!--species-->HOMO SAPIENS<TH><!--accession_number--><SCRIPT> document.writeln ( "<A HREF =\"" + accessLink + "P13645\"> P13645 </A>" );</SCRIPT><TD><!--entry_name-->K1CJ_HUMAN Keratin
+<TR><TH><!--rank--><A HREF="#3">4</A><TH><!--mowse_score-->444<TH NOWRAP>6/85 (7%)<TH NOWRAP><!--protein_mw--> 43903.6 / <!--protein_pI-->4.58<TD><!--species-->SACCHAROMYCES CEREVISIAE<TH><!--accession_number--><SCRIPT> document.writeln ( "<A HREF =\"" + accessLink + "YLR449W\"> YLR449W </A>" );</SCRIPT><TD><!--entry_name-->FPR4
+<TR><TH><!--rank--><A HREF="#4">5</A><TH><!--mowse_score-->398<TH NOWRAP>8/85 (9%)<TH NOWRAP><!--protein_mw--> 56719.7 / <!--protein_pI-->5.90<TD><!--species-->SACCHAROMYCES CEREVISIAE<TH><!--accession_number--><SCRIPT> document.writeln ( "<A HREF =\"" + accessLink + "YMR300C\"> YMR300C </A>" );</SCRIPT><TD><!--entry_name-->ADE4
+</TABLE><HR><P>
+
+<H3 ALIGN=center>Detailed Results</H3>
+<BR><A NAME="0"></A><!--rank-->1. <!--fraction_matched-->15/85 matches (17%). <!--prot_mw--> 55488.9 Da, pI = <!--prot_pI-->9.52. Acc. # <!--accession_number-->YNR053C. <!--species-->SACCHAROMYCES CEREVISIAE. <!--entry_name-->NOG2.
+
+<TABLE>
+<TR><TH>m/z<BR>submitted</TH><TH> MH<SUP>+</SUP><BR>matched</TH><TH>Delta <BR>ppm</TH><TH>start</TH><TH>end</TH><TH ALIGN=left>Peptide Sequence <BR>(Click for Fragment Ions)</TH><TH ALIGN=left>Modifications</TH>
+<TR><TH ALIGN=right><!--in_mass-->780.3832<TH ALIGN=right><!--matched_mass-->780.3793<TH ALIGN=right><!--delta_mass-->5.0008<TH> 77<TH> 82<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=WFGNTR\">WFGNTR</A>");</SCRIPT>(V)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->899.5570<TH ALIGN=right><!--matched_mass-->899.5678<TH ALIGN=right><!--delta_mass-->-12.0353<TH> 297<TH> 304<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=GSLIQLLR\">GSLIQLLR</A>");</SCRIPT>(Q)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1012.5215<TH ALIGN=right><!--matched_mass-->1012.5216<TH ALIGN=right><!--delta_mass-->-0.1034<TH> 24<TH> 31<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=VKGENFYR\">VKGENFYR</A>");</SCRIPT>(D)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1134.5652<TH ALIGN=right><!--matched_mass-->1134.5782<TH ALIGN=right><!--delta_mass-->-11.4323<TH> 305<TH> 313<TH ALIGN=left><NOBR>(R)QFSQLHTDR(K)</NOBR><TH>1D3
+<TR><TH ALIGN=right><!--in_mass-->1280.6694<TH ALIGN=right><!--matched_mass-->1280.6976<TH ALIGN=right><!--delta_mass-->-22.0328<TH> 423<TH> 433<TH ALIGN=left><NOBR>(K)DATEFIEILAR(K)</NOBR><TH>1D3
+<TR><TH ALIGN=right><!--in_mass-->1313.6723<TH ALIGN=right><!--matched_mass-->1313.6966<TH ALIGN=right><!--delta_mass-->-18.5043<TH> 83<TH> 93<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=VISQDALQHFR\">VISQDALQHFR</A>");</SCRIPT>(S)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1316.6871<TH ALIGN=right><!--matched_mass-->1316.7201<TH ALIGN=right><!--delta_mass-->-25.0502<TH> 83<TH> 93<TH ALIGN=left><NOBR>(R)VISQDALQHFR(S)</NOBR><TH>1D3
+<TR><TH ALIGN=right><!--in_mass-->1426.7383<TH ALIGN=right><!--matched_mass-->1426.7728<TH ALIGN=right><!--delta_mass-->-24.1878<TH> 339<TH> 351<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=KVCQVAPIPGETK\">KVCQVAPIPGETK</A>");</SCRIPT>(V)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1637.8480<TH ALIGN=right><!--matched_mass-->1637.8863<TH ALIGN=right><!--delta_mass-->-23.3596<TH> 218<TH> 232<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=VIDSSDVVIHVLDAR\">VIDSSDVVIHVLDAR</A>");</SCRIPT>(D)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1821.9176<TH ALIGN=right><!--matched_mass-->1821.9711<TH ALIGN=right><!--delta_mass-->-29.3378<TH> 94<TH> 109<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=SALGETQKDTYQVLLR\">SALGETQKDTYQVLLR</A>");</SCRIPT>(R)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1845.9513<TH ALIGN=right><!--matched_mass-->1845.9863<TH ALIGN=right><!--delta_mass-->-18.9648<TH> 390<TH> 405<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=VEHVTHPEQYIPGVLK\">VEHVTHPEQYIPGVLK</A>");</SCRIPT>(R)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1875.9294<TH ALIGN=right><!--matched_mass-->1875.9717<TH ALIGN=right><!--delta_mass-->-22.5597<TH> 280<TH> 296<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=ERPTLAFHASITNSFGK\">ERPTLAFHASITNSFGK</A>");</SCRIPT>(G)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1878.9498<TH ALIGN=right><!--matched_mass-->1878.9952<TH ALIGN=right><!--delta_mass-->-24.1600<TH> 280<TH> 296<TH ALIGN=left><NOBR>(K)ERPTLAFHASITNSFGK(G)</NOBR><TH>1D3
+<TR><TH ALIGN=right><!--in_mass-->2002.0392<TH ALIGN=right><!--matched_mass-->2002.0874<TH ALIGN=right><!--delta_mass-->-24.0848<TH> 390<TH> 406<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=VEHVTHPEQYIPGVLKR\">VEHVTHPEQYIPGVLKR</A>");</SCRIPT>(C)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->2005.0623<TH ALIGN=right><!--matched_mass-->2005.1109<TH ALIGN=right><!--delta_mass-->-24.2356<TH> 390<TH> 406<TH ALIGN=left><NOBR>(R)VEHVTHPEQYIPGVLKR(C)</NOBR><TH>1D3
+</TD>
+</TABLE>
+<BR>70 unmatched masses: <!--in_mass-->807.4103 <!--in_mass-->842.5100 <!--in_mass-->844.4115 <!--in_mass-->870.5324 <!--in_mass-->876.4886 <!--in_mass-->882.5242 <!--in_mass-->905.4814 <!--in_mass-->908.5322 <!--in_mass-->909.4996 <!--in_mass-->1034.5536 <!--in_mass-->1043.5967 <!--in_mass-->1068.5926 <!--in_mass-->1071.6061 <!--in_mass-->1084.5853 <!--in_mass-->1087.5954 <!--in_mass-->1090.5345 <!--in_mass-->1114.5542 <!--in_mass-->1119.5808 <!--in_mass-->1124.5976 <!--in_mass-->1165.5794 <!--in_mass-->1191.6559 <!--in_mass-->1196.6204 <!--in_mass-->1199.6401 <!--in_mass-->1211.5929 <!--in_mass-->1227.6725 <!--in_mass-->1233.6940 <!--in_mass-->1234.6639 <!--in_mass-->1300.5785 <!--in_mass-->1307.6607 <!--in_mass-->1347.7553 <!--in_mass-->1360.6193 <!--in_mass-->1384.7265 <!--in_mass-->1413.6466 <!--in_mass-->1434.7436 <!--in_mass-->1474.6897 <!--in_mass-->1478.7466 <!--in_mass-->1490.6869 <!--in_mass-->1493.7047 <!--in_mass-->1521.6975 <!--in_mass-->1522.7052 <!--in_mass-->1525.8075 <!--in_mass-->1535.7197 <!--in_mass-->1549.7436 <!--in_mass-->1584.7361 <!--in_mass-->1587.7484 <!--in_mass-->1591.7540 <!--in_mass-->1640.8589 <!--in_mass-->1649.8864 <!--in_mass-->1656.8509 <!--in_mass-->1703.8614 <!--in_mass-->1707.7505 <!--in_mass-->1749.8157 <!--in_mass-->1764.8774 <!--in_mass-->1779.7966 <!--in_mass-->1829.9373 <!--in_mass-->1848.9478 <!--in_mass-->1920.9815 <!--in_mass-->1971.9244 <!--in_mass-->2027.0247 <!--in_mass-->2081.0136 <!--in_mass-->2096.9674 <!--in_mass-->2157.0632 <!--in_mass-->2211.1046 <!--in_mass-->2225.1109 <!--in_mass-->2283.1102 <!--in_mass-->2356.9758 <!--in_mass-->2360.0876 <!--in_mass-->2717.0585 <!--in_mass-->2807.2543 <!--in_mass-->2845.2805 <P><NOBR> The matched peptides cover <B><!--protein_coverage-->26%</B> (131/487 AA's) of the protein.</NOBR>
+<BR>Coverage Map for This Hit (MS-Digest index #): <SCRIPT> document.write ( "<A HREF = \"" + msdigestLink + "dna_reading_frame=1&access_method=Index+Number&open_reading_frame=1&coverage_map=0+23+8+45+33+108+15+47+34+25+13+38+17+16+11+54&index_num=5522\"> 5522 </A>" );</SCRIPT><P>
+<BR><A NAME="1"></A><!--rank-->2. <!--fraction_matched-->6/85 matches (7%). <!--prot_mw--> 46681.7 Da, pI = <!--prot_pI-->7.19. Acc. # <!--accession_number-->YOL140W. <!--species-->SACCHAROMYCES CEREVISIAE. <!--entry_name-->ARG8.
+
+<TABLE>
+<TR><TH>m/z<BR>submitted</TH><TH> MH<SUP>+</SUP><BR>matched</TH><TH>Delta <BR>ppm</TH><TH>start</TH><TH>end</TH><TH ALIGN=left>Peptide Sequence <BR>(Click for Fragment Ions)</TH><TH ALIGN=left>Modifications</TH>
+<TR><TH ALIGN=right><!--in_mass-->1313.6723<TH ALIGN=right><!--matched_mass-->1313.6649<TH ALIGN=right><!--delta_mass-->5.6049<TH> 160<TH> 171<TH ALIGN=left><NOBR>(R)TMGALSVTWNSK(Y)</NOBR><TH>1D3 1Met-ox
+<TR><TH ALIGN=right><!--in_mass-->1829.9373<TH ALIGN=right><!--matched_mass-->1829.9723<TH ALIGN=right><!--delta_mass-->-19.1250<TH> 361<TH> 377<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=GLMLGAEFVEPPTEVIK\">GLMLGAEFVEPPTEVIK</A>");</SCRIPT>(K)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1845.9513<TH ALIGN=right><!--matched_mass-->1845.9672<TH ALIGN=right><!--delta_mass-->-8.6204<TH> 361<TH> 377<TH ALIGN=left><NOBR>(K)GLMLGAEFVEPPTEVIK(K)</NOBR><TH>1Met-ox
+<TR><TH ALIGN=right><!--in_mass-->1848.9478<TH ALIGN=right><!--matched_mass-->1848.9907<TH ALIGN=right><!--delta_mass-->-23.1954<TH> 361<TH> 377<TH ALIGN=left><NOBR>(K)GLMLGAEFVEPPTEVIK(K)</NOBR><TH>1D3 1Met-ox
+<TR><TH ALIGN=right><!--in_mass-->2283.1102<TH ALIGN=right><!--matched_mass-->2283.1331<TH ALIGN=right><!--delta_mass-->-10.0341<TH> 83<TH> 101<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=LVHSSNLYFTKECLDLSEK\">LVHSSNLYFTKECLDLSEK</A>");</SCRIPT>(I)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->2807.2543<TH ALIGN=right><!--matched_mass-->2807.3171<TH ALIGN=right><!--delta_mass-->-22.3755<TH> 108<TH> 133<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=QFGGQHDASRVFLCNSGTEANEAALK\">QFGGQHDASRVFLCNSGTEANEAALK</A>");</SCRIPT>(F)</NOBR><TH>
+</TD>
+</TABLE>
+<BR>79 unmatched masses: <!--in_mass-->780.3832 <!--in_mass-->807.4103 <!--in_mass-->842.5100 <!--in_mass-->844.4115 <!--in_mass-->870.5324 <!--in_mass-->876.4886 <!--in_mass-->882.5242 <!--in_mass-->899.5570 <!--in_mass-->905.4814 <!--in_mass-->908.5322 <!--in_mass-->909.4996 <!--in_mass-->1012.5215 <!--in_mass-->1034.5536 <!--in_mass-->1043.5967 <!--in_mass-->1068.5926 <!--in_mass-->1071.6061 <!--in_mass-->1084.5853 <!--in_mass-->1087.5954 <!--in_mass-->1090.5345 <!--in_mass-->1114.5542 <!--in_mass-->1119.5808 <!--in_mass-->1124.5976 <!--in_mass-->1134.5652 <!--in_mass-->1165.5794 <!--in_mass-->1191.6559 <!--in_mass-->1196.6204 <!--in_mass-->1199.6401 <!--in_mass-->1211.5929 <!--in_mass-->1227.6725 <!--in_mass-->1233.6940 <!--in_mass-->1234.6639 <!--in_mass-->1280.6694 <!--in_mass-->1300.5785 <!--in_mass-->1307.6607 <!--in_mass-->1316.6871 <!--in_mass-->1347.7553 <!--in_mass-->1360.6193 <!--in_mass-->1384.7265 <!--in_mass-->1413.6466 <!--in_mass-->1426.7383 <!--in_mass-->1434.7436 <!--in_mass-->1474.6897 <!--in_mass-->1478.7466 <!--in_mass-->1490.6869 <!--in_mass-->1493.7047 <!--in_mass-->1521.6975 <!--in_mass-->1522.7052 <!--in_mass-->1525.8075 <!--in_mass-->1535.7197 <!--in_mass-->1549.7436 <!--in_mass-->1584.7361 <!--in_mass-->1587.7484 <!--in_mass-->1591.7540 <!--in_mass-->1637.8480 <!--in_mass-->1640.8589 <!--in_mass-->1649.8864 <!--in_mass-->1656.8509 <!--in_mass-->1703.8614 <!--in_mass-->1707.7505 <!--in_mass-->1749.8157 <!--in_mass-->1764.8774 <!--in_mass-->1779.7966 <!--in_mass-->1821.9176 <!--in_mass-->1875.9294 <!--in_mass-->1878.9498 <!--in_mass-->1920.9815 <!--in_mass-->1971.9244 <!--in_mass-->2002.0392 <!--in_mass-->2005.0623 <!--in_mass-->2027.0247 <!--in_mass-->2081.0136 <!--in_mass-->2096.9674 <!--in_mass-->2157.0632 <!--in_mass-->2211.1046 <!--in_mass-->2225.1109 <!--in_mass-->2356.9758 <!--in_mass-->2360.0876 <!--in_mass-->2717.0585 <!--in_mass-->2845.2805 <P><NOBR> The matched peptides cover <B><!--protein_coverage-->17%</B> (74/424 AA's) of the protein.</NOBR>
+<BR>Coverage Map for This Hit (MS-Digest index #): <SCRIPT> document.write ( "<A HREF = \"" + msdigestLink + "dna_reading_frame=1&access_method=Index+Number&open_reading_frame=1&coverage_map=0+82+19+6+26+26+12+189+17+47&index_num=5698\"> 5698 </A>" );</SCRIPT><P>
+<BR><A NAME="2"></A><!--rank-->3. <!--fraction_matched-->8/85 matches (9%). <!--prot_mw--> 59518.9 Da, pI = <!--prot_pI-->5.13. Acc. # <!--accession_number-->P13645. <!--species-->HOMO SAPIENS. <!--entry_name-->K1CJ_HUMAN Keratin.
+
+<TABLE>
+<TR><TH>m/z<BR>submitted</TH><TH> MH<SUP>+</SUP><BR>matched</TH><TH>Delta <BR>ppm</TH><TH>start</TH><TH>end</TH><TH ALIGN=left>Peptide Sequence <BR>(Click for Fragment Ions)</TH><TH ALIGN=left>Modifications</TH>
+<TR><TH ALIGN=right><!--in_mass-->807.4103<TH ALIGN=right><!--matched_mass-->807.4001<TH ALIGN=right><!--delta_mass-->12.6424<TH> 229<TH> 235<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=LAADDFR\">LAADDFR</A>");</SCRIPT>(L)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1090.5345<TH ALIGN=right><!--matched_mass-->1090.5315<TH ALIGN=right><!--delta_mass-->2.7349<TH> 148<TH> 156<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=VTMQNLNDR\">VTMQNLNDR</A>");</SCRIPT>(L)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1165.5794<TH ALIGN=right><!--matched_mass-->1165.5853<TH ALIGN=right><!--delta_mass-->-5.0852<TH> 442<TH> 450<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=LENEIQTYR\">LENEIQTYR</A>");</SCRIPT>(S)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1234.6639<TH ALIGN=right><!--matched_mass-->1234.6796<TH ALIGN=right><!--delta_mass-->-12.6850<TH> 236<TH> 245<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=LKYENEVALR\">LKYENEVALR</A>");</SCRIPT>(Q)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1300.5785<TH ALIGN=right><!--matched_mass-->1300.5956<TH ALIGN=right><!--delta_mass-->-13.1281<TH> 286<TH> 295<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=NHEEEMKDLR\">NHEEEMKDLR</A>");</SCRIPT>(N)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1434.7436<TH ALIGN=right><!--matched_mass-->1434.7705<TH ALIGN=right><!--delta_mass-->-18.7502<TH> 440<TH> 450<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=IRLENEIQTYR\">IRLENEIQTYR</A>");</SCRIPT>(S)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1493.7047<TH ALIGN=right><!--matched_mass-->1493.7348<TH ALIGN=right><!--delta_mass-->-20.1810<TH> 323<TH> 334<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=SQYEQLAEQNRK\">SQYEQLAEQNRK</A>");</SCRIPT>(D)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1707.7505<TH ALIGN=right><!--matched_mass-->1707.7727<TH ALIGN=right><!--delta_mass-->-12.9919<TH> 41<TH> 59<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=GSLGGGFSSGGFSGGSFSR\">GSLGGGFSSGGFSGGSFSR</A>");</SCRIPT>(G)</NOBR><TH>
+</TD>
+</TABLE>
+<BR>77 unmatched masses: <!--in_mass-->780.3832 <!--in_mass-->842.5100 <!--in_mass-->844.4115 <!--in_mass-->870.5324 <!--in_mass-->876.4886 <!--in_mass-->882.5242 <!--in_mass-->899.5570 <!--in_mass-->905.4814 <!--in_mass-->908.5322 <!--in_mass-->909.4996 <!--in_mass-->1012.5215 <!--in_mass-->1034.5536 <!--in_mass-->1043.5967 <!--in_mass-->1068.5926 <!--in_mass-->1071.6061 <!--in_mass-->1084.5853 <!--in_mass-->1087.5954 <!--in_mass-->1114.5542 <!--in_mass-->1119.5808 <!--in_mass-->1124.5976 <!--in_mass-->1134.5652 <!--in_mass-->1191.6559 <!--in_mass-->1196.6204 <!--in_mass-->1199.6401 <!--in_mass-->1211.5929 <!--in_mass-->1227.6725 <!--in_mass-->1233.6940 <!--in_mass-->1280.6694 <!--in_mass-->1307.6607 <!--in_mass-->1313.6723 <!--in_mass-->1316.6871 <!--in_mass-->1347.7553 <!--in_mass-->1360.6193 <!--in_mass-->1384.7265 <!--in_mass-->1413.6466 <!--in_mass-->1426.7383 <!--in_mass-->1474.6897 <!--in_mass-->1478.7466 <!--in_mass-->1490.6869 <!--in_mass-->1521.6975 <!--in_mass-->1522.7052 <!--in_mass-->1525.8075 <!--in_mass-->1535.7197 <!--in_mass-->1549.7436 <!--in_mass-->1584.7361 <!--in_mass-->1587.7484 <!--in_mass-->1591.7540 <!--in_mass-->1637.8480 <!--in_mass-->1640.8589 <!--in_mass-->1649.8864 <!--in_mass-->1656.8509 <!--in_mass-->1703.8614 <!--in_mass-->1749.8157 <!--in_mass-->1764.8774 <!--in_mass-->1779.7966 <!--in_mass-->1821.9176 <!--in_mass-->1829.9373 <!--in_mass-->1845.9513 <!--in_mass-->1848.9478 <!--in_mass-->1875.9294 <!--in_mass-->1878.9498 <!--in_mass-->1920.9815 <!--in_mass-->1971.9244 <!--in_mass-->2002.0392 <!--in_mass-->2005.0623 <!--in_mass-->2027.0247 <!--in_mass-->2081.0136 <!--in_mass-->2096.9674 <!--in_mass-->2157.0632 <!--in_mass-->2211.1046 <!--in_mass-->2225.1109 <!--in_mass-->2283.1102 <!--in_mass-->2356.9758 <!--in_mass-->2360.0876 <!--in_mass-->2717.0585 <!--in_mass-->2807.2543 <!--in_mass-->2845.2805 <P><NOBR> The matched peptides cover <B><!--protein_coverage-->13%</B> (78/593 AA's) of the protein.</NOBR>
+<BR>Coverage Map for This Hit (MS-Digest index #): <SCRIPT> document.write ( "<A HREF = \"" + msdigestLink + "dna_reading_frame=1&access_method=Index+Number&open_reading_frame=1&coverage_map=0+40+19+88+9+72+17+40+10+27+12+105+11+143&index_num=6704\"> 6704 </A>" );</SCRIPT><P>
+<BR><A NAME="3"></A><!--rank-->4. <!--fraction_matched-->6/85 matches (7%). <!--prot_mw--> 43903.6 Da, pI = <!--prot_pI-->4.58. Acc. # <!--accession_number-->YLR449W. <!--species-->SACCHAROMYCES CEREVISIAE. <!--entry_name-->FPR4.
+
+<TABLE>
+<TR><TH>m/z<BR>submitted</TH><TH> MH<SUP>+</SUP><BR>matched</TH><TH>Delta <BR>ppm</TH><TH>start</TH><TH>end</TH><TH ALIGN=left>Peptide Sequence <BR>(Click for Fragment Ions)</TH><TH ALIGN=left>Modifications</TH>
+<TR><TH ALIGN=right><!--in_mass-->909.4996<TH ALIGN=right><!--matched_mass-->909.4980<TH ALIGN=right><!--delta_mass-->1.7235<TH> 309<TH> 316<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=VGMRYVGK\">VGMRYVGK</A>");</SCRIPT>(L)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1191.6559<TH ALIGN=right><!--matched_mass-->1191.6778<TH ALIGN=right><!--delta_mass-->-18.3531<TH> 360<TH> 370<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=IVIPAPYAYGK\">IVIPAPYAYGK</A>");</SCRIPT>(Q)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1227.6725<TH ALIGN=right><!--matched_mass-->1227.6949<TH ALIGN=right><!--delta_mass-->-18.2274<TH> 285<TH> 295<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=LLEGGIIIEDR\">LLEGGIIIEDR</A>");</SCRIPT>(V)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1347.7553<TH ALIGN=right><!--matched_mass-->1347.7789<TH ALIGN=right><!--delta_mass-->-17.4970<TH> 359<TH> 370<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=RIVIPAPYAYGK\">RIVIPAPYAYGK</A>");</SCRIPT>(Q)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1474.6897<TH ALIGN=right><!--matched_mass-->1474.7113<TH ALIGN=right><!--delta_mass-->-14.6285<TH> 344<TH> 358<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=GWDIGVAGMAVGGER\">GWDIGVAGMAVGGER</A>");</SCRIPT>(R)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1490.6869<TH ALIGN=right><!--matched_mass-->1490.7062<TH ALIGN=right><!--delta_mass-->-12.9385<TH> 344<TH> 358<TH ALIGN=left><NOBR>(K)GWDIGVAGMAVGGER(R)</NOBR><TH>1Met-ox
+</TD>
+</TABLE>
+<BR>79 unmatched masses: <!--in_mass-->780.3832 <!--in_mass-->807.4103 <!--in_mass-->842.5100 <!--in_mass-->844.4115 <!--in_mass-->870.5324 <!--in_mass-->876.4886 <!--in_mass-->882.5242 <!--in_mass-->899.5570 <!--in_mass-->905.4814 <!--in_mass-->908.5322 <!--in_mass-->1012.5215 <!--in_mass-->1034.5536 <!--in_mass-->1043.5967 <!--in_mass-->1068.5926 <!--in_mass-->1071.6061 <!--in_mass-->1084.5853 <!--in_mass-->1087.5954 <!--in_mass-->1090.5345 <!--in_mass-->1114.5542 <!--in_mass-->1119.5808 <!--in_mass-->1124.5976 <!--in_mass-->1134.5652 <!--in_mass-->1165.5794 <!--in_mass-->1196.6204 <!--in_mass-->1199.6401 <!--in_mass-->1211.5929 <!--in_mass-->1233.6940 <!--in_mass-->1234.6639 <!--in_mass-->1280.6694 <!--in_mass-->1300.5785 <!--in_mass-->1307.6607 <!--in_mass-->1313.6723 <!--in_mass-->1316.6871 <!--in_mass-->1360.6193 <!--in_mass-->1384.7265 <!--in_mass-->1413.6466 <!--in_mass-->1426.7383 <!--in_mass-->1434.7436 <!--in_mass-->1478.7466 <!--in_mass-->1493.7047 <!--in_mass-->1521.6975 <!--in_mass-->1522.7052 <!--in_mass-->1525.8075 <!--in_mass-->1535.7197 <!--in_mass-->1549.7436 <!--in_mass-->1584.7361 <!--in_mass-->1587.7484 <!--in_mass-->1591.7540 <!--in_mass-->1637.8480 <!--in_mass-->1640.8589 <!--in_mass-->1649.8864 <!--in_mass-->1656.8509 <!--in_mass-->1703.8614 <!--in_mass-->1707.7505 <!--in_mass-->1749.8157 <!--in_mass-->1764.8774 <!--in_mass-->1779.7966 <!--in_mass-->1821.9176 <!--in_mass-->1829.9373 <!--in_mass-->1845.9513 <!--in_mass-->1848.9478 <!--in_mass-->1875.9294 <!--in_mass-->1878.9498 <!--in_mass-->1920.9815 <!--in_mass-->1971.9244 <!--in_mass-->2002.0392 <!--in_mass-->2005.0623 <!--in_mass-->2027.0247 <!--in_mass-->2081.0136 <!--in_mass-->2096.9674 <!--in_mass-->2157.0632 <!--in_mass-->2211.1046 <!--in_mass-->2225.1109 <!--in_mass-->2283.1102 <!--in_mass-->2356.9758 <!--in_mass-->2360.0876 <!--in_mass-->2717.0585 <!--in_mass-->2807.2543 <!--in_mass-->2845.2805 <P><NOBR> The matched peptides cover <B><!--protein_coverage-->11%</B> (46/393 AA's) of the protein.</NOBR>
+<BR>Coverage Map for This Hit (MS-Digest index #): <SCRIPT> document.write ( "<A HREF = \"" + msdigestLink + "dna_reading_frame=1&access_method=Index+Number&open_reading_frame=1&coverage_map=0+284+11+13+8+27+27+23&index_num=4574\"> 4574 </A>" );</SCRIPT><P>
+<BR><A NAME="4"></A><!--rank-->5. <!--fraction_matched-->8/85 matches (9%). <!--prot_mw--> 56719.7 Da, pI = <!--prot_pI-->5.90. Acc. # <!--accession_number-->YMR300C. <!--species-->SACCHAROMYCES CEREVISIAE. <!--entry_name-->ADE4.
+
+<TABLE>
+<TR><TH>m/z<BR>submitted</TH><TH> MH<SUP>+</SUP><BR>matched</TH><TH>Delta <BR>ppm</TH><TH>start</TH><TH>end</TH><TH ALIGN=left>Peptide Sequence <BR>(Click for Fragment Ions)</TH><TH ALIGN=left>Modifications</TH>
+<TR><TH ALIGN=right><!--in_mass-->1307.6607<TH ALIGN=right><!--matched_mass-->1307.6530<TH ALIGN=right><!--delta_mass-->5.8658<TH> 340<TH> 349<TH ALIGN=left><NOBR>(R)TFIMPNQRER(V)</NOBR><TH>1Met-ox
+<TR><TH ALIGN=right><!--in_mass-->1384.7265<TH ALIGN=right><!--matched_mass-->1384.7371<TH ALIGN=right><!--delta_mass-->-7.6503<TH> 64<TH> 77<TH ALIGN=left><NOBR>(R)VSGLAGSMGIAHLR(Y)</NOBR><TH>1Met-ox
+<TR><TH ALIGN=right><!--in_mass-->1764.8774<TH ALIGN=right><!--matched_mass-->1764.8795<TH ALIGN=right><!--delta_mass-->-1.1887<TH> 151<TH> 165<TH ALIGN=left><NOBR>(R)VNNEDVFHALEGVYR(L)</NOBR><TH>1D3
+<TR><TH ALIGN=right><!--in_mass-->1875.9294<TH ALIGN=right><!--matched_mass-->1875.9580<TH ALIGN=right><!--delta_mass-->-15.2378<TH> 169<TH> 186<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=GGYACVGLLAGFALFGFR\">GGYACVGLLAGFALFGFR</A>");</SCRIPT>(D)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->1878.9498<TH ALIGN=right><!--matched_mass-->1878.9815<TH ALIGN=right><!--delta_mass-->-16.8499<TH> 169<TH> 186<TH ALIGN=left><NOBR>(R)GGYACVGLLAGFALFGFR(D)</NOBR><TH>1D3
+<TR><TH ALIGN=right><!--in_mass-->2005.0623<TH ALIGN=right><!--matched_mass-->2005.0970<TH ALIGN=right><!--delta_mass-->-17.2967<TH> 296<TH> 313<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=QLKPEDIDVVIPVPDTAR\">QLKPEDIDVVIPVPDTAR</A>");</SCRIPT>(T)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->2081.0136<TH ALIGN=right><!--matched_mass-->2081.0205<TH ALIGN=right><!--delta_mass-->-3.2977<TH> 149<TH> 165<TH ALIGN=left><NOBR>(K)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=YRVNNEDVFHALEGVYR\">YRVNNEDVFHALEGVYR</A>");</SCRIPT>(L)</NOBR><TH>
+<TR><TH ALIGN=right><!--in_mass-->2225.1109<TH ALIGN=right><!--matched_mass-->2225.1315<TH ALIGN=right><!--delta_mass-->-9.2442<TH> 187<TH> 206<TH ALIGN=left><NOBR>(R)<SCRIPT> document.write ( "<A HREF = \"" + msprodLink + "sequence=DPNGIRPLLFGERENPDGTK\">DPNGIRPLLFGERENPDGTK</A>");</SCRIPT>(D)</NOBR><TH>
+</TD>
+</TABLE>
+<BR>77 unmatched masses: <!--in_mass-->780.3832 <!--in_mass-->807.4103 <!--in_mass-->842.5100 <!--in_mass-->844.4115 <!--in_mass-->870.5324 <!--in_mass-->876.4886 <!--in_mass-->882.5242 <!--in_mass-->899.5570 <!--in_mass-->905.4814 <!--in_mass-->908.5322 <!--in_mass-->909.4996 <!--in_mass-->1012.5215 <!--in_mass-->1034.5536 <!--in_mass-->1043.5967 <!--in_mass-->1068.5926 <!--in_mass-->1071.6061 <!--in_mass-->1084.5853 <!--in_mass-->1087.5954 <!--in_mass-->1090.5345 <!--in_mass-->1114.5542 <!--in_mass-->1119.5808 <!--in_mass-->1124.5976 <!--in_mass-->1134.5652 <!--in_mass-->1165.5794 <!--in_mass-->1191.6559 <!--in_mass-->1196.6204 <!--in_mass-->1199.6401 <!--in_mass-->1211.5929 <!--in_mass-->1227.6725 <!--in_mass-->1233.6940 <!--in_mass-->1234.6639 <!--in_mass-->1280.6694 <!--in_mass-->1300.5785 <!--in_mass-->1313.6723 <!--in_mass-->1316.6871 <!--in_mass-->1347.7553 <!--in_mass-->1360.6193 <!--in_mass-->1413.6466 <!--in_mass-->1426.7383 <!--in_mass-->1434.7436 <!--in_mass-->1474.6897 <!--in_mass-->1478.7466 <!--in_mass-->1490.6869 <!--in_mass-->1493.7047 <!--in_mass-->1521.6975 <!--in_mass-->1522.7052 <!--in_mass-->1525.8075 <!--in_mass-->1535.7197 <!--in_mass-->1549.7436 <!--in_mass-->1584.7361 <!--in_mass-->1587.7484 <!--in_mass-->1591.7540 <!--in_mass-->1637.8480 <!--in_mass-->1640.8589 <!--in_mass-->1649.8864 <!--in_mass-->1656.8509 <!--in_mass-->1703.8614 <!--in_mass-->1707.7505 <!--in_mass-->1749.8157 <!--in_mass-->1779.7966 <!--in_mass-->1821.9176 <!--in_mass-->1829.9373 <!--in_mass-->1845.9513 <!--in_mass-->1848.9478 <!--in_mass-->1920.9815 <!--in_mass-->1971.9244 <!--in_mass-->2002.0392 <!--in_mass-->2027.0247 <!--in_mass-->2096.9674 <!--in_mass-->2157.0632 <!--in_mass-->2211.1046 <!--in_mass-->2283.1102 <!--in_mass-->2356.9758 <!--in_mass-->2360.0876 <!--in_mass-->2717.0585 <!--in_mass-->2807.2543 <!--in_mass-->2845.2805 <P><NOBR> The matched peptides cover <B><!--protein_coverage-->18%</B> (97/511 AA's) of the protein.</NOBR>
+<BR>Coverage Map for This Hit (MS-Digest index #): <SCRIPT> document.write ( "<A HREF = \"" + msdigestLink + "dna_reading_frame=1&access_method=Index+Number&open_reading_frame=1&coverage_map=0+63+14+71+17+3+38+89+18+26+10+162&index_num=5076\"> 5076 </A>" );</SCRIPT><P>
+
+<HR>MS-Fit 3.1.1, ProteinProspector 3.2.1 <BR>© Copyright (1995-1999) The Regents of the University of California.</BODY><!--end_html_file-->
\ No newline at end of file
diff --git a/samples/Spectra/A_25.txt b/samples/Spectra/A_25.txt
new file mode 100644
index 0000000000000000000000000000000000000000..48f690aca56e21b751bb39b1c462608fa1e673ae
--- /dev/null
+++ b/samples/Spectra/A_25.txt
@@ -0,0 +1,41357 @@
+TITLE "<<020205 Cosmin Silac 20012005-01-A25_F1_a_0001>> Voyager Spec #1 MC[BP = 842.5, 12470]"
+TYPE MASSSPEC
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diff --git a/samples/Spectra/B_25.txt b/samples/Spectra/B_25.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c201571139619ad9272727499ae45d16ac538578
--- /dev/null
+++ b/samples/Spectra/B_25.txt
@@ -0,0 +1,41360 @@
+TITLE "<<020205 Cosmin Silac 20012005-01-B25_F2_a_0001>> Voyager Spec #1 MC[BP = 1475.7, 17579]"
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diff --git a/samples/Spectra/C_25.txt b/samples/Spectra/C_25.txt
new file mode 100644
index 0000000000000000000000000000000000000000..17cbd06c448321dded15e222dc7d00ba0b65f0bb
--- /dev/null
+++ b/samples/Spectra/C_25.txt
@@ -0,0 +1,41360 @@
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diff --git a/samples/Spectra/D_25.txt b/samples/Spectra/D_25.txt
new file mode 100644
index 0000000000000000000000000000000000000000..699ecaeeb759ee43ffa312b4eeddbaceee1903a7
--- /dev/null
+++ b/samples/Spectra/D_25.txt
@@ -0,0 +1,41358 @@
+TITLE "<<020205 Cosmin Silac 20012005-01-D25_F4_a_0001>> Voyager Spec #1 MC[BP = 1707.8, 19756]"
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diff --git a/samples/XML_output/.DS_Store b/samples/XML_output/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/samples/XML_output/.DS_Store differ
diff --git a/samples/XML_output/C25plst02_A_25.xml b/samples/XML_output/C25plst02_A_25.xml
new file mode 100644
index 0000000000000000000000000000000000000000..7aded98501ad8fff083554218a48c4dae57dc75f
--- /dev/null
+++ b/samples/XML_output/C25plst02_A_25.xml
@@ -0,0 +1 @@
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248.8970 220.3540 181.1550 162.8870 164.0290 176.5880 195.2360 280.4850 359.2640 393.1350 391.9930 376.7700 326.5340 260.3140 226.8240 183.4380 173.9240 183.0580 196.3780 212.7430 231.3910 245.0910 205.1310 181.9160 201.3250 238.6220 331.1010 394.6570 411.4020 398.4630 339.4740 255.7480 224.1600 206.6530 194.0950 207.4150 208.5560 164.7900 175.4460 192.1920 196.3780 183.8190 193.3330 237.8610 272.8730 323.1090 353.9360 365.7330 311.6920 249.6580 226.8240 197.1390 172.4020 168.5960 166.3130 171.6410 174.6850 160.6040 165.9320 189.5280 204.3700 259.1730 318.9230 429.2890 469.6300 419.0140 332.2430 276.6790 221.1150 195.9970 171.6410 184.9610 210.8400 228.7270 243.9500 237.0990 198.6610 184.9610 211.9810 240.9050 264.8810 327.6760 365.3530 383.2400 346.7050 270.5900 238.2410 227.5850 189.5280 188.7660 197.9000 197.9000 170.1180 201.7060 212.3620 189.5280 199.8030 243.5690 288.8570 326.1540 346.7050 374.4870 389.3290 332.2430 209.6980 175.4460 172.7820 146.1420 161.7460 163.6490 189.5280 199.0420 215.4070 221.4960 193.3330 202.0870 273.2540 328.4370 343.6600 355.4580 295.3270 243.9500 193.7140 181.5360 172.7820 180.3940 181.1550 185.3410 152.9920 150.3280 175.8270 175.8270 218.8320 241.6660 240.1440 270.2090 329.1980 357.3610 340.6150 290.3800 253.8450 224.5400 230.6300 221.1150 196.3780 176.5880 170.4990 176.9690 184.5800 161.3650 174.3050 246.9940 330.7210 419.3940 505.7850 512.2540 452.1240 304.8420 216.1680 185.7220 165.9320 176.2080 178.8720 183.0580 207.7950 209.6980 192.9530 197.9000 195.9970 156.7980 242.0470 411.0220 554.8790 578.8550 460.8770 379.0530 320.0650 242.0470 175.0660 153.7540 165.1710 188.3860 211.2200 192.5720 165.1710 130.5390 146.1420 183.8190 258.4120 369.5390 519.1050 631.3740 573.9070 429.2890 329.1980 275.9180 236.3380 171.2600 144.6200 163.6490 210.0790 208.5560 174.3050 192.9530 209.6980 184.5800 203.6090 304.8420 404.9320 437.2810 391.9930 310.1700 220.7350 178.4910 189.9080 215.4070 243.9500 230.2490 185.7220 154.8950 150.3290 176.5880 214.6460 229.8680 197.1390 258.0310 384.0010 468.8690 471.9130 325.7730 237.4800 234.8160 204.3700 168.5960 165.9320 153.7540 151.8510 172.4020 175.0660 162.5070 199.4230 224.5400 229.4880 246.6140 310.9310 411.0220 399.6040 321.9670 274.7760 224.9210 192.9530 214.6450 169.7380 129.7770 122.9270 129.0160 149.5670 148.8060 147.6640 185.3410 215.7870 266.4040 288.8570 329.1980 407.9770 394.2760 296.0880 235.9580 170.8790 169.7380 176.9690 146.1420 136.2470 152.9930 158.3210 143.4780 148.4260 172.4020 234.4350 278.9620 283.9100 328.8180 375.6280 378.2920 272.8730 181.1550 171.2600 158.3210 160.6040 173.5440 188.0050 176.2080 145.7620 140.0530 131.3000 135.1060 171.2600 221.4960 288.4770 338.3320 375.6280 370.3000 318.1620 239.0020 179.2520 173.9240 164.0290 154.5150 141.5750 167.8350 204.3700 237.4800 243.9500 245.4720 248.8970 238.2410 299.5130 370.3000 401.8880 419.7750 333.3850 271.7320 216.9290 189.1470 187.2440 175.4460 205.1310 184.9610 152.6120 152.9930 173.5440 203.6090 248.5170 276.2980 314.3560 344.4210 342.8990 317.7810 258.4110 226.4430 255.7470 229.4880 168.2150 152.9920 159.4620 197.1390 228.7270 173.1630 143.0980 168.9770 210.0790 267.9260 312.8340 347.8460 328.4370 268.3060 227.2040 218.4510 224.1600 209.6980 170.8790 159.0820 141.9560 145.7620 135.8670 125.5910 138.5310 167.8350 183.0580 221.4960 269.4480 321.5870 376.3890 352.0330 274.0150 234.0550 206.2730 196.3780 210.4590 188.0050 179.6330 198.6610 176.2080 149.9480 160.6040 199.4230 201.7060 227.2040 303.7000 435.7590 591.0330 613.8680 514.5380 321.5870 227.9660 210.8400 179.6330 190.2890 226.4430 226.8240 204.7510 199.4230 192.5720 163.2680 174.6850 231.7710 409.4990 637.8440 845.6370 893.5900 676.6620 424.3420 290.3800 230.6300 222.2570 198.6620 156.7980 160.6040 194.8560 191.4310 179.6330 176.9690 197.1390 246.2330 366.8750 551.4540 715.1000 817.4750 699.8770 469.6300 333.3850 302.5580 265.6430 195.6170 162.8880 152.6120 182.6770 243.5690 223.7790 162.1260 167.4540 276.2990 428.1480 663.7230 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401.5070 341.3770 242.0470 167.0740 138.1500 146.5230 160.6040 182.2970 235.5770 216.5480 177.3490 183.4380 165.5520 211.6010 312.8340 393.8960 459.7350 505.7850 429.2890 288.0960 216.9290 202.0870 205.8920 188.0050 183.8190 186.8640 170.8800 174.3050 206.6540 200.5640 186.1030 223.3990 281.6270 361.5470 483.7110 478.7640 414.8280 324.6320 227.2050 174.3050 169.7380 165.5520 176.2080 160.6040 150.3290 150.7090 140.8140 156.7980 191.8110 258.0310 367.2560 479.5250 542.7000 557.1620 598.6450 589.8920 437.2810 277.4400 240.9050 233.2940 196.7590 174.3050 164.4100 185.3410 228.3460 232.9130 242.8080 304.4610 334.9070 348.9880 426.6250 536.6110 581.1380 555.6400 419.0140 278.9630 218.0710 190.6690 205.8920 221.8770 217.6900 200.1840 197.5200 177.3490 178.4910 234.4350 305.2220 391.2320 445.6540 399.6050 372.9640 374.1060 321.9670 248.8970 230.2490 235.5770 188.7670 159.0820 165.9320 168.2160 188.0050 203.9900 239.3830 282.7680 264.5010 302.5580 384.0010 431.1920 416.7300 357.7410 271.3510 221.8770 199.8030 201.7060 194.8560 180.0130 183.8190 179.6330 176.2080 184.5800 208.5560 286.1940 358.8830 362.6890 408.3580 430.0510 404.9330 353.5550 296.8500 227.5850 205.5120 194.4750 136.6280 110.7490 136.6280 161.3650 150.3290 153.3730 178.4910 200.1840 242.4280 283.1490 326.1540 385.5230 393.8960 299.1330 196.3780 170.4990 210.4590 201.7060 158.7010 138.9110 168.9770 169.3570 157.9400 171.6410 183.4390 199.0420 233.2940 251.1810 266.4040 292.6630 332.2430 320.4450 270.9710 221.4960 214.2650 202.8480 192.9530 193.3340 217.3100 200.5640 150.3290 146.1420 224.1600 266.4040 291.1410 344.0410 412.9250 484.0920 452.1240 328.4370 250.8000 221.4960 192.1920 183.4390 189.5280 179.6330 199.4230 211.9820 176.2080 188.3860 230.2490 257.2700 307.1250 391.9930 443.7510 455.1680 405.6940 335.6680 266.4040 195.2360 178.4910 190.2890 206.2730 206.2730 184.9610 167.8350 195.2360 194.0950 171.2600 227.2050 275.5370 347.0850 430.8120 449.4600 377.9120 329.1980 247.3750 216.1680 191.4310 185.7220 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164.4090 165.9310 186.1020 176.5870 183.0570 217.3090 227.9650 223.0170 231.0090 258.7910 271.7310 331.4810 387.4250 419.7740 458.5930 419.3940 329.9590 232.5320 184.9600 186.8630 190.2880 210.4580 192.5710 180.7740 172.0200 149.5670 180.3930 195.9970 173.9230 211.6000 231.7710 207.0330 232.9120 243.5680 248.5160 251.5600 275.1560 322.7280 380.5750 409.1180 427.3860 342.8980 261.4550 232.9120 192.9520 172.4010 161.7450 157.1780 183.8180 188.0050 198.2800 227.9650 207.4140 196.7580 206.6530 203.2280 221.8760 240.1430 215.4060 208.1750 278.5810 359.6430 452.8840 554.8780 538.1330 401.1260 285.0510 243.5680 204.3690 147.6640 146.1410 160.9840 167.4540 164.4090 160.2230 181.5350 211.6000 208.1750 191.4300 225.6810 256.8880 262.5970 230.2480 231.3900 232.1510 239.3820 306.3630 359.6430 356.2180 360.4050 327.6750 221.1150 178.4900 199.8020 185.3410 165.5510 165.1700 159.8420 192.1910 189.9080 204.3690 238.2400 203.9890 150.3280 155.6560 215.7870 255.3660 243.1880 248.1350 337.1900 432.3330 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211.6010 186.4830 169.7370 245.0910 324.2500 354.6960 344.4210 352.0320 597.1220 1299.2800 2564.3100 3510.8000 2805.5900 1440.4700 842.2110 670.5720 498.5530 350.8900 235.5760 196.7580 228.7260 280.4840 246.9940 156.7980 176.9680 198.6610 173.9230 206.2720 218.4510 191.8100 210.4580 255.3660 405.3120 692.6460 1163.8000 1584.7100 1554.2700 1062.9400 646.9770 384.3810 273.2530 244.3300 273.6340 240.1430 179.2510 184.5800 251.9410 232.9120 216.5480 207.4140 205.1300 205.1300 180.3930 218.8310 237.8600 251.9410 313.2140 395.0370 520.2460 678.1840 631.7540 464.3010 328.4360 258.0300 200.9440 198.6610 219.9730 176.2070 132.0600 163.2670 186.8630 206.2720 200.9440 236.7180 250.7990 256.5080 234.4350 184.9600 186.4820 189.9080 252.3220 382.4780 448.3170 398.0810 330.7200 339.4730 350.5100 280.8650 185.7210 164.4090 153.3720 172.0210 152.6110 149.9470 149.9470 181.9150 199.8020 190.6690 155.6560 168.2150 224.5400 235.5760 221.4950 254.9860 329.5780 418.6320 460.1150 396.9400 360.4050 348.2260 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367.2540 393.1330 359.2620 292.6620 234.4340 237.4790 243.9480 193.3320 160.9830 173.5420 225.3000 259.9330 247.7540 207.4130 205.1300 191.8100 159.8420 143.8580 170.8780 205.1300 215.7860 245.8510 307.8850 339.4730 310.5490 356.2180 485.6130 477.2400 362.6880 325.0110 289.9980 227.9640 200.5630 166.6920 157.1780 177.3480 205.5110 186.1010 148.0440 162.8860 174.3030 160.2220 172.0200 189.5260 204.7490 200.5630 243.1870 298.3710 312.4520 299.5120 374.8660 589.1290 844.1140 908.0500 701.3980 419.3930 282.7670 324.2500 289.6170 216.1670 164.7890 192.1900 218.8310 218.0690 221.8750 205.5110 189.9070 194.8540 230.6280 227.5840 234.0540 239.3820 240.1430 251.1790 271.3500 317.7800 336.8090 335.6670 442.6080 536.6100 503.1190 344.0390 226.0620 237.8590 273.2530 255.7460 218.0690 182.2960 156.0360 171.6390 187.6240 152.6110 143.4770 138.9100 160.9830 192.5710 166.3110 148.8050 159.0800 198.6600 252.3210 273.6330 308.2650 312.0710 393.5140 549.1690 592.5540 474.9570 303.3180 226.8230 197.5180 168.2140 180.3930 200.9440 187.2430 174.6840 172.7810 177.7290 194.0930 195.9960 165.1700 133.9630 151.4690 159.0800 171.6390 206.6520 189.5260 195.9960 219.9720 259.5520 306.3630 380.9550 417.8710 369.1570 328.4360 313.9740 265.2610 176.9670 160.6030 176.2060 181.5340 175.0650 170.4980 177.3480 169.7370 146.1410 133.2010 159.8420 152.6110 154.8940 165.9310 185.7210 211.6000 234.0540 283.1480 338.7110 406.0730 483.7100 513.7750 487.1350 448.6970 360.7850 236.3370 172.0200 163.6470 151.0880 171.2590 186.4820 157.9390 171.2590 191.4290 170.8780 156.0360 167.4530 154.1330 191.4290 240.9040 252.7020 218.4500 237.4790 271.7300 266.7830 333.0030 398.8420 419.3930 410.6400 378.6720 307.8850 211.2190 184.1980 207.0330 217.3080 195.2350 180.7730 193.3320 212.7410 169.7370 108.0840 156.0360 223.0170 222.6360 188.3850 155.6550 137.3880 169.3560 220.3530 255.3660 273.2530 270.5890 321.5860 319.3020 307.5040 307.5040 268.6860 267.1640 326.5330 314.7350 280.1030 227.9640 183.8180 173.9230 170.1170 172.0200 156.0360 139.6710 170.4980 167.8340 159.4610 171.6390 185.7210 205.8910 193.3320 207.0330 228.7260 273.2530 318.5410 317.7800 343.6590 328.4360 365.7320 500.8360 695.3090 803.7730 583.8010 272.8720 185.3400 181.9150 167.0730 172.7810 183.4370 186.4820 167.4530 137.7680 147.6630 154.8940 134.7240 154.5140 178.8700 208.5550 232.9120 234.0540 246.9930 256.1270 306.3630 356.9790 374.1050 403.4090 488.6580 482.5680 391.6110 278.2000 194.8540 159.8420 160.2220 180.7730 194.8540 184.1980 183.4370 179.2510 168.2140 151.8500 168.9750 179.2510 181.9150 182.6760 216.9280 250.7990 254.2240 245.0900 246.6130 368.7770 568.9590 609.6800 487.8960 374.1050 292.2810 243.9490 236.3370 196.7570 157.5580 124.0680 127.8730 133.9630 148.8050 187.2430 192.1900 175.8260 163.2670 165.5500 159.4610 191.0490 267.9250 291.9010 248.8960 263.3580 358.5010 392.7530 467.3450 540.0350 493.2240 347.4650 282.3870 208.5550 202.8470 218.0700 220.3530 194.0930 181.5340 208.5550 168.5950 154.1330 121.0230 94.3830 103.8970 147.6630 173.5420 209.3160 231.7700 266.4020 327.6750 299.5120 246.2320 325.7720 436.9000 466.2040 401.1260 277.8200 254.6050 288.4760 285.8120 196.7570 151.4690 176.9670 152.6110 133.2010 128.2540 106.5610 126.3510 121.7840 136.2460 154.8940 186.4820 209.3160 226.8230 289.9980 345.9420 340.2340 337.1890 353.1730 390.0890 404.5510 331.4810 287.3340 203.9880 162.8860 195.2350 173.5420 132.8210 155.2750 211.2190 242.8070 238.6200 172.0200 146.5220 152.6110 164.4090 170.1170 174.3030 200.5630 199.0410 233.6730 302.5570 347.4650 371.8210 376.3880 447.9360 503.8800 462.0170 361.9260 261.8350 218.8310 183.4370 186.4820 199.4210 207.7940 173.9230 139.6710 167.8340 198.6600 180.0120 173.5420 201.7050 197.1380 206.6520 235.5760 217.6890 256.5070 353.5540 430.4300 391.9920 317.3990 324.2500 380.5750 432.3330 419.0130 336.8090 270.2080 227.5840 191.8100 168.2140 163.6470 183.4370 177.3480 196.3770 188.7650 194.8540 225.3000 241.2850 224.9200 189.9070 165.9310 179.6320 218.4500 287.3340 382.4770 428.1460 336.8090 319.6830 337.5700 304.8400 314.7350 242.4260 156.4170 151.8500 182.2960 199.4210 168.9750 138.5300 146.1410 148.0440 160.2220 170.8780 170.4980 172.7810 183.4370 215.4050 273.6330 336.8090 369.1570 396.1780 332.2420 333.3830 333.3830 350.8900 419.0130 404.5510 323.1080 265.6410 197.1380 155.2750 142.7160 145.3800 186.1010 176.9670 175.0650 210.8390 216.9280 209.6970 182.6760 149.5660 200.5630 196.3770 168.5950 168.2140 232.9120 277.0580 300.2730 320.0630 326.5330 344.8010 382.0970 409.1180 404.1700 455.9280 436.8990 310.1680 211.9800 187.2430 193.3320 156.0360 175.4450 205.8910 198.6600 168.5950 169.7370 175.0650 156.7970 169.3560 149.9470 147.2830 219.9720 318.5410 360.4040 350.5090 331.1000 336.4280 396.1780 510.3500 461.2560 373.3440 393.5140 317.7800 192.9520 156.4160 159.0800 199.4210 194.4740 156.0360 149.5660 188.0040 217.3080 207.0330 200.5630 222.6360 237.4790 200.1820 215.4050 260.6940 308.6460 326.1520 583.4200 1562.6400 3252.0000 3994.5000 2705.8800 979.2170 344.4200 318.1600 380.9550 282.0060 177.7290 173.1620 192.1900 223.0170 191.8100 151.8500 185.7210 205.8910 164.7890 161.7440 203.2270 188.3850 145.3800 146.5220 194.0930 256.8880 379.4330 708.6290 1489.1900 2055.4800 1561.1100 705.5850 315.8770 273.6330 288.4760 240.9040 161.7440 156.0360 200.9440 237.0980 187.2430 148.0440 160.9830 189.9070 180.7730 158.7000 168.5950 152.2300 165.1700 234.4340 251.1790 237.8590 250.7990 348.6060 538.5130 706.7260 606.2550 403.4090 340.9950 279.3420 217.6890 206.2720 162.5060 159.4610 172.7810 165.9310 156.0360 154.8940 157.9390 162.5060 177.3480 199.4210 195.6160 214.2640 246.2320 228.7250 229.8670 289.9980 332.2420 325.0110 350.5090 417.1100 401.8870 323.4880 270.9690 230.6280 200.9440 181.5340 152.9910 132.4400 173.5420 178.4900 178.1090 194.0930 183.4370 200.9440 223.0170 186.4820 165.5500 169.3560 182.6760 193.3320 191.4290 188.7650 267.5440 360.4040 374.4850 355.0760 299.1320 282.0060 266.0220 237.0980 222.6360 199.4210 181.5340 153.3720 135.1040 156.7970 185.7210 193.7130 203.9880 192.1900 174.6840 158.3190 151.0880 160.6030 180.7730 165.5500 176.5870 226.8230 288.4760 337.9500 377.1490 420.9150 379.4330 347.0840 312.4520 266.7830 217.3080 182.2950 146.9020 104.2780 137.7680 143.0960 106.5610 120.6420 159.0800 164.7890 168.5950 169.3560 146.9020 164.7890 211.2190 213.8830 205.8910 224.9200 256.1270 277.4390 302.9370 403.0280 420.5350 370.6800 336.0470 274.3940 208.5550 200.5630 218.4500 180.7730 168.9750 186.4820 167.0720 138.1490 162.1250 187.6230 176.2060 130.1570 147.2830 181.5340 195.9960 209.6970 188.7650 188.7650 248.5150 288.4760 286.5730 349.3670 443.3690 417.4900 372.2020 318.9220 234.8150 193.3320 188.7650 163.2670 164.7890 196.3770 215.7860 177.3480 155.6550 170.1170 175.8260 164.4080 167.4530 173.9230 181.1540 226.8230 232.9120 224.1590 291.5200 340.2340 329.1970 304.8400 336.4280 359.2620 329.9580 251.1790 194.0930 170.4980 148.4240 172.4010 216.5470 233.6730 230.6280 204.7490 160.2220 150.7080 165.9310 149.9470 136.2460 141.9550 163.2670 178.1090 214.2640 202.4660 246.6120 284.6700 274.7750 291.9010 362.6870 430.0490 350.8900 280.4830 251.9400 199.8020 165.9310 137.0070 152.6110 186.4820 205.5100 194.4740 170.4980 171.6390 207.7940 213.5020 202.4660 213.1220 215.7860 229.4870 271.3500 260.3130 253.4630 286.9530 296.0870 305.6010 328.4360 368.0150 335.6670 285.0500 234.8150 231.7700 194.4740 148.4240 133.9620 151.8490 179.6310 195.2350 183.4370 149.1850 138.1490 134.7240 138.5290 161.7440 202.0850 245.8510 243.1870 232.5310 226.8230 215.7860 294.9450 379.8130 390.0890 354.6950 323.4880 288.0950 220.3530 187.6230 212.3610 199.8020 156.0360 158.3190 188.7650 181.5340 175.0640 160.9830 160.2220 176.5870 162.1250 159.0800 195.6150 242.8070 238.2400 234.0530 237.8590 396.1780 801.1090 1207.5600 1125.3600 705.2040 344.4200 248.1350 227.2030 207.7940 209.6970 174.3030 163.6470 184.9590 165.1690 151.4690 180.7730 184.9590 157.5580 195.6150 230.6280 194.0930 177.7280 239.3810 285.0500 265.2600 275.1550 409.4980 537.7510 721.1880 788.1690 591.0320 377.9100 262.9770 256.5070 239.0010 192.5710 202.0850 224.5390 186.4820 140.0520 141.9540 161.7440 177.7280 189.9070 189.1460 155.2740 150.3270 172.7810 204.7490 249.6570 270.9690 288.0950 333.3830 348.9870 392.7530 351.6510 259.1710 194.4740 216.1660 231.7700 202.8460 161.3640 157.1770 183.4370 179.6310 181.5340 177.7280 148.8050 175.8250 176.5870 151.4690 177.3480 150.3270 135.1040 199.0400 231.7700 246.6120 285.8110 312.0710 363.8290 400.7450 433.4740 355.8370 253.0820 215.0250 203.6070 175.8260 156.7970 164.7890 157.1770 165.9310 229.1060 241.6650 247.7540 234.4340 186.4820 164.0280 132.4400 140.4320 154.5130 200.5630 258.7910 286.5730 304.4600 315.1160 415.2070 514.1560 482.1880 381.3350 282.0060 225.6810 210.0770 224.1580 192.9510 183.4370 157.1770 176.2060 218.8300 231.3890 215.7860 203.6070 175.8260 200.1820 178.8700 144.6180 154.5130 209.3160 287.7140 272.4910 239.0010 284.2890 390.4690 447.1750 427.3850 355.4560 257.2680 252.7010 235.5760 203.6070 168.2140 172.0200 181.9150 175.0640 193.7130 196.7570 169.7360 169.3560 172.4000 156.4160 132.0600 152.6110 189.1460 190.2870 197.1380 213.5020 214.2640 254.2240 308.6460 354.6950 353.5540 354.3150 348.9870 313.9740 283.5280 216.5470 151.8490 138.1490 164.7890 207.7940 184.1980 158.3190 157.1770 179.2510 225.3000 189.9070 154.8940 192.1900 259.5520 270.5880 257.2680 219.9720 191.0490 285.0500 355.0760 414.0650 446.0330 410.2590 304.0790 227.5840 177.7280 124.0670 128.2540 143.4770 163.2670 127.1120 125.5900 169.3560 181.5340 182.6760 196.3760 213.5020 196.3760 180.3920 211.5990 223.3970 241.2840 272.4910 297.6090 326.5330 366.8740 405.6920 403.0280 419.0120 371.8210 242.0450 207.4130 204.7490 176.2060 151.0880 122.1650 166.6920 205.1300 200.5630 188.0040 178.8700 155.6550 168.2140 178.1090 188.0040 217.6890 220.3530 244.3290 264.4990 242.4260 276.6780 370.6790 404.9310 380.5740 340.9950 240.5230 200.1820 183.4370 184.1980 196.7570 185.3400 156.0360 146.1410 173.1620 215.0250 219.2110 177.3480 210.4580 199.0410 151.4690 179.2510 228.7250 244.7090 247.3730 267.1630 274.7750 280.4830 348.6060 417.4900 423.5790 327.6750 228.7250 229.1060 198.2790 151.8490 202.8460 207.4130 157.5580 148.0440 143.8570 156.0360 146.9020 141.5740 137.0070 125.9700 131.6790 155.6550 203.2270 215.4050 228.7250 240.5230 270.5880 380.9550 665.2440 881.0290 728.7990 424.7210 242.0450 180.7730 191.8100 189.9070 160.2220 148.8050 178.4900 192.1900 161.7440 149.5660 151.0880 165.5500 170.4980 129.7760 132.4400 197.1380 252.7020 242.8070 274.7750 309.4070 344.0390 375.6270 466.9650 578.8530 506.5440 371.4410 310.1680 233.6730 184.9590 202.4660 187.6230 168.2140 161.7440 162.1250 180.3920 194.4740 226.0610 201.7050 178.1090 194.0930 176.9670 163.2670 162.1250 218.4500 251.9400 286.5730 291.5200 360.4040 466.9650 439.5630 347.0840 272.8720 200.1820 180.0120 188.0040 163.6470 138.5290 141.9540 148.4240 158.7000 149.9470 182.6760 192.1900 177.3480 180.0120 213.5020 212.3610 208.1740 241.6650 261.8350 289.6170 312.4520 343.6590 489.4180 617.2910 632.5140 465.4420 266.4020 182.2950 181.1540 190.2870 173.5420 183.4370 207.7940 213.5020 191.0480 171.6390 181.9150 159.0800 146.9020 204.3690 234.4340 216.9280 188.0040 190.6680 195.2350 278.5810 532.0430 949.9130 1343.8100 1351.8000 864.6640 414.8260 248.5150 241.2840 226.0610 208.9360 183.8180 162.5050 144.2380 133.2010 139.2900 128.2540 142.7160 157.5580 133.9620 127.8730 162.8860 159.4610 133.5820 221.4940 327.6750 334.5250 406.8340 659.5350 847.9190 718.1430 465.0620 297.6090 273.2530 265.2600 156.0360 118.7400 137.7680 166.3110 192.5710 188.3850 178.4900 182.6760 190.6680 175.0640 170.1170 140.4320 145.7600 154.1330 202.0850 270.2080 262.2160 207.7940 237.4790 357.7400 507.6860 479.1430 309.7880 245.0900 239.7620 233.6730 204.7490 227.2030 224.9200 195.6150 162.8860 146.9020 182.6760 239.3810 197.5180 158.3190 175.0640 179.6310 187.2430 180.3920 181.1540 178.4900 208.5550 291.9010 377.9100 375.6270 322.7270 313.9740 293.4230 289.6170 245.4710 187.2430 179.6310 168.5950 146.1410 149.9470 141.9550 153.3720 181.9150 141.1930 122.1650 151.8490 143.0960 179.6310 235.9560 246.2320 249.2760 249.2760 227.5840 221.1140 269.8270 347.4640 335.6670 279.3420 </int_list></spectrum></measured><measured><pepseq>VEHVTHPEQYIPGVLKR</pepseq><mzh>2002.0392</mzh><calc_mzh>2002.0875</calc_mzh><leucines>1</leucines><mono_iso_intensity>331</mono_iso_intensity><deuterated_intensity>792</deuterated_intensity><ratio>2.39</ratio><validated>YES</validated><local_bg>95</local_bg><corrected_ratio>2.95</corrected_ratio><spectrum><mz_list>1977.5970 1977.6579 1977.7188 1977.7797 1977.8406 1977.9015 1977.9624 1978.0233 1978.0842 1978.1451 1978.2060 1978.2669 1978.3278 1978.3887 1978.4496 1978.5105 1978.5714 1978.6324 1978.6933 1978.7542 1978.8151 1978.8760 1978.9369 1978.9978 1979.0588 1979.1197 1979.1806 1979.2415 1979.3024 1979.3634 1979.4243 1979.4852 1979.5461 1979.6071 1979.6680 1979.7289 1979.7898 1979.8508 1979.9117 1979.9726 1980.0336 1980.0945 1980.1554 1980.2164 1980.2773 1980.3382 1980.3992 1980.4601 1980.5211 1980.5820 1980.6429 1980.7039 1980.7648 1980.8258 1980.8867 1980.9477 1981.0086 1981.0696 1981.1305 1981.1915 1981.2524 1981.3134 1981.3743 1981.4353 1981.4962 1981.5572 1981.6181 1981.6791 1981.7401 1981.8010 1981.8620 1981.9229 1981.9839 1982.0449 1982.1058 1982.1668 1982.2278 1982.2887 1982.3497 1982.4107 1982.4716 1982.5326 1982.5936 1982.6545 1982.7155 1982.7765 1982.8375 1982.8984 1982.9594 1983.0204 1983.0814 1983.1424 1983.2033 1983.2643 1983.3253 1983.3863 1983.4473 1983.5083 1983.5693 1983.6302 1983.6912 1983.7522 1983.8132 1983.8742 1983.9352 1983.9962 1984.0572 1984.1182 1984.1792 1984.2402 1984.3012 1984.3622 1984.4232 1984.4842 1984.5452 1984.6062 1984.6672 1984.7282 1984.7892 1984.8502 1984.9112 1984.9722 1985.0332 1985.0942 1985.1552 1985.2163 1985.2773 1985.3383 1985.3993 1985.4603 1985.5213 1985.5823 1985.6434 1985.7044 1985.7654 1985.8264 1985.8874 1985.9485 1986.0095 1986.0705 1986.1315 1986.1926 1986.2536 1986.3146 1986.3757 1986.4367 1986.4977 1986.5588 1986.6198 1986.6808 1986.7419 1986.8029 1986.8639 1986.9250 1986.9860 1987.0471 1987.1081 1987.1691 1987.2302 1987.2912 1987.3523 1987.4133 1987.4744 1987.5354 1987.5965 1987.6575 1987.7186 1987.7796 1987.8407 1987.9017 1987.9628 1988.0238 1988.0849 1988.1459 1988.2070 1988.2681 1988.3291 1988.3902 1988.4512 1988.5123 1988.5734 1988.6344 1988.6955 1988.7566 1988.8176 1988.8787 1988.9398 1989.0008 1989.0619 1989.1230 1989.1841 1989.2451 1989.3062 1989.3673 1989.4284 1989.4894 1989.5505 1989.6116 1989.6727 1989.7338 1989.7948 1989.8559 1989.9170 1989.9781 1990.0392 1990.1003 1990.1613 1990.2224 1990.2835 1990.3446 1990.4057 1990.4668 1990.5279 1990.5890 1990.6501 1990.7112 1990.7723 1990.8334 1990.8945 1990.9556 1991.0167 1991.0778 1991.1389 1991.2000 1991.2611 1991.3222 1991.3833 1991.4444 1991.5055 1991.5666 1991.6277 1991.6889 1991.7500 1991.8111 1991.8722 1991.9333 1991.9944 1992.0555 1992.1167 1992.1778 1992.2389 1992.3000 1992.3611 1992.4223 1992.4834 1992.5445 1992.6056 1992.6668 1992.7279 1992.7890 1992.8501 1992.9113 1992.9724 1993.0335 1993.0947 1993.1558 1993.2169 1993.2781 1993.3392 1993.4004 1993.4615 1993.5226 1993.5838 1993.6449 1993.7061 1993.7672 1993.8283 1993.8895 1993.9506 1994.0118 1994.0729 1994.1341 1994.1952 1994.2564 1994.3175 1994.3787 1994.4398 1994.5010 1994.5622 1994.6233 1994.6845 1994.7456 1994.8068 1994.8679 1994.9291 1994.9903 1995.0514 1995.1126 1995.1738 1995.2349 1995.2961 1995.3573 1995.4184 1995.4796 1995.5408 1995.6019 1995.6631 1995.7243 1995.7855 1995.8466 1995.9078 1995.9690 1996.0302 1996.0913 1996.1525 1996.2137 1996.2749 1996.3361 1996.3973 1996.4584 1996.5196 1996.5808 1996.6420 1996.7032 1996.7644 1996.8256 1996.8868 1996.9480 1997.0091 1997.0703 1997.1315 1997.1927 1997.2539 1997.3151 1997.3763 1997.4375 1997.4987 1997.5599 1997.6211 1997.6823 1997.7435 1997.8047 1997.8659 1997.9272 1997.9884 1998.0496 1998.1108 1998.1720 1998.2332 1998.2944 1998.3556 1998.4168 1998.4781 1998.5393 1998.6005 1998.6617 1998.7229 1998.7842 1998.8454 1998.9066 1998.9678 1999.0290 1999.0903 1999.1515 1999.2127 1999.2739 1999.3352 1999.3964 1999.4576 1999.5189 1999.5801 1999.6413 1999.7026 1999.7638 1999.8250 1999.8863 1999.9475 2000.0088 2000.0700 2000.1312 2000.1925 2000.2537 2000.3150 2000.3762 2000.4375 2000.4987 2000.5599 2000.6212 2000.6824 2000.7437 2000.8049 2000.8662 2000.9275 2000.9887 2001.0500 2001.1112 2001.1725 2001.2337 2001.2950 2001.3563 2001.4175 2001.4788 2001.5400 2001.6013 2001.6626 2001.7238 2001.7851 2001.8464 2001.9076 2001.9689 2002.0302 2002.0914 2002.1527 2002.2140 2002.2753 2002.3365 2002.3978 2002.4591 2002.5204 2002.5816 2002.6429 2002.7042 2002.7655 2002.8268 2002.8880 2002.9493 2003.0106 2003.0719 2003.1332 2003.1945 2003.2558 2003.3171 2003.3783 2003.4396 2003.5009 2003.5622 2003.6235 2003.6848 2003.7461 2003.8074 2003.8687 2003.9300 2003.9913 2004.0526 2004.1139 2004.1752 2004.2365 2004.2978 2004.3591 2004.4204 2004.4817 2004.5430 2004.6044 2004.6657 2004.7270 2004.7883 2004.8496 2004.9109 2004.9722 2005.0335 2005.0949 2005.1562 2005.2175 2005.2788 2005.3401 2005.4015 2005.4628 2005.5241 2005.5854 2005.6468 2005.7081 2005.7694 2005.8307 2005.8921 2005.9534 2006.0147 2006.0761 2006.1374 2006.1987 2006.2601 2006.3214 2006.3827 2006.4441 2006.5054 2006.5667 2006.6281 2006.6894 2006.7508 2006.8121 2006.8735 2006.9348 2006.9962 2007.0575 2007.1188 2007.1802 2007.2415 2007.3029 2007.3642 2007.4256 2007.4870 2007.5483 2007.6097 2007.6710 2007.7324 2007.7937 2007.8551 2007.9165 2007.9778 2008.0392 2008.1005 2008.1619 2008.2233 2008.2846 2008.3460 2008.4074 2008.4687 2008.5301 2008.5915 2008.6528 2008.7142 2008.7756 2008.8370 2008.8983 2008.9597 2009.0211 2009.0825 2009.1438 2009.2052 2009.2666 2009.3280 2009.3894 2009.4508 2009.5121 2009.5735 2009.6349 2009.6963 2009.7577 2009.8191 2009.8805 2009.9419 2010.0032 2010.0646 2010.1260 2010.1874 2010.2488 2010.3102 2010.3716 2010.4330 2010.4944 2010.5558 2010.6172 2010.6786 2010.7400 2010.8014 2010.8628 2010.9242 2010.9856 2011.0471 2011.1085 2011.1699 2011.2313 2011.2927 2011.3541 2011.4155 2011.4769 2011.5384 2011.5998 2011.6612 2011.7226 2011.7840 2011.8454 2011.9069 2011.9683 2012.0297 2012.0911 2012.1526 2012.2140 2012.2754 2012.3368 2012.3983 2012.4597 2012.5211 2012.5826 2012.6440 2012.7054 2012.7669 2012.8283 2012.8897 2012.9512 2013.0126 2013.0740 2013.1355 2013.1969 2013.2584 2013.3198 2013.3812 2013.4427 2013.5041 2013.5656 2013.6270 2013.6885 2013.7499 2013.8114 2013.8728 2013.9343 2013.9957 2014.0572 2014.1186 2014.1801 2014.2416 2014.3030 2014.3645 2014.4259 2014.4874 2014.5489 2014.6103 2014.6718 2014.7332 2014.7947 2014.8562 2014.9176 2014.9791 2015.0406 2015.1020 2015.1635 2015.2250 2015.2865 2015.3479 2015.4094 2015.4709 2015.5324 2015.5938 2015.6553 2015.7168 2015.7783 2015.8398 2015.9012 2015.9627 2016.0242 2016.0857 2016.1472 2016.2087 2016.2701 2016.3316 2016.3931 2016.4546 2016.5161 2016.5776 2016.6391 2016.7006 2016.7621 2016.8236 2016.8851 2016.9466 2017.0081 2017.0696 2017.1311 2017.1926 2017.2541 2017.3156 2017.3771 2017.4386 2017.5001 2017.5616 2017.6231 2017.6846 2017.7461 2017.8076 2017.8692 2017.9307 2017.9922 2018.0537 2018.1152 2018.1767 2018.2382 2018.2998 2018.3613 2018.4228 2018.4843 2018.5458 2018.6074 2018.6689 2018.7304 2018.7919 2018.8535 2018.9150 2018.9765 2019.0381 2019.0996 2019.1611 2019.2226 2019.2842 2019.3457 2019.4073 2019.4688 2019.5303 2019.5919 2019.6534 2019.7149 2019.7765 2019.8380 2019.8996 2019.9611 2020.0227 2020.0842 2020.1457 2020.2073 2020.2688 2020.3304 2020.3919 2020.4535 2020.5150 2020.5766 2020.6382 2020.6997 2020.7613 2020.8228 2020.8844 2020.9459 2021.0075 2021.0691 2021.1306 2021.1922 2021.2537 2021.3153 2021.3769 2021.4384 2021.5000 2021.5616 2021.6231 2021.6847 2021.7463 2021.8079 2021.8694 2021.9310 2021.9926 2022.0542 2022.1157 2022.1773 2022.2389 2022.3005 2022.3621 2022.4236 2022.4852 2022.5468 2022.6084 2022.6700 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192.1920 228.3470 210.4600 167.4550 178.8720 178.8720 140.0540 142.7180 186.4840 218.8330 247.7560 259.9350 290.0000 233.2940 181.9170 194.8560 179.6340 169.3580 137.0090 97.0490 127.4950 198.6620 218.0710 164.7910 156.0380 209.3180 250.4200 245.8530 227.2050 236.3390 262.9790 257.2710 219.5940 172.7830 139.2930 129.0170 140.0540 135.4870 142.7180 167.0750 155.2770 157.1800 208.1770 264.8820 255.7480 224.1610 259.9350 282.7690 234.8170 182.6780 167.8360 149.5680 176.2080 168.9770 125.2110 116.8390 162.1270 184.2000 187.2450 180.3950 202.0870 262.5990 278.2020 233.2940 188.3870 188.3870 183.8200 194.0950 187.2450 157.1800 121.0250 101.2350 132.4420 189.5280 224.9220 246.9950 268.3070 267.9270 256.8900 241.2870 220.3550 209.6990 250.4200 253.8450 219.9740 192.1930 138.9120 135.8680 135.8680 164.7910 190.2900 206.2740 199.4230 202.4680 231.7720 285.0530 267.9270 229.4890 207.4150 169.3580 154.8960 143.0980 144.2400 145.0010 132.4420 152.6130 187.2450 221.4970 252.3230 285.0530 303.7010 328.4380 287.3360 241.2870 246.2340 189.9090 153.3740 149.1880 132.0620 154.1350 165.5520 197.1400 221.8770 205.8930 262.5990 321.9680 354.3170 352.7950 290.7610 277.8220 282.0080 216.5490 181.1560 190.2900 180.7750 174.6860 145.3820 114.1750 119.8830 146.5240 219.5940 272.4940 277.4410 297.9920 340.2360 310.9320 251.5620 201.3260 177.3500 177.3500 163.6490 148.4260 186.8640 227.9660 198.6620 168.9770 166.3130 186.4840 232.9140 237.1000 210.0790 219.5940 286.9550 258.4120 209.3180 184.5810 149.9490 131.6810 150.3290 156.0380 134.3450 149.9490 166.6940 189.1480 245.0920 288.8580 301.0370 254.2260 202.8490 193.3340 191.0510 179.6340 155.2770 122.1670 127.8750 150.3290 142.7180 129.7780 148.8070 176.5890 208.5570 276.2990 343.6610 361.9280 339.0940 227.5860 167.4550 135.4870 111.1300 127.1140 149.1880 126.3530 115.3170 162.8880 197.1400 173.9250 199.4230 266.7850 282.7690 286.9550 302.5590 291.9030 240.1450 202.4680 190.6700 175.8280 149.9490 155.6570 165.9330 160.9850 138.9120 103.8990 165.1720 287.3360 391.6130 403.4110 332.6240 262.9790 246.6150 275.1580 262.9790 198.6620 164.7910 161.3660 190.2900 214.6460 176.2080 164.4110 200.5650 272.4940 353.5560 369.5400 333.7660 272.1130 176.2080 160.9850 160.2240 142.7180 113.7940 147.2850 185.3420 162.1270 157.5600 151.4710 176.9700 248.8980 272.4940 278.9630 299.5140 277.0600 217.6910 167.4550 148.4260 154.1350 137.7700 150.3290 167.4550 144.2400 145.7620 170.1190 185.3420 205.5130 261.8380 338.7130 345.9440 320.8260 264.1210 221.1160 190.6700 159.4630 164.7910 161.3660 161.3660 159.0830 140.4340 170.5000 208.1770 216.9300 260.6960 287.7170 314.7370 343.2800 318.5430 252.7040 198.6620 182.6780 203.9900 208.1770 177.3500 166.3130 144.2400 156.4190 184.9620 189.1480 217.3100 258.4120 353.1750 390.8520 318.1620 255.3680 214.6460 199.4230 193.7150 179.6340 169.3580 179.6340 173.5440 167.0750 151.0900 175.4470 261.4570 339.4750 340.2360 275.5380 264.1210 269.4490 222.2580 226.0640 221.8770 179.2530 152.6130 147.6650 148.8070 194.0950 157.5600 149.9490 214.2660 247.7560 281.6270 285.8140 256.5090 242.4280 180.3950 179.2530 181.1560 153.7540 175.4470 155.2770 163.6490 165.5520 151.0900 136.2480 175.4470 226.0640 296.0890 380.5770 442.6100 473.0560 405.6940 326.1550 271.7320 245.4730 213.1240 186.1030 170.1190 154.8960 164.4110 196.3790 216.5490 232.1530 272.8740 308.2680 371.0620 436.5210 490.5620 434.2370 292.2830 170.1190 117.6000 134.3450 189.9090 209.3180 177.3500 165.1720 191.8120 251.5620 277.4410 327.6770 401.5080 511.8750 519.1060 392.3740 286.5750 227.2050 215.0270 188.3870 211.2210 229.1080 219.5940 209.6990 199.8040 190.2900 219.9740 388.1880 568.9610 768.3810 980.3610 1032.8800 813.6700 535.4700 326.9160 224.1610 205.1320 183.4390 163.2690 160.9850 176.2080 223.4000 278.2020 392.3740 571.2440 799.2080 1008.9000 1069.8000 938.8790 667.9100 428.1480 261.8380 170.1190 180.0140 192.5730 202.0870 242.0480 235.5780 211.6020 266.7850 336.0490 457.8330 713.9590 898.5380 773.7100 503.1210 302.5590 208.9380 172.4030 187.6260 187.2450 155.2770 154.8960 149.1880 159.8440 184.9620 228.7280 297.6120 398.4640 447.1770 439.9460 393.5160 301.7980 203.2290 178.1110 191.4310 196.7590 180.7750 150.3290 178.4920 233.2950 211.6020 213.1240 249.6590 267.1660 288.8580 279.3440 240.9060 222.6390 240.5250 251.1820 194.8570 149.5680 151.4710 168.5970 166.3140 176.9700 178.8720 181.5360 199.0430 240.1450 271.3520 287.3360 277.8220 188.0060 156.7990 199.8040 179.6340 168.5970 163.6500 172.7830 170.8800 161.3660 166.6940 180.0140 194.0950 219.2130 229.4890 242.0480 254.2260 217.3100 164.7910 160.6050 176.9700 184.9620 176.5890 175.0670 210.0800 221.8770 194.8570 178.4920 221.1160 227.9660 195.9980 208.5570 218.4520 216.9300 195.2370 188.7670 182.6780 172.4030 161.3660 172.7830 158.3210 171.6420 184.5810 162.5080 158.7020 197.5210 228.7280 235.1970 248.8980 274.7770 255.3680 203.6100 195.2370 212.7440 219.5940 217.3100 182.2980 154.8960 187.6260 213.8850 209.6990 252.3230 306.7450 292.2840 254.2260 264.8820 260.6960 195.6180 149.5680 181.1560 198.2820 180.0140 161.3660 154.8960 172.4030 186.8650 213.1240 242.8090 265.2630 278.5830 274.0160 245.0920 184.2010 177.3500 200.1850 194.4760 184.5810 190.6700 190.6700 208.1770 221.4970 209.6990 224.9220 283.9110 298.3730 264.5020 248.5180 222.6390 177.7310 148.4270 147.6650 181.1560 198.6620 185.3420 192.1930 181.9170 195.9980 216.5490 228.7280 229.4890 251.1820 271.7330 258.7930 263.3600 232.1530 182.2980 164.0300 192.9540 182.6780 143.4790 141.5760 142.3370 158.7020 130.5400 125.9730 185.7230 269.0690 278.2020 266.7850 274.3970 240.1450 190.6700 179.6340 177.3500 174.6860 156.4190 167.0750 185.3420 179.6340 183.8200 234.8170 253.8460 217.6910 246.2340 348.2280 347.0860 254.6070 228.3470 215.0270 152.6130 137.0090 152.9940 153.7550 159.8440 170.1190 142.3370 151.0910 160.9860 193.3340 241.2870 244.3310 269.4490 227.2050 168.5970 148.8070 149.5680 162.1270 173.9250 184.9620 180.3950 172.7830 186.4840 199.8040 174.6860 184.9620 224.5410 234.8170 209.3190 203.9900 212.7440 178.1110 151.4710 150.7100 156.4190 149.5680 158.3220 171.2610 175.8280 187.2450 200.5650 212.3630 220.7360 266.7850 248.5180 219.5940 243.9510 237.8620 175.4470 140.4350 151.4710 155.6580 150.7100 168.2170 140.0540 116.0780 134.7260 229.8700 258.7930 220.3550 236.3390 247.3760 240.9060 222.2580 171.6420 104.6610 131.6810 145.3820 153.3740 181.5370 146.5240 129.0170 165.5530 187.6260 208.1770 235.1980 255.7490 221.4970 217.6910 210.0800 173.5450 136.2480 156.4190 148.4270 142.3380 165.1720 187.2450 173.5450 164.7910 156.7990 174.6860 227.2060 287.7170 320.4460 302.9400 243.9510 198.6620 210.8410 190.2900 149.1880 141.1960 129.7790 133.9650 153.3740 183.4390 208.5570 223.0190 224.9220 246.6150 299.5150 317.4010 310.9320 281.6280 215.0270 212.7440 186.1030 157.9410 169.3580 183.8200 182.6780 185.3420 202.0880 210.8410 269.0690 403.0310 505.4050 516.4420 439.9460 326.5350 261.0770 213.1240 193.7150 171.2610 173.9250 187.6260 189.9090 184.5810 186.1030 224.1610 262.9790 318.1630 369.9210 432.3350 394.2770 300.6560 237.4810 218.4520 223.7800 216.5490 182.6780 153.7550 155.2770 147.2850 164.4110 194.0960 191.8120 219.9750 285.4330 332.6240 337.1910 307.5070 263.7410 222.6390 211.9830 187.2450 151.8520 168.9780 207.4160 206.6550 211.2210 202.4680 193.3340 257.2710 341.3780 366.4960 317.0210 231.3920 213.1240 233.6750 248.5180 231.7720 215.4080 207.4160 211.2210 192.1930 166.3140 157.1800 172.4030 236.3390 299.8950 336.0500 317.4020 307.5070 267.5460 192.9540 166.3140 154.1350 134.3450 157.9410 185.7230 186.4840 201.7070 189.1480 216.5490 247.3760 295.3280 313.2150 293.8060 242.0480 229.8690 211.6020 148.4270 116.8390 147.6660 180.0140 </int_list></spectrum></measured></pepdata></protdata>
\ No newline at end of file
diff --git a/samples/XML_output/C25plst02_B_25.xml b/samples/XML_output/C25plst02_B_25.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fda94d10bcfbc750ab7496efe208bccb4d62ce47
--- /dev/null
+++ b/samples/XML_output/C25plst02_B_25.xml
@@ -0,0 +1 @@
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420.6170 364.2850 304.7340 291.8580 285.9560 297.2230 266.1060 233.3790 240.8900 245.7190 261.8140 324.5840 396.4750 497.3370 586.3960 567.0820 441.5410 357.8470 323.5110 283.8100 313.3180 295.6130 276.2990 282.2010 262.3500 257.5220 248.4010 266.6420 258.0580 271.4710 348.7260 392.7190 395.9380 385.7450 323.5110 256.4490 261.8140 296.6860 276.8360 259.1310 280.5910 265.5690 245.7190 253.7660 273.0800 265.5690 319.2190 444.2230 548.8410 530.6000 417.3980 346.0440 358.3830 384.6720 345.5070 290.2480 272.5440 257.5220 254.3030 232.3060 230.6970 263.4230 314.3910 401.3030 506.9940 620.7320 570.3010 440.4680 364.8220 319.2190 311.7080 331.0220 319.7560 312.7810 287.5660 249.4740 249.4740 254.8390 266.1060 351.9460 452.8070 452.8070 453.3440 500.5560 498.4100 392.1830 300.9780 287.0290 302.5880 296.1500 292.3940 250.5470 225.3320 236.5980 282.2010 325.6570 341.7520 392.7190 429.2010 496.8000 514.5050 417.3980 330.4860 324.5840 346.0440 362.1390 317.0730 255.3760 239.8170 252.6930 240.8900 256.9850 271.4710 331.5590 390.5730 447.9790 437.2490 402.3760 410.9600 361.0660 271.4710 233.3790 258.0580 273.6170 275.2260 332.0950 373.9420 353.5550 343.8980 324.5840 280.0550 270.9340 333.1680 409.8870 474.8040 422.2270 314.9270 264.4960 261.8140 270.3980 260.7410 245.7190 227.4780 258.0580 249.4740 222.1130 221.0400 295.0770 409.8870 421.6900 416.3250 462.4640 453.8800 345.5070 301.5150 249.4740 245.1820 278.9820 277.9090 265.0330 209.7730 219.9670 256.9850 253.7660 285.4200 353.5550 456.0260 530.0630 542.4030 458.7090 412.5700 397.0110 317.6100 257.5220 241.4270 238.7440 272.0070 302.5880 275.2260 267.7150 279.5180 309.0260 394.8650 448.5150 493.5810 517.1870 419.0080 316.5360 309.0260 301.5150 267.7150 259.1310 273.0800 277.9090 275.2260 285.4200 283.2740 259.1310 302.0510 360.5290 414.7160 442.6140 385.7450 381.9890 312.7810 260.2040 270.9340 290.7850 295.0770 263.4230 294.5400 340.6790 353.5550 297.2230 247.3280 269.8610 310.0990 354.0910 388.9640 372.3320 371.2590 361.6020 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215.1360 216.7450 263.9570 249.4720 202.7960 179.1900 195.2850 226.4020 240.8880 222.6470 216.2090 238.2050 246.7890 277.3700 303.1220 344.4320 354.6260 329.9470 347.6510 468.3630 627.7040 561.1780 438.8560 365.3560 317.0710 267.7130 200.6500 195.8220 203.3330 226.4020 256.4460 254.3000 299.3660 317.0710 311.7060 241.9610 193.6760 219.4280 239.8150 281.6620 289.1730 281.6620 355.6990 377.6950 400.2280 459.2430 494.1150 480.7030 418.4690 361.0640 342.8230 294.5380 246.7890 273.6140 234.4500 197.9680 231.7670 232.8400 226.9390 201.7230 250.5450 328.8740 334.7750 299.9030 292.9280 292.9280 225.8660 234.9860 307.4140 370.1840 419.5420 467.2900 436.7100 354.6260 312.2420 300.4390 275.7600 283.2710 303.6580 249.4720 203.8690 202.2600 229.6210 243.0340 276.8330 295.6110 263.9570 232.8400 259.6650 274.6870 240.3510 244.1070 265.0300 241.9610 285.4170 360.5270 415.7860 443.1480 531.1340 636.2880 775.7770 804.2120 627.1670 425.9800 306.3410 304.7310 307.4140 280.5890 289.1730 278.9790 232.8400 240.3510 250.5450 262.3480 271.4680 254.8370 243.5700 231.7670 283.8080 343.8950 350.3330 321.8990 351.9430 416.3230 492.5060 522.0130 579.9550 596.0500 504.3090 358.9170 263.9570 248.3990 234.9860 223.7200 209.2340 214.5990 282.7340 328.8730 355.6980 305.8040 247.8620 246.2530 265.5660 253.7640 278.9790 261.8110 263.9570 383.5960 856.7890 2337.5300 4111.1900 3945.4100 2070.3500 715.6890 358.9170 421.6880 389.4980 312.2420 264.4940 269.8590 376.6220 359.4540 261.8110 238.7420 253.7640 267.7130 233.3770 231.7670 255.9100 275.2240 250.0080 245.7160 297.7570 412.0310 571.9080 990.3770 1781.7100 1982.3600 1258.0900 575.6630 351.9430 415.2500 439.3920 362.1360 275.2240 289.1730 337.4570 276.8330 247.8620 308.4870 323.5080 274.6870 244.6430 255.3730 278.9790 256.4460 229.6210 216.7450 262.8840 350.3330 365.3550 426.5160 611.6090 761.2920 629.8490 453.3410 442.6110 393.2530 319.2170 266.6400 253.7640 289.7090 313.3150 263.4210 231.2310 248.9350 274.6870 289.1730 265.5670 251.0810 269.8590 261.8110 296.1470 364.8190 351.4060 284.8810 252.6910 302.5850 411.4940 473.7280 449.0490 408.8120 326.1910 344.9690 340.1400 295.0740 247.3260 229.0850 252.1540 260.2020 296.1470 313.8520 263.9570 261.2750 318.6800 300.9760 262.8840 279.5160 251.0810 226.4020 330.4830 368.0380 312.7790 347.1150 450.1220 523.6230 519.8670 483.3850 444.2210 416.3230 349.2610 261.2750 230.1580 219.4280 248.3990 246.2530 231.2310 258.5920 341.2130 328.8740 255.9100 224.2560 259.6650 287.0270 304.1950 344.9690 401.8370 370.1840 297.7570 381.4510 511.2830 574.0540 513.4290 426.5160 348.7240 314.3880 341.2130 317.0710 277.9060 278.4430 265.0300 267.1760 245.1800 214.0630 232.8400 246.2530 237.6690 244.6430 247.8620 263.4210 313.3150 318.6800 291.8550 323.5090 372.8670 363.7460 366.4290 423.2970 495.1880 505.3820 407.2020 299.9030 262.8840 263.4210 221.0370 195.2850 219.9640 253.7640 255.3730 225.8660 222.1100 243.0340 238.2050 265.0300 251.6180 221.5740 234.9860 232.8400 245.1800 313.8520 355.1620 326.1910 378.7680 452.2680 500.5530 492.5060 451.1950 372.8660 305.8040 302.0490 317.6070 281.6620 256.4460 251.6180 222.6470 196.3580 234.9860 253.7640 252.6910 247.3260 233.9130 206.5520 290.7820 364.2830 348.1880 306.3410 314.9250 392.7170 517.7210 613.7550 630.3860 522.0130 406.1290 359.9910 348.7240 319.7530 280.5890 283.2710 285.4170 296.1470 275.2240 268.7860 260.7380 241.4240 204.4060 246.2530 293.4650 322.4360 289.1730 330.4830 371.7940 359.9910 302.5850 322.4360 419.5420 518.2580 594.4410 621.8020 532.2070 411.4940 333.1660 312.2420 300.4390 298.8300 262.3480 226.9390 242.4970 337.9940 342.2860 281.1250 272.0050 296.1470 300.4390 313.3150 326.1910 284.8810 268.2490 270.3950 289.1730 337.9940 430.8090 460.8520 446.9030 466.7540 417.3960 351.4070 333.7020 315.4610 264.4940 270.3950 294.0010 275.2240 243.0340 212.9900 238.2050 272.5410 274.1510 237.1320 261.2750 295.6110 288.6360 314.3880 335.3120 324.5820 353.5530 420.6150 495.7250 533.2800 502.6990 458.1700 394.8630 310.0960 303.6580 344.9690 316.5340 284.3440 277.3700 261.2750 238.2050 232.8400 275.7600 304.1950 294.0010 290.2460 284.3440 238.7420 240.8880 300.9760 308.4870 301.5120 409.8850 491.9690 577.8090 703.8870 720.5180 521.4770 404.5200 381.4510 358.3810 326.7280 250.5450 260.2020 275.7600 273.0780 240.8880 214.5990 202.7960 223.1830 269.3220 264.4940 245.1800 300.4390 335.3120 331.5560 361.6000 435.1000 412.0310 431.8810 525.2320 562.7870 549.3750 504.3090 484.4580 438.8560 319.2170 246.2530 239.8150 267.7130 304.1950 261.2750 224.2560 216.7450 233.9130 255.9100 295.6110 290.2460 272.0050 262.8840 243.0340 287.5630 333.7020 315.4610 329.4100 408.2750 495.1880 473.7280 434.5640 449.0490 391.1080 336.3850 287.0270 281.6620 297.2200 312.2420 281.6620 217.8180 181.3360 185.0920 238.2050 286.4900 256.4460 237.6690 278.9790 279.5160 251.0810 311.7060 333.1660 311.7060 307.9500 414.7140 552.0570 657.7480 608.3900 480.7030 361.0640 329.4100 322.9720 279.5160 233.9130 219.4280 233.3770 254.8370 288.6360 274.6870 260.7380 246.7890 196.3580 213.5260 239.8150 270.9320 321.8990 363.7460 352.4800 371.2570 405.0570 420.0780 502.6990 623.9480 718.3720 811.7230 763.9740 592.8310 414.1770 317.0710 265.5670 285.9540 243.0340 187.2380 217.8180 310.0960 337.4580 272.0050 226.9390 289.7090 300.4390 256.4460 259.1290 273.6140 324.0450 378.2310 385.2060 408.2750 440.4650 468.9000 498.4070 539.7180 583.7110 474.8010 322.4350 276.2970 289.7090 267.1760 277.3700 316.5340 296.6840 262.8840 269.3220 233.9130 261.2750 270.3950 256.4460 235.5230 259.1290 281.1250 260.2020 270.3950 370.7200 454.4140 506.9910 544.5460 523.6230 518.7940 548.8380 441.0020 303.6580 261.8110 235.5230 253.2270 274.6870 244.6430 250.0080 218.3550 224.2560 266.1030 281.1250 279.5160 262.3480 221.5740 231.2310 261.8110 360.5270 432.4180 401.3010 375.0120 428.6620 518.2580 536.4990 457.0970 368.0380 362.1360 335.8480 327.8010 265.5670 230.1580 264.4940 290.7820 284.3440 307.4140 314.3880 260.2020 289.7090 314.9250 299.9030 309.0230 309.0230 344.9680 395.3990 364.8190 326.1910 378.2310 483.3850 571.9080 565.4700 477.4840 400.2280 366.9650 327.8010 316.5340 273.0780 231.7670 228.0120 268.7860 278.4430 278.4430 300.9760 306.3410 268.7860 281.1250 351.9430 338.5300 256.4460 243.0340 273.0780 319.2170 340.6760 375.0120 441.0020 453.3410 446.9030 432.9540 382.5230 369.6470 318.6800 267.1760 291.3190 300.9760 283.8080 248.9350 210.3070 233.9130 277.3700 267.7130 226.4020 213.5260 228.5480 240.3510 232.3040 296.1470 368.5740 369.1110 394.3260 442.0750 517.1850 554.7400 458.1700 361.0630 310.0960 287.5630 261.8110 249.4720 269.3220 262.3480 254.3000 237.6690 243.0340 240.8880 262.8840 246.7890 235.5230 254.8370 272.5410 289.7090 338.5300 327.8000 350.3330 398.6180 442.6110 644.8710 886.8330 934.0440 726.9560 462.4620 330.4830 311.1690 267.7130 296.6840 315.9970 253.7640 251.0810 325.1180 343.8950 290.2460 246.7890 230.6940 250.0080 245.1800 260.2020 288.1000 308.4860 310.6320 339.6030 390.5710 460.3160 628.2400 747.8790 706.5690 539.1810 413.6400 332.0920 319.7530 363.2090 312.7780 243.0340 233.9130 286.4900 314.3880 285.4170 261.2750 282.1980 272.5410 283.8070 295.0740 291.3180 319.2160 345.5050 333.1650 315.4610 357.8440 476.4110 625.0210 726.9560 668.4770 513.4290 402.3740 361.6000 349.7970 280.5880 243.0340 232.3040 225.3290 274.6870 346.5780 340.6760 251.0810 240.8880 271.4680 258.5920 231.7670 290.2450 327.2640 333.7020 331.0190 395.3990 452.2680 490.8960 688.3280 1025.7900 1056.3700 680.8170 392.1800 326.1910 300.4390 252.6910 237.6690 250.0080 206.0150 180.2630 231.2310 267.7130 276.8330 284.8800 270.3950 216.2090 223.7200 280.0520 337.4570 407.2020 409.8850 620.7290 1318.7100 2627.2400 3541.4300 2819.3000 1315.5000 483.9220 356.2350 422.2240 384.1330 331.5560 321.3620 322.4350 343.8950 304.1940 226.4020 227.4750 245.1790 251.0810 257.5190 230.1580 221.0370 238.7420 273.0770 299.3660 365.8920 467.2900 738.7590 1286.5200 1609.5000 1225.3600 623.4110 296.6830 305.2670 407.2020 355.1620 226.4020 182.4090 258.0550 295.6100 239.8140 199.0400 260.2010 308.4860 264.4930 272.0040 280.0520 258.5920 256.4460 259.1280 303.6580 319.7530 371.7930 568.6880 806.8940 864.8360 608.9260 427.0530 342.8220 321.8990 269.8580 197.4310 225.8650 268.7850 267.7120 236.0590 217.2810 227.4750 252.6900 257.5190 232.3030 200.6500 265.0300 340.1400 344.9680 359.4540 376.6220 374.4760 355.6980 377.6950 468.9000 556.3490 507.5270 385.7420 344.4320 300.4390 276.2960 285.4170 270.9310 232.8400 216.2080 248.3980 244.1060 240.8870 261.8110 247.3250 248.9350 248.9350 277.3690 296.1470 318.1430 323.5080 339.0670 370.1840 448.5130 524.6950 502.6990 523.0860 </int_list></spectrum></measured><measured><pepseq>VEHVTHPEQYIPGVLKR</pepseq><mzh>2002.0392</mzh><calc_mzh>2002.0875</calc_mzh><leucines>1</leucines><mono_iso_intensity>1134</mono_iso_intensity><deuterated_intensity>111</deuterated_intensity><ratio>0.10</ratio><validated>YES</validated><local_bg>117</local_bg><corrected_ratio>-0.01</corrected_ratio><spectrum><mz_list>1977.6233 1977.6842 1977.7451 1977.8060 1977.8669 1977.9278 1977.9887 1978.0496 1978.1105 1978.1714 1978.2324 1978.2933 1978.3542 1978.4151 1978.4760 1978.5369 1978.5978 1978.6587 1978.7196 1978.7805 1978.8414 1978.9024 1978.9633 1979.0242 1979.0851 1979.1460 1979.2070 1979.2679 1979.3288 1979.3897 1979.4506 1979.5116 1979.5725 1979.6334 1979.6943 1979.7553 1979.8162 1979.8771 1979.9381 1979.9990 1980.0599 1980.1209 1980.1818 1980.2427 1980.3037 1980.3646 1980.4255 1980.4865 1980.5474 1980.6084 1980.6693 1980.7303 1980.7912 1980.8521 1980.9131 1980.9740 1981.0350 1981.0959 1981.1569 1981.2178 1981.2788 1981.3397 1981.4007 1981.4616 1981.5226 1981.5836 1981.6445 1981.7055 1981.7664 1981.8274 1981.8884 1981.9493 1982.0103 1982.0712 1982.1322 1982.1932 1982.2541 1982.3151 1982.3761 1982.4370 1982.4980 1982.5590 1982.6200 1982.6809 1982.7419 1982.8029 1982.8639 1982.9248 1982.9858 1983.0468 1983.1078 1983.1688 1983.2297 1983.2907 1983.3517 1983.4127 1983.4737 1983.5347 1983.5956 1983.6566 1983.7176 1983.7786 1983.8396 1983.9006 1983.9616 1984.0226 1984.0836 1984.1446 1984.2056 1984.2666 1984.3276 1984.3886 1984.4496 1984.5106 1984.5716 1984.6326 1984.6936 1984.7546 1984.8156 1984.8766 1984.9376 1984.9986 1985.0596 1985.1206 1985.1816 1985.2427 1985.3037 1985.3647 1985.4257 1985.4867 1985.5477 1985.6088 1985.6698 1985.7308 1985.7918 1985.8528 1985.9139 1985.9749 1986.0359 1986.0969 1986.1580 1986.2190 1986.2800 1986.3410 1986.4021 1986.4631 1986.5241 1986.5852 1986.6462 1986.7072 1986.7683 1986.8293 1986.8904 1986.9514 1987.0124 1987.0735 1987.1345 1987.1956 1987.2566 1987.3176 1987.3787 1987.4397 1987.5008 1987.5618 1987.6229 1987.6839 1987.7450 1987.8060 1987.8671 1987.9281 1987.9892 1988.0503 1988.1113 1988.1724 1988.2334 1988.2945 1988.3555 1988.4166 1988.4777 1988.5387 1988.5998 1988.6609 1988.7219 1988.7830 1988.8441 1988.9051 1988.9662 1989.0273 1989.0883 1989.1494 1989.2105 1989.2716 1989.3326 1989.3937 1989.4548 1989.5159 1989.5770 1989.6380 1989.6991 1989.7602 1989.8213 1989.8824 1989.9434 1990.0045 1990.0656 1990.1267 1990.1878 1990.2489 1990.3100 1990.3711 1990.4322 1990.4933 1990.5543 1990.6154 1990.6765 1990.7376 1990.7987 1990.8598 1990.9209 1990.9820 1991.0431 1991.1042 1991.1653 1991.2264 1991.2875 1991.3487 1991.4098 1991.4709 1991.5320 1991.5931 1991.6542 1991.7153 1991.7764 1991.8375 1991.8987 1991.9598 1992.0209 1992.0820 1992.1431 1992.2042 1992.2654 1992.3265 1992.3876 1992.4487 1992.5099 1992.5710 1992.6321 1992.6932 1992.7544 1992.8155 1992.8766 1992.9378 1992.9989 1993.0600 1993.1211 1993.1823 1993.2434 1993.3046 1993.3657 1993.4268 1993.4880 1993.5491 1993.6103 1993.6714 1993.7325 1993.7937 1993.8548 1993.9160 1993.9771 1994.0383 1994.0994 1994.1606 1994.2217 1994.2829 1994.3440 1994.4052 1994.4663 1994.5275 1994.5886 1994.6498 1994.7110 1994.7721 1994.8333 1994.8944 1994.9556 1995.0168 1995.0779 1995.1391 1995.2002 1995.2614 1995.3226 1995.3838 1995.4449 1995.5061 1995.5673 1995.6284 1995.6896 1995.7508 1995.8120 1995.8731 1995.9343 1995.9955 1996.0567 1996.1178 1996.1790 1996.2402 1996.3014 1996.3626 1996.4238 1996.4849 1996.5461 1996.6073 1996.6685 1996.7297 1996.7909 1996.8521 1996.9133 1996.9745 1997.0356 1997.0968 1997.1580 1997.2192 1997.2804 1997.3416 1997.4028 1997.4640 1997.5252 1997.5864 1997.6476 1997.7088 1997.7700 1997.8313 1997.8925 1997.9537 1998.0149 1998.0761 1998.1373 1998.1985 1998.2597 1998.3209 1998.3821 1998.4434 1998.5046 1998.5658 1998.6270 1998.6882 1998.7495 1998.8107 1998.8719 1998.9331 1998.9943 1999.0556 1999.1168 1999.1780 1999.2392 1999.3005 1999.3617 1999.4229 1999.4842 1999.5454 1999.6066 1999.6679 1999.7291 1999.7903 1999.8516 1999.9128 1999.9740 2000.0353 2000.0965 2000.1578 2000.2190 2000.2803 2000.3415 2000.4027 2000.4640 2000.5252 2000.5865 2000.6477 2000.7090 2000.7702 2000.8315 2000.8927 2000.9540 2001.0152 2001.0765 2001.1378 2001.1990 2001.2603 2001.3215 2001.3828 2001.4441 2001.5053 2001.5666 2001.6278 2001.6891 2001.7504 2001.8116 2001.8729 2001.9342 2001.9954 2002.0567 2002.1180 2002.1793 2002.2405 2002.3018 2002.3631 2002.4244 2002.4856 2002.5469 2002.6082 2002.6695 2002.7308 2002.7920 2002.8533 2002.9146 2002.9759 2003.0372 2003.0985 2003.1597 2003.2210 2003.2823 2003.3436 2003.4049 2003.4662 2003.5275 2003.5888 2003.6501 2003.7114 2003.7727 2003.8340 2003.8953 2003.9566 2004.0179 2004.0792 2004.1405 2004.2018 2004.2631 2004.3244 2004.3857 2004.4470 2004.5083 2004.5696 2004.6309 2004.6922 2004.7535 2004.8149 2004.8762 2004.9375 2004.9988 2005.0601 2005.1214 2005.1828 2005.2441 2005.3054 2005.3667 2005.4280 2005.4894 2005.5507 2005.6120 2005.6733 2005.7347 2005.7960 2005.8573 2005.9186 2005.9800 2006.0413 2006.1026 2006.1640 2006.2253 2006.2866 2006.3480 2006.4093 2006.4707 2006.5320 2006.5933 2006.6547 2006.7160 2006.7774 2006.8387 2006.9000 2006.9614 2007.0227 2007.0841 2007.1454 2007.2068 2007.2681 2007.3295 2007.3908 2007.4522 2007.5135 2007.5749 2007.6363 2007.6976 2007.7590 2007.8203 2007.8817 2007.9430 2008.0044 2008.0658 2008.1271 2008.1885 2008.2499 2008.3112 2008.3726 2008.4340 2008.4953 2008.5567 2008.6181 2008.6794 2008.7408 2008.8022 2008.8636 2008.9249 2008.9863 2009.0477 2009.1091 2009.1705 2009.2318 2009.2932 2009.3546 2009.4160 2009.4774 2009.5387 2009.6001 2009.6615 2009.7229 2009.7843 2009.8457 2009.9071 2009.9685 2010.0299 2010.0913 2010.1526 2010.2140 2010.2754 2010.3368 2010.3982 2010.4596 2010.5210 2010.5824 2010.6438 2010.7052 2010.7666 2010.8280 2010.8895 2010.9509 2011.0123 2011.0737 2011.1351 2011.1965 2011.2579 2011.3193 2011.3807 2011.4421 2011.5036 2011.5650 2011.6264 2011.6878 2011.7492 2011.8106 2011.8721 2011.9335 2011.9949 2012.0563 2012.1178 2012.1792 2012.2406 2012.3020 2012.3635 2012.4249 2012.4863 2012.5478 2012.6092 2012.6706 2012.7321 2012.7935 2012.8549 2012.9164 2012.9778 2013.0392 2013.1007 2013.1621 2013.2236 2013.2850 2013.3464 2013.4079 2013.4693 2013.5308 2013.5922 2013.6537 2013.7151 2013.7766 2013.8380 2013.8995 2013.9609 2014.0224 2014.0838 2014.1453 2014.2067 2014.2682 2014.3297 2014.3911 2014.4526 2014.5140 2014.5755 2014.6370 2014.6984 2014.7599 2014.8214 2014.8828 2014.9443 2015.0058 2015.0672 2015.1287 2015.1902 2015.2516 2015.3131 2015.3746 2015.4361 2015.4975 2015.5590 2015.6205 2015.6820 2015.7435 2015.8049 2015.8664 2015.9279 2015.9894 2016.0509 2016.1123 2016.1738 2016.2353 2016.2968 2016.3583 2016.4198 2016.4813 2016.5428 2016.6043 2016.6658 2016.7273 2016.7887 2016.8502 2016.9117 2016.9732 2017.0347 2017.0962 2017.1577 2017.2192 2017.2807 2017.3422 2017.4038 2017.4653 2017.5268 2017.5883 2017.6498 2017.7113 2017.7728 2017.8343 2017.8958 2017.9573 2018.0189 2018.0804 2018.1419 2018.2034 2018.2649 2018.3264 2018.3880 2018.4495 2018.5110 2018.5725 2018.6340 2018.6956 2018.7571 2018.8186 2018.8802 2018.9417 2019.0032 2019.0647 2019.1263 2019.1878 2019.2493 2019.3109 2019.3724 2019.4339 2019.4955 2019.5570 2019.6186 2019.6801 2019.7416 2019.8032 2019.8647 2019.9263 2019.9878 2020.0494 2020.1109 2020.1724 2020.2340 2020.2955 2020.3571 2020.4186 2020.4802 2020.5417 2020.6033 2020.6649 2020.7264 2020.7880 2020.8495 2020.9111 2020.9726 2021.0342 2021.0958 2021.1573 2021.2189 2021.2805 2021.3420 2021.4036 2021.4652 2021.5267 2021.5883 2021.6499 2021.7114 2021.7730 2021.8346 2021.8961 2021.9577 2022.0193 2022.0809 2022.1424 2022.2040 2022.2656 2022.3272 2022.3888 2022.4503 2022.5119 2022.5735 2022.6351 2022.6967 2022.7583 2022.8199 2022.8814 2022.9430 2023.0046 2023.0662 2023.1278 2023.1894 2023.2510 2023.3126 2023.3742 2023.4358 2023.4974 2023.5590 2023.6206 2023.6822 2023.7438 2023.8054 2023.8670 2023.9286 2023.9902 2024.0518 2024.1134 2024.1750 2024.2366 2024.2982 2024.3598 2024.4215 2024.4831 2024.5447 2024.6063 2024.6679 2024.7295 2024.7912 2024.8528 2024.9144 2024.9760 2025.0376 2025.0993 2025.1609 2025.2225 2025.2841 2025.3457 2025.4074 2025.4690 2025.5306 2025.5923 2025.6539 2025.7155 2025.7772 2025.8388 2025.9004 2025.9621 2026.0237 2026.0853 2026.1470 2026.2086 2026.2702 2026.3319 2026.3935 2026.4552 2026.5168 2026.5785 2026.6401 2026.7018 2026.7634 2026.8250 2026.8867 2026.9483 2027.0100 2027.0717 2027.1333 2027.1950 2027.2566 2027.3183 2027.3799 2027.4416 2027.5032 2027.5649 2027.6266 2027.6882 2027.7499 2027.8116 2027.8732 2027.9349 2027.9965 2028.0582 2028.1199 2028.1816 2028.2432 2028.3049 2028.3666 2028.4282 2028.4899 2028.5516 2028.6133 2028.6749 2028.7366 2028.7983 2028.8600 2028.9217 2028.9833 2029.0450 2029.1067 2029.1684 2029.2301 2029.2918 2029.3534 2029.4151 2029.4768 2029.5385 2029.6002 2029.6619 2029.7236 2029.7853 2029.8470 2029.9087 2029.9704 2030.0321 2030.0938 2030.1555 2030.2172 2030.2789 2030.3406 2030.4023 2030.4640 2030.5257 2030.5874 2030.6491 2030.7108 2030.7725 2030.8342 2030.8959 2030.9576 2031.0193 2031.0811 2031.1428 2031.2045 2031.2662 2031.3279 2031.3896 2031.4514 2031.5131 2031.5748 2031.6365 2031.6982 2031.7600 2031.8217 2031.8834 2031.9451 2032.0069 2032.0686 2032.1303 2032.1920 2032.2538 2032.3155 2032.3772 2032.4390 2032.5007 </mz_list><int_list>259.1320 278.9830 309.5630 298.8330 339.6070 379.3080 423.8380 463.5380 364.2860 279.5190 247.8660 205.4820 201.7270 261.2780 284.3480 265.5700 254.3040 250.5480 238.2090 290.7860 358.3850 404.5240 408.8160 443.1510 442.6150 385.7460 330.4870 269.3260 250.0120 272.5450 295.0780 260.2050 212.4570 174.9020 201.7270 267.1800 304.1980 375.0160 416.3270 397.5490 364.2860 310.6360 265.5700 235.5260 224.7960 224.7960 228.0150 217.2850 226.4060 265.0340 313.3190 313.3190 335.3150 407.2060 450.1260 409.8890 383.6000 343.8990 317.0740 294.0050 261.2780 256.4500 241.4280 231.7710 230.6980 217.2850 204.9460 205.4820 201.1900 291.3220 396.4760 395.4030 349.8010 353.5560 349.2640 325.6580 284.8840 244.6470 253.7670 233.9170 206.5550 211.3840 230.6980 251.6210 246.2560 272.0080 284.8840 333.1690 393.2570 387.8920 385.7460 346.5820 269.3260 244.6470 263.9610 270.9350 280.0560 272.0080 269.8620 251.6210 256.9860 276.8370 273.6180 311.7090 450.1260 559.0350 497.8740 349.2640 321.9030 360.5310 298.2970 231.2340 218.3580 213.5300 237.1360 245.7200 259.1320 289.1760 322.4390 331.5600 394.8670 472.6590 466.2210 347.6550 261.2780 248.9390 270.3990 263.4240 248.9390 203.8730 185.0950 237.1360 259.1320 238.7450 305.2710 348.1910 361.0670 390.5750 392.1840 319.7570 289.1760 284.3480 230.6980 198.5080 282.2020 372.8700 310.6360 240.3550 221.0410 204.4090 220.5040 283.2750 345.5090 422.7650 441.5420 376.0890 343.8990 349.2640 297.7600 196.8980 170.6100 196.3620 261.8150 272.5450 233.3800 245.1830 237.1360 246.2560 303.6620 340.6800 380.9180 468.3670 461.9290 349.8010 299.9060 316.0010 336.3880 310.1000 302.5890 294.0050 322.4390 306.3440 291.8590 304.7350 363.7500 411.4980 422.7650 432.9580 385.2100 331.5600 285.9570 231.2340 225.8690 240.3550 256.4500 275.2270 250.0120 237.1360 216.2120 227.4790 291.3220 303.6620 301.5160 376.6260 398.0860 310.1000 256.9860 239.8180 233.9170 245.7200 226.4060 199.0440 202.8000 231.2340 272.5450 300.9790 296.1510 316.0010 355.1660 355.1660 348.7280 332.0960 256.9860 205.4820 192.6060 208.7010 252.6940 259.1320 239.2820 183.4860 188.8510 260.7420 320.2930 312.7820 352.4830 414.1810 445.2970 406.6700 384.1370 339.6070 273.6180 231.2340 249.4750 261.2780 233.9170 197.4350 221.0410 227.4790 244.1100 266.6430 339.6070 447.4430 457.6370 383.6000 326.1950 294.5410 279.5190 312.7820 335.3150 306.8810 306.8810 272.0080 242.5010 248.4020 324.5850 508.0680 864.8400 1211.9500 1189.4200 914.1980 625.5610 423.3010 359.4580 313.3190 297.7600 289.1760 269.8620 251.6210 265.0340 266.1070 281.1290 420.6190 753.2480 1170.1100 1386.8500 1222.6800 826.7480 547.7690 414.7170 332.6330 310.6360 290.2490 248.9390 229.6250 239.2820 264.4970 284.8840 336.3880 435.6410 672.2370 899.7120 1005.4000 828.8940 512.3600 372.8700 361.6040 334.2420 317.0740 290.7860 284.3480 285.9570 277.3730 253.7670 295.6140 435.6410 576.2030 703.3540 775.7810 707.1090 531.1370 373.9430 308.4900 309.0270 294.0050 293.4680 304.1980 267.7160 237.6720 231.7710 254.8400 306.3440 436.1770 586.3970 637.9010 619.1230 569.2290 443.1520 312.2460 301.5160 344.9720 322.9760 284.8840 280.0560 260.2050 272.5450 298.2970 295.0780 338.5340 449.5900 525.7720 525.7720 501.6300 418.4730 310.6360 307.9540 322.9760 302.5890 267.1800 281.6650 295.0780 243.5740 222.1140 282.7380 307.4170 375.0160 478.5600 492.5090 465.1480 423.8380 337.4610 280.0560 258.0590 246.2560 255.3770 240.3550 226.9420 257.5230 316.5380 292.9320 261.2780 335.8520 454.4180 471.5860 407.7430 353.5560 344.4360 281.1290 254.8400 247.8660 247.8660 261.8150 285.4210 281.1290 252.1580 241.4280 350.3370 492.5090 661.5070 916.3440 1177.6200 1355.7400 1248.9700 828.8940 481.7800 371.2610 367.5050 344.9720 334.2420 318.1470 250.5480 230.6980 234.9900 316.0010 520.4070 840.6970 1238.2400 1528.4900 1441.5800 1061.7300 691.0140 473.1950 365.8960 339.6070 302.5890 246.2560 233.3800 252.1580 280.5920 306.8810 388.9650 579.9590 765.0510 917.9530 987.1620 834.2590 555.8160 391.1110 295.6140 281.6650 312.2460 326.7310 299.9060 265.5700 239.8180 282.2020 332.6330 413.6440 535.4290 644.8750 672.2370 568.6920 434.0310 346.5820 320.2930 326.1950 274.6910 247.3290 249.4750 238.2090 253.2310 277.3730 312.2460 374.4800 474.8050 518.7980 496.2650 431.8850 366.4320 309.0270 213.5300 216.7490 290.7860 269.3260 253.2310 263.4240 277.3730 291.3220 308.4900 351.4100 431.3490 479.6330 469.9760 365.3590 304.7350 296.6870 268.2530 259.6690 261.8150 282.2020 256.4500 222.1140 228.0150 240.8910 239.2820 281.6650 345.5090 379.8450 391.6480 354.0930 319.2200 243.5740 246.7930 265.5700 269.8620 292.9320 265.5700 265.5700 300.4430 316.5380 295.0780 305.2710 312.7820 313.8550 356.7750 380.3810 331.0230 263.9610 237.1360 234.4530 255.3770 273.6180 275.2270 280.5920 248.4020 206.5550 202.2630 256.4500 333.1690 377.1620 341.7530 295.6140 307.4170 315.4650 267.7160 245.7200 234.4530 229.6250 237.1360 233.9170 243.5740 252.6940 266.1070 267.1800 304.7350 352.4830 368.5780 354.6290 334.7790 291.8590 280.5920 273.0810 237.6720 230.1610 291.3220 310.6360 258.0590 252.1580 269.3260 274.1540 288.1030 312.2460 341.7530 351.4100 348.7280 318.1470 266.1070 259.1320 303.6620 297.2240 271.4720 280.0560 270.3990 238.2090 241.9640 269.3260 301.5160 274.1540 291.8590 362.6770 381.4540 287.0300 208.1650 197.4350 213.5300 254.3040 289.7130 279.5190 266.1070 299.3700 319.7570 286.4940 278.9830 303.6620 371.7970 394.3300 337.9980 334.7790 332.0960 294.5410 242.5010 234.4530 233.9170 238.2090 245.1830 239.2820 266.1070 290.7860 303.1250 294.5410 326.1950 375.5530 396.4760 341.7530 338.5340 333.7060 288.1030 286.4940 347.6550 305.2710 272.5450 282.2020 275.7640 272.5450 280.5920 277.9100 312.7820 385.7460 437.7860 397.5490 280.5920 247.3290 229.6250 253.7670 283.2750 270.3990 255.3770 277.3730 262.3510 233.3800 260.2050 265.0340 323.5120 368.0420 358.3850 383.0640 391.6470 310.6360 288.6400 262.3510 292.3950 288.6400 272.5450 272.0080 244.1100 219.4310 238.7450 266.6430 316.5380 369.1150 395.4030 371.7970 348.7280 295.6140 248.9390 250.5480 270.3990 272.0080 261.8150 276.8370 276.3000 241.9640 215.6760 309.0270 424.9100 436.7130 431.3480 427.5930 392.7210 323.5120 321.9030 300.9790 277.9100 243.5740 219.4310 186.7050 190.4600 215.1390 209.2380 212.9930 242.5010 310.1000 343.3630 375.0160 394.3300 386.8190 291.8590 255.3770 246.2560 218.8950 211.9200 204.9460 228.0150 219.9680 196.8980 197.4350 215.6760 287.0300 353.5560 375.5530 377.6990 351.9470 304.7350 278.4460 230.1610 199.0440 175.9750 219.4310 251.6210 188.8510 147.0040 193.1430 221.0410 233.9170 297.2240 322.9760 312.7820 354.0930 349.2640 287.0300 238.7450 211.9200 248.4020 288.1030 223.7230 194.2160 198.5080 208.7010 258.5960 327.8040 363.2130 387.8920 398.0860 402.9140 344.4360 310.1000 292.3950 301.5160 307.9540 285.9570 280.0560 225.8690 192.0700 211.9200 240.8910 291.8590 371.2610 415.2530 431.3480 434.0310 399.6950 360.5310 269.8620 245.1830 275.2270 269.8620 258.5960 276.8370 240.3550 215.1390 265.5700 295.0780 299.9060 323.5120 327.2680 396.4760 422.7640 365.8960 299.3700 252.1580 226.4060 250.0120 253.7670 214.0660 207.0920 193.1430 185.6320 222.6500 320.2930 401.8410 370.1880 343.3630 346.5820 335.8520 285.9570 257.5230 199.0440 175.9750 221.5770 261.2780 255.9130 200.6540 213.5300 234.9900 316.5380 459.2460 574.5940 591.2250 500.0200 446.3700 334.7790 239.2820 261.8150 261.2780 237.1360 250.0120 224.7960 227.4790 267.7160 287.5670 315.4650 413.1070 530.6010 595.5170 591.2250 468.9030 353.5560 245.7200 227.4790 238.2090 266.1070 263.4240 216.7490 199.0440 243.5740 247.8660 246.2560 290.2490 442.0780 571.3750 524.1630 388.9650 300.4430 265.5700 266.1070 244.6470 233.3800 200.1170 190.9970 240.3550 269.3260 273.0810 279.5190 303.6620 453.8810 644.8750 745.7370 682.4300 540.2580 407.7430 309.0270 270.3990 272.0080 275.2270 273.6180 256.9860 252.6940 256.9860 291.3220 388.4290 472.1220 561.1810 644.8750 655.6050 518.2610 369.1150 324.5850 283.2750 294.5410 293.4680 248.9390 214.0660 243.5740 285.9570 274.6910 260.2050 349.2640 478.0240 549.3780 506.9950 405.5970 340.1440 319.7570 278.9830 233.3800 253.2310 247.8660 </int_list></spectrum></measured></pepdata></protdata>
\ No newline at end of file
diff --git a/samples/XML_output/C25plst02_C_25.xml b/samples/XML_output/C25plst02_C_25.xml
new file mode 100644
index 0000000000000000000000000000000000000000..77b7f00e162f7006d1e976f69bd092ae704dcb20
--- /dev/null
+++ b/samples/XML_output/C25plst02_C_25.xml
@@ -0,0 +1 @@
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181.7110 158.5050 158.5050 183.2840 199.8030 184.0710 150.6390 132.5470 160.0790 177.7780 164.0120 154.5720 165.5850 195.4770 245.0340 307.9650 352.4090 362.6350 317.4040 232.8420 167.1580 149.8520 152.9990 140.8060 152.6060 165.1920 171.8780 150.2460 136.0860 141.5930 160.0790 189.1840 152.2120 134.5130 158.5050 171.8780 192.7240 217.8960 300.8850 424.7790 492.0360 352.8030 206.8830 152.9990 147.8860 163.2250 155.3590 137.6600 145.1330 110.5210 121.5340 134.5130 135.3000 148.6720 147.0990 184.0710 167.1580 171.0910 210.4230 217.8960 258.8010 401.1800 533.3340 492.8230 351.2290 254.8670 200.9830 165.9780 151.8190 167.1580 170.6980 179.3510 175.0250 176.5980 164.0120 151.8190 153.7860 173.0580 173.0580 127.0400 116.8140 124.2870 206.0960 322.9110 400.3940 458.6040 486.9230 402.3600 318.1910 257.2270 201.3770 186.8240 182.8910 147.4930 148.6730 184.8570 204.9160 199.4100 152.2120 124.6800 112.8810 158.1120 180.1380 167.1580 232.4480 244.2480 276.5000 443.2650 696.9530 786.6280 586.0380 359.8820 231.2690 181.7110 170.6980 177.7780 180.1380 173.0580 157.7190 155.7520 187.6110 172.6650 145.9190 158.8990 174.2380 187.6110 202.9500 250.5410 271.3870 287.5130 337.0700 460.5710 610.0300 678.0740 565.9790 390.1680 249.3610 162.0450 133.3330 155.7520 147.4930 131.3670 143.5590 155.3590 169.5180 173.0580 159.2920 133.7270 136.0870 144.3460 138.0530 175.0250 222.2220 298.9190 396.0670 521.1410 534.5140 430.6790 300.4920 194.2970 185.2510 182.8910 172.2710 145.9190 123.8940 132.9400 160.4720 179.7440 175.4180 162.8320 177.7780 176.9910 170.6980 173.0580 176.9910 188.3970 294.1990 407.4730 429.1060 412.5870 361.4560 303.6380 212.3900 150.2460 136.4800 129.0070 145.5260 142.3800 152.6060 163.2250 170.3050 217.8960 203.7370 173.0580 180.1380 190.3640 183.2840 185.2510 238.7420 283.5790 353.1960 446.0180 489.6760 396.4610 294.1990 220.6490 193.1170 197.8370 185.2510 152.2120 144.3460 144.3460 167.1580 213.5700 215.5360 186.0370 177.7780 175.0250 171.0920 175.4180 185.6440 231.6620 304.4250 365.3890 411.8000 422.8130 388.5940 280.0400 234.8090 218.2890 181.3180 171.0920 138.8400 122.3210 141.5930 151.4260 150.6390 133.3330 136.8730 156.5390 178.1710 188.7910 180.9240 193.5100 228.1220 270.6000 313.4710 362.2420 381.1210 361.8490 301.6720 258.4070 229.6950 222.2220 181.7110 153.7860 153.3920 185.6440 205.7030 205.7030 199.4100 197.0500 216.3230 211.6030 186.0380 178.9580 186.4310 232.4490 297.7390 414.1600 558.9000 624.1900 482.2030 311.8980 237.5620 213.1760 163.6190 152.6060 161.6520 143.9530 171.0920 180.1380 205.7030 259.5870 246.6080 213.5700 186.0370 186.0370 199.0170 212.3900 219.0760 265.0940 466.0770 818.0940 1035.2000 881.0240 504.2290 289.8720 195.4770 217.5030 199.4100 190.7570 154.5720 154.5720 173.4510 148.6730 162.4390 198.6230 221.0420 203.7370 171.0910 176.2050 205.3100 198.6230 237.5620 370.1090 617.1100 752.8030 619.0770 397.6410 274.5330 197.4440 178.9580 195.8700 183.2840 143.9530 128.2200 147.0990 191.5440 188.3970 171.8780 180.9240 164.0120 152.9990 175.4180 195.0840 213.1760 285.9390 432.2520 701.2790 896.7570 765.7830 538.8400 390.1680 290.6590 238.7420 195.0840 159.2920 176.2050 181.7110 141.5930 155.3590 188.7910 214.3560 187.2170 154.5720 155.3590 174.6310 164.7980 152.9990 219.0760 350.8360 512.4880 581.7120 506.9820 391.7410 250.1480 203.3430 182.4980 159.6850 167.1580 156.1450 177.7780 164.4050 161.6520 160.4720 136.8730 134.1200 135.6930 123.8940 152.6060 211.2100 259.9800 309.9310 330.7770 463.7170 632.4490 629.3030 477.0900 326.0570 283.9730 254.0810 214.7490 168.3380 165.1920 212.3890 223.0090 171.4850 138.0530 130.9730 140.8060 170.3050 178.5640 191.9370 176.9910 183.6770 221.8290 291.4460 388.2010 505.0150 549.4600 419.2730 283.1860 225.3690 185.2510 169.5180 154.9660 117.2070 116.4210 156.1450 179.3510 197.0500 175.8110 174.6310 220.2560 202.1630 171.0910 152.9990 151.0320 197.8370 260.7670 373.2550 446.4110 409.0470 350.0490 270.2070 239.9210 233.6280 220.2560 184.0710 150.2460 159.6850 195.4770 163.6180 131.3670 132.9400 170.3050 198.2300 186.0370 178.5640 182.4970 226.5490 240.3150 340.2170 481.4160 489.2830 390.1680 292.6260 267.8470 230.8750 184.4640 159.6850 158.1120 143.1660 159.2920 166.3720 172.6650 172.2710 153.3920 160.8650 168.3380 173.0580 223.7960 214.7490 217.5030 243.0680 341.0030 429.1060 439.7250 425.1720 365.7820 252.1140 190.7570 154.9650 138.0530 140.8060 164.4050 130.5800 106.1940 113.6670 119.9600 169.5180 185.6440 161.6520 169.1250 173.0580 154.9650 224.5820 378.3680 731.9580 1395.0900 1789.5800 1341.6000 597.8380 234.4150 178.1710 184.8570 190.7570 193.5100 172.6650 151.0320 162.8320 162.8320 204.1300 257.2270 251.7210 205.7030 157.3250 160.0790 164.4050 176.9910 279.6460 571.0920 1024.9800 1232.2500 991.5450 584.8580 329.5970 265.4870 254.4740 198.6240 174.6310 157.7190 167.5520 180.5310 178.9580 173.0580 166.3720 158.5050 144.7390 186.0370 236.7750 248.1810 238.7420 280.8260 336.6770 497.9360 657.2280 654.4750 483.7770 257.6210 155.3590 177.3850 216.3230 191.5440 136.0870 107.3750 113.2740 148.6730 176.5980 153.7860 148.2790 174.2380 163.6190 166.7650 199.4100 250.1480 306.3920 381.1210 492.0360 567.9460 579.3520 434.6120 254.4740 189.5770 175.4180 158.8990 171.8780 184.4640 175.4180 156.1460 148.2790 169.9120 185.2510 183.2840 182.4980 187.2170 210.0300 258.8010 267.4540 334.7100 452.3110 602.9510 749.6570 692.6270 411.4070 213.9630 148.6730 189.9710 200.5900 164.4050 153.7860 153.7860 137.6600 123.5010 135.6930 162.8320 188.3970 162.0450 150.2460 164.7990 211.2100 247.7880 315.8310 429.8930 529.4010 558.1130 506.9820 427.1390 340.2170 245.8210 220.2560 213.1760 162.4390 132.5470 156.5390 165.1920 178.1710 172.6650 155.3590 178.5650 180.9250 186.0380 197.0500 181.3180 191.9370 243.4620 325.2710 372.4690 408.6540 401.1810 309.5380 221.4360 193.5110 174.2380 173.4520 173.4520 168.7320 193.5110 197.8370 190.3640 200.1970 203.3430 210.0300 183.2840 183.6780 198.2300 229.6960 310.3250 468.8310 887.7110 1452.9000 1460.7700 868.0450 419.6660 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196.6560 266.6660 410.2260 591.1510 695.3790 641.1020 457.8170 337.8560 269.4190 238.3480 219.4690 232.4480 226.5480 205.7020 248.9670 273.3530 297.3450 245.0340 220.2550 219.4680 189.9700 221.8280 325.2700 505.4080 661.1610 596.2640 462.9300 355.1620 294.1980 256.4400 223.7950 212.7820 261.9460 262.7330 219.8620 180.9240 204.5230 250.5400 251.7200 257.6200 257.6200 261.9460 350.8360 532.9400 707.9650 698.5250 558.8990 397.2470 293.8050 277.6790 252.1140 236.7740 226.9410 256.8330 264.3060 232.4480 211.2090 183.6770 193.9030 230.0880 219.0750 211.6020 292.6250 462.5370 666.2740 752.4100 655.2610 457.0300 318.9770 265.8800 213.9620 186.4300 240.3140 272.1730 235.2010 261.5530 294.5920 251.3270 251.7200 257.6200 235.2010 231.2680 270.5990 384.2670 512.0940 588.0040 567.9450 490.0690 386.2340 293.4120 239.1340 220.6480 202.9490 192.3300 189.5770 200.9830 206.8820 205.7020 199.8030 193.1160 199.0160 214.3550 238.3480 311.1110 402.3600 526.2540 575.4180 547.8860 427.5320 310.3240 264.7000 222.2220 179.7440 194.2960 248.9670 228.9080 180.5300 149.4590 163.6180 199.4090 197.0500 200.9830 206.4890 258.8000 426.3520 562.4390 626.9420 571.0920 444.0510 300.4910 250.9340 256.0470 258.0130 254.8670 226.5480 245.8210 287.5120 264.3060 264.7000 295.3780 292.6250 342.5760 655.2610 1275.1200 1841.5000 1980.3400 1599.6100 1020.2600 625.7620 515.6340 445.6240 367.7480 305.2110 251.7200 263.1260 256.8330 250.9340 225.3680 242.6740 249.7540 235.2010 279.6460 463.3230 725.2710 1208.6500 1719.9600 1841.1000 1475.7100 896.3630 506.5880 387.0200 357.9150 294.9850 236.3810 226.5480 236.7740 297.3450 287.9050 259.9800 266.2730 241.1010 234.0210 292.6250 486.1360 789.7740 1117.4100 1390.7600 1373.4500 1111.5100 736.2840 411.4060 285.5450 239.5280 248.1810 252.1140 238.3480 238.7410 257.6200 224.9750 199.8030 244.2470 259.9800 264.3060 320.9440 464.1100 687.9060 878.6640 1043.0700 1090.6600 883.3830 594.6910 377.5810 296.5580 272.5660 248.9670 204.5230 201.7700 212.7820 201.7700 161.6510 175.8110 192.3300 213.5690 214.7490 253.6870 396.8530 554.5730 725.2710 753.1960 602.5570 403.5400 273.7460 200.1960 191.1500 205.3090 212.3890 182.1040 159.2910 184.0700 226.1550 248.9670 219.8620 206.4890 268.6330 347.2960 404.7200 457.0300 549.8530 612.7830 562.8320 452.7040 350.0490 283.9720 269.4190 197.8360 173.4510 192.3300 193.5100 200.5890 197.8360 210.0290 205.7030 222.6150 257.6200 317.7970 359.8820 409.4390 497.9350 561.6520 540.0200 409.0460 311.1110 249.7540 190.3630 178.5640 174.2370 206.4890 214.7490 190.7570 215.9290 238.7410 226.1550 213.1760 300.8850 398.8200 460.5700 871.1910 1700.6900 2149.4600 1696.3600 892.0360 425.5650 319.7640 346.1160 341.3960 300.8850 259.9800 248.9670 324.0900 363.8150 341.7890 340.6100 379.1540 330.3830 345.7230 508.9480 891.2500 1547.6900 1972.8600 1601.5800 925.4680 470.7970 340.6090 294.9850 270.9930 252.1140 253.6870 267.8460 312.6840 349.2620 308.7510 326.4500 361.4550 364.9950 369.3210 426.3520 613.1760 976.9920 1324.6800 1212.1900 762.6360 464.8970 329.5970 279.2520 255.2600 242.6740 268.6330 298.5250 299.7050 290.6580 275.7130 283.9720 283.5790 233.6280 211.2090 264.7000 424.3850 645.8210 841.2990 763.4220 533.3330 409.4390 299.7050 234.0210 247.3940 265.8800 276.1060 274.5330 315.8310 357.5220 354.3750 321.3370 313.8640 301.2780 253.2940 250.5400 345.7220 564.0120 726.8440 703.6380 575.0250 397.2470 257.6200 230.0880 245.8200 232.0540 238.3480 256.0470 270.2060 290.2650 293.0180 301.2780 296.9510 284.7590 300.4910 327.2370 353.1950 482.5960 695.7720 818.0930 720.9440 474.7300 328.0230 271.3860 246.2140 214.7490 186.4300 236.7740 293.4120 292.2320 271.7790 234.4140 228.1210 250.5400 309.9310 374.4340 497.5420 1029.7000 2283.5800 3474.1500 3118.9800 1635.4000 598.6240 355.5550 390.1670 392.9200 281.6120 194.2970 197.0500 237.1680 232.4480 210.4220 206.8830 260.7670 254.8670 251.3270 394.1000 829.4990 1823.4000 2949.8600 3064.7100 2039.7300 959.6860 479.4500 347.2960 297.3450 282.7920 254.0800 225.7620 232.4480 276.8930 291.0520 278.0730 281.6120 265.4870 298.1320 365.3880 534.5140 1033.6300 1771.0900 2125.8600 1657.8200 932.1540 483.7760 326.8440 322.1240 283.1860 239.1340 211.9960 206.0960 260.3730 283.5790 272.5660 244.2480 276.8930 369.3220 501.4750 881.0240 1990.5600 3845.8300 4968.7400 3887.5200 1765.5900 628.1230 471.1900 592.3310 495.5760 322.5170 291.0520 370.1080 400.0000 304.0320 221.4360 235.9880 289.8720 329.2040 459.3910 747.2970 1382.1100 2459.7900 3341.6000 3025.3700 1675.1300 639.1350 376.7950 404.7200 420.0590 358.3090 304.4250 297.3450 381.5140 390.5610 316.6180 246.6080 241.4950 320.9440 466.4700 724.4850 1322.3200 2343.7600 2981.3200 2328.8100 1145.3300 456.2440 308.3580 335.4970 305.6050 255.2610 249.7540 295.7720 359.0960 331.9570 278.4660 223.0090 220.2560 315.4380 396.0670 471.5840 810.6210 1489.8700 1834.4200 1426.9400 798.0350 436.1850 290.2660 260.3740 238.7420 231.2690 252.1140 312.2910 318.1910 304.4250 294.5920 249.7540 253.2940 307.1780 428.3190 594.2980 812.5870 1010.8200 1070.6000 880.2370 541.2000 353.1960 291.8390 258.4070 221.8290 170.6980 204.5230 243.0680 237.9550 258.4070 223.7960 222.2220 255.6540 261.9470 263.5200 400.3940 707.1790 916.4220 918.7820 779.9420 527.0410 307.5720 247.0010 240.7080 241.8880 205.3100 143.9530 197.0500 264.7000 287.1190 267.4530 230.4820 213.9630 221.4360 267.4530 406.6870 619.4700 772.4690 753.1970 589.1850 428.3190 305.9980 266.2740 251.7210 216.7160 200.1970 192.7240 214.3560 201.7700 207.6700 218.6830 271.3870 285.1530 284.3660 335.8900 449.1650 610.8170 853.4920 1067.4600 890.0700 567.5520 391.7410 284.7590 248.1810 237.5620 227.7290 240.7080 251.7210 274.1400 285.1530 275.7130 264.7000 241.4950 259.9810 273.3530 326.0570 560.4730 764.9960 819.2740 759.8830 571.0920 386.2350 296.1660 253.6880 234.4150 234.8090 207.6700 231.2690 284.7590 280.4330 277.2870 252.5080 235.2020 238.7420 254.8680 371.2890 567.5530 755.5570 995.0850 1065.1000 897.9370 613.9640 415.7330 336.6770 260.3740 261.1610 254.4740 266.6670 282.4000 263.9140 256.8340 216.7160 224.9760 252.1140 292.6260 308.3580 397.2470 614.3570 919.1760 1072.9600 964.8000 709.5390 475.5170 286.3330 241.4950 224.5820 225.3690 240.3150 234.0220 214.3560 217.1090 183.6780 180.1380 207.6700 265.4870 338.6430 412.5870 486.1360 630.4830 774.0430 710.7190 505.8020 350.4430 254.8680 217.5030 227.3360 198.2300 187.6110 234.4150 237.9550 193.1170 189.5770 218.6830 228.9090 227.7290 251.7210 376.7950 542.3800 687.5130 777.9760 701.2790 518.7820 356.3430 252.1140 223.7960 189.5770 195.0840 219.8630 197.4440 202.5570 204.1300 167.9450 153.7860 162.4390 210.8160 311.1120 416.5200 506.5890 638.7420 720.5520 669.4210 492.8230 313.4710 235.5950 250.5410 246.2150 182.4980 161.2590 195.4770 242.2820 227.3360 247.0010 237.1680 211.2100 237.1680 267.8470 361.0630 481.0230 598.6240 661.9480 598.2310 473.9440 365.7820 272.5670 233.2350 244.2480 278.8600 293.8060 350.8360 383.4810 374.4350 349.2630 335.4970 298.5250 239.1350 299.3120 444.0520 558.1130 640.7090 641.8890 507.7690 337.4640 237.1680 222.6160 239.5280 215.1430 256.4410 307.1780 295.7720 314.6510 336.6770 344.5430 323.6980 304.0320 327.2370 392.9210 496.3630 534.1210 565.1930 649.3620 578.9590 398.8210 275.3200 216.3230 229.6950 261.1610 267.4540 235.9880 231.6620 246.2150 194.6900 176.2050 190.7570 263.5200 312.6850 366.9620 440.9050 535.3010 648.9690 674.9270 614.7500 480.2370 320.9440 279.6460 263.5200 235.5950 231.6620 218.6830 183.6780 203.7370 211.9960 191.5440 217.8960 263.5200 321.7310 366.1760 387.4140 478.6630 612.7840 597.4440 470.7970 409.4400 376.4020 374.4350 377.1880 284.7590 204.1300 178.1710 224.9760 262.3400 215.9290 216.7160 213.9630 193.1170 199.4100 221.0420 284.7590 443.2650 577.3850 650.1480 647.3950 508.1620 418.0930 406.2940 373.6480 324.0910 279.6460 273.7470 244.2480 206.4900 195.8700 188.7910 184.0710 199.0170 263.1270 316.6180 412.9800 549.8530 669.4210 717.4050 593.1180 429.1060 322.9110 283.5790 267.4540 238.7420 229.3020 222.6160 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227.7290 216.7160 238.3480 210.8160 254.8680 279.2530 315.8310 307.9650 266.6670 358.7030 468.8310 514.8480 514.0620 492.0360 425.9590 333.1370 269.0270 213.9630 221.4360 213.5700 222.2220 231.6620 223.0090 198.6240 229.3020 309.9320 409.0470 501.8690 617.5030 680.4340 697.3460 651.3290 479.8430 345.3300 272.1730 218.6830 260.3740 278.0730 254.0810 227.3360 217.8960 246.2150 280.0400 370.5020 517.6020 655.6550 746.1170 771.6830 606.8840 344.9370 237.5620 247.3950 265.0940 270.6000 248.5750 232.4490 223.0090 242.2820 249.7550 250.1480 285.9400 440.5120 639.1360 680.8270 632.8430 530.5810 431.4660 374.4350 310.3250 245.0350 228.9090 242.6750 221.0430 180.1380 171.8780 224.9760 265.0940 314.2580 437.3660 554.5730 640.3160 609.2440 492.8230 369.7160 281.6130 244.2480 255.2610 256.4410 228.1220 270.6000 268.6340 234.8090 222.6160 229.6960 252.1150 344.9370 459.7850 508.9490 458.9980 356.7360 285.5460 245.4280 219.4690 177.7780 167.9450 197.4440 248.1810 262.7340 268.2400 270.9940 242.2820 239.9220 279.6470 371.6820 431.4660 388.2010 329.2040 239.5290 199.4100 199.8040 196.6570 204.9170 202.9500 215.1430 211.2100 201.3770 216.3230 268.6340 308.3590 308.7520 313.0780 368.5360 412.1940 339.4300 254.8680 212.3900 193.1170 160.4720 196.6570 230.4820 223.4030 230.4820 204.5240 208.0630 248.5750 264.3070 258.0140 293.8060 331.5640 359.4890 359.8830 320.1580 264.3070 274.5330 225.3690 183.6780 197.8370 241.4950 279.2530 282.7930 290.6590 287.9060 295.7720 337.4640 405.5070 454.6710 436.1860 360.6690 297.7390 255.6540 226.5490 252.1150 210.8170 150.2460 141.9860 183.2850 207.6700 220.6490 218.2890 259.5870 327.6310 400.0010 436.9720 416.1270 331.9570 282.7930 238.7420 223.7960 225.3690 197.8370 202.1640 226.1560 277.2870 294.1990 263.1270 268.6340 289.8730 314.2580 404.7200 654.0820 851.5260 756.3440 497.9360 351.6230 314.2580 298.9190 258.0140 249.7550 238.3490 208.0630 228.9090 205.3100 199.0170 228.5160 332.7440 549.0670 800.0020 941.2010 814.9480 559.6860 376.7950 288.3000 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273.3530 309.5380 243.0680 186.4300 211.9960 235.2010 222.6150 295.3780 499.1150 814.1600 1092.2300 1176.4000 901.0830 525.4670 300.8850 274.1390 265.0930 186.8240 197.8360 211.6020 235.9880 252.5070 223.4020 177.7770 171.4840 215.9290 276.4990 313.4710 378.7610 559.6860 770.1090 760.2760 586.8240 435.7920 328.8100 254.0800 227.3350 221.0420 191.1500 240.7080 266.6660 277.6790 265.0930 213.9620 192.7230 205.7030 205.3090 241.4940 383.8740 527.0410 771.2890 960.8660 809.8340 505.4080 311.8980 270.9930 226.5480 200.9830 178.1710 188.3970 235.9880 230.4810 202.9490 219.0750 262.3400 250.9340 226.9420 252.5070 307.9640 440.5110 619.4690 772.8620 761.0630 609.6370 384.2670 261.1600 253.2940 252.5070 220.2550 204.1290 230.4820 271.7800 276.1060 247.7870 221.4350 206.0960 206.4890 257.2270 287.9050 345.3290 539.6270 735.8910 744.5430 599.4100 486.1360 392.5270 315.8310 270.6000 270.2060 254.8670 266.6660 292.2320 282.7920 252.5070 236.7750 227.3350 259.9800 248.1810 268.6330 344.1490 475.9100 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194.6900 196.6560 186.8230 239.1340 270.2060 194.2960 143.5590 164.4040 192.7230 196.6560 266.6660 410.2260 591.1510 695.3790 641.1020 457.8170 337.8560 269.4190 238.3480 219.4690 232.4480 226.5480 205.7020 248.9670 273.3530 297.3450 245.0340 220.2550 219.4680 189.9700 221.8280 325.2700 505.4080 661.1610 596.2640 462.9300 355.1620 294.1980 256.4400 223.7950 212.7820 261.9460 262.7330 219.8620 180.9240 204.5230 250.5400 251.7200 257.6200 257.6200 261.9460 350.8360 532.9400 707.9650 698.5250 558.8990 397.2470 293.8050 277.6790 252.1140 236.7740 226.9410 256.8330 264.3060 232.4480 211.2090 183.6770 193.9030 230.0880 219.0750 211.6020 292.6250 462.5370 666.2740 752.4100 655.2610 457.0300 318.9770 265.8800 213.9620 186.4300 240.3140 272.1730 235.2010 261.5530 294.5920 251.3270 251.7200 257.6200 235.2010 231.2680 270.5990 384.2670 512.0940 588.0040 567.9450 490.0690 386.2340 293.4120 239.1340 220.6480 202.9490 192.3300 189.5770 200.9830 206.8820 205.7020 199.8030 193.1160 199.0160 214.3550 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248.9680 165.5850 158.1120 149.0660 141.9860 191.1510 206.0970 209.6360 217.8960 224.9760 285.9390 380.7280 432.6460 536.0870 647.0020 541.5940 364.2090 267.8470 229.6950 280.8260 278.0730 271.7800 248.5750 220.6490 196.6570 185.6440 141.5930 164.7990 185.2510 149.4590 156.5390 191.5440 191.5440 191.5440 248.5750 325.2710 355.5560 383.4810 359.4890 291.8390 235.2020 194.2970 196.2640 200.5900 172.6650 187.6110 193.1170 181.7110 219.8630 220.2560 208.8500 205.3100 181.3180 192.7240 208.0630 184.0710 197.8370 213.1760 193.9040 239.1350 333.1370 388.5950 405.1140 390.9540 284.7600 185.6440 166.7650 171.0920 174.2380 149.4590 161.6520 193.5110 206.0970 186.8240 155.7520 123.8940 111.3080 107.7680 133.7270 202.5570 210.0300 177.7780 213.9630 270.6000 387.8080 552.2130 648.1820 536.0870 325.6640 207.2770 165.1920 169.1250 187.6110 193.5110 159.6860 163.6190 173.8450 167.9450 178.1710 163.2250 144.3460 132.1540 141.5930 164.0120 186.4310 211.2100 235.5950 267.8470 335.1040 510.9150 723.6980 684.7600 408.6540 228.1220 154.9660 127.0400 153.3920 201.7700 153.3920 124.2870 130.9740 157.3260 178.9580 180.5310 175.8110 181.7110 188.7910 228.1220 216.7160 207.2770 261.5540 551.8200 1537.0700 2981.3200 3277.1000 2032.6500 873.1580 469.6170 429.4990 354.7690 250.1480 187.6110 191.9370 208.8500 171.0920 140.4130 192.3310 222.2220 186.0380 149.4590 165.5850 178.5650 177.3850 168.3380 188.3970 334.7100 764.9960 1656.6400 2235.6000 1876.9000 1145.3300 674.1410 481.0230 301.6720 199.4100 150.6390 140.8060 151.4260 177.7780 175.8110 187.6110 177.3850 161.2590 155.7520 173.0580 258.0140 309.5380 289.8720 246.6080 270.6000 361.4560 586.8250 896.3630 1028.5200 981.3190 782.3020 489.6760 259.5870 188.7910 204.9170 186.0370 151.4260 145.1330 166.3720 182.1040 180.1380 163.6190 171.8780 180.1380 200.1970 241.1020 275.3200 255.2610 241.1020 357.1290 829.1070 1572.8600 1824.9800 1491.0500 1282.2000 1159.8800 796.0680 395.6740 220.6490 159.2920 157.7190 185.2510 200.1970 199.8030 191.9370 169.1250 155.3590 163.6180 201.7700 244.2480 256.4410 254.8670 240.3150 394.1010 820.4530 1476.1100 1885.9400 1537.8600 982.1060 761.0630 607.2770 368.9290 213.1760 146.7060 171.4850 218.2890 239.1350 216.3230 165.1920 152.6060 144.3460 149.4590 176.2040 188.7910 205.3100 202.9500 192.7240 253.2940 452.3110 761.4560 946.3140 795.2810 551.8200 425.1730 311.5050 181.7110 165.9780 178.1710 173.0580 154.5720 155.3590 176.9910 185.2510 194.6900 183.6770 167.1580 181.7110 194.6900 196.6570 197.8370 200.1970 230.8750 359.8820 463.3240 503.0490 501.4750 431.8590 314.2580 239.5280 211.6030 168.7320 147.4930 158.1120 190.3640 188.7910 188.7910 224.5820 206.0960 167.1580 145.5260 156.1450 165.9780 196.2640 190.7570 179.3510 220.6490 312.6850 374.8280 343.7560 314.2580 312.6850 321.3370 272.9600 206.4900 193.1170 186.4310 128.6130 125.0740 136.8730 163.6180 175.4180 144.3460 147.4930 152.6060 155.3590 150.2460 160.4720 167.1580 228.9090 263.5200 350.4430 362.6350 344.1500 354.7690 310.3250 223.0090 187.6110 211.6030 217.5020 206.8830 153.3920 146.7060 181.7110 170.3050 139.2330 143.1660 155.3590 146.7060 147.8860 171.4850 173.8450 222.6160 221.4360 200.1970 225.3690 290.2660 372.4680 436.9720 385.4480 263.5200 245.4280 195.4770 175.0240 175.4180 129.7930 145.9190 165.9780 151.8190 156.1450 166.3720 158.5050 141.9860 123.1070 154.5720 167.5520 177.7780 223.4020 246.2140 317.7980 391.3470 405.9000 405.1130 296.1650 223.0090 179.3510 180.5310 208.0630 175.0250 132.9400 117.6010 133.3330 153.7860 184.0710 213.5690 173.0580 158.8990 142.3790 151.0320 202.9500 195.4770 165.1920 196.2630 246.2140 308.3580 393.7070 436.9720 397.6400 291.0520 216.7160 171.4850 131.3670 103.4410 145.1330 191.1500 150.2460 135.6930 151.0320 170.6980 155.3590 162.0450 166.7650 175.0250 255.6540 407.8670 443.6580 376.7950 347.2960 425.1720 535.6940 510.5220 420.8460 334.3170 251.3280 207.6700 203.3430 195.8700 182.4970 148.2790 136.8730 145.1330 122.3200 128.6130 181.3180 162.8320 163.2250 189.1840 206.4900 244.2480 283.5790 340.6100 331.5640 375.6150 534.9070 619.0770 469.2240 331.5640 263.9140 219.0760 165.5850 146.3130 152.6060 130.1870 147.0990 117.6010 106.1950 134.5130 158.8990 156.5390 142.7730 169.9110 176.5980 187.6110 223.0090 263.9140 290.6590 337.4630 410.6200 450.7380 431.4660 373.6480 244.2480 136.8730 127.4340 138.8400 127.0400 128.6130 112.8810 130.9730 167.9450 177.3840 157.7190 156.1450 152.2120 148.6730 153.3920 170.6980 155.3590 170.3050 233.6280 279.2530 403.9340 550.2470 518.3880 332.7440 191.9370 163.6180 154.9660 147.8860 134.5130 143.5590 144.3460 149.0660 143.5590 164.4050 163.2250 144.3460 113.6680 131.7600 165.9780 165.9780 171.0910 210.0300 251.3280 258.0140 353.1960 461.3570 418.8800 314.6510 276.5000 268.6330 232.4490 172.2710 145.1330 151.0320 148.6730 163.6180 163.6180 174.2380 161.6520 167.1580 175.4180 134.9070 134.5130 163.6180 180.5310 202.9500 188.7910 216.7160 303.2450 374.0420 375.2220 318.1910 202.1630 154.5720 155.7520 156.9320 145.1330 158.5050 175.4180 168.3380 149.8520 143.5590 130.1870 158.1120 175.8110 162.4390 146.7060 136.8730 168.7320 179.3510 186.4310 265.8800 352.4090 392.5270 370.5020 339.8230 287.9060 208.0630 178.1710 161.2590 132.1530 148.2790 155.3590 149.4590 175.8110 191.9370 164.4050 138.0530 152.6060 182.1040 188.0040 178.5640 162.4390 184.8570 194.2970 208.8500 294.5920 344.5430 302.8520 225.3690 169.9120 133.7270 140.4130 166.3720 177.3850 142.3800 104.2280 112.8810 135.3000 173.4510 188.7910 181.7110 152.6060 153.7860 159.2920 185.6440 196.6570 179.7440 176.5980 198.2300 283.1860 398.4270 416.9130 352.0160 234.8080 175.0250 171.8780 197.8370 185.2510 169.1250 168.3380 163.6190 150.6390 141.2000 167.9450 177.3850 136.8730 127.8270 126.6470 120.7470 156.9320 193.5100 198.2300 234.4150 323.3040 476.6970 501.0820 342.1830 207.6700 140.0200 130.5800 130.1870 134.9070 140.8060 143.1660 137.2660 156.5390 162.0450 143.5600 108.5550 129.7940 119.1740 110.1280 121.5340 170.6980 230.8750 250.1480 269.0270 361.4560 437.3650 424.3860 384.2680 282.3990 206.4900 169.5180 121.9270 134.9070 130.9730 162.0450 180.9240 180.5310 184.4640 140.0200 154.9660 162.0450 145.5260 121.9270 135.6930 163.6190 188.0040 211.6030 243.4610 306.3920 429.1060 542.7740 519.9610 342.1830 163.2250 153.3920 177.3850 162.0450 115.2410 101.0820 147.0990 153.3920 134.1200 112.4880 121.1410 150.6390 172.6650 167.1580 150.2460 152.2120 206.0960 240.3150 269.4200 343.7570 414.5530 412.1930 368.9290 241.4950 159.6850 140.8060 147.4930 177.3840 139.2330 127.4340 147.4930 141.9860 142.7730 157.3250 171.8780 143.5590 107.3750 90.4620 95.9684 129.0070 189.9710 </int_list></spectrum></measured><measured><pepseq>WFGNTR</pepseq><mzh>780.3832</mzh><calc_mzh>780.3793</calc_mzh><leucines>0</leucines><mono_iso_intensity>4868</mono_iso_intensity><deuterated_intensity>0</deuterated_intensity><ratio>0.00</ratio><validated>UNKNOWN</validated><local_bg>0.0000</local_bg><corrected_ratio>0.00</corrected_ratio><spectrum><mz_list>755.6870 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364.2090 295.7730 208.0630 198.6240 151.0330 103.4420 120.7480 148.2800 146.7060 123.5010 128.6140 159.6860 150.6390 124.2870 112.4880 99.5086 141.2000 160.4720 147.1000 173.8450 196.2640 226.1560 278.8600 322.5180 296.5590 250.9350 290.6590 293.0190 213.5700 173.8450 192.3310 196.6570 168.7320 154.5730 166.7650 145.1330 134.5140 162.0460 133.7270 115.6340 127.8270 152.6060 156.5390 142.3800 178.9580 219.8630 210.0300 205.7030 287.1200 353.9830 350.0500 316.6180 269.0270 240.7080 205.3100 154.9660 138.4470 145.9200 104.2280 78.6629 111.3080 133.7270 131.7600 140.4130 130.9740 120.7480 114.4550 131.7600 136.4800 169.5190 202.5570 173.0580 188.7910 261.1610 314.2580 356.3430 332.3510 294.1990 252.5080 215.1430 200.5900 165.5850 115.2410 111.7010 121.1410 112.8810 137.2670 170.6990 140.8070 154.1790 158.8990 166.7650 183.6780 185.6440 166.7650 149.0660 147.4930 182.4980 208.8500 247.3950 283.9730 317.7980 313.0780 254.4740 225.7630 199.8040 186.8240 182.1050 156.9330 136.8730 131.7600 118.3880 99.9019 142.7730 144.3460 131.3670 140.8070 180.1380 214.3560 184.4650 142.3800 162.8320 169.5190 197.4440 208.4570 281.6130 408.2600 451.1320 371.6820 283.1860 211.2100 179.3510 142.7730 131.7600 106.5880 105.0150 120.7480 145.1330 127.0410 116.0280 119.1740 157.7190 156.9330 141.5930 146.3130 146.7060 186.0380 207.6700 198.2310 206.0970 247.3950 388.5950 616.3240 769.7160 642.2830 400.0010 243.4620 183.2850 222.2230 223.0090 147.1000 125.8610 149.8530 141.5930 127.0410 125.4670 157.7190 193.1180 171.0920 138.0540 153.7860 182.1050 203.3440 192.3310 200.9840 211.9970 253.6880 349.2630 416.5200 429.1060 366.9630 279.2530 225.3690 179.7450 155.3590 161.2590 163.6190 175.8120 166.3720 144.7400 140.4130 143.1670 144.7400 162.8320 128.2210 153.0000 184.8580 173.4520 147.1000 143.9530 217.5030 294.5930 331.9580 380.7290 390.9550 392.9210 367.7490 272.1740 205.7040 190.7580 136.8740 125.8610 159.6860 151.8200 134.1200 142.7730 147.8860 139.2330 115.6350 127.8270 124.6810 129.4010 119.5680 120.7480 130.5810 153.3930 169.5190 195.0840 240.3150 342.1840 472.7640 484.5640 359.4900 257.2280 157.7190 142.3800 150.6400 140.8070 140.8070 158.5060 152.9990 108.1620 156.9330 175.4180 154.1790 152.9990 169.9120 178.1720 148.6730 145.5260 172.6650 238.7420 329.2040 579.3520 1229.1100 1867.8500 1766.7700 1034.8100 396.4610 165.1920 154.9660 174.2380 152.9990 152.9990 158.8990 162.8320 201.3770 211.9970 160.4720 121.1410 124.2870 127.4340 132.1540 140.8070 147.4930 172.2720 189.1840 196.6570 247.0020 391.7410 743.3640 1078.8600 929.7950 556.9330 292.6260 212.7830 229.6960 187.2180 131.3670 117.9940 153.3930 189.5780 165.1920 129.7940 126.2540 138.8400 145.5260 116.0280 108.5550 108.1610 106.9820 108.5550 154.5730 182.8910 223.7960 325.2710 447.9850 422.0260 264.3070 174.6320 166.3720 237.1690 195.8710 124.2870 136.8730 200.9840 227.3360 201.3770 169.5180 168.3390 146.3130 143.5600 129.0070 154.1790 195.0840 196.6570 182.4980 183.6780 185.2510 190.7570 216.3230 295.7720 351.6230 323.6980 284.7600 286.3330 238.7420 160.0790 154.9660 148.6730 154.1790 153.3930 159.6860 147.8860 112.8810 160.8660 169.9120 134.9070 159.6860 180.5310 164.0120 159.6860 191.5440 217.1100 217.8960 218.6830 278.8600 291.4460 278.4670 280.0400 </int_list></spectrum></measured><measured><pepseq>VEHVTHPEQYIPGVLKR</pepseq><mzh>2002.0392</mzh><calc_mzh>2002.0875</calc_mzh><leucines>1</leucines><mono_iso_intensity>847</mono_iso_intensity><deuterated_intensity>1046</deuterated_intensity><ratio>1.24</ratio><validated>YES</validated><local_bg>174</local_bg><corrected_ratio>1.30</corrected_ratio><spectrum><mz_list>1977.5795 1977.6404 1977.7013 1977.7622 1977.8231 1977.8840 1977.9449 1978.0058 1978.0667 1978.1276 1978.1885 1978.2494 1978.3103 1978.3712 1978.4321 1978.4931 1978.5540 1978.6149 1978.6758 1978.7367 1978.7976 1978.8585 1978.9194 1978.9804 1979.0413 1979.1022 1979.1631 1979.2240 1979.2849 1979.3459 1979.4068 1979.4677 1979.5286 1979.5896 1979.6505 1979.7114 1979.7723 1979.8333 1979.8942 1979.9551 1980.0161 1980.0770 1980.1379 1980.1989 1980.2598 1980.3207 1980.3817 1980.4426 1980.5035 1980.5645 1980.6254 1980.6864 1980.7473 1980.8083 1980.8692 1980.9301 1980.9911 1981.0520 1981.1130 1981.1739 1981.2349 1981.2958 1981.3568 1981.4177 1981.4787 1981.5397 1981.6006 1981.6616 1981.7225 1981.7835 1981.8444 1981.9054 1981.9664 1982.0273 1982.0883 1982.1493 1982.2102 1982.2712 1982.3322 1982.3931 1982.4541 1982.5151 1982.5760 1982.6370 1982.6980 1982.7590 1982.8199 1982.8809 1982.9419 1983.0029 1983.0638 1983.1248 1983.1858 1983.2468 1983.3078 1983.3687 1983.4297 1983.4907 1983.5517 1983.6127 1983.6737 1983.7347 1983.7956 1983.8566 1983.9176 1983.9786 1984.0396 1984.1006 1984.1616 1984.2226 1984.2836 1984.3446 1984.4056 1984.4666 1984.5276 1984.5886 1984.6496 1984.7106 1984.7716 1984.8326 1984.8936 1984.9546 1985.0156 1985.0766 1985.1377 1985.1987 1985.2597 1985.3207 1985.3817 1985.4427 1985.5037 1985.5648 1985.6258 1985.6868 1985.7478 1985.8088 1985.8699 1985.9309 1985.9919 1986.0529 1986.1139 1986.1750 1986.2360 1986.2970 1986.3581 1986.4191 1986.4801 1986.5412 1986.6022 1986.6632 1986.7243 1986.7853 1986.8463 1986.9074 1986.9684 1987.0294 1987.0905 1987.1515 1987.2126 1987.2736 1987.3347 1987.3957 1987.4567 1987.5178 1987.5788 1987.6399 1987.7009 1987.7620 1987.8230 1987.8841 1987.9451 1988.0062 1988.0673 1988.1283 1988.1894 1988.2504 1988.3115 1988.3725 1988.4336 1988.4947 1988.5557 1988.6168 1988.6779 1988.7389 1988.8000 1988.8611 1988.9221 1988.9832 1989.0443 1989.1053 1989.1664 1989.2275 1989.2886 1989.3496 1989.4107 1989.4718 1989.5329 1989.5939 1989.6550 1989.7161 1989.7772 1989.8383 1989.8993 1989.9604 1990.0215 1990.0826 1990.1437 1990.2048 1990.2659 1990.3270 1990.3880 1990.4491 1990.5102 1990.5713 1990.6324 1990.6935 1990.7546 1990.8157 1990.8768 1990.9379 1990.9990 1991.0601 1991.1212 1991.1823 1991.2434 1991.3045 1991.3656 1991.4267 1991.4878 1991.5490 1991.6101 1991.6712 1991.7323 1991.7934 1991.8545 1991.9156 1991.9767 1992.0379 1992.0990 1992.1601 1992.2212 1992.2823 1992.3435 1992.4046 1992.4657 1992.5268 1992.5879 1992.6491 1992.7102 1992.7713 1992.8325 1992.8936 1992.9547 1993.0158 1993.0770 1993.1381 1993.1992 1993.2604 1993.3215 1993.3826 1993.4438 1993.5049 1993.5661 1993.6272 1993.6883 1993.7495 1993.8106 1993.8718 1993.9329 1993.9941 1994.0552 1994.1164 1994.1775 1994.2387 1994.2998 1994.3610 1994.4221 1994.4833 1994.5444 1994.6056 1994.6667 1994.7279 1994.7891 1994.8502 1994.9114 1994.9725 1995.0337 1995.0949 1995.1560 1995.2172 1995.2784 1995.3395 1995.4007 1995.4619 1995.5230 1995.5842 1995.6454 1995.7065 1995.7677 1995.8289 1995.8901 1995.9512 1996.0124 1996.0736 1996.1348 1996.1960 1996.2571 1996.3183 1996.3795 1996.4407 1996.5019 1996.5631 1996.6242 1996.6854 1996.7466 1996.8078 1996.8690 1996.9302 1996.9914 1997.0526 1997.1138 1997.1750 1997.2362 1997.2974 1997.3586 1997.4198 1997.4810 1997.5422 1997.6034 1997.6646 1997.7258 1997.7870 1997.8482 1997.9094 1997.9706 1998.0318 1998.0930 1998.1542 1998.2154 1998.2766 1998.3378 1998.3991 1998.4603 1998.5215 1998.5827 1998.6439 1998.7051 1998.7664 1998.8276 1998.8888 1998.9500 1999.0113 1999.0725 1999.1337 1999.1949 1999.2562 1999.3174 1999.3786 1999.4398 1999.5011 1999.5623 1999.6235 1999.6848 1999.7460 1999.8072 1999.8685 1999.9297 1999.9909 2000.0522 2000.1134 2000.1747 2000.2359 2000.2972 2000.3584 2000.4196 2000.4809 2000.5421 2000.6034 2000.6646 2000.7259 2000.7871 2000.8484 2000.9096 2000.9709 2001.0321 2001.0934 2001.1546 2001.2159 2001.2772 2001.3384 2001.3997 2001.4609 2001.5222 2001.5835 2001.6447 2001.7060 2001.7673 2001.8285 2001.8898 2001.9511 2002.0123 2002.0736 2002.1349 2002.1961 2002.2574 2002.3187 2002.3800 2002.4412 2002.5025 2002.5638 2002.6251 2002.6864 2002.7476 2002.8089 2002.8702 2002.9315 2002.9928 2003.0540 2003.1153 2003.1766 2003.2379 2003.2992 2003.3605 2003.4218 2003.4831 2003.5444 2003.6057 2003.6670 2003.7282 2003.7895 2003.8508 2003.9121 2003.9734 2004.0347 2004.0960 2004.1573 2004.2186 2004.2799 2004.3412 2004.4026 2004.4639 2004.5252 2004.5865 2004.6478 2004.7091 2004.7704 2004.8317 2004.8930 2004.9543 2005.0157 2005.0770 2005.1383 2005.1996 2005.2609 2005.3223 2005.3836 2005.4449 2005.5062 2005.5675 2005.6289 2005.6902 2005.7515 2005.8128 2005.8742 2005.9355 2005.9968 2006.0582 2006.1195 2006.1808 2006.2422 2006.3035 2006.3648 2006.4262 2006.4875 2006.5488 2006.6102 2006.6715 2006.7329 2006.7942 2006.8555 2006.9169 2006.9782 2007.0396 2007.1009 2007.1623 2007.2236 2007.2850 2007.3463 2007.4077 2007.4690 2007.5304 2007.5917 2007.6531 2007.7145 2007.7758 2007.8372 2007.8985 2007.9599 2008.0212 2008.0826 2008.1440 2008.2053 2008.2667 2008.3281 2008.3894 2008.4508 2008.5122 2008.5735 2008.6349 2008.6963 2008.7577 2008.8190 2008.8804 2008.9418 2009.0031 2009.0645 2009.1259 2009.1873 2009.2487 2009.3100 2009.3714 2009.4328 2009.4942 2009.5556 2009.6170 2009.6783 2009.7397 2009.8011 2009.8625 2009.9239 2009.9853 2010.0467 2010.1081 2010.1695 2010.2309 2010.2923 2010.3537 2010.4151 2010.4765 2010.5379 2010.5993 2010.6607 2010.7221 2010.7835 2010.8449 2010.9063 2010.9677 2011.0291 2011.0905 2011.1519 2011.2133 2011.2747 2011.3361 2011.3975 2011.4590 2011.5204 2011.5818 2011.6432 2011.7046 2011.7660 2011.8275 2011.8889 2011.9503 2012.0117 2012.0731 2012.1346 2012.1960 2012.2574 2012.3188 2012.3803 2012.4417 2012.5031 2012.5646 2012.6260 2012.6874 2012.7489 2012.8103 2012.8717 2012.9332 2012.9946 2013.0560 2013.1175 2013.1789 2013.2404 2013.3018 2013.3632 2013.4247 2013.4861 2013.5476 2013.6090 2013.6705 2013.7319 2013.7934 2013.8548 2013.9163 2013.9777 2014.0392 2014.1006 2014.1621 2014.2235 2014.2850 2014.3464 2014.4079 2014.4694 2014.5308 2014.5923 2014.6537 2014.7152 2014.7767 2014.8381 2014.8996 2014.9611 2015.0225 2015.0840 2015.1455 2015.2069 2015.2684 2015.3299 2015.3914 2015.4528 2015.5143 2015.5758 2015.6373 2015.6987 2015.7602 2015.8217 2015.8832 2015.9447 2016.0062 2016.0676 2016.1291 2016.1906 2016.2521 2016.3136 2016.3751 2016.4366 2016.4980 2016.5595 2016.6210 2016.6825 2016.7440 2016.8055 2016.8670 2016.9285 2016.9900 2017.0515 2017.1130 2017.1745 2017.2360 2017.2975 2017.3590 2017.4205 2017.4820 2017.5435 2017.6050 2017.6665 2017.7281 2017.7896 2017.8511 2017.9126 2017.9741 2018.0356 2018.0971 2018.1586 2018.2202 2018.2817 2018.3432 2018.4047 2018.4662 2018.5278 2018.5893 2018.6508 2018.7123 2018.7739 2018.8354 2018.8969 2018.9584 2019.0200 2019.0815 2019.1430 2019.2046 2019.2661 2019.3276 2019.3892 2019.4507 2019.5122 2019.5738 2019.6353 2019.6968 2019.7584 2019.8199 2019.8815 2019.9430 2020.0045 2020.0661 2020.1276 2020.1892 2020.2507 2020.3123 2020.3738 2020.4354 2020.4969 2020.5585 2020.6200 2020.6816 2020.7431 2020.8047 2020.8663 2020.9278 2020.9894 2021.0509 2021.1125 2021.1741 2021.2356 2021.2972 2021.3587 2021.4203 2021.4819 2021.5434 2021.6050 2021.6666 2021.7282 2021.7897 2021.8513 2021.9129 2021.9744 2022.0360 2022.0976 2022.1592 2022.2207 2022.2823 2022.3439 2022.4055 2022.4671 2022.5286 2022.5902 2022.6518 2022.7134 2022.7750 2022.8366 2022.8982 2022.9598 2023.0213 2023.0829 2023.1445 2023.2061 2023.2677 2023.3293 2023.3909 2023.4525 2023.5141 2023.5757 2023.6373 2023.6989 2023.7605 2023.8221 2023.8837 2023.9453 2024.0069 2024.0685 2024.1301 2024.1917 2024.2533 2024.3149 2024.3766 2024.4382 2024.4998 2024.5614 2024.6230 2024.6846 2024.7462 2024.8079 2024.8695 2024.9311 2024.9927 2025.0543 2025.1160 2025.1776 2025.2392 2025.3008 2025.3624 2025.4241 2025.4857 2025.5473 2025.6090 2025.6706 2025.7322 2025.7938 2025.8555 2025.9171 2025.9788 2026.0404 2026.1020 2026.1637 2026.2253 2026.2869 2026.3486 2026.4102 2026.4719 2026.5335 2026.5952 2026.6568 2026.7184 2026.7801 2026.8417 2026.9034 2026.9650 2027.0267 2027.0883 2027.1500 2027.2116 2027.2733 2027.3350 2027.3966 2027.4583 2027.5199 2027.5816 2027.6432 2027.7049 2027.7666 2027.8282 2027.8899 2027.9516 2028.0132 2028.0749 2028.1366 2028.1982 2028.2599 2028.3216 2028.3832 2028.4449 2028.5066 2028.5683 2028.6299 2028.6916 2028.7533 2028.8150 2028.8766 2028.9383 2029.0000 2029.0617 2029.1234 2029.1850 2029.2467 2029.3084 2029.3701 2029.4318 2029.4935 2029.5552 2029.6169 2029.6786 2029.7402 2029.8019 2029.8636 2029.9253 2029.9870 2030.0487 2030.1104 2030.1721 2030.2338 2030.2955 2030.3572 2030.4189 2030.4806 2030.5423 2030.6040 2030.6657 2030.7274 2030.7891 2030.8509 2030.9126 2030.9743 2031.0360 2031.0977 2031.1594 2031.2211 2031.2828 2031.3446 2031.4063 2031.4680 2031.5297 2031.5914 2031.6532 2031.7149 2031.7766 2031.8383 2031.9000 2031.9618 2032.0235 2032.0852 2032.1470 2032.2087 2032.2704 2032.3321 2032.3939 2032.4556 </mz_list><int_list>178.5640 180.5310 223.0090 331.1700 425.1720 453.8840 435.7920 400.7870 363.0290 311.5050 273.7460 238.7410 202.5570 211.2090 261.5540 250.5410 223.7960 199.8030 190.3640 236.3820 287.9060 423.2060 496.7560 445.6250 357.5220 355.9490 351.6230 314.6510 288.2990 267.4530 255.2610 200.9830 167.9450 165.9780 219.0760 247.3940 263.1270 330.7770 391.7410 431.8590 396.0670 334.3170 319.7640 256.4410 228.1220 266.2740 266.6670 236.7750 207.6700 219.8620 232.8420 205.3100 197.8370 245.4280 355.1630 420.0590 402.7540 335.8900 323.6970 283.9730 222.2220 209.2430 149.0660 118.3870 169.9110 189.5770 198.2300 216.7160 197.4440 211.6030 264.3070 320.1580 409.4400 413.7660 310.7180 254.8670 220.6490 224.1890 239.9210 205.7030 173.8450 168.3380 198.2300 224.5820 211.2090 213.1760 251.7210 330.7770 383.0880 371.2880 323.3040 274.1400 245.4280 228.1220 213.9630 203.7370 170.3050 185.2510 162.0450 154.5720 169.9110 230.0890 331.9570 382.3010 387.4140 404.3270 383.0880 322.1240 271.7800 207.2760 191.1500 199.4100 191.1500 188.3970 193.1170 158.8990 160.4720 237.9550 289.4790 282.3990 324.4840 344.1500 342.1830 301.6720 289.0860 247.7880 188.7910 195.4770 200.9830 162.8320 137.6600 149.0660 145.1330 174.2380 199.4100 220.6490 286.7260 360.6690 408.2600 401.5740 308.7510 230.0890 232.0550 259.9800 213.5690 221.0420 238.7410 209.2430 189.1840 197.0500 208.0630 241.8880 336.6770 429.4990 430.2860 424.3860 364.6020 344.9360 291.8390 241.1010 235.9880 256.0470 282.0060 228.1220 180.9240 185.6440 219.0760 282.7930 359.0960 411.8000 471.5840 465.2910 426.7460 369.7150 292.2320 241.4950 223.0090 226.1550 217.8960 241.8880 271.7800 242.6750 213.1760 235.2020 245.8210 297.7390 399.2140 460.5710 418.0930 307.9650 249.7540 208.4560 180.9240 165.5850 183.2840 224.9750 221.4360 178.9580 149.4590 168.3380 229.6950 280.0390 310.7180 346.9030 322.1240 257.2270 219.4690 211.6030 198.2300 191.5440 191.1500 175.0250 171.4850 169.5180 199.0170 267.0600 315.8310 358.7020 414.9460 436.9720 363.8160 287.1190 302.4580 297.3450 204.9160 192.7240 227.3350 205.7030 170.6980 160.8650 188.7910 240.3150 229.3020 218.6820 303.2450 474.3370 499.5090 422.4190 315.8310 246.6080 275.3200 245.4280 179.7440 181.3180 187.6110 209.2430 197.0500 179.7440 231.2690 285.5460 324.0910 405.5070 471.9770 461.3570 431.4660 368.1420 254.8670 196.2640 201.7700 180.5310 175.8110 197.4430 203.7370 261.9470 289.4790 327.2370 523.5010 846.0190 1130.3900 1128.4200 870.0110 561.6530 400.3940 317.7980 283.1860 266.6670 260.3740 258.8000 244.6410 252.5070 282.0060 314.2580 491.2490 858.9980 1224.7800 1310.9200 1060.7700 644.2490 364.6020 280.0390 271.7800 250.9340 244.2480 227.3350 227.3350 243.0680 234.4150 278.8590 392.9210 565.9790 757.9160 880.2370 813.3740 630.8760 425.1720 266.2730 254.8670 215.1430 182.4970 219.0760 230.0890 228.9090 227.7290 249.3610 286.3320 400.7870 542.3800 648.9680 647.7880 511.7020 398.0340 317.4040 269.4200 252.1140 239.1350 239.5280 206.8830 181.3180 179.3510 186.8240 214.7490 319.3710 501.8690 613.9630 617.8970 553.3930 427.1390 322.1240 278.4660 315.8310 312.6850 292.6260 298.1320 250.1480 174.6310 184.8570 245.0350 297.7390 382.3010 507.3750 504.2290 449.9510 412.5870 381.9080 337.8570 293.0190 270.2070 268.2400 249.3610 231.2690 248.5740 263.9140 271.7800 262.3400 312.2910 419.2730 511.3080 534.9070 463.7170 387.8080 312.2910 238.3480 226.5490 217.5030 199.4100 194.6900 211.2100 224.9760 245.4280 287.1190 360.2760 495.5760 562.0460 532.5470 500.2960 405.9000 328.4170 285.5460 241.1010 209.2430 203.7370 197.4430 165.1920 159.2920 207.6700 217.5030 297.3450 443.6580 571.0920 818.0940 1048.1800 1050.5400 810.6210 493.2160 339.4300 288.2990 252.5070 250.9340 230.8750 212.3890 243.4610 235.2020 255.2610 352.4090 506.9820 760.2760 1067.0600 1228.7100 1056.8400 702.0660 452.3110 326.8440 291.4460 247.0010 247.0010 239.5280 217.8960 211.6030 285.1530 378.3680 465.2910 566.3720 720.5520 931.3680 937.6610 685.1530 468.0440 327.6310 255.6540 257.6210 266.6670 251.3280 237.1680 211.6030 254.0810 328.0240 473.1570 680.0400 981.3190 1349.4600 1502.8500 1222.0300 799.2140 520.7480 350.4430 280.8260 287.1190 282.7930 224.1890 203.7360 221.8290 236.7750 299.7050 484.9560 800.0010 1165.3900 1369.1300 1205.9000 790.9550 468.8300 356.7360 339.4300 310.3250 252.1140 230.8750 225.7620 235.5950 287.5120 344.9360 451.9180 594.6910 726.8450 867.2580 937.2680 794.8880 542.7730 350.8360 315.0440 325.2710 289.8720 211.6030 181.3180 217.1090 273.3530 299.7050 302.4580 383.8740 535.3010 559.2930 492.0360 388.2010 325.6640 279.2530 185.2510 149.4590 182.1040 224.9750 215.9290 183.6770 145.1330 204.9160 302.4580 354.7690 339.0370 355.5560 365.3890 314.6510 269.4200 212.7830 190.7570 211.6030 195.8700 204.1300 200.9830 226.9420 250.1480 232.0550 253.2940 318.9780 338.6430 317.0110 318.1910 326.4510 299.7050 232.4480 211.6030 253.2940 235.2020 204.5230 217.8960 228.1220 248.5740 233.2350 227.7290 289.4790 332.7440 335.1030 313.4710 255.2610 210.0300 191.9370 227.7290 262.3400 260.3740 258.0140 239.9210 245.4280 217.8960 184.4640 197.4430 255.2610 299.7050 306.7850 314.6510 311.1110 299.7050 258.0140 210.8160 191.9370 229.3020 256.0470 272.9600 276.8930 248.5740 190.3640 178.5640 209.6360 277.2860 361.4560 357.5220 313.0780 299.7050 293.0190 232.8420 204.5230 232.0550 262.3400 259.1940 247.0010 221.4360 205.7030 241.4950 235.9880 225.7620 313.0780 408.6530 345.3300 249.7540 235.9880 212.3890 196.6570 209.6360 204.1300 182.8910 184.0710 243.8550 271.3870 226.9420 233.6280 250.1480 307.5710 346.9030 368.5350 372.8620 333.1370 259.5870 205.7030 173.4510 185.6440 236.7750 244.2480 225.3690 200.9830 197.0500 238.3480 342.1830 393.3140 376.0080 349.2630 320.5510 303.2450 259.1940 264.3070 275.7130 234.0220 193.9040 183.2840 186.8240 206.4900 225.3690 240.3150 265.4870 339.0370 343.3630 331.5640 324.0910 248.1810 207.2760 206.4900 218.6820 212.7830 192.7240 188.7900 194.6900 221.0420 253.2940 268.2400 287.5120 326.4510 356.7360 386.6280 351.2290 274.9260 239.5280 219.8620 182.1040 175.8110 196.2630 225.7620 246.6080 206.4900 162.0450 197.8370 272.1730 324.8770 359.8820 381.5150 356.7360 289.8720 229.3020 206.0960 211.9960 225.3690 210.0290 179.3510 175.0240 176.2040 188.0040 217.1090 259.9800 276.8930 297.7390 338.6430 324.0910 281.6130 280.8260 279.6460 264.3070 243.0680 200.5900 224.1890 258.4070 235.5950 210.0290 221.0420 264.3070 260.3740 263.5200 319.3710 356.3420 376.0080 368.1420 332.3500 244.6410 153.7860 148.2790 173.4510 206.8830 223.0090 174.6310 148.6720 174.6310 207.2760 251.3270 350.0490 388.9880 360.2760 302.4580 306.7850 247.7880 161.6520 165.1920 202.5560 212.3890 190.7570 159.6850 163.6180 195.8700 238.7410 280.0390 370.5020 435.0050 410.6200 401.1800 359.0960 287.9060 207.2760 151.4260 157.7190 156.9320 156.5390 176.5980 178.5640 199.8030 212.7830 248.9680 324.0910 383.0880 444.8380 403.5400 304.0320 269.4200 226.5490 206.0960 228.5150 221.4360 201.7700 206.4900 195.0830 194.6900 199.4100 260.3740 325.2710 346.9030 376.4010 390.1670 362.6350 298.1320 237.9550 206.0960 181.7110 190.7570 189.1840 192.7240 194.6900 221.0420 226.9420 236.3810 315.0440 378.3680 407.8670 476.3030 509.3420 424.3860 259.1940 236.7750 241.8880 202.5560 212.7830 234.8080 219.4690 217.1090 251.7210 251.7210 328.0240 538.4470 818.8800 905.4090 758.7030 546.7060 375.2210 335.1030 269.4200 248.9670 219.4690 229.3020 261.5540 258.0140 245.8210 247.3940 331.5640 471.5830 718.5850 978.9590 914.8490 565.9790 338.2500 277.6800 303.6380 269.4200 241.4950 259.9800 247.0010 208.0630 231.2680 234.0220 270.6000 363.0290 530.9740 702.0660 705.6060 540.0200 375.6150 283.1860 224.1890 202.5560 205.3100 234.0220 225.7620 179.3510 164.0120 203.3430 276.1060 410.6200 578.9580 705.2120 670.9940 571.4850 485.7430 362.2420 327.6300 317.4040 249.7540 210.0290 195.0830 231.6620 276.8930 279.2530 278.8590 310.7180 398.0340 545.1330 597.8370 556.1460 452.7040 305.9980 231.6620 259.9800 274.1400 248.9680 220.2560 192.7240 193.5100 224.1890 257.6200 304.0320 346.5100 400.3940 437.7580 439.7250 363.8150 283.1860 254.4740 221.0420 218.2890 243.0680 </int_list></spectrum></measured></pepdata></protdata>
\ No newline at end of file
diff --git a/samples/XML_output/C25plst02_D_25.xml b/samples/XML_output/C25plst02_D_25.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4235407526eb2e1da773f2bf4c0dc59daeb588a5
--- /dev/null
+++ b/samples/XML_output/C25plst02_D_25.xml
@@ -0,0 +1 @@
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1042.4522 1042.4964 1042.5406 1042.5848 1042.6290 1042.6733 1042.7175 1042.7617 1042.8059 1042.8501 1042.8943 1042.9386 1042.9828 1043.0270 1043.0712 1043.1155 1043.1597 1043.2039 1043.2481 1043.2924 1043.3366 1043.3808 1043.4251 1043.4693 1043.5135 1043.5578 1043.6020 1043.6462 1043.6905 1043.7347 1043.7789 </mz_list><int_list>167.6130 100.0850 125.4080 140.4810 130.8340 149.5250 139.2750 125.4080 142.8930 159.1720 152.5400 164.5980 154.9510 95.2621 91.0416 113.9530 98.2767 97.0708 139.2750 183.8920 221.2730 244.1840 232.7280 191.7300 144.0990 139.2750 122.3940 95.2621 88.0270 88.6299 98.8796 102.4970 100.0850 122.3940 138.0700 131.4370 107.9230 127.2170 169.4210 162.1860 153.7450 185.7000 208.0080 198.9650 215.2430 239.9630 224.2870 195.3470 142.2900 114.5560 105.5120 81.3949 71.7481 86.8212 125.4080 103.1000 80.7920 104.9090 116.3640 106.1150 124.2020 141.0840 130.8340 115.1590 113.9530 146.5100 183.8920 240.5660 219.4640 156.7600 117.5700 121.7910 118.1730 97.0709 86.8212 96.4680 110.3350 136.8640 103.1000 83.8066 99.4826 147.7160 133.2460 80.1891 80.7920 106.7180 168.8190 202.5820 201.3760 195.9500 216.4490 223.0810 165.8040 109.1290 110.9380 105.5120 103.1000 124.8050 124.2020 114.5560 97.6738 94.0562 85.6153 97.0709 86.8212 85.6153 120.5850 132.0400 119.9820 113.3500 113.3500 133.2460 168.8190 220.0670 237.5520 181.4800 146.5100 134.4520 124.8050 88.6300 92.8504 91.6446 74.1598 91.0416 75.9686 85.0124 112.1440 113.9530 81.3949 77.7774 104.3060 110.3350 110.9380 131.4370 290.0060 641.5090 1038.8300 1003.2600 543.8360 238.7570 179.6710 146.5100 122.3940 97.6738 113.3500 129.6290 122.9970 112.1440 118.7760 127.8200 130.8340 113.3500 92.8504 108.5260 137.4670 147.7160 151.3340 199.5680 373.8120 678.8900 761.4910 490.1760 244.1840 182.6860 150.7310 135.6580 104.3060 69.3365 78.3803 109.1290 128.4230 105.5120 82.6008 101.8940 103.7030 104.9090 105.5120 87.4241 89.8358 114.5560 242.3750 540.2180 1059.9400 1425.3100 1082.8500 444.9570 188.7150 164.5980 171.8330 152.5400 119.9820 109.7320 118.7760 127.2170 117.5700 133.8490 144.0990 154.9510 130.8340 128.4230 173.6420 144.7020 112.7470 171.2300 309.2990 628.2450 890.5160 752.4470 415.4140 211.6260 131.4370 144.7020 111.5410 77.1745 87.4241 95.2621 107.3210 107.3210 115.1590 125.4080 117.5700 121.7910 147.1130 138.6720 107.9230 83.8066 118.7760 193.5380 320.7550 423.2510 423.2510 308.0930 166.4070 93.4534 87.4242 85.6154 63.3073 60.2927 77.7774 85.6154 91.0417 95.2621 91.0417 135.0550 148.9220 133.2460 143.4960 135.0550 130.2320 126.0110 121.1880 176.6570 238.7570 247.8010 210.4200 195.9500 161.5840 122.9970 127.8200 132.0400 112.7470 129.6290 125.4080 102.4970 101.2910 115.7610 125.4080 121.1880 107.9230 109.7320 115.7610 118.7760 127.8200 161.5840 267.0950 342.4600 352.1070 318.9460 254.4330 180.8770 126.0110 91.6446 91.6446 100.0850 110.3350 121.7910 132.0400 121.7910 111.5410 94.0563 80.1891 91.0417 83.8066 95.8650 109.1290 151.3340 165.2010 209.8170 257.4480 296.0350 303.8730 227.3020 163.3920 109.1290 106.7180 89.2329 92.2475 83.2037 133.8490 150.1280 129.0260 127.2170 130.8340 114.5560 92.2475 111.5410 119.3790 130.8340 184.4940 218.2580 193.5380 285.7850 355.1210 348.4890 257.4480 165.8040 131.4370 138.6720 153.7460 143.4960 138.6720 113.3500 83.8066 102.4970 121.7910 174.8480 185.0970 154.9510 101.8940 91.6446 114.5560 155.5540 206.8030 307.4910 470.2790 523.9390 441.3390 321.9610 205.5970 157.3630 134.4520 119.3790 118.7760 97.6738 94.6592 126.0110 117.5700 102.4970 95.2621 113.9530 100.0850 89.8358 101.2910 113.3500 124.8050 160.3780 365.9740 1009.8900 1967.3300 2181.3700 1249.2500 380.4440 198.3620 191.1270 180.2740 128.4230 89.2328 98.8795 136.2610 133.8490 91.0416 105.5120 127.8200 159.7750 148.3190 97.6737 107.3200 145.3050 167.0100 238.7570 532.3800 1013.5100 1190.1700 731.3440 294.8290 163.9950 129.0260 75.9685 85.6153 92.8503 104.9090 122.3940 142.8930 120.5850 100.0850 104.9090 113.9530 132.0400 162.7890 170.0240 164.5980 146.5100 236.9490 405.1640 532.9830 534.7920 410.5900 214.0380 142.2900 150.1280 130.8340 106.1150 114.5560 124.8050 126.6140 119.9820 106.1150 121.1880 117.5700 101.2910 94.0562 107.3200 118.7760 121.1880 164.5980 225.4930 294.2260 341.2540 321.3580 212.8320 122.9960 115.1580 118.1730 114.5560 92.2474 85.6153 105.5120 99.4825 89.8357 70.5422 81.3948 78.3802 71.1452 86.8211 108.5260 130.8340 118.1730 121.1880 135.6580 251.4190 464.8530 557.7030 416.0160 232.7280 140.4810 123.5990 121.1880 102.4970 113.3500 135.6580 112.7470 95.2620 93.4533 88.0270 76.5715 96.4679 107.3200 111.5410 120.5850 124.2020 155.5540 197.1560 275.5360 367.1800 414.8110 334.0190 265.2860 204.9940 142.2900 109.7320 99.4825 102.4970 111.5410 110.9380 105.5120 124.8050 127.2170 119.3790 106.7180 89.2328 81.3949 115.7610 146.5100 156.7600 160.3780 200.1700 244.1840 228.5080 198.3620 186.3030 157.3630 164.5980 132.0400 115.7610 116.9670 99.4825 116.9670 103.7030 71.7481 64.5130 100.6880 102.4970 112.1440 103.1000 84.4094 101.8940 167.6130 229.7140 238.1540 214.6410 208.0080 210.4200 164.5980 119.9820 118.7760 116.3640 91.6445 85.6153 63.9101 74.1598 106.1150 124.8050 118.7760 88.0270 88.6299 108.5260 109.1290 92.2474 113.9530 157.3630 207.4050 287.5940 320.7550 264.6830 212.8320 153.7450 121.7910 110.3350 101.2910 113.9530 111.5410 99.4825 86.2182 109.1290 112.1440 103.7030 106.1150 90.4387 86.2182 94.6591 99.4825 108.5260 157.9660 419.0310 982.1600 1409.0300 1038.2300 457.6180 220.6700 153.7450 119.9820 109.1290 95.2621 105.5120 109.7320 104.3060 121.1880 121.7910 114.5560 115.1590 107.9230 112.1440 119.3790 85.0124 77.7774 154.3480 323.1660 637.8920 908.6030 736.1680 360.5480 243.5810 197.7590 150.7310 102.4970 119.3790 112.7470 99.4825 104.9090 139.8780 157.3630 124.2020 106.1150 119.9820 122.3940 136.8640 138.0700 114.5560 105.5120 187.5090 346.0770 462.4410 384.0620 253.8300 158.5690 108.5260 96.4679 77.1744 73.5569 99.4825 126.0110 130.2320 129.0260 133.8490 125.4080 112.7470 86.2183 101.2910 165.8040 173.0390 154.9510 173.0390 212.8320 293.0200 343.6660 329.7990 280.3590 202.5820 145.9080 117.5700 115.1590 104.9090 105.5120 107.3210 135.0550 141.6870 144.0990 171.2300 135.0550 92.8504 82.6007 89.2329 91.6446 98.2767 160.9810 277.9470 438.3250 535.3950 440.7360 225.4930 139.8780 145.9080 148.3190 101.8940 120.5850 129.6290 115.1590 100.0850 86.2183 75.9686 97.0709 150.7310 145.9080 106.7180 103.7030 110.3350 147.1130 179.6710 224.2870 328.5930 446.1630 377.4290 235.1400 161.5830 139.2750 129.0260 103.7030 87.4241 100.0850 113.3500 124.2020 123.5990 112.7470 117.5700 117.5700 147.7160 179.0680 162.7890 143.4960 144.7020 147.7160 182.6860 277.3440 340.0480 285.7850 168.2160 117.5700 108.5260 118.7760 128.4230 117.5700 127.2170 129.0260 132.6430 106.7180 75.9686 87.4241 115.1590 106.7180 114.5560 107.9230 110.9380 162.1860 306.8880 770.5340 1481.3800 1602.5700 964.6750 378.0320 195.9500 197.1560 145.3050 105.5120 104.9090 119.3790 129.6290 124.2020 96.4680 115.1590 133.8490 116.3640 126.6140 151.3340 188.7150 186.3030 185.7000 292.4180 607.7460 1061.1400 1117.8200 714.4630 320.7550 173.6420 171.2300 135.6580 97.0710 119.9820 144.0990 115.7620 92.8505 121.1880 122.3940 133.2460 115.7620 115.7620 111.5410 114.5560 132.0400 152.5400 256.8450 506.4550 806.1070 783.7990 471.4850 253.8310 194.7440 179.6710 133.8490 100.0860 128.4230 135.0550 121.1880 93.4534 78.9833 103.7030 98.2768 96.4680 90.4388 110.3350 149.5250 160.9810 167.0100 238.1550 466.0590 703.0070 668.6410 422.0460 246.5960 164.5980 96.4681 94.0564 106.1150 94.0564 93.4535 97.0710 108.5260 121.1880 124.8050 153.1430 174.2450 176.0540 197.7590 212.8320 228.5080 225.4930 238.7580 393.1060 529.3660 514.2930 435.9130 320.1520 243.5810 159.1720 136.2610 151.9370 122.9970 112.1440 129.0260 136.8640 145.3050 152.5400 139.8780 149.5250 148.9220 154.3490 165.2010 214.0380 231.5230 215.2440 323.1670 429.8840 373.2090 259.8600 191.1270 160.3780 147.7160 124.2020 129.6290 124.8050 104.9090 102.4970 75.3658 98.8798 160.9810 157.9660 129.6290 136.8640 153.1430 188.1120 194.7440 213.4350 261.0660 322.5640 288.8000 243.5810 246.5960 235.1400 183.8920 156.1570 131.4380 96.4681 91.0418 98.8798 98.8798 99.4827 101.8940 112.7470 127.8200 153.1430 148.9220 131.4380 158.5690 176.6570 176.0540 228.5080 301.4610 331.6080 291.8150 211.6260 150.1280 107.9240 85.6156 94.0565 82.6010 65.7191 80.7922 87.4243 94.6594 109.1300 118.1730 119.3790 146.5110 167.6130 142.2900 124.8050 197.7590 283.9770 335.2250 376.2240 306.8880 233.3310 183.8920 153.7460 166.4070 147.1140 123.6000 121.7910 99.4828 106.1150 118.1730 106.1150 122.9970 153.1430 139.2760 116.3650 121.1880 138.0700 185.7010 177.8630 159.7750 225.4930 239.9640 227.9050 192.3330 165.2010 155.5550 142.2900 132.6430 136.2610 140.4810 105.5120 109.1300 141.0840 124.8060 89.8361 94.6594 103.1000 121.1880 149.5250 162.1870 182.6860 177.8630 160.9810 221.2730 308.6970 305.0790 211.0230 149.5250 132.6430 159.7750 139.2760 116.9680 139.8790 151.9370 136.2610 141.0840 157.9660 142.8930 109.1300 91.6448 115.7620 133.2460 154.9520 186.9060 181.4800 263.4770 324.9750 288.1970 203.7880 138.0700 118.7760 113.9530 85.6156 77.1747 145.3050 152.5400 101.2920 69.9396 77.1747 102.4970 93.4536 111.5410 127.8200 126.0110 130.2320 130.2320 116.9680 159.1720 242.3750 335.2250 390.6940 419.0310 337.0340 183.8920 130.2320 107.9240 127.8200 113.3500 66.9250 57.2783 69.3367 83.8068 100.6890 95.8653 94.6594 109.1300 118.1730 123.6000 133.2460 122.3940 113.9530 175.4510 240.5660 304.4760 318.3430 227.9050 170.0250 171.8330 159.1720 138.0700 113.3500 74.7630 88.0273 115.1590 126.0110 133.2460 144.0990 131.4380 93.4536 98.8799 121.1880 129.6290 217.6550 465.4560 827.2090 883.2810 568.5560 261.6690 142.8930 135.0550 135.0550 129.6290 108.5270 94.0565 119.3790 99.4827 84.4097 91.0418 121.1880 130.2320 115.1590 112.7470 139.2760 124.2030 133.8490 207.4060 534.7920 1054.5100 1254.0800 852.5320 375.6210 210.4200 150.7310 131.4380 114.5560 122.3940 120.5850 108.5270 95.2622 107.9240 106.1150 125.4080 154.3490 163.3920 134.4520 113.3500 78.9834 79.5863 186.3030 393.7080 695.1690 804.9010 545.6450 248.4040 118.7760 101.8940 100.0860 118.1730 130.8350 116.9670 101.8940 102.4970 104.9090 118.1730 126.6140 97.0711 104.9090 114.5560 118.7760 140.4810 160.3780 192.3330 253.8310 405.1640 437.1190 315.9320 249.0070 195.3470 137.4670 106.1150 110.3350 136.2610 133.8490 126.0110 121.1880 110.9380 109.1300 123.6000 101.2920 129.0260 122.3940 118.1730 146.5110 223.6850 432.2960 718.6830 745.8150 478.7200 249.6100 141.6870 142.8930 126.6140 115.1590 104.9090 105.5120 111.5410 103.1000 111.5410 109.1290 98.2769 104.9090 119.9820 125.4080 144.7020 151.9370 134.4520 189.9210 413.6050 601.7160 525.1450 332.2110 202.5820 150.1280 130.8350 109.1300 118.1730 144.0990 134.4520 118.7760 118.7760 146.5110 179.6710 141.0840 109.1300 104.9090 122.3940 117.5700 92.8506 118.7760 187.5090 294.2260 379.8410 328.5930 206.8030 156.7600 147.1140 129.6290 109.7320 89.8360 98.8798 90.4389 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928.1686 928.2103 928.2521 928.2938 928.3355 928.3772 928.4189 928.4607 928.5024 928.5441 928.5858 928.6276 928.6693 928.7110 928.7528 928.7945 928.8362 928.8779 928.9197 928.9614 929.0032 929.0449 929.0866 929.1284 929.1701 929.2118 929.2536 929.2953 929.3371 929.3788 929.4206 929.4623 929.5040 929.5458 929.5875 929.6293 929.6710 929.7128 929.7545 929.7963 929.8381 929.8798 929.9216 929.9633 930.0051 930.0468 930.0886 930.1304 930.1721 930.2139 930.2556 930.2974 </mz_list><int_list>86.8211 103.7030 112.7470 99.4824 116.3640 119.9820 119.3790 121.1880 156.1570 208.6110 247.8010 255.6390 183.8910 95.8649 78.9831 114.5550 132.0400 93.4532 100.0850 109.7320 110.3350 89.8357 100.0850 119.9820 92.2474 85.0123 72.3509 76.5714 103.1000 132.6430 169.4210 171.8330 165.2010 197.7590 273.7270 362.3560 358.7390 225.4930 122.3930 85.6152 62.7042 86.8211 119.9820 115.7610 83.8065 70.5422 81.3948 117.5700 125.4080 77.7773 68.1305 74.7626 97.0707 110.9380 127.2170 138.0690 133.2460 147.1130 243.5810 321.9610 326.7840 293.6230 242.3750 135.0550 68.1305 82.6006 91.0415 83.8064 110.3350 135.6580 114.5550 85.0123 83.2035 83.2035 89.8357 107.9230 87.4240 67.5276 94.6590 159.7750 177.2590 139.2750 148.3190 176.6560 217.0520 212.2290 206.8020 170.0240 115.1580 88.6298 89.8356 95.2619 100.6880 105.5120 107.9230 116.3640 113.9520 98.8795 96.4678 88.0269 109.1290 141.6870 153.7450 151.3340 145.9070 129.6280 116.9670 165.2010 235.7430 361.1500 392.5020 293.6230 176.0530 125.4080 103.1000 92.2473 100.0850 106.1150 111.5410 111.5410 101.2910 104.9090 118.7760 133.8490 127.2170 115.1580 116.3640 112.7470 128.4230 131.4370 89.2327 106.1150 193.5380 265.8890 297.2410 253.8300 171.2300 130.8340 143.4960 147.7160 127.2170 106.7170 91.6444 101.8940 106.1150 85.6152 59.6895 80.7918 92.8502 80.1889 78.3801 88.6298 135.0550 150.7310 151.3340 180.2740 203.7880 230.9190 271.9180 244.7860 216.4490 160.9800 124.8050 115.7610 116.3640 133.2460 128.4230 150.1280 140.4810 123.5990 119.9820 97.0707 107.9230 110.9380 136.8640 139.8780 141.0840 156.7600 176.0530 167.6130 185.0970 220.6700 262.2710 406.3690 610.1570 646.3320 471.4850 317.1370 236.3460 209.2140 215.2430 226.6990 195.3470 164.5980 162.7890 130.8340 132.0400 133.2460 143.4960 136.8630 95.8648 98.2765 147.1130 156.7600 144.7010 168.8180 198.9640 276.7410 294.8290 340.6510 343.6660 217.6550 157.9660 140.4810 150.1280 145.3040 126.0110 106.1140 98.8794 104.3060 117.5700 107.3200 102.4970 108.5260 105.5120 127.2170 142.8930 130.8340 140.4810 166.4070 143.4960 151.9370 192.9350 252.6240 250.2130 209.2140 194.7440 185.7000 157.9660 116.3640 116.3640 107.3200 105.5120 106.1140 120.5850 118.1730 117.5700 104.9090 91.0414 105.5120 125.4080 127.8200 166.4070 189.9210 200.1700 228.5080 203.1850 214.6400 230.3160 203.1850 162.1860 133.2460 130.8340 136.2610 108.5260 92.2473 80.7918 73.5567 68.1304 65.7187 64.5129 65.7187 98.8794 129.0260 153.1420 161.5830 183.8910 175.4500 157.9660 211.0230 260.4620 258.6540 222.4780 191.1260 147.1130 114.5550 110.9380 101.2910 72.9538 79.5859 79.5859 75.9684 94.6590 89.8356 83.2035 100.6880 90.4385 82.6005 106.1140 156.1570 171.2300 163.3920 162.1860 121.7900 150.1280 218.8610 239.9630 201.3760 149.5250 125.4080 132.6430 157.3630 138.0690 105.5120 107.9230 104.9090 90.4385 91.0415 97.6736 101.8940 117.5700 130.8340 140.4810 152.5390 183.8910 163.9950 130.2310 131.4370 150.1280 198.3620 252.6240 279.1530 259.2570 235.7430 146.5100 94.6590 90.4386 88.6298 103.1000 103.1000 100.6880 95.8648 100.0850 101.8940 112.7470 127.8200 101.8940 113.3500 133.8490 157.3630 173.0390 142.2900 135.6580 154.3480 203.7880 254.4330 209.2140 156.1570 129.0260 121.7900 115.7610 110.3350 109.1290 104.9090 117.5700 123.5990 104.9090 118.1730 111.5410 103.7030 116.3640 142.2900 131.4370 170.0240 178.4650 137.4660 142.2900 174.2450 234.5370 260.4620 207.4050 167.0100 151.3340 146.5100 138.0690 95.2619 65.7188 92.8503 113.9530 130.2310 151.3340 119.9820 108.5260 97.6736 78.9830 112.1440 103.7030 112.7470 151.9370 180.8770 177.8620 174.2450 198.3620 218.8610 202.5820 206.8020 211.0230 160.3770 147.1130 150.1280 139.8780 157.3630 118.7760 90.4386 94.0561 85.6152 76.5714 101.2910 129.0260 131.4370 140.4810 161.5830 195.9500 192.3320 198.9640 174.2450 144.7020 204.9940 283.9760 253.2270 182.6860 174.2450 135.0550 109.1290 107.9230 138.0690 142.2900 113.3500 107.3200 119.3790 123.5990 113.3500 106.1150 126.6140 132.0400 134.4520 127.2170 140.4810 160.9800 173.6420 202.5820 238.7570 240.5660 187.5090 137.4660 120.5850 121.7900 113.9520 111.5410 109.7320 100.6880 107.9230 118.7760 100.0850 85.6152 89.2327 103.1000 90.4386 81.3947 111.5410 144.7020 145.3040 153.1420 126.0110 130.2310 169.4210 193.5380 192.3320 188.1120 156.7600 143.4960 121.7900 116.3640 96.4678 79.5860 89.2327 100.6880 103.7030 76.5714 68.1304 80.7918 92.8502 110.9380 130.2310 133.2460 151.9370 171.8330 157.3630 137.4660 186.3030 238.7570 240.5660 198.3610 137.4660 126.6140 136.2610 148.3190 123.5990 109.7320 120.5850 126.6140 115.7610 124.2020 119.3790 88.0268 94.6590 106.7170 130.2310 143.4960 159.1720 127.8200 109.7320 156.1570 189.9210 231.5220 285.7850 249.0070 188.7150 159.7750 164.5980 139.2750 93.4532 85.6152 69.9392 75.3655 128.4230 124.8050 130.2310 132.6430 126.6140 123.5990 99.4824 103.7030 157.9660 170.0240 152.5390 170.0240 235.7430 352.7090 423.8540 378.6350 314.7250 232.7280 155.5540 125.4080 129.0260 117.5700 92.8502 112.1440 127.8200 101.8940 93.4532 103.7030 99.4824 107.9230 101.2910 115.7610 153.1420 130.8340 116.3640 142.8930 212.2290 259.2570 299.6520 305.6820 299.6520 246.5950 209.8170 204.9940 168.2150 126.0110 83.8064 74.7626 89.8357 96.4678 88.6298 85.6152 101.8940 125.4080 121.7910 120.5850 129.6280 142.8930 163.3920 188.1120 182.0830 195.9500 220.6700 335.8280 573.9820 1049.0800 1374.6600 1028.5800 449.1770 215.8460 173.0390 267.0950 338.2390 314.7250 248.4040 183.8910 167.6120 158.5690 129.0250 105.5120 128.4230 153.7450 200.1700 217.0520 185.0970 173.6420 201.9790 227.9050 334.0190 551.0710 795.2540 697.5810 361.7530 174.2450 122.9960 107.9230 167.0100 208.6110 179.0680 141.6870 123.5990 135.6580 144.0990 115.1580 123.5990 141.6870 159.1720 180.8770 208.0080 215.8460 200.7730 198.3610 229.1100 317.7400 365.9740 358.1360 258.6540 153.1420 124.8050 128.4230 130.2310 144.0990 146.5100 132.0400 124.8050 113.3490 122.9960 127.8200 110.3350 136.2610 150.1280 166.4070 154.9510 161.5830 190.5230 197.1560 215.8460 218.2580 212.2290 185.0970 133.2460 106.1140 93.4531 80.7917 87.4239 114.5550 139.8780 145.9070 131.4370 81.9976 54.2632 78.3800 91.0414 121.7900 128.4230 130.8340 158.5690 167.6120 198.9640 246.5950 302.6670 446.1620 554.6880 487.1610 318.3430 183.2880 123.5990 128.4230 141.0840 137.4660 107.3200 91.0414 92.2472 107.3200 100.0850 92.8502 103.1000 103.7030 88.0268 100.6880 151.3340 163.9950 163.3920 196.5530 261.6680 332.8130 393.7080 367.7820 257.4480 200.7730 163.3920 125.4080 107.9230 98.8794 87.4238 68.1303 88.0268 107.9230 110.3350 97.0706 113.9520 104.3060 102.4970 120.5850 162.7890 189.3180 157.3630 165.2010 234.5370 334.0190 448.5740 409.3840 282.1680 223.0810 187.5090 139.2750 127.8200 147.7160 163.9950 156.7600 130.8340 100.6880 94.0560 97.6735 116.9670 116.9670 112.7470 94.0560 107.3200 167.0100 176.6560 172.4360 215.2430 310.5050 397.9280 422.0450 355.1210 259.2570 188.1120 132.6430 95.2618 78.3800 102.4970 116.3640 98.8793 100.6880 116.3640 102.4970 83.2034 100.6880 158.5690 232.1250 323.1660 329.1950 262.8740 202.5820 218.2580 255.6390 294.2260 336.4300 332.2100 294.8290 202.5820 135.6580 127.2170 90.4384 65.7186 45.2193 63.3069 101.8940 121.1870 117.5700 109.1290 126.0110 153.7450 198.3610 303.2700 309.2990 179.6710 124.8050 133.8490 232.1250 484.7490 652.9640 542.0270 423.8540 394.9140 343.0630 223.6840 124.8050 88.6297 80.7917 124.2020 159.1710 110.9380 97.6735 138.0690 176.0530 147.7160 127.8200 138.6720 130.8340 131.4370 147.7160 157.3630 242.3750 382.2530 477.5140 390.6930 255.6390 249.0070 247.8010 191.7290 118.1730 110.3350 84.4092 89.2326 122.9960 154.9510 142.8930 113.3490 88.0268 80.1888 110.9380 160.3770 179.6710 169.4210 144.0980 143.4960 161.5830 212.8320 238.7570 240.5660 212.8320 177.8620 138.6720 141.0840 143.4960 138.6720 134.4520 113.3490 99.4822 106.1140 92.2472 75.3654 80.1888 89.2326 97.6735 135.0550 151.9360 148.3190 122.3930 119.9820 136.2600 149.5250 174.2450 212.2290 188.1120 159.7740 128.4230 117.5700 116.9670 113.3490 100.0850 85.6151 103.1000 127.2170 103.7030 85.6151 101.2910 110.3350 121.1870 133.8490 132.0400 161.5830 189.3180 167.0090 138.6720 191.7290 213.4340 198.9640 165.2010 155.5540 136.2600 118.7760 113.3490 130.2310 130.2310 108.5260 101.8940 112.1440 105.5110 96.4677 91.6443 78.3800 75.3654 80.7917 102.4970 111.5410 143.4960 180.8770 215.8460 244.1830 240.5660 211.6260 190.5230 156.7600 147.1130 137.4660 140.4810 122.9960 135.0550 142.8930 129.0250 88.6297 68.1303 99.4823 138.0690 110.9380 135.6580 153.7450 160.9800 149.5250 133.2460 155.5540 236.3450 314.7250 312.3140 228.5080 162.1860 164.5980 150.7310 104.3060 80.7917 97.6735 122.3930 127.2170 133.2460 104.3060 72.3508 88.6297 97.6735 91.0414 110.3350 124.8050 159.1720 161.5830 167.0100 177.8620 195.3470 212.2290 206.8020 219.4640 247.1980 209.2140 138.0690 125.4080 122.3930 102.4970 90.4384 92.8501 112.1440 113.3490 111.5410 113.9520 103.1000 101.2910 88.0268 113.9520 160.3770 174.2450 122.9960 126.0110 163.9950 173.0390 183.2880 224.2870 242.3750 197.1560 157.9660 132.6430 130.8340 147.7160 102.4970 80.1888 79.5859 70.5420 103.7030 118.7760 120.5850 116.3640 102.4970 132.0400 223.0810 295.4320 398.5310 408.1780 302.0640 208.6110 187.5090 183.2880 165.2010 163.3920 171.2300 147.7160 97.6736 76.5713 75.3655 83.8064 87.4239 88.6297 85.0122 83.2034 116.3640 123.5990 108.5260 101.2910 157.3630 255.0360 288.8000 280.9620 236.9480 191.1260 235.1400 286.9910 201.3760 136.8630 126.6140 88.0268 77.7771 80.1888 94.0560 95.2619 87.4239 98.2765 97.6736 92.2473 94.0560 93.4531 89.2327 142.8930 174.2450 154.9510 170.6270 185.0970 139.8780 148.9220 195.9500 221.8750 236.3460 185.7000 124.8050 86.8210 87.4239 96.4677 90.4385 107.3200 132.0400 122.9960 84.4093 75.3655 89.8356 96.4677 105.5120 85.6151 100.6880 113.9520 128.4230 150.1280 132.0400 144.7010 173.6420 245.3890 264.0800 208.0080 152.5390 118.7760 100.6880 85.6151 76.5713 102.4970 122.3930 94.6590 88.6298 85.6151 81.3947 100.0850 92.8502 101.8940 101.8940 118.7760 119.3790 94.0560 101.8940 116.9670 158.5690 242.3750 257.4480 249.0070 224.8900 141.0840 97.0707 80.1889 75.9684 92.8502 97.6736 112.7470 115.1580 90.4385 85.6152 93.4531 92.8502 92.2473 106.1140 133.2460 133.8490 127.2170 138.6720 135.6580 188.7150 263.4770 236.3460 161.5830 181.4800 191.1260 161.5830 132.6430 122.9960 106.1140 102.4970 87.4239 69.3363 76.5713 63.3070 77.1742 104.3060 148.3190 179.6710 192.9350 173.6420 170.0240 190.5240 149.5250 198.3610 235.7430 203.1850 180.2740 138.6720 138.0690 165.2010 150.1280 109.7320 75.9684 97.0707 108.5260 95.8648 84.4093 78.9830 78.3801 104.3060 113.9520 112.1440 136.2610 150.7310 132.0400 124.2020 136.8630 162.7890 201.9790 182.6860 164.5980 122.9960 109.7320 92.8502 60.8954 63.3071 68.7334 81.3947 94.0561 110.9380 116.3640 121.7900 91.0415 101.2910 173.6420 169.4210 154.9510 143.4960 109.7320 102.4970 126.6140 171.2300 192.9350 182.0830 174.8480 144.7010 118.7760 89.8356 69.3363 84.4093 95.2619 104.9090 94.6590 103.7030 101.2910 88.6298 63.3071 69.9392 102.4970 106.1150 98.2765 125.4080 138.6720 126.6140 125.4080 161.5830 180.2740 168.8180 165.2010 165.8040 138.0690 116.3640 102.4970 85.0123 106.1150 106.7170 81.3947 85.0123 138.6720 143.4960 100.0850 76.5714 83.8064 103.1000 113.9530 129.0260 116.9670 143.4960 161.5830 170.0240 186.9060 211.0230 201.3760 151.9370 142.2900 122.9960 101.2910 109.1290 124.8050 97.6736 76.5714 100.0850 108.5260 106.7170 122.3930 132.0400 112.7470 99.4824 92.2473 106.7170 105.5120 119.3790 166.4070 227.9050 243.5810 243.5810 215.8460 198.3620 176.0530 135.0550 106.1150 97.0707 78.9831 97.6736 104.9090 105.5120 81.3948 86.2181 103.1000 86.2181 84.4094 92.8503 116.9670 144.7020 143.4960 137.4660 153.1420 181.4800 212.8320 230.9190 212.8320 186.3030 171.8330 162.1860 120.5850 81.3948 68.7334 75.3656 97.0707 111.5410 108.5260 113.3500 100.6880 71.7480 77.1743 84.4094 92.2474 138.0690 174.8480 </int_list></spectrum></measured><measured><pepseq>WFGNTR</pepseq><mzh>780.3832</mzh><calc_mzh>780.3793</calc_mzh><leucines>0</leucines><mono_iso_intensity>2700</mono_iso_intensity><deuterated_intensity>0</deuterated_intensity><ratio>0.00</ratio><validated>UNKNOWN</validated><local_bg>0.0000</local_bg><corrected_ratio>0.00</corrected_ratio><spectrum><mz_list>755.7211 755.7587 755.7964 755.8340 755.8717 755.9093 755.9470 755.9846 756.0223 756.0599 756.0976 756.1352 756.1729 756.2105 756.2482 756.2858 756.3235 756.3612 756.3988 756.4365 756.4741 756.5118 756.5495 756.5871 756.6248 756.6625 756.7001 756.7378 756.7755 756.8131 756.8508 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188.7150 222.4780 215.2430 153.1420 127.2170 131.4370 124.8050 102.4970 121.1870 108.5260 78.3799 91.6442 78.3799 51.2485 88.0267 125.4080 132.0400 130.2310 144.0980 121.1870 138.0690 156.7600 154.3480 194.7440 208.6110 174.8470 195.9500 255.0360 277.3440 250.2130 200.7730 130.8340 111.5410 99.4822 96.4676 106.1140 94.6588 67.5274 65.7186 78.3799 92.2471 80.1887 105.5110 115.1580 93.4530 87.4238 106.1140 123.5990 136.2600 189.3180 189.3180 169.4210 189.3180 228.5070 256.2420 245.9920 211.6260 179.6710 155.5540 135.6580 88.0267 51.8514 74.7624 103.1000 81.3946 71.7478 84.4092 88.6296 102.4970 86.2179 69.9390 93.4530 119.9820 114.5550 106.7170 163.3920 263.4770 271.9180 223.0810 205.5960 224.8900 211.0230 163.3920 135.6580 156.7600 116.9670 85.0121 86.2179 88.6296 86.2179 85.0121 83.8063 80.1887 94.6588 100.6880 110.3350 97.0705 97.0705 102.4970 95.2618 106.7170 162.1860 224.2870 197.1560 202.5820 275.5350 323.1660 282.7700 196.5530 167.0090 142.2900 109.7320 97.0705 100.0850 95.2618 111.5410 118.7760 95.8647 101.2910 97.0705 63.3069 63.3069 91.0413 90.4384 59.0865 54.8660 85.0121 134.4520 177.2590 208.0080 208.0080 171.2300 188.7150 227.9050 222.4780 200.7730 183.2880 143.4950 130.2310 110.9380 92.2471 118.1730 118.1730 82.6004 62.1010 93.4530 106.1140 88.6296 102.4970 105.5110 104.9080 122.9960 131.4370 152.5390 150.1280 176.6560 216.4490 230.3160 231.5220 232.7280 218.8610 186.9060 153.7450 124.8050 103.7030 107.9230 119.9820 106.7170 63.3069 73.5566 92.2471 75.9683 72.9537 90.4384 90.4384 67.5274 71.1449 87.4238 81.3946 108.5260 159.7740 154.3480 136.8630 160.9800 217.0520 277.3440 304.4760 262.2710 228.5070 160.9800 100.6880 110.3350 135.0550 128.4220 104.9080 106.1140 95.2617 85.6150 113.3490 116.9670 94.6588 106.1140 129.0250 103.1000 85.6150 97.6734 93.4530 91.6442 110.3350 157.9660 192.3320 186.3030 232.7280 267.6970 203.1850 141.0840 133.2460 131.4370 113.3490 90.4384 106.7170 129.0250 129.0250 116.9670 104.9080 83.8062 62.7040 72.3507 88.0267 104.3060 133.8490 134.4520 151.3330 176.6560 171.2300 197.1550 233.9340 269.5060 280.3590 226.0960 160.3770 145.9070 152.5390 133.2460 113.9520 100.0850 95.8646 108.5260 126.0110 118.7760 110.3350 100.6880 94.0559 103.1000 97.0705 98.8792 78.9828 72.3507 76.5711 92.2471 145.9070 170.6270 174.8470 199.5670 230.3160 250.2130 218.2580 189.3180 189.9200 172.4360 144.0980 110.3350 94.6588 100.0850 130.2310 119.3790 105.5110 112.7460 97.0705 80.1887 67.5273 80.1887 91.0413 103.1000 118.1730 157.3630 182.0820 204.9930 230.3160 254.4330 244.1830 211.6260 211.0230 165.2010 129.0250 110.3350 91.6442 87.4238 95.8647 96.4676 111.5410 125.4080 101.2910 88.6296 112.7460 126.6140 97.6734 72.3507 80.1887 100.6880 104.3060 103.7030 118.1730 140.4810 203.1850 219.4640 201.3760 229.1100 206.1990 165.8040 222.4780 402.1490 469.0730 321.3570 147.7160 107.9230 114.5550 117.5700 97.0705 69.9391 76.5712 97.0705 88.0267 81.3946 81.9975 81.9975 115.1580 136.2600 139.2750 133.8490 139.2750 135.6580 165.2010 178.4650 141.0840 145.9070 153.7450 204.9940 329.7980 314.1220 180.8770 104.9090 110.3350 113.3490 121.1870 110.3350 109.7320 111.5410 82.6004 71.7478 89.2326 94.0559 93.4530 119.9820 141.0840 162.7890 176.6560 190.5230 205.5960 206.8020 209.2140 226.0960 228.5070 192.9350 197.1560 227.9050 209.2140 167.6120 129.6280 93.4530 72.3508 98.2764 104.9090 99.4823 100.6880 88.0267 92.8501 123.5990 124.8050 115.7610 116.3640 178.4650 214.6400 195.3470 205.5960 214.0370 246.5950 270.1090 236.3450 187.5090 150.1280 144.7010 136.2600 113.9520 98.8793 88.0267 82.6004 87.4238 69.3362 59.6894 116.3640 156.1570 152.5390 140.4810 100.6880 75.3654 97.6735 160.9800 219.4640 278.5500 242.3750 180.2740 183.8910 204.9940 224.8900 211.6260 187.5090 162.1860 143.4950 115.1580 101.8940 92.2472 106.1140 126.6140 100.0850 65.7186 64.5128 88.0267 113.9520 129.0250 153.7450 123.5990 79.5858 97.0705 164.5980 168.8180 153.7450 195.3470 214.0370 184.4940 170.6270 150.7310 151.9360 160.3770 179.6710 154.9510 108.5260 106.1140 108.5260 131.4370 141.6870 170.6270 170.6270 124.8050 110.3350 114.5550 114.5550 103.7030 83.2033 89.2325 139.2750 208.6110 242.3750 206.8020 185.7000 157.3630 136.2600 150.7310 185.7000 183.2880 158.5690 142.8930 115.7610 115.1580 88.0267 67.5273 62.7040 89.8354 114.5550 118.1730 109.1290 109.1290 129.0250 118.1730 101.8940 113.3490 157.3630 200.1700 211.0230 208.6110 196.5530 174.8470 187.5090 177.8620 170.0240 152.5390 130.8340 115.1580 105.5110 104.3060 106.7170 99.4822 93.4530 107.9230 104.9080 93.4530 88.6296 93.4530 93.4530 113.9520 142.2900 123.5990 119.3790 153.7450 204.9930 208.6110 206.8020 191.1260 154.9510 185.7000 203.1850 153.1420 133.2460 119.9820 116.3640 124.8050 128.4220 117.5700 105.5110 95.8646 85.6150 85.0121 92.8500 92.8500 94.6588 85.0121 97.6734 108.5260 133.2460 162.7890 216.4490 231.5220 204.3910 212.8310 219.4640 206.8020 233.3310 235.1400 165.2010 125.4080 129.6280 100.0850 91.0413 99.4822 101.2910 103.1000 90.4384 80.7916 87.4238 91.0413 93.4530 116.3640 139.8780 129.6280 123.5990 171.2300 201.9790 189.9200 150.1280 169.4210 219.4640 253.2270 302.6670 311.7110 274.3290 172.4360 140.4810 129.6280 126.0110 104.3060 116.9670 115.7610 116.3640 115.1580 113.3490 109.7320 98.8793 88.0267 83.2033 91.0413 129.6280 153.7450 151.9360 162.1860 186.9060 194.1410 230.9190 224.8900 187.5090 171.2300 162.1860 136.8630 142.2900 143.4950 128.4220 113.9520 112.1440 113.3490 94.6588 101.2910 102.4970 113.9520 113.9520 118.1730 101.2910 110.9380 153.7450 165.8040 156.7600 160.3770 276.1380 828.4140 2048.1300 2768.6200 1866.0400 580.6140 150.1280 156.1570 198.3610 178.4650 129.0250 126.0110 133.2460 118.1730 88.0268 72.3508 85.6151 108.5260 109.1290 80.7917 66.3216 107.9230 126.6140 146.5100 168.8180 182.6860 222.4780 344.8710 780.1810 1216.7000 961.6600 438.9270 182.0830 141.6870 176.0530 154.9510 103.7030 83.2035 95.2619 107.9230 103.1000 100.6880 91.6444 101.8940 112.1440 87.4239 87.4239 122.9960 121.7900 110.9380 92.8502 127.2170 174.8480 211.0230 281.5650 359.9450 319.5490 232.1250 207.4050 212.2290 197.1560 149.5250 120.5850 109.7320 81.3947 116.3640 103.7030 94.0561 117.5700 107.3200 68.1304 65.7188 114.5550 127.2170 113.3500 94.6590 113.3500 151.3340 166.4070 176.0530 192.3320 209.2140 189.9210 164.5980 178.4650 174.2450 160.3770 151.9370 143.4960 126.6140 115.1580 93.4532 104.9090 95.8648 78.9830 95.8648 95.8648 74.7626 68.1304 91.6444 129.6280 162.7890 178.4650 162.1860 142.2900 172.4360 195.9500 236.9490 297.8440 277.3440 198.9640 151.3340 118.7760 90.4386 102.4970 139.8780 153.1420 131.4370 139.8780 136.2610 103.7030 103.1000 88.0269 82.6006 85.0123 86.8211 93.4532 86.8211 88.6298 122.3930 164.5980 160.9800 228.5080 277.3440 232.7280 165.8040 163.3920 166.4070 156.7600 113.9530 95.2620 89.8357 113.3500 131.4370 133.8490 139.8780 133.2460 118.7760 102.4970 107.3200 115.7610 91.6444 80.1889 90.4386 108.5260 141.0840 179.6710 183.2890 175.4510 168.8180 176.6560 182.0830 197.1560 184.4940 136.2610 124.8050 116.3640 151.3340 146.5100 110.9380 133.8490 106.1150 107.3200 102.4970 105.5120 110.3350 109.7320 113.3500 121.1880 126.0110 118.1730 94.6590 113.9530 159.1720 187.5090 184.4940 176.0530 171.2300 170.0240 160.9800 150.7310 132.6430 122.3930 145.3040 99.4824 65.7188 79.5860 71.1451 54.2633 63.3071 66.9246 92.2473 104.9090 122.9960 121.1880 107.9230 121.1880 138.0690 159.7750 193.5380 190.5240 194.1410 179.6710 198.9640 243.5810 215.8460 138.6720 93.4532 85.6152 107.9230 118.7760 94.0561 87.4240 97.6736 103.7030 103.1000 103.1000 80.1889 63.9100 79.5860 101.8940 138.0690 186.9060 182.6860 144.7010 134.4520 156.1570 177.2590 168.8180 161.5830 151.9370 136.2610 124.8050 110.9380 92.8503 71.1451 86.2181 94.6590 88.6298 89.2327 94.0561 94.0561 98.2766 129.6280 129.6280 92.8503 87.4240 135.0550 178.4650 183.2890 174.2450 197.1560 212.2290 282.1680 326.7840 245.9920 197.1560 182.6860 134.4520 107.3200 100.0850 103.7030 97.0707 97.6736 143.4960 135.0550 88.6298 88.6298 98.8795 100.0850 126.0110 122.3930 115.7610 110.3350 132.6430 135.6580 183.8910 192.9350 165.2010 188.1120 241.7720 238.1540 197.1560 151.3340 110.3350 109.7320 97.6736 74.1597 81.9977 101.2910 91.0415 78.3801 93.4532 110.3350 113.9530 106.1150 83.2035 63.9100 44.0136 86.2181 149.5250 163.3920 197.1560 306.8870 629.4510 1024.3600 976.1300 520.9250 211.6260 110.9380 123.5990 150.7310 132.0400 129.0260 129.6280 132.6430 141.6870 133.2460 88.6298 89.8357 117.5700 116.9670 109.1290 79.5860 83.8064 109.1290 136.2610 167.0100 165.8040 194.7440 299.6520 496.2050 542.0270 362.9590 250.2130 192.9350 142.8930 106.1150 83.8064 98.2765 121.1880 165.2010 136.8640 95.8649 92.8502 106.7170 112.7470 131.4370 160.3770 116.9670 109.1290 137.4660 156.7600 182.6860 180.8770 191.7290 244.7860 268.3000 239.3600 198.3620 178.4650 162.7890 135.6580 97.0707 70.5421 68.7334 85.0123 104.3060 95.2619 108.5260 138.6720 140.4810 102.4970 74.7626 83.8064 111.5410 112.7470 113.9520 124.2020 132.0400 144.7010 179.6710 245.3890 294.2260 248.4040 179.6710 110.3350 88.0268 113.9520 103.1000 121.7900 117.5700 77.1742 64.5129 70.5421 103.1000 155.5540 137.4660 112.1440 106.7170 98.2765 87.4239 86.2181 103.7030 121.1880 136.8630 163.9950 216.4490 282.1680 291.2110 218.8610 164.5980 212.2290 232.1250 170.6270 134.4520 108.5260 98.8794 116.3640 118.1730 88.6298 73.5567 81.3947 95.2619 101.8940 107.3200 109.7320 110.3350 100.6880 110.9380 124.2020 167.6120 189.3180 182.6860 207.4050 222.4780 180.2740 182.6860 190.5240 162.7890 117.5700 101.8940 101.8940 127.2170 139.8780 119.9820 103.7030 77.7772 77.1742 94.0561 81.3947 102.4970 142.2900 104.9090 126.0110 152.5390 134.4520 153.7450 138.0690 133.8490 169.4210 171.2300 160.3770 201.9790 259.2570 227.9050 153.1420 110.9380 97.6736 85.6151 78.9830 82.6005 88.6297 110.9380 110.3350 87.4239 86.8210 94.6589 101.2910 88.0268 109.7320 165.8040 177.2590 159.1720 171.8330 170.0240 154.9510 195.3470 233.9340 203.1850 157.9660 136.2610 125.4080 97.0706 67.5275 53.6603 60.2924 76.5713 105.5120 123.5990 125.4080 92.2473 77.1742 100.0850 125.4080 126.6140 112.7470 106.1140 124.8050 136.8630 135.0550 167.6120 206.1990 219.4640 195.9500 173.0390 150.7310 126.6140 116.3640 131.4370 141.6870 124.8050 121.7900 122.9960 106.7170 101.2910 117.5700 104.3060 75.9684 59.0866 57.8807 83.2034 147.1130 148.9220 113.3500 104.9090 101.8940 112.7470 203.1850 260.4620 220.0670 185.0970 163.9950 125.4080 88.6297 71.1450 79.5859 94.6589 117.5700 99.4823 97.0706 110.9380 110.3350 89.2326 83.2034 97.6735 103.7030 87.4239 84.4092 107.3200 154.3480 173.6420 190.5230 179.0680 175.4500 228.5080 211.0230 140.4810 110.3350 133.2460 153.1420 130.8340 81.9975 83.8063 105.5110 95.8647 85.6151 105.5110 121.7900 115.7610 107.9230 100.6880 108.5260 141.6870 123.5990 85.0122 93.4531 113.9520 163.3920 201.3760 261.0650 327.9900 290.0060 218.2580 160.9800 124.8050 138.6720 99.4823 67.5275 72.3508 98.8794 95.2618 86.2180 72.9538 82.6005 121.7900 121.1870 96.4677 103.7030 96.4677 104.3060 149.5250 178.4650 195.9500 193.5380 227.9050 242.9780 206.8020 176.6560 158.5690 156.1570 138.0690 121.7900 124.2020 99.4823 74.1596 72.3508 85.0122 98.8794 102.4970 101.8940 104.3060 98.2765 88.6297 107.9230 129.0250 127.2170 136.2610 148.9220 177.2590 178.4650 220.6700 255.0360 241.7720 177.8620 132.0400 121.7900 116.9670 116.3640 113.9520 89.2326 91.0414 92.2472 80.7917 103.1000 139.2750 143.4960 119.9820 99.4823 112.7470 120.5850 113.9520 119.9820 161.5830 195.9500 209.2140 227.9050 240.5660 263.4770 270.7120 235.7430 167.0100 121.1870 107.9230 119.3790 107.3200 98.2765 113.9520 113.3500 105.5120 85.6151 89.2326 121.7900 113.3500 90.4385 86.8209 85.6151 103.7030 119.3790 162.1860 245.9920 668.6400 1751.4900 2703.5000 2365.2600 1176.3000 382.2530 196.5530 175.4500 175.4500 113.3490 104.3060 119.3790 141.0840 122.3930 111.5410 123.5990 97.6735 89.2326 92.2472 106.7170 156.1570 188.1120 142.8930 122.9960 144.0980 204.9940 429.2800 933.9260 1298.0900 963.4690 399.7370 159.7740 120.5840 186.9060 138.0690 93.4530 95.2618 94.6588 110.3350 106.1140 86.2179 101.2910 129.0250 166.4070 159.7740 133.8490 132.0400 125.4080 93.4530 112.7460 154.3480 159.7740 262.8740 466.0590 592.6720 487.7640 240.5660 106.7170 103.7030 107.9230 97.6735 93.4530 118.7760 114.5550 99.4822 74.7624 78.3800 98.8793 136.8630 121.7900 86.8209 101.2910 104.9090 78.3800 81.3946 97.6735 113.3490 173.0390 269.5060 318.9460 305.6810 230.3160 165.8040 157.3630 119.3790 94.6589 99.4822 121.7900 137.4660 138.0690 121.1870 148.3190 134.4520 77.1741 56.0718 86.8208 83.2033 79.5858 101.8940 133.2460 153.7450 156.1570 152.5390 142.8930 177.2590 203.1850 210.4200 183.8910 </int_list></spectrum></measured><measured><pepseq>VEHVTHPEQYIPGVLKR</pepseq><mzh>2002.0392</mzh><calc_mzh>2002.0875</calc_mzh><leucines>1</leucines><mono_iso_intensity>636</mono_iso_intensity><deuterated_intensity>201</deuterated_intensity><ratio>0.32</ratio><validated>YES</validated><local_bg>26</local_bg><corrected_ratio>0.29</corrected_ratio><spectrum><mz_list>1977.6266 1977.6875 1977.7484 1977.8093 1977.8702 1977.9311 1977.9920 1978.0529 1978.1138 1978.1747 1978.2356 1978.2965 1978.3574 1978.4183 1978.4792 1978.5402 1978.6011 1978.6620 1978.7229 1978.7838 1978.8447 1978.9056 1978.9665 1979.0275 1979.0884 1979.1493 1979.2102 1979.2711 1979.3320 1979.3930 1979.4539 1979.5148 1979.5757 1979.6367 1979.6976 1979.7585 1979.8194 1979.8804 1979.9413 1980.0022 1980.0632 1980.1241 1980.1850 1980.2460 1980.3069 1980.3678 1980.4288 1980.4897 1980.5507 1980.6116 1980.6725 1980.7335 1980.7944 1980.8554 1980.9163 1980.9773 1981.0382 1981.0992 1981.1601 1981.2211 1981.2820 1981.3430 1981.4039 1981.4649 1981.5258 1981.5868 1981.6477 1981.7087 1981.7696 1981.8306 1981.8916 1981.9525 1982.0135 1982.0744 1982.1354 1982.1964 1982.2573 1982.3183 1982.3793 1982.4402 1982.5012 1982.5622 1982.6232 1982.6841 1982.7451 1982.8061 1982.8670 1982.9280 1982.9890 1983.0500 1983.1110 1983.1719 1983.2329 1983.2939 1983.3549 1983.4159 1983.4769 1983.5378 1983.5988 1983.6598 1983.7208 1983.7818 1983.8428 1983.9038 1983.9648 1984.0258 1984.0867 1984.1477 1984.2087 1984.2697 1984.3307 1984.3917 1984.4527 1984.5137 1984.5747 1984.6357 1984.6967 1984.7577 1984.8187 1984.8798 1984.9408 1985.0018 1985.0628 1985.1238 1985.1848 1985.2458 1985.3068 1985.3678 1985.4288 1985.4899 1985.5509 1985.6119 1985.6729 1985.7339 1985.7950 1985.8560 1985.9170 1985.9780 1986.0390 1986.1001 1986.1611 1986.2221 1986.2831 1986.3442 1986.4052 1986.4662 1986.5273 1986.5883 1986.6493 1986.7104 1986.7714 1986.8324 1986.8935 1986.9545 1987.0156 1987.0766 1987.1376 1987.1987 1987.2597 1987.3208 1987.3818 1987.4428 1987.5039 1987.5649 1987.6260 1987.6870 1987.7481 1987.8091 1987.8702 1987.9312 1987.9923 1988.0534 1988.1144 1988.1755 1988.2365 1988.2976 1988.3586 1988.4197 1988.4808 1988.5418 1988.6029 1988.6640 1988.7250 1988.7861 1988.8472 1988.9082 1988.9693 1989.0304 1989.0914 1989.1525 1989.2136 1989.2746 1989.3357 1989.3968 1989.4579 1989.5189 1989.5800 1989.6411 1989.7022 1989.7633 1989.8243 1989.8854 1989.9465 1990.0076 1990.0687 1990.1298 1990.1909 1990.2519 1990.3130 1990.3741 1990.4352 1990.4963 1990.5574 1990.6185 1990.6796 1990.7407 1990.8018 1990.8629 1990.9240 1990.9851 1991.0462 1991.1073 1991.1684 1991.2295 1991.2906 1991.3517 1991.4128 1991.4739 1991.5350 1991.5961 1991.6572 1991.7184 1991.7795 1991.8406 1991.9017 1991.9628 1992.0239 1992.0850 1992.1462 1992.2073 1992.2684 1992.3295 1992.3906 1992.4518 1992.5129 1992.5740 1992.6351 1992.6963 1992.7574 1992.8185 1992.8796 1992.9408 1993.0019 1993.0630 1993.1242 1993.1853 1993.2464 1993.3076 1993.3687 1993.4298 1993.4910 1993.5521 1993.6133 1993.6744 1993.7355 1993.7967 1993.8578 1993.9190 1993.9801 1994.0413 1994.1024 1994.1636 1994.2247 1994.2859 1994.3470 1994.4082 1994.4693 1994.5305 1994.5916 1994.6528 1994.7139 1994.7751 1994.8363 1994.8974 1994.9586 1995.0197 1995.0809 1995.1421 1995.2032 1995.2644 1995.3256 1995.3867 1995.4479 1995.5091 1995.5702 1995.6314 1995.6926 1995.7538 1995.8149 1995.8761 1995.9373 1995.9985 1996.0596 1996.1208 1996.1820 1996.2432 1996.3043 1996.3655 1996.4267 1996.4879 1996.5491 1996.6103 1996.6715 1996.7326 1996.7938 1996.8550 1996.9162 1996.9774 1997.0386 1997.0998 1997.1610 1997.2222 1997.2834 1997.3446 1997.4058 1997.4670 1997.5282 1997.5894 1997.6506 1997.7118 1997.7730 1997.8342 1997.8954 1997.9566 1998.0178 1998.0790 1998.1402 1998.2014 1998.2626 1998.3239 1998.3851 1998.4463 1998.5075 1998.5687 1998.6299 1998.6912 1998.7524 1998.8136 1998.8748 1998.9360 1998.9973 1999.0585 1999.1197 1999.1809 1999.2422 1999.3034 1999.3646 1999.4258 1999.4871 1999.5483 1999.6095 1999.6708 1999.7320 1999.7932 1999.8545 1999.9157 1999.9769 2000.0382 2000.0994 2000.1607 2000.2219 2000.2831 2000.3444 2000.4056 2000.4669 2000.5281 2000.5894 2000.6506 2000.7119 2000.7731 2000.8344 2000.8956 2000.9569 2001.0181 2001.0794 2001.1406 2001.2019 2001.2631 2001.3244 2001.3857 2001.4469 2001.5082 2001.5694 2001.6307 2001.6920 2001.7532 2001.8145 2001.8758 2001.9370 2001.9983 2002.0596 2002.1208 2002.1821 2002.2434 2002.3047 2002.3659 2002.4272 2002.4885 2002.5498 2002.6110 2002.6723 2002.7336 2002.7949 2002.8562 2002.9174 2002.9787 2003.0400 2003.1013 2003.1626 2003.2239 2003.2852 2003.3465 2003.4077 2003.4690 2003.5303 2003.5916 2003.6529 2003.7142 2003.7755 2003.8368 2003.8981 2003.9594 2004.0207 2004.0820 2004.1433 2004.2046 2004.2659 2004.3272 2004.3885 2004.4498 2004.5111 2004.5724 2004.6337 2004.6951 2004.7564 2004.8177 2004.8790 2004.9403 2005.0016 2005.0629 2005.1242 2005.1856 2005.2469 2005.3082 2005.3695 2005.4308 2005.4922 2005.5535 2005.6148 2005.6761 2005.7375 2005.7988 2005.8601 2005.9214 2005.9828 2006.0441 2006.1054 2006.1668 2006.2281 2006.2894 2006.3508 2006.4121 2006.4734 2006.5348 2006.5961 2006.6575 2006.7188 2006.7801 2006.8415 2006.9028 2006.9642 2007.0255 2007.0869 2007.1482 2007.2096 2007.2709 2007.3323 2007.3936 2007.4550 2007.5163 2007.5777 2007.6390 2007.7004 2007.7617 2007.8231 2007.8845 2007.9458 2008.0072 2008.0685 2008.1299 2008.1913 2008.2526 2008.3140 2008.3754 2008.4367 2008.4981 2008.5595 2008.6208 2008.6822 2008.7436 2008.8049 2008.8663 2008.9277 2008.9891 2009.0504 2009.1118 2009.1732 2009.2346 2009.2960 2009.3573 2009.4187 2009.4801 2009.5415 2009.6029 2009.6643 2009.7256 2009.7870 2009.8484 2009.9098 2009.9712 2010.0326 2010.0940 2010.1554 2010.2168 2010.2782 2010.3396 2010.4010 2010.4624 2010.5238 2010.5852 2010.6466 2010.7080 2010.7694 2010.8308 2010.8922 2010.9536 2011.0150 2011.0764 2011.1378 2011.1992 2011.2606 2011.3220 2011.3834 2011.4448 2011.5063 2011.5677 2011.6291 2011.6905 2011.7519 2011.8133 2011.8748 2011.9362 2011.9976 2012.0590 2012.1205 2012.1819 2012.2433 2012.3047 2012.3662 2012.4276 2012.4890 2012.5504 2012.6119 2012.6733 2012.7347 2012.7962 2012.8576 2012.9190 2012.9805 2013.0419 2013.1034 2013.1648 2013.2262 2013.2877 2013.3491 2013.4106 2013.4720 2013.5334 2013.5949 2013.6563 2013.7178 2013.7792 2013.8407 2013.9021 2013.9636 2014.0250 2014.0865 2014.1479 2014.2094 2014.2709 2014.3323 2014.3938 2014.4552 2014.5167 2014.5782 2014.6396 2014.7011 2014.7625 2014.8240 2014.8855 2014.9469 2015.0084 2015.0699 2015.1313 2015.1928 2015.2543 2015.3158 2015.3772 2015.4387 2015.5002 2015.5616 2015.6231 2015.6846 2015.7461 2015.8076 2015.8690 2015.9305 2015.9920 2016.0535 2016.1150 2016.1765 2016.2379 2016.2994 2016.3609 2016.4224 2016.4839 2016.5454 2016.6069 2016.6684 2016.7299 2016.7914 2016.8529 2016.9144 2016.9758 2017.0373 2017.0988 2017.1603 2017.2218 2017.2833 2017.3449 2017.4064 2017.4679 2017.5294 2017.5909 2017.6524 2017.7139 2017.7754 2017.8369 2017.8984 2017.9599 2018.0214 2018.0830 2018.1445 2018.2060 2018.2675 2018.3290 2018.3905 2018.4521 2018.5136 2018.5751 2018.6366 2018.6982 2018.7597 2018.8212 2018.8827 2018.9443 2019.0058 2019.0673 2019.1288 2019.1904 2019.2519 2019.3134 2019.3750 2019.4365 2019.4980 2019.5596 2019.6211 2019.6827 2019.7442 2019.8057 2019.8673 2019.9288 2019.9904 2020.0519 2020.1135 2020.1750 2020.2365 2020.2981 2020.3596 2020.4212 2020.4827 2020.5443 2020.6058 2020.6674 2020.7290 2020.7905 2020.8521 2020.9136 2020.9752 2021.0367 2021.0983 2021.1599 2021.2214 2021.2830 2021.3446 2021.4061 2021.4677 2021.5293 2021.5908 2021.6524 2021.7140 2021.7755 2021.8371 2021.8987 2021.9602 2022.0218 2022.0834 2022.1450 2022.2065 2022.2681 2022.3297 2022.3913 2022.4529 2022.5144 2022.5760 2022.6376 2022.6992 2022.7608 2022.8224 2022.8840 2022.9455 2023.0071 2023.0687 2023.1303 2023.1919 2023.2535 2023.3151 2023.3767 2023.4383 2023.4999 2023.5615 2023.6231 2023.6847 2023.7463 2023.8079 2023.8695 2023.9311 2023.9927 2024.0543 2024.1159 2024.1775 2024.2391 2024.3007 2024.3623 2024.4239 2024.4856 2024.5472 2024.6088 2024.6704 2024.7320 2024.7936 2024.8552 2024.9169 2024.9785 2025.0401 2025.1017 2025.1633 2025.2250 2025.2866 2025.3482 2025.4098 2025.4715 2025.5331 2025.5947 2025.6564 2025.7180 2025.7796 2025.8412 2025.9029 2025.9645 2026.0261 2026.0878 2026.1494 2026.2111 2026.2727 2026.3343 2026.3960 2026.4576 2026.5193 2026.5809 2026.6426 2026.7042 2026.7658 2026.8275 2026.8891 2026.9508 2027.0124 2027.0741 2027.1357 2027.1974 2027.2590 2027.3207 2027.3824 2027.4440 2027.5057 2027.5673 2027.6290 2027.6907 2027.7523 2027.8140 2027.8756 2027.9373 2027.9990 2028.0606 2028.1223 2028.1840 2028.2456 2028.3073 2028.3690 2028.4307 2028.4923 2028.5540 2028.6157 2028.6773 2028.7390 2028.8007 2028.8624 2028.9241 2028.9857 2029.0474 2029.1091 2029.1708 2029.2325 2029.2942 2029.3558 2029.4175 2029.4792 2029.5409 2029.6026 2029.6643 2029.7260 2029.7877 2029.8494 2029.9111 2029.9727 2030.0344 2030.0961 2030.1578 2030.2195 2030.2812 2030.3429 2030.4046 2030.4663 2030.5280 2030.5898 2030.6515 2030.7132 2030.7749 2030.8366 2030.8983 2030.9600 2031.0217 2031.0834 2031.1451 2031.2068 2031.2686 2031.3303 2031.3920 2031.4537 2031.5154 2031.5772 2031.6389 2031.7006 2031.7623 2031.8240 2031.8858 2031.9475 2032.0092 2032.0709 2032.1327 2032.1944 2032.2561 2032.3179 2032.3796 2032.4413 2032.5031 </mz_list><int_list>87.4225 107.9220 113.3480 161.5820 175.4490 188.7130 192.3310 218.2560 206.1980 138.6710 106.7160 113.9510 122.9950 104.3040 132.0390 127.2150 101.2900 119.3770 139.2740 127.8180 161.5820 241.7700 271.3140 244.7850 218.2570 177.8610 119.3770 123.5980 162.1850 136.2590 91.0400 94.6576 116.9660 146.5090 136.2590 120.5830 171.2290 228.5060 261.6670 261.6670 217.6540 162.7880 135.0530 115.1570 117.5690 126.6120 116.9660 117.5690 128.4210 129.6270 141.0830 150.7290 163.9940 170.0230 157.9640 188.1100 218.8590 170.6260 141.6850 135.0530 141.6850 146.5090 134.4500 109.7310 88.6284 67.5261 86.2167 100.0840 110.9370 137.4650 159.1700 199.5660 215.8450 201.9780 171.8320 139.2740 136.2590 130.2300 122.9950 109.7310 92.2459 95.2605 115.1570 129.0240 141.0830 138.6710 135.6560 155.5530 165.8020 158.5670 133.2450 127.8180 124.8040 107.9220 90.4372 81.9963 68.7320 69.3349 82.5992 92.8488 122.9950 126.6120 133.8480 167.0080 170.0230 195.9480 206.8010 150.7290 95.8634 76.5699 108.5250 129.6270 100.0840 77.1729 86.2167 86.2167 99.4810 130.8330 141.6850 162.1850 171.8320 146.5090 134.4500 127.8180 116.9660 121.7890 107.3190 108.5250 126.6120 130.2300 97.0693 66.3203 88.0255 132.6420 167.6110 158.5670 178.4640 197.1540 191.7280 156.7580 112.1420 114.5540 122.9950 106.7160 106.7160 118.1720 93.4517 81.9962 90.4371 117.5690 149.5230 142.2880 139.8770 146.5090 173.0370 163.3910 148.3180 143.4940 114.5540 98.2751 110.3340 112.7450 110.9360 113.3480 109.7310 97.0693 120.5830 144.0970 154.3470 179.6700 179.0670 165.1990 143.4940 134.4500 145.3030 116.9660 85.6137 103.7010 132.0390 112.7450 78.3787 69.9378 103.0980 156.7580 182.6840 156.7580 168.8170 215.8450 204.9920 169.4200 141.0830 113.9510 113.3480 118.1720 127.2150 119.9800 108.5250 127.8180 144.7000 138.0680 108.5250 133.8470 155.5530 167.0080 173.0370 154.3470 111.5390 101.2900 103.0980 71.7466 78.3787 124.8040 121.7890 101.2900 69.3349 73.5553 103.0980 138.0680 181.4780 193.5370 153.7440 131.4360 97.6722 85.6137 83.2020 88.0254 98.2751 117.5690 112.1420 95.2605 92.2459 110.9360 100.0840 101.2900 169.4200 205.5950 211.0210 166.4050 136.2590 154.9500 136.2590 112.1420 110.3340 107.3190 116.9660 141.0830 139.2740 128.4210 146.5090 146.5090 151.9350 160.9790 163.3910 144.0970 140.4800 130.8330 156.1560 174.8460 119.9800 65.1144 72.3495 95.8634 104.9070 106.7160 146.5090 241.7700 422.0440 669.8450 757.8710 584.2300 373.2070 273.7250 245.3880 203.7860 144.7000 124.2010 136.2590 126.6120 108.5250 117.5690 146.5090 245.9910 416.6180 627.6400 786.2090 681.3000 436.5140 236.3440 142.2880 133.2450 121.1860 105.5100 87.4225 99.4809 95.8634 86.8196 104.9070 167.0080 253.8290 416.0150 526.3490 449.7780 320.7530 234.5350 151.9350 118.1710 116.3630 127.8180 156.1560 153.1410 127.2150 106.7160 127.8180 177.2580 276.1370 429.2790 557.0980 581.2150 485.3510 338.8410 224.8890 167.6110 140.4800 116.3630 94.6576 115.1570 172.4340 174.8460 156.1560 171.2290 247.8000 381.6480 496.8060 568.5540 541.4220 388.2800 247.8000 154.3470 150.1260 139.8770 135.0530 154.3470 127.8180 129.6270 151.3320 151.9350 179.6690 254.4320 321.3560 362.9580 364.7660 290.6070 224.2860 174.8460 130.8330 116.3630 98.2751 110.3340 130.8330 106.1130 94.6576 108.5250 138.6710 198.3600 247.1970 285.7840 316.5330 267.0930 245.3880 175.4490 109.7310 86.2166 106.1130 130.2300 126.6120 122.3920 95.8634 75.3641 88.6283 127.8180 214.6390 286.9900 289.4010 217.0510 143.4940 116.9660 104.9070 121.1860 163.3910 147.7150 141.6850 146.5090 157.9640 150.7290 153.1410 198.9630 230.9180 250.2110 382.2510 601.7150 729.5340 608.9500 374.4130 226.0940 197.1540 211.0210 181.4780 139.2740 137.4650 138.6710 131.4360 121.7890 148.9200 222.4770 347.2820 575.7890 790.4290 768.7240 513.6880 299.0480 180.8750 146.5090 154.9500 113.3480 98.2750 106.7160 94.0545 125.4060 171.8310 208.0070 281.5630 404.5590 512.4820 488.9680 403.9560 298.4450 203.1830 138.0680 116.3630 84.4077 107.9220 145.3030 157.9640 154.3470 163.3900 192.3310 215.2420 285.7840 403.3530 484.7480 436.5140 326.7820 201.3750 175.4490 164.5960 142.8910 103.7010 92.8486 115.7600 121.7890 105.5100 164.5960 212.2270 267.6960 371.3980 391.2950 343.6640 250.8140 174.8460 153.7440 121.7890 100.0840 117.5680 113.3480 103.0980 125.4060 142.2880 174.2430 215.8450 240.5640 246.5940 296.6360 340.6490 288.1950 177.8610 157.3610 142.8910 123.5980 113.9510 129.0240 129.0240 121.7890 118.1710 101.8920 111.5390 163.9930 206.1980 201.3750 182.0810 182.6840 177.8610 156.7580 121.1860 133.2440 126.6120 116.3630 156.7580 171.2280 121.7890 91.6428 127.8180 201.3750 218.8590 206.1980 217.0510 183.2870 139.8770 113.3480 101.8920 83.2019 83.8048 103.0980 86.8194 71.1435 89.8340 118.7740 138.6710 134.4500 159.7730 182.0810 182.6840 182.0810 136.2590 104.3040 89.8340 91.6428 92.8486 75.3639 78.3785 85.0107 99.4808 112.1420 107.9220 141.0820 157.3610 130.2300 113.9510 103.7010 94.6574 116.3630 136.2590 120.5830 88.6282 90.4370 87.4224 71.1435 99.4808 151.9350 156.1550 140.4790 124.8030 139.2740 139.8770 142.2880 143.4940 129.0240 112.7450 119.9800 128.4210 131.4360 124.8030 107.9220 81.9960 93.4516 118.7740 122.9950 138.0680 168.2140 154.9500 128.4210 124.8030 134.4500 122.9950 91.6428 119.9800 126.0090 98.2749 107.9220 110.3330 107.3190 118.7740 127.2150 186.3010 213.4330 192.9340 143.4940 124.2010 116.3630 125.4060 151.9350 148.9200 130.8330 115.1570 133.8470 150.1260 119.9800 91.0399 104.3040 124.8030 129.6270 174.8460 191.7280 151.9350 119.3770 112.1420 129.6270 112.1420 98.2749 101.2900 81.9961 90.4370 104.3040 96.4662 115.1570 135.6560 145.9060 160.9790 166.4050 159.1700 148.9200 147.1120 122.3920 110.3330 136.8620 133.2440 106.1130 107.9220 98.8779 86.2165 91.6428 80.7902 100.6870 106.7160 133.2440 145.9060 126.6120 126.6120 127.8180 130.2300 121.7890 91.0399 106.7160 100.0840 89.8341 101.8920 119.9800 150.1260 163.3910 192.9340 248.4020 256.8430 191.7280 141.0820 102.4950 100.0840 120.5830 118.7740 104.9070 85.6136 107.3190 114.5540 105.5100 146.5090 196.5510 241.1670 270.7110 206.8010 133.8470 122.3920 153.7440 136.2590 100.6870 95.8633 132.0390 138.6710 136.2590 113.9510 108.5250 146.5090 203.1830 195.3450 183.8900 230.3150 251.4170 226.6970 154.9500 104.9070 93.4516 136.2590 145.3030 107.9220 86.2166 101.2900 130.2300 129.6270 138.0680 179.0660 245.9910 216.4480 198.9630 192.3310 153.7440 123.5980 103.7010 92.2458 105.5100 112.7450 122.9950 133.2440 109.7300 89.2311 118.7740 179.0660 192.9340 187.5070 182.6840 143.4940 99.4808 111.5390 108.5250 127.8180 136.8620 156.7580 127.2150 100.6870 103.0980 100.0840 118.7740 148.9200 181.4780 212.8300 247.8000 259.2550 215.2420 192.3310 135.0530 79.5844 114.5540 133.8470 106.1130 83.2019 63.3055 71.7464 92.2457 139.8770 172.4340 203.1830 274.9310 319.5470 290.0040 221.2710 165.1990 150.1260 122.3920 122.9950 139.8770 129.0240 106.7160 86.2166 110.9360 153.1410 173.6400 167.6110 181.4780 197.7570 187.5070 159.1700 132.0390 111.5390 96.4662 83.8049 77.7757 92.8487 112.1420 107.3190 86.8195 85.0107 126.6120 169.4200 204.9920 223.0800 183.8900 157.3610 138.0680 116.9660 110.3330 92.2458 111.5390 112.7450 104.9070 127.8180 140.4800 123.5980 126.0090 124.2010 154.3470 187.5070 180.8750 165.8020 136.8620 110.3330 112.1420 118.7740 97.6721 109.1280 112.7450 124.8040 110.9360 94.0546 130.8330 165.1990 163.9930 191.7280 198.9630 176.6550 165.1990 148.3180 103.0980 94.0546 113.3480 132.6420 147.7150 135.6560 107.3190 90.4370 87.4224 103.7010 115.1570 147.1120 166.4050 162.1850 156.7580 138.6710 121.7890 124.8040 116.9660 115.7600 121.1860 118.7740 132.6420 153.1410 154.9500 140.4800 126.0090 143.4940 175.4490 173.6400 133.8470 122.3920 94.6575 109.7310 125.4060 130.8330 109.7310 106.1130 91.0399 80.7903 95.2604 118.7740 158.5670 173.0370 162.1850 173.0370 170.6260 136.2590 93.4516 110.3330 119.3770 123.5980 141.6850 135.6560 119.9800 116.3630 121.7890 102.4950 118.1710 148.3180 168.8170 183.8900 149.5230 101.2900 125.4060 135.0530 100.6870 80.7903 68.1289 </int_list></spectrum></measured></pepdata></protdata>
\ No newline at end of file
diff --git a/samples/aggregated_output.txt b/samples/aggregated_output.txt
new file mode 100644
index 0000000000000000000000000000000000000000..230ce02ee42802c00df5f9c612410c737e9f9ad2
--- /dev/null
+++ b/samples/aggregated_output.txt
@@ -0,0 +1,5 @@
+file_name Mowse_score Database ppm_tolerance Spot_identification Identified_protein Accesion_number Peptide_coverage %_matched_peptides Number_of_valid_peptides Median_ratio Mean_ratio Std_Dev
+C25plst02_A_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 5 3.23 3.33 0.6219
+C25plst02_B_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 5 0.05 0.08 0.1322
+C25plst02_C_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 5 1.39 1.40 0.2643
+C25plst02_D_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 5 0.24 0.26 0.1112
diff --git a/samples/detailed_output.txt b/samples/detailed_output.txt
new file mode 100644
index 0000000000000000000000000000000000000000..14a55900dd14ed811d846af30b17aed1f210b6f9
--- /dev/null
+++ b/samples/detailed_output.txt
@@ -0,0 +1,21 @@
+file_name Mowse_score Database ppm_tolerance Spot_identification Identified_protein Accesion_number Peptide_coverage %_matched_peptides pepseq leucines mzh calc_mzh mono_iso_int deuterated_intensity ratio corrected_ratio local_bg validated Number_of_valid_peptides Median_ratio Mean_ratio Std_Dev
+C25plst02_A_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VISQDALQHFR 1 1313.6723 1313.6967 1537 5018 3.26 4.18 443 YES 5 3.23 3.33 0.6219
+C25plst02_A_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 SALGETQKDTYQVLLR 3 1821.9176 1821.9711 405 1150 2.84 3.68 127 YES 5 3.23 3.33 0.6219
+C25plst02_A_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLK 1 1845.9513 1845.9864 360 1018 2.83 3.23 65 YES 5 3.23 3.33 0.6219
+C25plst02_A_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 DATEFIEILAR 1 1277.6464 1277.6742 1139 2443 2.14 2.59 320 YES 5 3.23 3.33 0.6219
+C25plst02_A_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLKR 1 2002.0392 2002.0875 331 792 2.39 2.95 95 YES 5 3.23 3.33 0.6219
+C25plst02_B_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VISQDALQHFR 1 1313.6723 1313.6967 5606 859 0.15 0.05 617 YES 5 0.05 0.08 0.1322
+C25plst02_B_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 SALGETQKDTYQVLLR 3 1821.9176 1821.9711 1208 547 0.45 0.29 273 YES 5 0.05 0.08 0.1322
+C25plst02_B_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLK 1 1845.9513 1845.9864 1099 276 0.25 0.13 150 YES 5 0.05 0.08 0.1322
+C25plst02_B_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 DATEFIEILAR 1 1277.6464 1277.6742 5284 198 0.04 -0.04 415 YES 5 0.05 0.08 0.1322
+C25plst02_B_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLKR 1 2002.0392 2002.0875 1134 111 0.10 -0.01 117 YES 5 0.05 0.08 0.1322
+C25plst02_C_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VISQDALQHFR 1 1313.6723 1313.6967 3271 4477 1.37 1.44 521 YES 5 1.39 1.40 0.2643
+C25plst02_C_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 SALGETQKDTYQVLLR 3 1821.9176 1821.9711 890 1395 1.57 1.79 247 YES 5 1.39 1.40 0.2643
+C25plst02_C_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLK 1 1845.9513 1845.9864 675 854 1.27 1.39 221 YES 5 1.39 1.40 0.2643
+C25plst02_C_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 DATEFIEILAR 1 1277.6464 1277.6742 2352 2468 1.05 1.06 248 YES 5 1.39 1.40 0.2643
+C25plst02_C_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLKR 1 2002.0392 2002.0875 847 1046 1.24 1.30 174 YES 5 1.39 1.40 0.2643
+C25plst02_D_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VISQDALQHFR 1 1313.6723 1313.6967 3526 1024 0.29 0.24 224 YES 5 0.24 0.26 0.1112
+C25plst02_D_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 SALGETQKDTYQVLLR 3 1821.9176 1821.9711 691 231 0.33 0.19 125 YES 5 0.24 0.26 0.1112
+C25plst02_D_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLK 1 1845.9513 1845.9864 613 279 0.45 0.43 24 YES 5 0.24 0.26 0.1112
+C25plst02_D_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 DATEFIEILAR 1 1277.6464 1277.6742 3265 658 0.20 0.14 247 YES 5 0.24 0.26 0.1112
+C25plst02_D_25.xml 1.0 PA.cosyeast200409 30.000 C25plst.txt NOG2 YNR053C 26 15 VEHVTHPEQYIPGVLKR 1 2002.0392 2002.0875 636 201 0.32 0.29 26 YES 5 0.24 0.26 0.1112
diff --git a/samples/orfnog2.txt b/samples/orfnog2.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f7394a4a155f1119641fc29f793a30d2b76ecf5a
--- /dev/null
+++ b/samples/orfnog2.txt
@@ -0,0 +1 @@
+YNR053C
\ No newline at end of file
diff --git a/samples/pairsnog2.txt b/samples/pairsnog2.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3d527d044080cd401f6ef8cfab83e6b4728f6dca
--- /dev/null
+++ b/samples/pairsnog2.txt
@@ -0,0 +1,4 @@
+Spectra/A_25.txt MS_Fit_files/C25plst02.html
+Spectra/B_25.txt MS_Fit_files/C25plst02.html
+Spectra/C_25.txt MS_Fit_files/C25plst02.html
+Spectra/D_25.txt MS_Fit_files/C25plst02.html
\ No newline at end of file
diff --git a/silactof.dtd b/silactof.dtd
new file mode 100644
index 0000000000000000000000000000000000000000..bd7393b51db63e130f0af27ec139282b4401f48b
--- /dev/null
+++ b/silactof.dtd
@@ -0,0 +1,113 @@
+<?xml encoding="UTF-8"?>
+
+<!ELEMENT protdata (id_parameters,accession_number,entry_name,prot_mw,
+ prot_pi,pepdata)>
+<!ATTLIST protdata
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT id_parameters (spot_id,database,ppm_tolerance,mowse_score,
+ pep_coverage,no_matched_pept)>
+<!ATTLIST id_parameters
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT accession_number (#PCDATA)>
+<!ATTLIST accession_number
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT entry_name (#PCDATA)>
+<!ATTLIST entry_name
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT prot_mw (#PCDATA)>
+<!ATTLIST prot_mw
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT prot_pi (#PCDATA)>
+<!ATTLIST prot_pi
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT pepdata (measured)+>
+<!ATTLIST pepdata
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT spot_id (#PCDATA)>
+<!ATTLIST spot_id
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT database (#PCDATA)>
+<!ATTLIST database
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT ppm_tolerance (#PCDATA)>
+<!ATTLIST ppm_tolerance
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT mowse_score (#PCDATA)>
+<!ATTLIST mowse_score
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT pep_coverage (#PCDATA)>
+<!ATTLIST pep_coverage
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT no_matched_pept (#PCDATA)>
+<!ATTLIST no_matched_pept
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT measured (pepseq,mzh,calc_mzh,leucines,mono_iso_intensity,
+ deuterated_intensity,ratio,validated,local_bg,
+ corrected_ratio,spectrum)>
+<!ATTLIST measured
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT pepseq (#PCDATA)>
+<!ATTLIST pepseq
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT mzh (#PCDATA)>
+<!ATTLIST mzh
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT calc_mzh (#PCDATA)>
+<!ATTLIST calc_mzh
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT leucines (#PCDATA)>
+<!ATTLIST leucines
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT mono_iso_intensity (#PCDATA)>
+<!ATTLIST mono_iso_intensity
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT deuterated_intensity (#PCDATA)>
+<!ATTLIST deuterated_intensity
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT ratio (#PCDATA)>
+<!ATTLIST ratio
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT validated (#PCDATA)>
+<!ATTLIST validated
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT local_bg (#PCDATA)>
+<!ATTLIST local_bg
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT corrected_ratio (#PCDATA)>
+<!ATTLIST corrected_ratio
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT spectrum (mz_list,int_list)>
+<!ATTLIST spectrum
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT mz_list (#PCDATA)>
+<!ATTLIST mz_list
+ xmlns CDATA #FIXED ''>
+
+<!ELEMENT int_list (#PCDATA)>
+<!ATTLIST int_list
+ xmlns CDATA #FIXED ''>
diff --git a/silactof.xsd b/silactof.xsd
new file mode 100644
index 0000000000000000000000000000000000000000..df64450492f6da7acd7703dc37d99441f180bd3a
--- /dev/null
+++ b/silactof.xsd
@@ -0,0 +1,81 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified">
+ <xs:element name="protdata">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="id_parameters"/>
+ <xs:element ref="accession_number"/>
+ <xs:element ref="entry_name"/>
+ <xs:element ref="prot_mw"/>
+ <xs:element ref="prot_pi"/>
+ <xs:element ref="pepdata"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="id_parameters">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="spot_id"/>
+ <xs:element ref="database"/>
+ <xs:element ref="ppm_tolerance"/>
+ <xs:element ref="mowse_score"/>
+ <xs:element ref="pep_coverage"/>
+ <xs:element ref="no_matched_pept"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="spot_id" type="xs:NMTOKEN"/>
+ <xs:element name="database" type="xs:NCName"/>
+ <xs:element name="ppm_tolerance" type="xs:decimal"/>
+ <xs:element name="mowse_score" type="xs:decimal"/>
+ <xs:element name="pep_coverage" type="xs:string"/>
+ <xs:element name="no_matched_pept" type="xs:integer"/>
+ <xs:element name="accession_number" type="xs:NCName"/>
+ <xs:element name="entry_name" type="xs:NCName"/>
+ <xs:element name="prot_mw" type="xs:decimal"/>
+ <xs:element name="prot_pi" type="xs:decimal"/>
+ <xs:element name="pepdata">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" ref="measured"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="measured">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="pepseq"/>
+ <xs:element ref="mzh"/>
+ <xs:element ref="calc_mzh"/>
+ <xs:element ref="leucines"/>
+ <xs:element ref="mono_iso_intensity"/>
+ <xs:element ref="deuterated_intensity"/>
+ <xs:element ref="ratio"/>
+ <xs:element ref="validated"/>
+ <xs:element ref="local_bg"/>
+ <xs:element ref="corrected_ratio"/>
+ <xs:element ref="spectrum"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="pepseq" type="xs:NCName"/>
+ <xs:element name="mzh" type="xs:decimal"/>
+ <xs:element name="calc_mzh" type="xs:decimal"/>
+ <xs:element name="leucines" type="xs:integer"/>
+ <xs:element name="mono_iso_intensity" type="xs:integer"/>
+ <xs:element name="deuterated_intensity" type="xs:integer"/>
+ <xs:element name="ratio" type="xs:decimal"/>
+ <xs:element name="validated" type="xs:NCName"/>
+ <xs:element name="local_bg" type="xs:decimal"/>
+ <xs:element name="corrected_ratio" type="xs:decimal"/>
+ <xs:element name="spectrum">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="mz_list"/>
+ <xs:element ref="int_list"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="mz_list" type="xs:string"/>
+ <xs:element name="int_list" type="xs:string"/>
+</xs:schema>
diff --git a/src/.DS_Store b/src/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/src/.DS_Store differ
diff --git a/src/Collect_SILAC_XML.py b/src/Collect_SILAC_XML.py
new file mode 100644
index 0000000000000000000000000000000000000000..81f1abb9685ca1614d2b100f1f3f965386a96708
--- /dev/null
+++ b/src/Collect_SILAC_XML.py
@@ -0,0 +1,303 @@
+"""
+Collect_SILAC_XML.py
+
+Allow collection of SILAC XML file results after
+validation, calculates statistics and generates
+a table with results, aggregating the results
+for each protein (as an option)
+
+Usage: python Collect_SILAC_XML.py -f <folder with XML SILAC files> -s
+(switch to obtain the output in aggregated or summary form)
+
+Output is to stdout
+
+First argument - folder with XML files
+Output - table in tab delimited format containing
+the statistics for each validated protein, printed to stdout
+
+This script is provided "as is" and works well with correctly
+formatted XML SILAC files. However, no exceptions have been
+implemented and the code will fail if not fed correct data
+
+Cosmin Saveanu, last modifications 2008-04-14
+Genetique des Interactions Macromoleculaires,
+Alain Jacquier's lab, Institut Pasteur,
+CNRS-URA 2171, France
+csaveanu@pasteur.fr for any questions
+"""
+
+#import cElementTree as ET (for versions of Python < 2.5)
+import xml.etree.cElementTree as ET #latest version integrated in Python 2.5
+import sys, os, math, getopt
+
+#a dictionary that holds the position of the different
+#informations available in the SILAC XML file
+#used by GetValXML
+XMLdict = {'pepseq': 0, 'mzh':1, 'calc_mzh':2, 'leucines':3,
+ 'mono_iso_int':4, 'deuterated_intensity':5,
+ 'ratio':6, 'validated':7,
+ 'local_bg':8, 'corrected_ratio':9}
+
+
+def Mean(inlist):
+ """
+ Obtain the mean of the values from a list
+ Returns 0 if the list is empty
+ """
+ sum = 0
+ for item in inlist:
+ sum = sum + item
+ if len(inlist)>0:
+ return sum/float(len(inlist))
+ else:
+ return 0
+
+def SumSquares(inlist):
+ """
+ Squares each value in the passed list, adds up these squares and
+ returns the result.
+ """
+ ss = 0
+ for item in inlist:
+ ss = ss + item*item
+ return ss
+
+
+def Variance(inlist):
+ """
+ Calculates the variance for a sample
+ Returns 100 if less than 2 values are provided
+ """
+ n = len(inlist)
+ mn = Mean(inlist)
+ ssq = SumSquares(inlist)
+ if n >1:
+ vari = (ssq - n*mn*mn)/(n-1)
+ else:
+ vari = 100
+ return vari
+
+def StdDev(inlist):
+ """
+ Returns the standard deviation of the values in the passed list
+ using N-1 in the denominator (i.e., to estimate population stdev).
+
+ """
+ return math.sqrt(Variance(inlist))
+
+
+def Median(inlist):
+ """
+ Returns the median of the passed list.
+ Returns 0 or the element if less than 2 elements
+ are passed to the function
+ """
+ newlist = inlist
+ newlist.sort()
+ if len(newlist) == 0:
+ median = 0
+ elif len(newlist) == 1:
+ median = newlist[0]
+ elif len(newlist) % 2 == 0: # if even number, simple mean of middles
+ index = len(newlist)/2
+ median = float(newlist[index] + newlist[index-1]) /2
+ else:
+ index = len(newlist)/2
+ median = newlist[index]
+ return median
+
+
+
+def get_flist(dirname, ext = ".xml"):
+ """
+ Get all .ext file names from dirname, not recursive
+ returns list of complete paths for files
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (ext,):
+ try:
+ outlist.append(file)
+ except:
+ pass
+ return outlist
+
+def GetValXML(data, index=0, what='pepseq'):
+ """
+ Returns the text attribute of an entry in an ElementTree
+ object based on the XMLdict dictionary that maps
+ numbers to tags - definition in the init of the main
+ frame. By default it returns the peptide sequence of
+ the first record.
+
+ pdatapos - indicates the position of the <pepdata> in
+ the root of the pepdata xml entry
+ """
+ pdatapos = 5
+ return data[pdatapos][index][XMLdict[what]].text
+
+def GenerateListDict(xmldata):
+ """
+ Recovers the data about a peptide in the XML SILAC file
+ Returns a dictionary, each peptide has an integer as key
+ """
+ entriesdict = {}
+ for i in range(len(xmldata[5])):
+ entriesdict[i] = (GetValXML(xmldata, i, 'pepseq'),
+ GetValXML(xmldata, i, 'leucines'),
+ GetValXML(xmldata, i, 'mzh'),
+ GetValXML(xmldata, i, 'calc_mzh'),
+ GetValXML(xmldata, i, 'mono_iso_int'),
+ GetValXML(xmldata, i, 'deuterated_intensity'),
+ GetValXML(xmldata, i, 'ratio'),
+ GetValXML(xmldata, i, 'corrected_ratio'),
+ GetValXML(xmldata, i, 'local_bg'),
+ GetValXML(xmldata, i, 'validated'))
+ return entriesdict
+
+def CalcStatistics(datadict):
+ """
+ Returns statistics on a single data dictionary (corresponding to one protein)
+ as a multiple of strings <nr of valid peptides>, <median>, <mean>, <SD>
+ """
+ yeslist = []
+ yeskeylist = []
+ for key in datadict.keys():
+ if datadict[key][9] == "YES":
+ yeskeylist.append(key)
+ yeslist.append(float(datadict[key][7]))
+ #7 is calculated corrected ratio index
+ median = Median(yeslist)
+ mean = Mean(yeslist)
+ stddev = StdDev(yeslist)
+ nopep = len(yeslist)
+
+ return("%d"%nopep, "%.2f"%median, "%.2f"%mean, "%.4f"%stddev)
+
+
+def ExtractSILACDataFromXML(fname, peptides_also=True):
+ """Parses an XML Silac file and returns information
+ on all the validated peptides in the entry if peptides_also
+ is True. The origin of the peptide (protein) is
+ also recovered and used in the output. Uses:
+ - GenerateListDict - to obtain the peptide data
+ - CalcStatistics - to calculate protein SILAC statistics.
+ Returns a string, formatted differently if peptides_also
+ is true or false
+ """
+ tree = ET.parse(fname)
+ data = tree.getroot()
+ fsplit = os.path.split(fname)
+ endofname = fsplit[1]
+ #the root is a <protdata> entry
+ prot_data = "\t".join([endofname,
+ data[0][3].text,
+ data[0][1].text,
+ data[0][2].text,
+ data[0][0].text,
+ data[2].text,
+ data[1].text,
+ data[0][4].text[:-1],
+ data[0][5].text])
+ #print "> Mowse score: %s, database: %s, ppm tolerance: %s"%(data[0][3].text,
+ # data[0][1].text, data[0][2].text)
+ #print "> Spot identification: %s.\n"%data[0][0].text
+ #print "> Identified protein: %s, accesion number: %s."%(data[2].text, data[1].text)
+ #print "> Peptide coverage: %s percent, matched peptides: %s."%(data[0][4].text[:-1], data[0][5].text)
+ datadict = GenerateListDict(data)
+ stats = CalcStatistics(datadict)
+ stats_string = "\t".join(stats)
+ if peptides_also:
+ peptide_info_list = []
+ for peptkey in datadict.keys():
+ if datadict[peptkey][9] == "YES":
+ peptide_info_list.append("\t".join([prot_data, "\t".join(datadict[peptkey]), stats_string]))
+ return "\n".join(peptide_info_list)
+ else:
+ return "\t".join([prot_data, stats_string])
+
+
+class Usage(Exception):
+ """
+ used for catching exceptions generated
+ during command line parameter parsing
+ """
+ def __init__(self, msg):
+ self.msg = msg
+
+def main(argv=None):
+ global foldername, aggregate
+
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "hsf:", ["help", "summary",
+ "XMLfolder="])
+ except getopt.error, msg:
+ raise Usage(msg)
+ # option processing
+
+ foldername = ""
+ aggregate = False
+ for option, value in opts:
+ if option in ("-h", "--help"):
+ raise Usage(__doc__)
+ if option in ("-s", "--summary"):
+ aggregate = True
+ if option in ("-f", "--XMLfolder"):
+ foldername = value
+
+ if "" in (foldername,):
+ raise Usage("no input folder!")
+ sys.exit(2)
+ else:
+ try:
+ flist = get_flist(foldername)
+
+ header_identif = "\t".join(["file_name",
+ "Mowse_score",
+ "Database",
+ "ppm_tolerance",
+ "Spot_identification",
+ "Identified_protein",
+ "Accesion_number",
+ "Peptide_coverage",
+ "%_matched_peptides"])
+ header_stats = "\t".join(["Number_of_valid_peptides",
+ "Median_ratio", "Mean_ratio",
+ "Std_Dev"])
+ if not aggregate:
+ header_pep = "\t".join(['pepseq',
+ 'leucines',
+ 'mzh',
+ 'calc_mzh',
+ 'mono_iso_int',
+ 'deuterated_intensity',
+ 'ratio',
+ 'corrected_ratio',
+ 'local_bg',
+ 'validated'])
+ header = "\t".join([header_identif, header_pep, header_stats])
+ else:
+ header = "\t".join([header_identif, header_stats])
+ print header
+ for fname in flist:
+ print ExtractSILACDataFromXML(fname, peptides_also= not aggregate)
+
+ finally:
+ pass
+
+ except Usage, err:
+ print >>sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+ print >>sys.stderr, "\t for help use --help or -h"
+ return 2
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/src/Create_matrix_from_csv.py b/src/Create_matrix_from_csv.py
new file mode 100644
index 0000000000000000000000000000000000000000..0bec0080b0d91b85abf374536fd5b8b9fc851bc7
--- /dev/null
+++ b/src/Create_matrix_from_csv.py
@@ -0,0 +1,80 @@
+"""
+Will take a list of files as input, read data, and output
+a matrix of values. Used to see the SILAC data.
+"""
+
+import sys, getopt, pdb, os
+
+def Read_csv_rem_header(infname, sep='\t'):
+ """Reading csv file, separator should be provided, default is tab
+ """
+ fin = open(infname, 'rU')
+ throw = fin.readline()
+ data = [line.strip().split(sep) for line in fin]
+ fin.close()
+ return data
+
+class Usage(Exception):
+ def __init__(self, msg):
+ self.msg = msg
+
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "hi:o:", ["help", "output=", "input"])
+ except getopt.error, msg:
+ raise Usage(msg)
+
+ # option processing
+ for option, value in opts:
+ if option in ("-i", "--input"):
+ inputlist = value
+ flist = open(inputlist, 'r')
+ fvalues = [f.strip() for f in flist]
+ flist.close()
+ if option in ("-h", "--help"):
+ raise Usage(__doc__)
+ if option in ("-o", "--output"):
+ output = value
+
+ datalist = {}
+ for filename in fvalues:
+ p = os.path.split(filename)
+ datalist[p[1]]=Read_csv_rem_header(filename, sep=',')
+
+ proteindict = {}
+
+ for f in datalist.keys():
+# pdb.set_trace()
+ for protline in datalist[f]:
+ if proteindict.has_key(protline[1]):
+ proteindict[protline[1]].append((f, protline[2]))
+ else:
+ proteindict[protline[1]] = [(f, protline[2])]
+# print proteindict
+ header = datalist.keys()
+ result = [header]
+ for protein in proteindict.keys():
+ resprot= [protein]
+ for file in header:
+ files_available = [f_v[0] for f_v in proteindict[protein]]
+ if file in files_available:
+ for file_val in proteindict[protein]:
+ if file == file_val[0]:
+ resprot.append(file_val[1])
+ else:
+ resprot.append("NA")
+ result.append(resprot)
+ for res in result:
+ print '\t'.join(res)
+
+
+ except Usage, err:
+ print >>sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+ print >>sys.stderr, "\t for help use --help"
+ return 2
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/src/Create_matrix_from_csv.py~ b/src/Create_matrix_from_csv.py~
new file mode 100644
index 0000000000000000000000000000000000000000..1932e6df6861d9d0637a24e6901fbc52455e27a8
--- /dev/null
+++ b/src/Create_matrix_from_csv.py~
@@ -0,0 +1,38 @@
+"""
+An example of Main function as devised by
+Guido van Rossum. This string is obtained
+by calling the script with the -h or --h
+option
+"""
+
+import sys, getopt
+
+class Usage(Exception):
+ def __init__(self, msg):
+ self.msg = msg
+
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "hov:", ["help", "output="])
+ except getopt.error, msg:
+ raise Usage(msg)
+
+ # option processing
+ for option, value in opts:
+ if option == "-v":
+ verbose = True
+ if option in ("-h", "--help"):
+ raise Usage(__doc__)
+ if option in ("-o", "--output"):
+ output = value
+
+ except Usage, err:
+ print >>sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+ print >>sys.stderr, "\t for help use --help"
+ return 2
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/src/MSFit_to_txt.py b/src/MSFit_to_txt.py
new file mode 100644
index 0000000000000000000000000000000000000000..3f290c49680681003b41ab40d7c9206790625de7
--- /dev/null
+++ b/src/MSFit_to_txt.py
@@ -0,0 +1,338 @@
+#!/usr/bin/env pythonw
+"""
+MSFit to Table v 0.2
+
+New version, based on HTMLparser
+
+A tool with GUI to collect data from
+a series of MSFit HTML identification files
+in a unique table
+
+Written using wxPython in Python, August 2004, Cosmin
+Modified to be more general and flexible, Sept 2004
+Included the HTML parser in the script, 2008-04-29
+
+Alain Jacquier's laboratory, Institut Pasteur, Paris, France
+
+INSTRUCTIONS:
+
+Place the files with .html or .htm extension in a folder
+From the File menu select Choose directory...
+You will be able to see a list of the html files in your directory
+
+From the File menu choose Collect to..., the global file will
+be saved under the name you specify.
+
+"""
+import os, string, sys, re, wx
+from string import lstrip, rstrip
+#from MsFitHTMLparse02 import MSFit32ParserProt #now included
+from HTMLParser import HTMLParser
+
+pepseqRE = r"sequence=([A-Z]+)\*?\\"
+peplinePATT = re.compile(pepseqRE)
+pepseqmodRE = r"\)([A-Z]+)\*?\("
+peplinePATTmod = re.compile(pepseqmodRE)
+
+class MSFit32ParserProt(HTMLParser):
+ """
+ A parser for MSFit HTML results to obtain a
+ dictionary of data corresponding to the page
+ Only protein information is retained
+ """
+ def reset(self):
+ HTMLParser.reset(self)
+ self.parsedlist =[]
+ #list of text contained between tags
+ self.comments = []
+ #list of comment texts
+ self.aftercomment = 0
+ #true if the text to be handled
+ #follows a comment
+ self.accesionRE = re.compile('> (.+)')
+ #allows extraction of ORF name from the first table
+
+ #two variables to allow start of scanning for peptide sequences in file
+ self.seeksequence = False
+ self.seeksequencemod = False
+
+ self.seqlist = []
+ #contains the list of sequences of all peptides
+
+ def handle_starttag(self, tag, attrs):
+ #print tag, attrs
+ pass
+
+ def handle_comment(self, tag):
+ """
+ Overrides the handle_comment method
+ Builds a list of all the found comments
+ If a comment is found, the aftercomment
+ variable is set to True
+ """
+ self.comments.append(tag)
+ self.aftercomment = 1
+ #if tag == 'delta_mass':
+ #self.seeksequence = True
+
+
+ def handle_data(self, text):
+ """
+ Overrides the handle_data method
+ writes to a list the text following
+ any comment - modifies self.parsedlist
+ """
+ #print "text", text
+ if self.aftercomment:
+ cleantext = text.strip('\n\r ./')
+ self.parsedlist.append([self.comments[-1], cleantext])
+ #append the last comment and the text that follows
+ self.aftercomment = 0
+ #don't get any other value until the next comment
+ #appears
+ #however obtain the sequence of a peptide if we are in an in_mass tags
+ return 1
+
+
+ def get_dictionary(self):
+ """
+ Reorganizes data and treats some special cases
+ of data found after comment tags
+ Should be called after closing the parser
+ """
+ reccounter = 0
+ secreccounter = 0
+ list_out = []
+ list = self.parsedlist
+ details = 0
+ passedrank1 = 0
+
+ for i in range(len(list)):
+ if list[i][0] == 'rank':
+ passedrank1 = 1
+ if list[i+1][0] <> 'fraction_matched':
+ #we are not at the beginning of the details
+ #sometimes proteins have equal ranks
+ #we build the data dictionary for the identified proteins
+ reccounter+=1
+ list_out.append({'protdata':{'rank':list[i][1]}})
+ details = 0
+ else:
+ #we are at the beginning of the details
+ details = 1
+ secreccounter+=1
+ else:
+ if details == 0 and passedrank1 == 1:
+ #not yet in details but passed the first rank tags
+ #take care first of the accesion numbers
+ if list[i][0] == 'accession_number':
+ matches = self.accesionRE.search(self.parsedlist[i][1])
+ if matches:
+ entries = matches.groups()
+ list[i][1]=entries[0]
+ list_out[reccounter-1]['protdata'][list[i][0]] = list[i][1]
+ elif details == 1:
+ #we are in the details, we may build the peptide masses lists
+ if list[i][0] == 'protein_coverage':
+ list_out[secreccounter-1]['protdata'][list[i][0]] = list[i][1]
+ return list_out
+
+###################################
+##### INTERFACE ###################
+###################################
+[ID_CHOOSEDIR,
+ID_COLLECTTO,
+ID_EXIT,
+ID_ABOUT,
+] = map(lambda init_ctrls: wx.NewId(), range(4))
+
+def Read_Dir(dirname):
+ """
+ Recover information for all the files in a folder, recursively
+ Collect data in a list of complete path names, returned
+
+ """
+ filelist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ Read_Dir(file)
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".html", ".htm"):
+ filelist.append(file)
+ return filelist
+
+def WriteListToFile(filename, outlist):
+ """
+ Writes a list of lists to a tab delimited text file
+ """
+ fout = open(filename, "w")
+ for entry in outlist:
+ for element in entry:
+ fout.write(element+'\t')
+ fout.write('\n')
+ fout.close()
+ return 1
+
+class MainFrame(wx.Frame):
+ def __init__(self, parent, id, title):
+ wx.Frame.__init__(self, parent, id, title,
+ wx.DefaultPosition, (600, 600))
+
+ self.temp_outfile = "temp_data"
+ self.defaultdirname = "."
+ self.filelist = []
+
+ #default directory for saving, will be modified after first save
+ #self.maxy = 0
+
+ # Create the menu bar and items
+ self.menubar = wx.MenuBar()
+
+ filemenu = wx.Menu()
+ filemenu.Append(ID_CHOOSEDIR, 'Ch&oose folder...\tCtrl+O', 'Choose folder with html MSFit files')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_COLLECTTO, 'Collec&t data to...\tCtrl+S', 'Parse files and save data to the specified file')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_EXIT, '&Quit\tCtrl+Q', 'Exit program')
+
+ helpmenu = wx.Menu()
+ helpmenu.Append(ID_ABOUT, 'About...\tCtrl+H', 'About this program')
+
+ # Bind the events to methods
+ wx.EVT_MENU(self, ID_CHOOSEDIR, self.OnChooseFolder)
+ wx.EVT_MENU(self, ID_EXIT, self.OnFileExit)
+ wx.EVT_MENU(self, ID_COLLECTTO, self.OnCollectData)
+ wx.EVT_MENU(self, ID_ABOUT, self.OnHelpAbout)
+
+ # Attach menus to the menubar
+ self.menubar.Append(filemenu, '&File')
+ self.menubar.Append(helpmenu, '&Help')
+
+ self.SetMenuBar(self.menubar)
+
+ #Disable by default the Save data as menu
+ self.menubar.Enable(ID_COLLECTTO, 0)
+
+ self.autoscale = 1
+
+ # A status bar to tell people what's happening
+ self.CreateStatusBar(1)
+
+ lc = wx.ListCtrl(self, -1, style=wx.LC_REPORT|wx.SUNKEN_BORDER)
+ self.lc = lc
+ self.lc.InsertColumn(0, "Number")
+ self.lc.InsertColumn(1, "File name")
+ self.lc.SetColumnWidth(0, 100)
+ self.lc.SetColumnWidth(1, 400)
+ self.Show(True)
+
+ def OnChooseFolder(self, event):
+ """
+ Shows a directory select dialog, allows to set the self.defaultdirname
+ to a value where data collection will occur, also enables the menu item
+ corresponding to data collection.
+ """
+ dlg = wx.DirDialog(frame, "Choose a folder with MSFit files:",
+ style=wx.DD_DEFAULT_STYLE)
+ # If the user selects OK, then we process the dialog's data.
+ # This is done by getting the path data from the dialog - BEFORE
+ # we destroy it.
+ if dlg.ShowModal() == wx.ID_OK:
+ #log.WriteText('You selected: %s\n' % dlg.GetPath())
+ self.defaultdirname = dlg.GetPath()
+ # Only destroy a dialog after you're done with it.
+ dlg.Destroy()
+ self.menubar.Enable(ID_COLLECTTO, 1)
+ self.filelist = Read_Dir(self.defaultdirname)
+ self.lc.DeleteAllItems()
+ #self.txtout.WriteText("You chose "+self.defaultdirname+" that contains the following html files:\n\n")
+ counter = 0
+ for filename in self.filelist:
+ filepath = os.path.split(filename)
+ self.lc.InsertStringItem(counter, str(counter+1))
+ self.lc.SetStringItem(counter, 1, filepath[1])
+ counter+=1
+ self.SetStatusText("Now choose where to save the output file (File>Collect data to...)")
+
+ def ProcessFiles(self, filelist):
+ biglist = []
+ outlist = []
+ progcounter = 0
+ self.progbar = wx.ProgressDialog("Quantitating peptides...", "Working...",
+ maximum = len(self.filelist), parent = self,
+ style = wx.PD_CAN_ABORT| wx.PD_APP_MODAL)
+ for file in filelist:
+ shortname = os.path.split(file)[1]
+ try:
+ f = open(file, "r")
+ htmlpage = f.read()
+ f.close
+
+ parser = MSFit32ParserProt()
+ parser.feed(htmlpage)
+ parser.close()
+
+ biglist.append([file, parser.get_dictionary()])
+
+ self.progbar.Update(progcounter, str(progcounter)+" "+shortname+".")
+ progcounter+=1
+
+ except:
+ pass
+
+ #print len(biglist)
+ self.progbar.Destroy()
+
+ for entrieslist in biglist:
+ #print entrieslist
+ for dict in entrieslist[1]:
+ #print dict
+ outlist.append([entrieslist[0], dict['protdata']['rank'],
+ dict['protdata']['protein_coverage'], dict['protdata']['protein_mw'],
+ dict['protdata']['protein_pI'], dict['protdata']['accession_number'],
+ dict['protdata']['entry_name']])
+ return outlist
+
+ def OnCollectData(self, event):
+ """
+ Save data to a specified text file (new)
+ """
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ #might be os.getcwd()
+ dlg = wx.FileDialog(
+ self, message="Save collected data as ...", defaultDir = self.defaultdirname,
+ defaultFile="", wildcard=wildcard, style=wx.SAVE
+ )
+ dlg.SetFilterIndex(0)
+ if dlg.ShowModal() == wx.ID_OK:
+ #self.dirname=dlg.GetDirectory()
+ #self.defaultdirname = self.dirname
+ path = dlg.GetPath()
+ #print "You selected", path
+ try:
+ #filelist = Read_Dir(self.defaultdirname)
+ outlist = self.ProcessFiles(self.filelist)
+ WriteListToFile(path, outlist)
+ except IOError:
+ dlg = wx.MessageDialog(self, "Error. Maybe the output file is in use...", 'Problem saving data',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ dlg.Destroy()
+
+ def OnHelpAbout(self, event):
+ from wx.lib.dialogs import ScrolledMessageDialog
+ about = ScrolledMessageDialog(self, __doc__, "About...")
+ about.ShowModal()
+
+ def OnFileExit(self, event):
+ self.Close()
+
+
+app = wx.PySimpleApp()
+frame = MainFrame(None, -1, "MSFit to txt v. 0.2")
+app.SetTopWindow(frame)
+app.MainLoop()
diff --git a/src/MsFitHTMLparse02.py b/src/MsFitHTMLparse02.py
new file mode 100644
index 0000000000000000000000000000000000000000..2b4898c26953f668eca371ea245c1d96cf92f46f
--- /dev/null
+++ b/src/MsFitHTMLparse02.py
@@ -0,0 +1,271 @@
+from HTMLParser import HTMLParser
+import re
+
+"""
+A module providing the necessary tools to parse
+and transform to a data dictionary the first
+entry from an MSFit version 3.2 identification file
+
+Compared to the previous regular expression based parsing
+this version is more flexible
+
+Regular expression needed to extract sequences
+of peptides from MSFit lines are compiled outside
+functions to avoid repetition of re compilations
+"""
+pepseqRE = r"sequence=([A-Z]+)\*?\\"
+peplinePATT = re.compile(pepseqRE)
+pepseqmodRE = r"\)([A-Z]+)\*?\("
+peplinePATTmod = re.compile(pepseqmodRE)
+
+class MSFit32Parser(HTMLParser):
+ """
+ A parser for MSFit HTML results to obtain a
+ dictionary of data corresponding to the page
+ """
+ def reset(self):
+ HTMLParser.reset(self)
+ self.parsedlist =[]
+ #list of text contained between tags
+ self.comments = []
+ #list of comment texts
+ self.aftercomment = 0
+ #true if the text to be handled
+ #follows a comment
+ self.accesionRE = re.compile('> (.+)')
+ #allows extraction of ORF name from the first table
+
+ #two variables to allow start of scanning for peptide sequences in file
+ self.seeksequence = False
+ self.seeksequencemod = False
+
+ self.seqlist = []
+ #contains the list of sequences of all peptides
+
+ def handle_starttag(self, tag, attrs):
+ #print tag, attrs
+ if tag.lower() == "nobr":
+ self.seeksequencemod = True
+ elif tag.lower() == "script":
+ self.seeksequence = True
+ else:
+ self.seeksequencemod, self.seeksequence = False, False
+
+ def handle_comment(self, tag):
+ """
+ Overrides the handle_comment method
+ Builds a list of all the found comments
+ If a comment is found, the aftercomment
+ variable is set to True
+ """
+ self.comments.append(tag)
+ self.aftercomment = 1
+ #if tag == 'delta_mass':
+ #self.seeksequence = True
+
+
+ def handle_data(self, text):
+ """
+ Overrides the handle_data method
+ writes to a list the text following
+ any comment - modifies self.parsedlist
+ """
+ #print "text", text
+ if self.aftercomment:
+ cleantext = text.strip('\n\r ./')
+ self.parsedlist.append([self.comments[-1],cleantext])
+ #print cleantext, self.comments[-1]
+ #append the last comment and the text that follows
+ self.aftercomment = 0
+ #don't get any other value until the next comment
+ #appears
+ #however obtain the sequence of a peptide if we are in an in_mass tags
+ elif self.seeksequence:
+ #print text, "under seek sequence"
+ pepmatch = peplinePATT.search(text)
+ if pepmatch:
+ self.seqlist.append(pepmatch.groups()[0])
+ elif self.seeksequencemod:
+ pepmatch = peplinePATTmod.search(text)
+ if pepmatch:
+ self.seqlist.append(pepmatch.groups()[0])
+ return 1
+
+
+ def get_dictionary(self):
+ """
+ Reorganizes data and treats some special cases
+ of data found after comment tags
+ Should be called after closing the parser
+ """
+ reccounter = 0
+ secreccounter = 0
+ list_out = []
+ list = self.parsedlist
+ details = 0
+ passedrank1 = 0
+ seq_counter = 0 #a counter for the list of sequences, append to matched masses
+
+ for i in range(len(list)):
+ if list[i][0] == 'rank':
+ passedrank1 = 1
+ if list[i+1][0] <> 'fraction_matched':
+ #we are not at the beginning of the details
+ #sometimes proteins have equal ranks
+ #we build the data dictionary for the identified proteins
+ reccounter+=1
+ list_out.append({'protdata':{'rank':list[i][1]}, \
+ 'pepdata':{'matched':[], 'unmatched':[]}})
+ details = 0
+ list_out[reccounter-1]['protdata']['comment'] = list[0][1]
+ list_out[reccounter-1]['protdata']['database'] = list[1][1]
+ list_out[reccounter-1]['protdata']['parent_mass_tolerance'] = list[3][1]
+
+ else:
+ #we are at the beginning of the details
+ details = 1
+ secreccounter+=1
+ else:
+ if details == 0 and passedrank1 == 1:
+ #not yet in details but passed the first rank tags
+ #take care first of the accesion numbers
+ if list[i][0] == 'accession_number':
+ matches = self.accesionRE.search(self.parsedlist[i][1])
+ if matches:
+ entries = matches.groups()
+ list[i][1]=entries[0]
+ list_out[reccounter-1]['protdata'][list[i][0]] = list[i][1]
+ elif details == 1:
+ #we are in the details, we may build the peptide masses lists
+ if list[i][0] == 'protein_coverage':
+ list_out[secreccounter-1]['protdata'][list[i][0]] = list[i][1]
+ elif list[i][0] == 'in_mass':
+ if list[i+1][0] == 'matched_mass':
+ #we are in the matched masses
+ list_out[secreccounter-1]['pepdata']['matched'].append([list[i][1], self.seqlist[seq_counter]])
+
+ seq_counter+=1
+ #print seq_counter
+ else:
+ list_out[secreccounter-1]['pepdata']['unmatched'].append(list[i][1])
+
+
+ return list_out
+
+class MSFit32ParserProt(HTMLParser):
+ """
+ A parser for MSFit HTML results to obtain a
+ dictionary of data corresponding to the page
+ Only protein information is retained
+ """
+ def reset(self):
+ HTMLParser.reset(self)
+ self.parsedlist =[]
+ #list of text contained between tags
+ self.comments = []
+ #list of comment texts
+ self.aftercomment = 0
+ #true if the text to be handled
+ #follows a comment
+ self.accesionRE = re.compile('> (.+)')
+ #allows extraction of ORF name from the first table
+
+ #two variables to allow start of scanning for peptide sequences in file
+ self.seeksequence = False
+ self.seeksequencemod = False
+
+ self.seqlist = []
+ #contains the list of sequences of all peptides
+
+ def handle_starttag(self, tag, attrs):
+ #print tag, attrs
+ pass
+
+ def handle_comment(self, tag):
+ """
+ Overrides the handle_comment method
+ Builds a list of all the found comments
+ If a comment is found, the aftercomment
+ variable is set to True
+ """
+ self.comments.append(tag)
+ self.aftercomment = 1
+ #if tag == 'delta_mass':
+ #self.seeksequence = True
+
+
+ def handle_data(self, text):
+ """
+ Overrides the handle_data method
+ writes to a list the text following
+ any comment - modifies self.parsedlist
+ """
+ #print "text", text
+ if self.aftercomment:
+ cleantext = text.strip('\n\r ./')
+ self.parsedlist.append([self.comments[-1],cleantext])
+ #append the last comment and the text that follows
+ self.aftercomment = 0
+ #don't get any other value until the next comment
+ #appears
+ #however obtain the sequence of a peptide if we are in an in_mass tags
+ return 1
+
+
+ def get_dictionary(self):
+ """
+ Reorganizes data and treats some special cases
+ of data found after comment tags
+ Should be called after closing the parser
+ """
+ reccounter = 0
+ secreccounter = 0
+ list_out = []
+ list = self.parsedlist
+ details = 0
+ passedrank1 = 0
+
+ for i in range(len(list)):
+ if list[i][0] == 'rank':
+ passedrank1 = 1
+ if list[i+1][0] <> 'fraction_matched':
+ #we are not at the beginning of the details
+ #sometimes proteins have equal ranks
+ #we build the data dictionary for the identified proteins
+ reccounter+=1
+ list_out.append({'protdata':{'rank':list[i][1]}})
+ details = 0
+ else:
+ #we are at the beginning of the details
+ details = 1
+ secreccounter+=1
+ else:
+ if details == 0 and passedrank1 == 1:
+ #not yet in details but passed the first rank tags
+ #take care first of the accesion numbers
+ if list[i][0] == 'accession_number':
+ matches = self.accesionRE.search(self.parsedlist[i][1])
+ if matches:
+ entries = matches.groups()
+ list[i][1]=entries[0]
+ list_out[reccounter-1]['protdata'][list[i][0]] = list[i][1]
+ elif details == 1:
+ #we are in the details, we may build the peptide masses lists
+ if list[i][0] == 'protein_coverage':
+ list_out[secreccounter-1]['protdata'][list[i][0]] = list[i][1]
+ return list_out
+
+#an entry in the list_out looks like this:
+#{'comment': '120804 CS X07', 'protein_mw': '115945.3', 'protein_coverage': '26%', 'mowse_score': '1.64e+007', 'database': 'PA.yeastorf', 'accession_number': 'ORFP:YLR249W', 'rank': '1', 'entry_name': '>ORFP:YLR249W YEF3, Chr XII from 636780-639914', 'parent_mass_tolerance': '50.000', 'protein_pI': '5.73', 'species': 'UNREADABLE'}
+
+
+#~ f = open('/Volumes/Fire/CosminF/200409September/SILAC_Rlp24/Msfit/cs_x07b.htm', 'r')
+#~ htmlpage = f.read()
+#~ f.close()
+#~ parser = MSFit32Parser()
+#~ parser.feed(htmlpage)
+#~ parser.close()
+
+#~ result = parser.get_dictionary()
+#~ for record in result:
+ #~ print record['protdata']
diff --git a/src/Silacvalidator_20080123.py~ b/src/Silacvalidator_20080123.py~
new file mode 100644
index 0000000000000000000000000000000000000000..13efe03388befee888ec36c69a87be1feefedfd0
--- /dev/null
+++ b/src/Silacvalidator_20080123.py~
@@ -0,0 +1,1072 @@
+"""
+SILAC validator v. 0.2
+
+INSTRUCTIONS:
+
+This application recognizes XML files, as generated by lilamsXML. These files are
+obtained from a spectrum (in text format) and a MsFit3.2 results file (in html for-
+mat). Only the first entry in the file is quantified and generates an xml file.
+After opening an XML file, the first peptide-associated spectrum is displayed in
+the interactive plot window. You can zoom by drawing a rectangle with the left
+mouse click and unzoom with the menu >Plot>Full Unzoom. When clicking anywhere
+on the plot, the m/z value and intensity are shown in the status bar.
+To associate a local background to a spectrum double-click on the maximum and
+minimum of the peak considered as background. The difference of the two values
+is shown in the status bar. By clicking on the <Set Bgrnd.> button the last va-
+lue of the local background is inserted in the peptide table and the corrected
+ratio is automatically calculated. To validate the peptide quantification click
+on the <Validate> button.
+
+Clicking on the column titles allows sorting of the peptide list by any criteria.
+A visualisation program for XML files generated by lilamsxml. Allows validation
+of SILAC experiments, peptide by peptide.
+
+Written using wxPython, numarray, ElementTree et al., in Python, September 2004.
+Modified in January 2008, to be able to save in text format individual spectra
+regions.
+
+Cosmin Saveanu in Alain Jacquier's laboratory, Institut Pasteur, CNRS-URA2171.
+
+Many thanks to all the people contributing to the development of tools like wxPython,
+Python itself, ElementTree, and wx.lib.plot and the wonderful examples to get
+inspiration (and sometimes copy/paste) from.
+
+This program may be freely distributed as long as correct references to it are
+provided, with this included note.
+"""
+import wx
+import os, string
+from wx.lib.plot import *
+#the required plot module to draw spectra
+from elementtree import ElementTree as ET
+#elementtree is an excellent package written by Fredrik Lundh (effbot.org)
+#to deal with simple XML structures.
+
+#Imports for the ListCtrl class, copied from the wxPython documentation
+import wx.lib.mixins.listctrl as listmix
+from wx import ImageFromStream, BitmapFromImage
+
+import cStringIO
+
+try:
+ import Numeric
+except:
+ try:
+ import numarray as Numeric
+ except:
+ msg = """This program requires the Numeric or numarray
+ module to function - in fact is a requirement for the
+ wx.lib.plot module. Please install either Numeric or
+ numarray.
+ """
+ raise ImportError, "Numeric or numarray not found.\n"+msg
+
+#first - define unique identifiers for the different graphical elements
+[ID_OPEN,
+ID_OPENX,
+ID_CLOSE,
+ID_SAVEP,
+ID_SAVESP,
+ID_SAVEDATA,
+ID_EXIT,
+ID_ABOUT,
+ID_ENGRID,
+ID_UNZOOM,
+ID_NEXTF,
+ID_PREVF,
+ID_BTN1,
+ID_BTN2,
+ID_BTN3
+] = map(lambda init_ctrls: wx.NewId(), range(15))
+
+def get_flist_xml(dirname):
+ """get all .xml file names from dirname, not recursive
+ return only the file name, not the path
+
+ Needed by the OnPrevFile and OnNextFile functions
+ but called by <XMLOpen> to set the self.filelist list
+ of xml files from the current folder.
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".xml",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def get_flist_txt(dirname):
+ """get all .txt file names from dirname, not recursive
+ return only the file name, not the path
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".txt",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def map_pos_inlist(flist, fname):
+ """
+ Obtain the index of a file name in a file list
+ If file name not found return 0 as the position
+ Used in XMLOpen, generated a value for <self.where>
+ about the current position of a file in the file
+ list obtained with <get_flist_xml>.
+ """
+ for i in range(len(flist)):
+ if flist[i] == fname:
+ res = i
+ break
+ else:
+ res = 0
+ return res
+
+def ReadFromFileArray(file, skip=0):
+ """
+ Obtain floats from a tab delimited file into a numarray array
+ The <skip> parameter indicate the number of lines not
+ read.
+
+ This function is only used to directly open a complete spectrum
+ or a text delimited file with two columns - mz and intensity
+ """
+ data = []
+ err = 0
+ errmsg = ""
+ f=file
+ for i in range(skip):
+ f.readline()
+ #simple test to see if the file look like a float coercible text file
+ try:
+ for line in f:
+ data.append(map(float, line.strip().split("\t")))
+ data_array = Numeric.array(data)
+ except ValueError:
+ data = [[1, 1]]
+ data_array = Numeric.array(data)
+ err = 1
+ errmsg = "The file you are trying to open does not look like a tab delimited one"
+ return (data_array, err, errmsg)
+ #the returned data is a tuple with an array of floats, error and errmsg
+
+
+############################################
+# INTERFACE ############################
+############################################
+class MainFrame(wx.Frame):
+ """
+ The application main frame. Contains the following
+ graphic elements:
+ self.panel |---- self.lb - the text list control
+ |---- self.btnpanel1 - the panel containing
+ three buttons (Validate, Invalidate
+ and LocalBackground
+
+ self.panelplot - containing self.plotcanvas
+ to allow drawing of spectra files
+
+ self.log - a TextCtrl panel with information
+ on the analysed xml file
+ ______________________
+ --------------- ------
+ | || | self.lb and self.btnpanel1
+ -----------------------
+ | |
+ | | self.panelplot with self.plotcanvas
+ | |
+ -----------------------
+ | | self.log
+ -----------------------
+ """
+ def __init__(self, parent, id, title):
+ wx.Frame.__init__(self, parent, id, title,
+ wx.DefaultPosition, (800, 700))
+ self.defaultdirname = "."
+ #default directory for opening files, will be modified after first open
+ self.filelist = []
+ #list with all the xml files in a folder
+ self.where = 0
+ #position in the list of files
+ self.previousclick_y = 0.0
+ self.actualclick_y = 0.0
+ #local background is calculated by substracting
+ #self.previousclick_y from self.actualclick_y
+ #absolute value is returned anyway
+ self.localbg = 0.0
+
+ self.XMLdict = {'pepseq': 0, 'mzh':1, 'calc_mzh':2, 'leucines':3,
+ 'mono_iso_int':4, 'deuterated_intensity':5,
+ 'ratio':6, 'validated':7,
+ 'local_bg':8, 'corrected_ratio':9}
+ #the mapping of tags to numbers to allow easy orientation in the ElementTree
+ #Element object obtained by parsing a SILAC XML file. If the lilams XML format
+ #changes you should change accordingly these numbers
+ self.pdatapos = 5
+ #in the XML tree the pepdata values are in this position
+
+ ###################################################################
+ # Create the menu bar and items
+ self.menubar = wx.MenuBar()
+
+ filemenu = wx.Menu()
+ filemenu.Append(ID_OPENX, '&Open XML SILAC file...\tCtrl+O', 'Open XML file with SILAC data')
+ filemenu.Append(ID_SAVEDATA, 'Save XML &modifications\tCtrl+S', 'Save modifications with (validation/local background)')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_OPEN, 'O&pen text file...\tCtrl+T', 'Open tab delimited file for plotting')
+ filemenu.Append(ID_CLOSE, '&Close text file\tCtrl+W', 'Close text file')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVEP, '&Save plot image\tCtrl+I', 'Save plot image in a bmp, png or jpg format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVESP, 'Sa&ve plot data\tCtrl+D', 'Save the data corresponding to the plotted spectrum in text format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_EXIT, '&Quit\tCtrl+Q', 'Exit program')
+
+ navmenu = wx.Menu()
+ navmenu.Append(ID_NEXTF, '&Next XML file\tCtrl+N', 'Open next xml file in the current folder')
+ navmenu.Append(ID_PREVF, '&Previous XML file\tCtrl+P', 'Open previous xml file in the current folder')
+
+ plotmenu = wx.Menu()
+ plotmenu.Append(ID_UNZOOM, 'Full &Unzoom\tCtrl+U', 'Full unzoom for the current plot')
+ plotmenu.AppendSeparator()
+ plotmenu.Append(ID_ENGRID, 'Grid &enabled', 'Enable or disable grid when drawing', wx.ITEM_CHECK)
+
+ helpmenu = wx.Menu()
+ helpmenu.Append(ID_ABOUT, '&About...\tCtrl+E', 'About this program')
+
+ ###################################################################
+ # Bind the events to methods
+ wx.EVT_MENU(self, ID_OPENX, self.OnXMLOpen)
+ wx.EVT_MENU(self, ID_SAVEDATA, self.OnXMLSave)
+ wx.EVT_MENU(self, ID_OPEN, self.OnFileOpen)
+ wx.EVT_MENU(self, ID_CLOSE, self.OnFileClose)
+ wx.EVT_MENU(self, ID_SAVEP, self.OnSaveImage)
+ wx.EVT_MENU(self, ID_SAVESP, self.OnSpectrumSave)
+ wx.EVT_MENU(self, ID_EXIT, self.OnFileExit)
+ wx.EVT_MENU(self, ID_NEXTF, self.OnNextFile)
+ wx.EVT_MENU(self, ID_PREVF, self.OnPrevFile)
+ wx.EVT_MENU(self, ID_ENGRID, self.OnEnableGrid)
+ wx.EVT_MENU(self, ID_UNZOOM, self.OnFullUnzoom)
+ wx.EVT_MENU(self, ID_ABOUT, self.OnHelpAbout)
+
+ ###################################################################
+ # Attach menus to the menubar
+ self.menubar.Append(filemenu, '&File')
+ self.menubar.Append(navmenu, '&Next/Previous')
+ self.menubar.Append(plotmenu, '&Plot')
+ self.menubar.Append(helpmenu, '&Help')
+
+ self.SetMenuBar(self.menubar)
+
+ ###################################################################
+ #Disable by default some menus and buttons
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 0)
+ self.menubar.Enable(ID_SAVEP, 0)
+ self.menubar.Enable(ID_SAVESP, 0)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ # A status bar to tell people what's happening
+ self.CreateStatusBar(1)
+
+ self.SetAutoLayout(True)
+
+ ###################################################################
+ self.panel = wx.Panel(self, -1, style=wx.SIMPLE_BORDER)
+ #in this case and all the others we use layout constraints
+ #I couldn't understand easily the sizers, while layout constraints seem
+ #quite easy to set up and they work very well.
+ #self.panel will contain the listctrl and button panel
+
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self, wx.Top, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 30)
+ self.panel.SetConstraints(lc)
+
+ ###################################################################
+ #the peplistctrlpanel - with the list of peptides and interesting data
+ self.smalldict = {1:("pepseq", "0", "mzh", "mzhcalc", "mono", "deuter", "ratio", "corr",
+ "localbg", "valid")}
+ #we need this to fill up the listctrl at program initialization
+ self.lb = PepListCtrlPanel(self.panel, dictwithdata=self.smalldict)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.PercentOf(self.panel, wx.Right, 80) #it will take up 80% of the panel
+ lc.left.SameAs(self.panel, wx.Left, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.lb.SetConstraints(lc)
+ ###################################################################
+ self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.lb.list)
+ ###################################################################
+ #the panel to hold the three buttons
+ self.btnpanel1 = wx.Panel(self.panel, -1, style=wx.SIMPLE_BORDER)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.SameAs(self.panel, wx.Right, 10)
+ lc.left.SameAs(self.lb, wx.Right, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.btnpanel1.SetConstraints(lc)
+ ###################################################################
+ #set up the buttons and bind to the corresponding functions
+ self.btn1 = wx.Button(self.btnpanel1, ID_BTN1, " Validate ", wx.DefaultPosition)
+ self.btn2 = wx.Button(self.btnpanel1, ID_BTN2, "INvalidate", wx.DefaultPosition)
+ self.btn3 = wx.Button(self.btnpanel1, ID_BTN3, "Set Bgrnd.", wx.DefaultPosition)
+ wx.EVT_BUTTON(self, ID_BTN1, self.OnValidate)
+ wx.EVT_BUTTON(self, ID_BTN2, self.OnInvalidate)
+ wx.EVT_BUTTON(self, ID_BTN3, self.OnSetLocalBg)
+
+ #Disable by default the three buttons
+ self.btn1.Enable(False)
+ self.btn2.Enable(False)
+ self.btn3.Enable(False)
+ ###################################################################
+ #layout the buttons on the btnpanel1
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btnpanel1, wx.CentreX)
+ lc.top.SameAs(self.btnpanel1, wx.Top, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn1.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.centreY.SameAs(self.btnpanel1, wx.CentreY)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn2.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.bottom.SameAs(self.btnpanel1, wx.Bottom, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn3.SetConstraints(lc)
+
+ ###################################################################
+ #A black panel to give contrast to the plot
+ self.panelplot = wx.Window(self, -1)
+ self.panelplot.SetBackgroundColour(wx.BLACK)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panel, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 85)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.panelplot.SetConstraints(lc)
+ ###################################################################
+ #The plot itself in self.panelplot
+ self.plotcanvas = PlotCanvas(self.panelplot, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panelplot, wx.Top, 2)
+ lc.left.SameAs(self.panelplot, wx.Left, 2)
+ lc.bottom.SameAs(self.panelplot, wx.Bottom, 2)
+ lc.right.SameAs(self.panelplot, wx.Right, 2)
+ self.plotcanvas.SetConstraints(lc)
+ ###################################################################
+ #A panel to hold the TextCtrl called self.log
+ self.logpanel = wx.Window(self, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panelplot, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.SameAs(self, wx.Bottom, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.logpanel.SetConstraints(lc)
+ ###################################################################
+ #The text control that will hold informations on the protein and file used
+ self.log = wx.TextCtrl(self.logpanel, -1,
+ style = wx.TE_MULTILINE|wx.TE_READONLY|wx.HSCROLL)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.logpanel, wx.Top, 2)
+ lc.left.SameAs(self.logpanel, wx.Left, 0)
+ lc.bottom.SameAs(self.logpanel, wx.Bottom, 2)
+ lc.right.SameAs(self.logpanel, wx.Right, 0)
+ self.log.SetConstraints(lc)
+ self.log.AppendText("> Hello. Load a LILAMS XML file from the File> menu (or Cmd+O).")
+ ###################################################################
+ # Create mouse event for showing cursor coords in status bar
+ self.plotcanvas.Bind(wx.EVT_LEFT_DOWN, self.OnMouseLeftDown)
+ self.plotcanvas.Bind(wx.EVT_LEFT_DCLICK, self.OnMouseDClick)
+ self.plotcanvas.SetEnableZoom(1) #to ensure zoom by default
+
+ self.Show(True)
+
+ ###################################################################
+ ## Main Frame function definitions ################################
+ ###################################################################
+
+ def OnXMLOpen(self, event):
+ """
+ Opens a XML file with SILAC data and generates
+ an ElementTree instance containing the data
+ in the variable self.data
+ """
+ self.resetDefaults()
+ wildcard = "XML file (*.xml)|*.xml|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a SILAC XML file:",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ try:
+ if not self.XMLOpen(dirname, filename):
+ msg = """
+ The file you wanted to open does not
+ contain valid SILAC XML data. Try opening it with
+ a text editor to see what is the problem."""
+ dlg = wx.MessageDialog(self, msg, 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ finally:
+ dlg.Destroy()
+
+ def XMLOpen(self, dirname, filename):
+ """
+ Will allow calls for XMLOpen from Previous
+ and Next calls. Returns True if everything OK.
+
+ -uses get_flist_xml to set up the file list
+ -uses map_pos_inlist to set up self.where
+ -uses self.PlotSpectrumXML to plot the first peptide
+ in file
+ -uses self.PopulateList to populate the self.lb list
+ control with data
+ -uses self.GenerateListDict to generate the dictionary
+ used to describe the data in the self.lb control
+ """
+ filename=filename
+ dirname=dirname
+ self.defaultdirname = dirname
+ fname = os.path.join(dirname, filename)
+ #self.fnameout = fname+"x"
+ #we write in the same xml file, overwriting previous file
+ self.fnameout = fname
+ self.filelist = get_flist_xml(dirname)
+ self.where = map_pos_inlist(self.filelist, filename)
+ try:
+ tree = ET.parse(fname)
+ self.data = tree.getroot()
+ #the root is a <protdata> entry
+ self.PlotSpectrumXML(0, title="peptide 1")
+ self.PopulateList(self.GenerateListDict(self.data))
+ #Clear the log, write text to it about the opened file
+ self.log.Remove(0, self.log.GetLastPosition())
+ self.log.AppendText("\n> Opened %s xml file.\n"%filename)
+ self.log.AppendText("> Mowse score: %s, database: %s, ppm tolerance: %s.\n"%(self.data[0][3].text,
+ self.data[0][1].text, self.data[0][2].text))
+ self.log.AppendText("> Spot identification: %s.\n"%self.data[0][0].text)
+ self.log.AppendText("> Identified protein: %s, accesion number: %s.\n"%(self.data[2].text, self.data[1].text))
+ self.log.AppendText("> Peptide coverage: %s percent, matched peptides: %s.\n"%(self.data[0][4].text[:-1], self.data[0][5].text))
+ self.menubar.Enable(ID_NEXTF, 1)
+ self.menubar.Enable(ID_PREVF, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.btn1.Enable(True)
+ self.btn2.Enable(True)
+ self.btn3.Enable(True)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVESP, 0)
+ return True
+ except:
+ return False
+
+ def PlotSpectrumXML(self, index=0, title=""):
+ """
+ Recover and plot data for the record that has <index>
+ It is found in self.data[5] - that is pepdata,
+ the subnode is 10 for <spectrum> and 0, 1 for
+ the two lists mz and int. "5 "is contained in self.pdatapos
+
+ -uses self.PlotArray - a function to do the plotting
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+ self.PlotArray(dataforarray, "blue", title)
+
+ def PlotArray(self, data_array, color, title):
+ """
+ Used to plot on the plotcanvas the points of a data_array
+ Default is autoscale, used by PlotSpectrumXML
+ """
+ self.line = PolyLine(data_array, colour = color)
+ self.plotcanvas.Draw(PlotGraphics([self.line, ], title, "m/z", ""))
+ #self.plotcanvas.Redraw()
+
+ def GenerateListDict(self, xmldata):
+ """
+ forms a dictionary {1:["a", "b", "c"], 2:...}
+ for the PepListCtrlPanel widget - to populate
+ with XML data
+ """
+ self.entriesdict = {}
+ for i in range(len(xmldata[self.pdatapos])):
+ self.entriesdict[i] = (self.GetValXML(i, 'pepseq'),
+ self.GetValXML(i, 'leucines'),
+ self.GetValXML(i, 'mzh'),
+ self.GetValXML(i, 'calc_mzh'),
+ self.GetValXML(i, 'mono_iso_int'),
+ self.GetValXML(i, 'deuterated_intensity'),
+ self.GetValXML(i, 'ratio'),
+ self.GetValXML(i, 'corrected_ratio'),
+ self.GetValXML(i, 'local_bg'),
+ self.GetValXML(i, 'validated'))
+ return self.entriesdict
+
+ def PopulateList(self, externaldict):
+ """
+ a wrapper to the function with the same name in self.lb
+ """
+ self.lb.PopulateList(externaldict)
+
+ def OnItemSelected(self, event):
+ """
+ Activated when one item in the self.lb list control
+ is selected. Determines the generation of a unique key
+ that will allow a correspondence between the list
+ elements and the underlying ElementTree Element
+ - uses MapUniqueKey function
+ """
+ #print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.lb.list.GetItemText(self.currentItem)+self.lb.getColumnText(self.currentItem, 2)
+ self.index = self.MapUniqueKey(self.uniquekey)
+ #print self.index, "self.index"
+ self.PlotSpectrumXML(self.index, title = self.GetValXML(self.index, 'pepseq')+\
+ " / "+self.GetValXML(self.index, 'mzh'))
+ self.menubar.Enable(ID_SAVEDATA, 1)
+ self.menubar.Enable(ID_SAVESP, 1)
+ event.Skip()
+ #the self.index variable allows us to recover and change the data if validation occurs
+
+ def MapUniqueKey(self, uniquekey):
+ """
+ Used by <OnItemSelected> to allow a correspondence between
+ self.currentItem - in the list and self.index in the ElementTree
+ Element representing data read from the XML SILAC file
+ """
+ result = 0
+ for i in range(len(self.data[self.pdatapos])):
+ #testing [0] is peptide sequence [1] is submitted m/z+h mass
+ if uniquekey == self.data[self.pdatapos][i][0].text+\
+ self.data[self.pdatapos][i][1].text:
+ #the index of the correspoinding key was found
+ result = i
+ break
+ return result
+
+ def OnValidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "YES")
+ self.SetXMLValidated(self.index, "YES")
+ def OnInvalidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "NO")
+ self.SetXMLValidated(self.index, "NO")
+
+ def SetXMLValidated(self, index, what):
+ """
+ 7 is the actual position of the <validated> field
+ in the self.data - coming from the SILAC XML tree
+ """
+ self.data[self.pdatapos][index][7].text = what
+
+ def GetValXML(self, index=0, what='pepseq'):
+ """
+ Returns the text attribute of an entry in an Element
+ object based on the self.XMLdict dictionary that maps
+ numbers to tags - definition in the init of the main
+ frame. By default it returns the peptide sequence of
+ the first record.
+
+ self.pdatapos - indicates the position of the <pepdata> in
+ the root of the pepdata xml entry
+ """
+ return self.data[self.pdatapos][index][self.XMLdict[what]].text
+
+ def OnXMLSave(self, event):
+ """
+ Writes the contents of self.data to the self.fnameout
+ (established when the actual file was opened)
+ """
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ def OnSpectrumSave(self, event):
+ self.SpectrumSave(self.index)
+
+ def SpectrumSave(self, index=0):
+ """
+ Writes the contents of the actual selected spectrum
+ to a given file name, in tab delimited format
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(
+ self, message="Save plot data to ...", defaultDir = self.defaultdirname,
+ defaultFile="pepspecdata.txt", wildcard=wildcard, style=wx.SAVE
+ )
+ dlg.SetFilterIndex(0)
+ if dlg.ShowModal() == wx.ID_OK:
+ path = dlg.GetPath()
+ try:
+ fout = open(path, "w")
+ for line in dataforarray:
+ fout.write('%.3f\t%d\n'%(line[0], line[1]))
+ fout.close()
+
+ self.SetStatusText("Data saved to file %s"%path)
+ except IOError:
+ dlg = wx.MessageDialog(self, "Error. Maybe the output file is in use...", 'Problem saving data',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ dlg.Destroy()
+
+ def OnNextFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO| wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+ if len(self.filelist) > 0:
+ if self.where < len(self.filelist)-1:
+ #fname = os.path.split(self.filelist[self.where+1]
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where+1])
+ self.where += 1
+ else:
+ #we are at the end of the list
+ self.where = 0
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+ self.where += 1
+
+ def OnPrevFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO | wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ if len(self.filelist) > 0:
+ if self.where > 0:
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where-1])
+ self.where -= 1
+ else:
+ #we are at the beginning of the list
+ self.where = len(self.filelist)-1
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+ self.where -= 1
+
+ def OnFullUnzoom(self, event):
+ self.plotcanvas.Reset()
+
+ def OnFileOpen(self, event):
+ """
+ Opens and plots a tab delimited text file
+ If not a recognized file, a message is displayed
+ Sets also the actual directory name: self.defaultdirname
+ """
+ self.resetDefaults()
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a tab delimited text file",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ self.filename=dlg.GetFilename()
+ self.dirname=dlg.GetDirectory()
+ self.defaultdirname = self.dirname
+ self.filelist = get_flist_txt(self.dirname)
+ fname = os.path.join(self.dirname, self.filename)
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ dlg.Destroy()
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", self.filename)
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ def PlotFile(self, fname):
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", os.path.split(fname)[1])
+
+ def OnFileClose(self, event):
+ self.plotcanvas.Clear()
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+
+ def OnMouseLeftDown(self,event):
+ self.localbg = abs(self.actualclick_y - self.previousclick_y)
+ s= "(m/z : %.2f, Intensity : %.2f)"%self.plotcanvas.GetXY(event)+\
+ " Local background : %.0f"%self.localbg
+ self.SetStatusText(s)
+ event.Skip()
+
+ def OnMouseDClick(self, event):
+ self.previousclick_y = self.actualclick_y
+ self.actualclick_y = self.plotcanvas.GetXY(event)[1]
+
+ def OnSetLocalBg(self, event):
+ """
+ Updates the local background data both in the shown list
+ and in self.data. Recalculated the corrected ratio
+ """
+ self.data[self.pdatapos][self.index][8].text = "%0.f"%self.localbg
+ deut = float(self.GetValXML(self.index, 'deuterated_intensity'))-self.localbg
+ monoiso = float(self.GetValXML(self.index, 'mono_iso_int'))-self.localbg
+ self.data[self.pdatapos][self.index][9].text = "%.2f"%(deut/monoiso)
+ self.lb.SetBg(self.currentItem, self.localbg, (deut/monoiso))
+
+ def OnSaveImage(self, event):
+ self.plotcanvas.SaveFile()
+
+ def OnFileExit(self, event):
+ self.Close()
+
+ def OnPlotRedraw(self,event):
+ self.plotcanvas.Redraw()
+
+ def OnPlotClear(self,event):
+ self.plotcanvas.Clear()
+
+ def OnPlotScale(self, event):
+ if self.plotcanvas.last_draw != None:
+ graphics, xAxis, yAxis= self.plotcanvas.last_draw
+ self.plotcanvas.Draw(graphics,(1,3.05),(0,1))
+
+ def OnEnableZoom(self, event):
+ self.plotcanvas.SetEnableZoom(event.IsChecked())
+
+ def OnEnableGrid(self, event):
+ self.plotcanvas.SetEnableGrid(event.IsChecked())
+
+ def OnEnableLegend(self, event):
+ self.plotcanvas.SetEnableLegend(event.IsChecked())
+ def OnReset(self,event):
+ self.plotcanvas.Reset()
+
+ def OnHelpAbout(self, event):
+ from wx.lib.dialogs import ScrolledMessageDialog
+ about = ScrolledMessageDialog(self, __doc__, "About...")
+ about.ShowModal()
+
+ def resetDefaults(self):
+ """Just to reset the fonts back to the PlotCanvas defaults"""
+ self.plotcanvas.SetFont(wx.Font(10,wx.SWISS,wx.NORMAL,wx.NORMAL))
+ self.plotcanvas.SetFontSizeAxis(10)
+ self.plotcanvas.SetFontSizeLegend(7)
+ self.plotcanvas.SetXSpec('auto')
+ self.plotcanvas.SetYSpec('auto')
+ self.plotcanvas.SetEnableZoom(1)
+
+#######################################################
+#######################################################
+################ PepListCtrlPanel ###############
+################ and PepListCtrl classes###############
+#######################################################
+#######################################################
+#######################################################
+#----------------------------------------------------------------------------
+# Name: ListCtrl.py
+# Purpose: Testing lots of stuff, controls, window types, etc.
+#
+# Author: Robin Dunn & Gary Dumer
+#
+# Created:
+# RCS-ID: $Id: ListCtrl.py,v 1.3 2004/03/05 00:06:32 RD Exp $
+# Copyright: (c) 1998 by Total Control Software
+# Licence: wxWindows license
+#
+# Modified by Cosmin Saveanu, IP, September 2004
+# to be able to deal with peptide entries for SILAC
+#----------------------------------------------------------------------------
+def getSmallUpArrowData():
+ return \
+'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00<IDATx\x9ccddbf\xa0\x040Q\xa4{h\x18\xf0\xff\xdf\xdf\xffd\x1b\x00\xd3\
+\x8c\xcf\x10\x9c\x06\xa0k\xc2e\x08m\xc2\x00\x97m\xd8\xc41\x0c \x14h\xe8\xf2\
+\x8c\xa3)q\x10\x18\x00\x00R\xd8#\xec\x95{\xc4\x11\x00\x00\x00\x00IEND\xaeB`\
+\x82'
+
+def getSmallUpArrowBitmap():
+ return BitmapFromImage(getSmallUpArrowImage())
+def getSmallUpArrowImage():
+ stream = cStringIO.StringIO(getSmallUpArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+
+def getSmallDnArrowData():
+ return \
+"\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00HIDATx\x9ccddbf\xa0\x040Q\xa4{\xd4\x00\x06\x06\x06\x06\x06\x16t\x81\
+\xff\xff\xfe\xfe'\xa4\x89\x91\x89\x99\x11\xa7\x0b\x90%\ti\xc6j\x00>C\xb0\x89\
+\xd3.\x10\xd1m\xc3\xe5*\xbc.\x80i\xc2\x17.\x8c\xa3y\x81\x01\x00\xa1\x0e\x04e\
+\x1d\xc4;\xb7\x00\x00\x00\x00IEND\xaeB`\x82"
+def getSmallDnArrowBitmap():
+ return BitmapFromImage(getSmallDnArrowImage())
+
+def getSmallDnArrowImage():
+ stream = cStringIO.StringIO(getSmallDnArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+class PepListCtrl(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin):
+
+ def __init__(self, parent, ID, pos=wx.DefaultPosition,
+ size=wx.DefaultSize, style=0):
+ wx.ListCtrl.__init__(self, parent, ID, pos, size, style)
+ listmix.ListCtrlAutoWidthMixin.__init__(self)
+
+class PepListCtrlPanel(wx.Panel, listmix.ColumnSorterMixin):
+
+ def __init__(self, parent, dictwithdata={}):
+ wx.Panel.__init__(self, parent, -1, style=wx.WANTS_CHARS)
+ tID = wx.NewId()
+ self.il = wx.ImageList(16, 16)
+ self.sm_up = self.il.Add(getSmallUpArrowBitmap())
+ self.sm_dn = self.il.Add(getSmallDnArrowBitmap())
+ self.list = PepListCtrl(self, tID,
+ style=wx.LC_REPORT
+ | wx.SUNKEN_BORDER
+ | wx.LC_SINGLE_SEL
+ #| wx.LC_HRULES
+ #| wx.LC_EDIT_LABELS
+ #| wxLC_NO_HEADER
+ #| wxLC_VRULES
+ )
+ self.list.SetImageList(self.il, wx.IMAGE_LIST_SMALL)
+ self.PopulateList(dictwithdata)
+ # Now that the list exists we can init the other base class,
+ # see wxPython/lib/mixins/listctrl.py
+
+ listmix.ColumnSorterMixin.__init__(self, 10)
+ #self.SortListItems(0, True)
+ self.Bind(wx.EVT_SIZE, self.OnSize)
+ #self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.list)
+ self.Bind(wx.EVT_LIST_COL_CLICK, self.OnColClick, self.list)
+
+ def PopulateList(self, externaldict):
+ """
+ Constructs the headings of the list control
+ and populates it with data
+ """
+
+ self.itemDataMap = externaldict
+ self.list.ClearAll()
+ if 0:
+ # for normal, simple columns, you can add them like this:
+ self.list.InsertColumn(0, "Peptide")
+ self.list.InsertColumn(1, "Leucines", wx.LIST_FORMAT_RIGHT)
+ self.list.InsertColumn(2, "m/z measured")
+ #etc...
+ else:
+ # but since we want images on the column header we have to do it the hard way:
+ info = wx.ListItem()
+ info.m_mask = wx.LIST_MASK_TEXT | wx.LIST_MASK_IMAGE | wx.LIST_MASK_FORMAT
+ info.m_image = -1
+ info.m_format = 0
+ info.m_text = "Peptide"
+ self.list.InsertColumnInfo(0, info)
+ #info.m_format = wx.LIST_FORMAT_RIGHT
+ info.m_format = 0
+ info.m_text = "Leucines"
+ self.list.InsertColumnInfo(1, info)
+ info.m_format = 0
+ info.m_text = "m/z meas."
+ self.list.InsertColumnInfo(2, info)
+
+ info.m_format = 0
+ info.m_text = "m/z calc."
+ self.list.InsertColumnInfo(3, info)
+
+ info.m_format = 0
+ info.m_text = "Base_int."
+ self.list.InsertColumnInfo(4, info)
+
+ info.m_format = 0
+ info.m_text = "Deut_int."
+ self.list.InsertColumnInfo(5, info)
+
+ info.m_format = 0
+ info.m_text = "Ratio"
+ self.list.InsertColumnInfo(6, info)
+
+ info.m_format = 0
+ info.m_text = "Corr_ratio"
+ self.list.InsertColumnInfo(7, info)
+
+ info.m_format = 0
+ info.m_text = "Local_bg"
+ self.list.InsertColumnInfo(8, info)
+
+ info.m_format = 0
+ info.m_text = "Valid."
+ self.list.InsertColumnInfo(9, info)
+ #Now put inside the data from the dictionary
+ items = externaldict.items()
+ for x in range(len(items)):
+ key, data = items[x]
+ self.list.InsertStringItem(x, data[0])
+ #self.list.InsertImageStringItem(x, data[0], self.sm_up)
+ self.list.SetStringItem(x, 1, data[1])
+ self.list.SetStringItem(x, 2, data[2])
+ self.list.SetStringItem(x, 3, data[3])
+ self.list.SetStringItem(x, 4, data[4])
+ self.list.SetStringItem(x, 5, data[5])
+ self.list.SetStringItem(x, 6, data[6])
+ self.list.SetStringItem(x, 7, data[7])
+ self.list.SetStringItem(x, 8, data[8])
+ self.list.SetStringItem(x, 9, data[9])
+ self.list.SetItemData(x, key) #why is that necessary ?
+ #Set colors for the adnotation - is light grey if
+ #no leucine exists in the peptide sequence
+ if data[9] == "YES":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if data[9] == "NO":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+ if data[1] == "0":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.LIGHT_GREY)
+ self.list.SetItem(item)
+
+ for i in range(9):
+ self.list.SetColumnWidth(i, 60)
+ #self.list.SetColumnWidth(i, wx.LIST_AUTOSIZE)
+ self.list.SetColumnWidth(9, 100)
+ # show how to select an item
+ #self.list.SetItemState(5, wx.LIST_STATE_SELECTED, wx.LIST_STATE_SELECTED)
+ self.currentItem = 0
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetListCtrl(self):
+ return self.list
+
+ def SetValidated(self, where, what):
+ """
+ Called when the OnValidate or OnInvalidate are activated
+ Changes the 9th element in the current list item to "YES"
+ or "NO"
+ """
+ self.list.SetStringItem(where, 9, what)
+ if what == "YES":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if what == "NO":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+
+ def SetBg(self, where, bg, ratio):
+ """
+ Shows local background value in the list and
+ the updated value of corrected ratio
+ """
+ self.list.SetStringItem(where, 8, "%.0f"%bg)
+ self.list.SetStringItem(where, 7, "%.2f"%ratio)
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetSortImages(self):
+ return (self.sm_dn, self.sm_up)
+
+ def getColumnText(self, index, col):
+ item = self.list.GetItem(index, col)
+ return item.GetText()
+
+ def OnItemSelected(self, event):
+ """
+ Overwritten by its equivalent in MainFrame
+ """
+ ##print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.list.GetItemText(self.currentItem)+\
+ self.getColumnText(self.currentItem, 1)
+ #print self.uniquekey
+ event.Skip()
+
+ def OnColClick(self, event):
+ #print ("OnColClick: %d\n" % event.GetColumn())
+ event.Skip()
+
+ def OnSize(self, event):
+ w,h = self.GetClientSizeTuple()
+ self.list.SetDimensions(0, 0, w, h)
+
+#######################################################
+#the equivalent of a main function.
+app = wx.PySimpleApp()
+frame = MainFrame(None, -1, "SILAC validator v. 0.2")
+app.SetTopWindow(frame)
+app.MainLoop()
+#######################################################
diff --git a/src/Silacvalidator_20080123_debug.py~ b/src/Silacvalidator_20080123_debug.py~
new file mode 100644
index 0000000000000000000000000000000000000000..705ea89f1ce08f9051676ddb4ce552c6cc0ffa0e
--- /dev/null
+++ b/src/Silacvalidator_20080123_debug.py~
@@ -0,0 +1,1079 @@
+"""
+SILAC validator v. 0.2
+
+INSTRUCTIONS:
+
+This application recognizes XML files, as generated by lilamsXML. These files are
+obtained from a spectrum (in text format) and a MsFit3.2 results file (in html for-
+mat). Only the first entry in the file is quantified and generates an xml file.
+After opening an XML file, the first peptide-associated spectrum is displayed in
+the interactive plot window. You can zoom by drawing a rectangle with the left
+mouse click and unzoom with the menu >Plot>Full Unzoom. When clicking anywhere
+on the plot, the m/z value and intensity are shown in the status bar.
+To associate a local background to a spectrum double-click on the maximum and
+minimum of the peak considered as background. The difference of the two values
+is shown in the status bar. By clicking on the <Set Bgrnd.> button the last va-
+lue of the local background is inserted in the peptide table and the corrected
+ratio is automatically calculated. To validate the peptide quantification click
+on the <Validate> button.
+
+Clicking on the column titles allows sorting of the peptide list by any criteria.
+A visualisation program for XML files generated by lilamsxml. Allows validation
+of SILAC experiments, peptide by peptide.
+
+Written using wxPython, numarray, ElementTree et al., in Python, September 2004.
+Modified in January 2008, to be able to save in text format individual spectra
+regions. Several ergonomy amelioration also done and debugged the Next/Previous
+commands!
+
+Cosmin Saveanu in Alain Jacquier's laboratory, Institut Pasteur, CNRS-URA2171.
+
+Many thanks to all the people contributing to the development of tools like wxPython,
+Python itself, ElementTree, and wx.lib.plot and the wonderful examples to get
+inspiration (and sometimes copy/paste) from.
+
+This program may be freely distributed as long as correct references to it are
+provided, with this included note.
+"""
+import wx
+#import pdb
+import os, string
+from wx.lib.plot import *
+#the required plot module to draw spectra
+from elementtree import ElementTree as ET
+#elementtree is an excellent package written by Fredrik Lundh (effbot.org)
+#to deal with simple XML structures.
+
+#Imports for the ListCtrl class, copied from the wxPython documentation
+import wx.lib.mixins.listctrl as listmix
+from wx import ImageFromStream, BitmapFromImage
+
+import cStringIO
+
+try:
+ import Numeric
+except:
+ try:
+ import numarray as Numeric
+ except:
+ msg = """This program requires the Numeric or numarray
+ module to function - in fact is a requirement for the
+ wx.lib.plot module. Please install either Numeric or
+ numarray.
+ """
+ raise ImportError, "Numeric or numarray not found.\n"+msg
+
+#first - define unique identifiers for the different graphical elements
+[ID_OPEN,
+ID_OPENX,
+ID_CLOSE,
+ID_SAVEP,
+ID_SAVESP,
+ID_SAVEDATA,
+ID_EXIT,
+ID_ABOUT,
+ID_ENGRID,
+ID_UNZOOM,
+ID_NEXTF,
+ID_PREVF,
+ID_BTN1,
+ID_BTN2,
+ID_BTN3
+] = map(lambda init_ctrls: wx.NewId(), range(15))
+
+def get_flist_xml(dirname):
+ """get all .xml file names from dirname, not recursive
+ return only the file name, not the path
+
+ Needed by the OnPrevFile and OnNextFile functions
+ but called by <XMLOpen> to set the self.filelist list
+ of xml files from the current folder.
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".xml",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def get_flist_txt(dirname):
+ """get all .txt file names from dirname, not recursive
+ return only the file name, not the path
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".txt",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def map_pos_inlist(flist, fname):
+ """
+ Obtain the index of a file name in a file list
+ If file name not found return 0 as the position
+ Used in XMLOpen, generated a value for <self.where>
+ about the current position of a file in the file
+ list obtained with <get_flist_xml>.
+ """
+ for i in range(len(flist)):
+ if flist[i] == fname:
+ res = i
+ break
+ else:
+ res = 0
+ return res
+
+def ReadFromFileArray(file, skip=0):
+ """
+ Obtain floats from a tab delimited file into a numarray array
+ The <skip> parameter indicate the number of lines not
+ read.
+
+ This function is only used to directly open a complete spectrum
+ or a text delimited file with two columns - mz and intensity
+ """
+ data = []
+ err = 0
+ errmsg = ""
+ f=file
+ for i in range(skip):
+ f.readline()
+ #simple test to see if the file look like a float coercible text file
+ try:
+ for line in f:
+ data.append(map(float, line.strip().split("\t")))
+ data_array = Numeric.array(data)
+ except ValueError:
+ data = [[1, 1]]
+ data_array = Numeric.array(data)
+ err = 1
+ errmsg = "The file you are trying to open does not look like a tab delimited one"
+ return (data_array, err, errmsg)
+ #the returned data is a tuple with an array of floats, error and errmsg
+
+
+############################################
+# INTERFACE ############################
+############################################
+class MainFrame(wx.Frame):
+ """
+ The application main frame. Contains the following
+ graphic elements:
+ self.panel |---- self.lb - the text list control
+ |---- self.btnpanel1 - the panel containing
+ three buttons (Validate, Invalidate
+ and LocalBackground
+
+ self.panelplot - containing self.plotcanvas
+ to allow drawing of spectra files
+
+ self.log - a TextCtrl panel with information
+ on the analysed xml file
+ ______________________
+ --------------- ------
+ | || | self.lb and self.btnpanel1
+ -----------------------
+ | |
+ | | self.panelplot with self.plotcanvas
+ | |
+ -----------------------
+ | | self.log
+ -----------------------
+ """
+ def __init__(self, parent, id, title):
+ wx.Frame.__init__(self, parent, id, title,
+ wx.DefaultPosition, (800, 700))
+ self.defaultdirname = "."
+ #default directory for opening files, will be modified after first open
+ self.filelist = []
+ #list with all the xml files in a folder
+ self.where = 0
+ #position in the list of files
+ self.previousclick_y = 0.0
+ self.actualclick_y = 0.0
+ #local background is calculated by substracting
+ #self.previousclick_y from self.actualclick_y
+ #absolute value is returned anyway
+ self.localbg = 0.0
+
+ self.XMLdict = {'pepseq': 0, 'mzh':1, 'calc_mzh':2, 'leucines':3,
+ 'mono_iso_int':4, 'deuterated_intensity':5,
+ 'ratio':6, 'validated':7,
+ 'local_bg':8, 'corrected_ratio':9}
+ #the mapping of tags to numbers to allow easy orientation in the ElementTree
+ #Element object obtained by parsing a SILAC XML file. If the lilams XML format
+ #changes you should change accordingly these numbers
+ self.pdatapos = 5
+ #in the XML tree the pepdata values are in this position
+
+ ###################################################################
+ # Create the menu bar and items
+ self.menubar = wx.MenuBar()
+
+ filemenu = wx.Menu()
+ filemenu.Append(ID_OPENX, '&Open XML SILAC file...\tCtrl+O', 'Open XML file with SILAC data')
+ filemenu.Append(ID_SAVEDATA, 'Save XML &modifications\tCtrl+S', 'Save modifications with (validation/local background)')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_OPEN, 'O&pen text file...\tCtrl+T', 'Open tab delimited file for plotting')
+ filemenu.Append(ID_CLOSE, '&Close text file\tCtrl+W', 'Close text file')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVEP, '&Save plot image\tCtrl+I', 'Save plot image in a bmp, png or jpg format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVESP, 'Sa&ve plot data\tCtrl+D', 'Save the data corresponding to the plotted spectrum in text format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_EXIT, '&Quit\tCtrl+Q', 'Exit program')
+
+ navmenu = wx.Menu()
+ navmenu.Append(ID_NEXTF, '&Next XML file\tCtrl+N', 'Open next xml file in the current folder')
+ navmenu.Append(ID_PREVF, '&Previous XML file\tCtrl+P', 'Open previous xml file in the current folder')
+
+ plotmenu = wx.Menu()
+ plotmenu.Append(ID_UNZOOM, 'Full &Unzoom\tCtrl+U', 'Full unzoom for the current plot')
+ plotmenu.AppendSeparator()
+ plotmenu.Append(ID_ENGRID, 'Grid &enabled', 'Enable or disable grid when drawing', wx.ITEM_CHECK)
+
+ helpmenu = wx.Menu()
+ helpmenu.Append(ID_ABOUT, '&About...\tCtrl+E', 'About this program')
+
+ ###################################################################
+ # Bind the events to methods
+ wx.EVT_MENU(self, ID_OPENX, self.OnXMLOpen)
+ wx.EVT_MENU(self, ID_SAVEDATA, self.OnXMLSave)
+ wx.EVT_MENU(self, ID_OPEN, self.OnFileOpen)
+ wx.EVT_MENU(self, ID_CLOSE, self.OnFileClose)
+ wx.EVT_MENU(self, ID_SAVEP, self.OnSaveImage)
+ wx.EVT_MENU(self, ID_SAVESP, self.OnSpectrumSave)
+ wx.EVT_MENU(self, ID_EXIT, self.OnFileExit)
+ wx.EVT_MENU(self, ID_NEXTF, self.OnNextFile)
+ wx.EVT_MENU(self, ID_PREVF, self.OnPrevFile)
+ wx.EVT_MENU(self, ID_ENGRID, self.OnEnableGrid)
+ wx.EVT_MENU(self, ID_UNZOOM, self.OnFullUnzoom)
+ wx.EVT_MENU(self, ID_ABOUT, self.OnHelpAbout)
+
+ ###################################################################
+ # Attach menus to the menubar
+ self.menubar.Append(filemenu, '&File')
+ self.menubar.Append(navmenu, '&Next/Previous')
+ self.menubar.Append(plotmenu, '&Plot')
+ self.menubar.Append(helpmenu, '&Help')
+
+ self.SetMenuBar(self.menubar)
+
+ ###################################################################
+ #Disable by default some menus and buttons
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 0)
+ self.menubar.Enable(ID_SAVEP, 0)
+ self.menubar.Enable(ID_SAVESP, 0)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ # A status bar to tell people what's happening
+ self.CreateStatusBar(1)
+
+ self.SetAutoLayout(True)
+
+ ###################################################################
+ self.panel = wx.Panel(self, -1, style=wx.SIMPLE_BORDER)
+ #in this case and all the others we use layout constraints
+ #I couldn't understand easily the sizers, while layout constraints seem
+ #quite easy to set up and they work very well.
+ #self.panel will contain the listctrl and button panel
+
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self, wx.Top, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 30)
+ self.panel.SetConstraints(lc)
+
+ ###################################################################
+ #the peplistctrlpanel - with the list of peptides and interesting data
+ self.smalldict = {1:("pepseq", "0", "mzh", "mzhcalc", "mono", "deuter", "ratio", "corr",
+ "localbg", "valid")}
+ #we need this to fill up the listctrl at program initialization
+ self.lb = PepListCtrlPanel(self.panel, dictwithdata=self.smalldict)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.PercentOf(self.panel, wx.Right, 80) #it will take up 80% of the panel
+ lc.left.SameAs(self.panel, wx.Left, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.lb.SetConstraints(lc)
+ ###################################################################
+ self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.lb.list)
+ ###################################################################
+ #the panel to hold the three buttons
+ self.btnpanel1 = wx.Panel(self.panel, -1, style=wx.SIMPLE_BORDER)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.SameAs(self.panel, wx.Right, 10)
+ lc.left.SameAs(self.lb, wx.Right, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.btnpanel1.SetConstraints(lc)
+ ###################################################################
+ #set up the buttons and bind to the corresponding functions
+ self.btn1 = wx.Button(self.btnpanel1, ID_BTN1, " Validate ", wx.DefaultPosition)
+ self.btn2 = wx.Button(self.btnpanel1, ID_BTN2, "INvalidate", wx.DefaultPosition)
+ self.btn3 = wx.Button(self.btnpanel1, ID_BTN3, "Set Bgrnd.", wx.DefaultPosition)
+ wx.EVT_BUTTON(self, ID_BTN1, self.OnValidate)
+ wx.EVT_BUTTON(self, ID_BTN2, self.OnInvalidate)
+ wx.EVT_BUTTON(self, ID_BTN3, self.OnSetLocalBg)
+
+ #Disable by default the three buttons
+ self.btn1.Enable(False)
+ self.btn2.Enable(False)
+ self.btn3.Enable(False)
+ ###################################################################
+ #layout the buttons on the btnpanel1
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btnpanel1, wx.CentreX)
+ lc.top.SameAs(self.btnpanel1, wx.Top, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn1.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.centreY.SameAs(self.btnpanel1, wx.CentreY)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn2.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.bottom.SameAs(self.btnpanel1, wx.Bottom, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn3.SetConstraints(lc)
+
+ ###################################################################
+ #A black panel to give contrast to the plot
+ self.panelplot = wx.Window(self, -1)
+ self.panelplot.SetBackgroundColour(wx.BLACK)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panel, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 85)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.panelplot.SetConstraints(lc)
+ ###################################################################
+ #The plot itself in self.panelplot
+ self.plotcanvas = PlotCanvas(self.panelplot, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panelplot, wx.Top, 2)
+ lc.left.SameAs(self.panelplot, wx.Left, 2)
+ lc.bottom.SameAs(self.panelplot, wx.Bottom, 2)
+ lc.right.SameAs(self.panelplot, wx.Right, 2)
+ self.plotcanvas.SetConstraints(lc)
+ ###################################################################
+ #A panel to hold the TextCtrl called self.log
+ self.logpanel = wx.Window(self, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panelplot, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.SameAs(self, wx.Bottom, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.logpanel.SetConstraints(lc)
+ ###################################################################
+ #The text control that will hold informations on the protein and file used
+ self.log = wx.TextCtrl(self.logpanel, -1,
+ style = wx.TE_MULTILINE|wx.TE_READONLY|wx.HSCROLL)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.logpanel, wx.Top, 2)
+ lc.left.SameAs(self.logpanel, wx.Left, 0)
+ lc.bottom.SameAs(self.logpanel, wx.Bottom, 2)
+ lc.right.SameAs(self.logpanel, wx.Right, 0)
+ self.log.SetConstraints(lc)
+ self.log.AppendText("> Hello. Load a LILAMS XML file from the File> menu (or Cmd+O).")
+ ###################################################################
+ # Create mouse event for showing cursor coords in status bar
+ self.plotcanvas.Bind(wx.EVT_LEFT_DOWN, self.OnMouseLeftDown)
+ self.plotcanvas.Bind(wx.EVT_LEFT_DCLICK, self.OnMouseDClick)
+ self.plotcanvas.SetEnableZoom(1) #to ensure zoom by default
+
+ self.Show(True)
+
+ ###################################################################
+ ## Main Frame function definitions ################################
+ ###################################################################
+
+ def OnXMLOpen(self, event):
+ """
+ Opens a XML file with SILAC data and generates
+ an ElementTree instance containing the data
+ in the variable self.data
+ """
+ self.resetDefaults()
+ wildcard = "XML file (*.xml)|*.xml|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a SILAC XML file:",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ try:
+ if not self.XMLOpen(dirname, filename):
+ msg = """
+ The file you wanted to open does not
+ contain valid SILAC XML data. Try opening it with
+ a text editor to see what is the problem."""
+ dlg = wx.MessageDialog(self, msg, 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ finally:
+ dlg.Destroy()
+
+ def XMLOpen(self, dirname, filename):
+ """
+ Will allow calls for XMLOpen from Previous
+ and Next calls. Returns True if everything OK.
+
+ -uses get_flist_xml to set up the file list
+ -uses map_pos_inlist to set up self.where
+ -uses self.PlotSpectrumXML to plot the first peptide
+ in file
+ -uses self.PopulateList to populate the self.lb list
+ control with data
+ -uses self.GenerateListDict to generate the dictionary
+ used to describe the data in the self.lb control
+ """
+ filename=filename
+ dirname=dirname
+ self.defaultdirname = dirname
+ fname = os.path.join(dirname, filename)
+ #self.fnameout = fname+"x"
+ #we write in the same xml file, overwriting previous file
+ self.fnameout = fname
+ self.filelist = get_flist_xml(dirname)
+ self.where = map_pos_inlist(self.filelist, filename)
+ try:
+ tree = ET.parse(fname)
+ self.data = tree.getroot()
+ #the root is a <protdata> entry
+ self.PlotSpectrumXML(0, title="peptide 1")
+ self.PopulateList(self.GenerateListDict(self.data))
+ #Clear the log, write text to it about the opened file
+ self.log.Remove(0, self.log.GetLastPosition())
+ self.log.AppendText("\n> Opened %s xml file.\n"%filename)
+ self.log.AppendText("> Mowse score: %s, database: %s, ppm tolerance: %s.\n"%(self.data[0][3].text,
+ self.data[0][1].text, self.data[0][2].text))
+ self.log.AppendText("> Spot identification: %s.\n"%self.data[0][0].text)
+ self.log.AppendText("> Identified protein: %s, accesion number: %s.\n"%(self.data[2].text, self.data[1].text))
+ self.log.AppendText("> Peptide coverage: %s percent, matched peptides: %s.\n"%(self.data[0][4].text[:-1], self.data[0][5].text))
+ self.menubar.Enable(ID_NEXTF, 1)
+ self.menubar.Enable(ID_PREVF, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.btn1.Enable(True)
+ self.btn2.Enable(True)
+ self.btn3.Enable(True)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVESP, 0)
+ return True
+ except:
+ return False
+
+ def PlotSpectrumXML(self, index=0, title=""):
+ """
+ Recover and plot data for the record that has <index>
+ It is found in self.data[5] - that is pepdata,
+ the subnode is 10 for <spectrum> and 0, 1 for
+ the two lists mz and int. "5 "is contained in self.pdatapos
+
+ -uses self.PlotArray - a function to do the plotting
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+ self.PlotArray(dataforarray, "blue", title)
+
+ def PlotArray(self, data_array, color, title):
+ """
+ Used to plot on the plotcanvas the points of a data_array
+ Default is autoscale, used by PlotSpectrumXML
+ """
+ self.line = PolyLine(data_array, colour = color)
+ self.plotcanvas.Draw(PlotGraphics([self.line, ], title, "m/z", ""))
+ #self.plotcanvas.Redraw()
+
+ def GenerateListDict(self, xmldata):
+ """
+ forms a dictionary {1:["a", "b", "c"], 2:...}
+ for the PepListCtrlPanel widget - to populate
+ with XML data
+ """
+ self.entriesdict = {}
+ for i in range(len(xmldata[self.pdatapos])):
+ self.entriesdict[i] = (self.GetValXML(i, 'pepseq'),
+ self.GetValXML(i, 'leucines'),
+ self.GetValXML(i, 'mzh'),
+ self.GetValXML(i, 'calc_mzh'),
+ self.GetValXML(i, 'mono_iso_int'),
+ self.GetValXML(i, 'deuterated_intensity'),
+ self.GetValXML(i, 'ratio'),
+ self.GetValXML(i, 'corrected_ratio'),
+ self.GetValXML(i, 'local_bg'),
+ self.GetValXML(i, 'validated'))
+ return self.entriesdict
+
+ def PopulateList(self, externaldict):
+ """
+ a wrapper to the function with the same name in self.lb
+ """
+ self.lb.PopulateList(externaldict)
+
+ def OnItemSelected(self, event):
+ """
+ Activated when one item in the self.lb list control
+ is selected. Determines the generation of a unique key
+ that will allow a correspondence between the list
+ elements and the underlying ElementTree Element
+ - uses MapUniqueKey function
+ """
+ #print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.lb.list.GetItemText(self.currentItem)+self.lb.getColumnText(self.currentItem, 2)
+ self.index = self.MapUniqueKey(self.uniquekey)
+ #print self.index, "self.index"
+ self.PlotSpectrumXML(self.index, title = self.GetValXML(self.index, 'pepseq')+\
+ " / "+self.GetValXML(self.index, 'mzh'))
+ self.menubar.Enable(ID_SAVEDATA, 1)
+ self.menubar.Enable(ID_SAVESP, 1)
+ event.Skip()
+ #the self.index variable allows us to recover and change the data if validation occurs
+
+ def MapUniqueKey(self, uniquekey):
+ """
+ Used by <OnItemSelected> to allow a correspondence between
+ self.currentItem - in the list and self.index in the ElementTree
+ Element representing data read from the XML SILAC file
+ """
+ result = 0
+ for i in range(len(self.data[self.pdatapos])):
+ #testing [0] is peptide sequence [1] is submitted m/z+h mass
+ if uniquekey == self.data[self.pdatapos][i][0].text+\
+ self.data[self.pdatapos][i][1].text:
+ #the index of the correspoinding key was found
+ result = i
+ break
+ return result
+
+ def OnValidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "YES")
+ self.SetXMLValidated(self.index, "YES")
+ def OnInvalidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "NO")
+ self.SetXMLValidated(self.index, "NO")
+
+ def SetXMLValidated(self, index, what):
+ """
+ 7 is the actual position of the <validated> field
+ in the self.data - coming from the SILAC XML tree
+ """
+ self.data[self.pdatapos][index][7].text = what
+
+ def GetValXML(self, index=0, what='pepseq'):
+ """
+ Returns the text attribute of an entry in an Element
+ object based on the self.XMLdict dictionary that maps
+ numbers to tags - definition in the init of the main
+ frame. By default it returns the peptide sequence of
+ the first record.
+
+ self.pdatapos - indicates the position of the <pepdata> in
+ the root of the pepdata xml entry
+ """
+ return self.data[self.pdatapos][index][self.XMLdict[what]].text
+
+ def OnXMLSave(self, event):
+ """
+ Writes the contents of self.data to the self.fnameout
+ (established when the actual file was opened)
+ """
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ def OnSpectrumSave(self, event):
+ self.SpectrumSave(self.index)
+
+ def SpectrumSave(self, index=0):
+ """
+ Writes the contents of the actual selected spectrum
+ to a given file name, in tab delimited format
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(
+ self, message="Save plot data to ...", defaultDir = self.defaultdirname,
+ defaultFile="pepspecdata.txt", wildcard=wildcard, style=wx.SAVE
+ )
+ dlg.SetFilterIndex(0)
+ if dlg.ShowModal() == wx.ID_OK:
+ path = dlg.GetPath()
+ try:
+ fout = open(path, "w")
+ for line in dataforarray:
+ fout.write('%.3f\t%d\n'%(line[0], line[1]))
+ fout.close()
+
+ self.SetStatusText("Data saved to file %s"%path)
+ except IOError:
+ dlg = wx.MessageDialog(self, "Error. Maybe the output file is in use...", 'Problem saving data',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ dlg.Destroy()
+
+ def OnNextFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO| wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+ #debugging here
+ #pdb.set_trace()
+ if len(self.filelist) > 0:
+ #print self.filelist
+ #print self.where
+ if self.where < len(self.filelist)-1:
+ #fname = os.path.split(self.filelist[self.where+1]
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where+1])
+ #self.where += 1 there is a risk in using global variables
+ #this one is already modified by XMLOpen to the correct value
+ else:
+ #we are at the end of the list, going on from the beginning
+ self.where = 0
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+ #self.where += 1
+
+ def OnPrevFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO | wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ if len(self.filelist) > 0:
+ if self.where > 0:
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where-1])
+ #self.where -= 1
+ else:
+ #we are at the beginning of the list
+ self.where = len(self.filelist)-1
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+ #self.where -= 1
+
+ def OnFullUnzoom(self, event):
+ self.plotcanvas.Reset()
+
+ def OnFileOpen(self, event):
+ """
+ Opens and plots a tab delimited text file
+ If not a recognized file, a message is displayed
+ Sets also the actual directory name: self.defaultdirname
+ """
+ self.resetDefaults()
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a tab delimited text file",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ self.filename=dlg.GetFilename()
+ self.dirname=dlg.GetDirectory()
+ self.defaultdirname = self.dirname
+ self.filelist = get_flist_txt(self.dirname)
+ fname = os.path.join(self.dirname, self.filename)
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ dlg.Destroy()
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", self.filename)
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ def PlotFile(self, fname):
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", os.path.split(fname)[1])
+
+ def OnFileClose(self, event):
+ self.plotcanvas.Clear()
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+
+ def OnMouseLeftDown(self,event):
+ self.localbg = abs(self.actualclick_y - self.previousclick_y)
+ s= "(m/z : %.2f, Intensity : %.2f)"%self.plotcanvas.GetXY(event)+\
+ " Local background : %.0f"%self.localbg
+ self.SetStatusText(s)
+ event.Skip()
+
+ def OnMouseDClick(self, event):
+ self.previousclick_y = self.actualclick_y
+ self.actualclick_y = self.plotcanvas.GetXY(event)[1]
+
+ def OnSetLocalBg(self, event):
+ """
+ Updates the local background data both in the shown list
+ and in self.data. Recalculated the corrected ratio
+ """
+ self.data[self.pdatapos][self.index][8].text = "%0.f"%self.localbg
+ deut = float(self.GetValXML(self.index, 'deuterated_intensity'))-self.localbg
+ monoiso = float(self.GetValXML(self.index, 'mono_iso_int'))-self.localbg
+ self.data[self.pdatapos][self.index][9].text = "%.2f"%(deut/monoiso)
+ self.lb.SetBg(self.currentItem, self.localbg, (deut/monoiso))
+
+ def OnSaveImage(self, event):
+ self.plotcanvas.SaveFile()
+
+ def OnFileExit(self, event):
+ self.Close()
+
+ def OnPlotRedraw(self,event):
+ self.plotcanvas.Redraw()
+
+ def OnPlotClear(self,event):
+ self.plotcanvas.Clear()
+
+ def OnPlotScale(self, event):
+ if self.plotcanvas.last_draw != None:
+ graphics, xAxis, yAxis= self.plotcanvas.last_draw
+ self.plotcanvas.Draw(graphics,(1,3.05),(0,1))
+
+ def OnEnableZoom(self, event):
+ self.plotcanvas.SetEnableZoom(event.IsChecked())
+
+ def OnEnableGrid(self, event):
+ self.plotcanvas.SetEnableGrid(event.IsChecked())
+
+ def OnEnableLegend(self, event):
+ self.plotcanvas.SetEnableLegend(event.IsChecked())
+ def OnReset(self,event):
+ self.plotcanvas.Reset()
+
+ def OnHelpAbout(self, event):
+ from wx.lib.dialogs import ScrolledMessageDialog
+ about = ScrolledMessageDialog(self, __doc__, "About...")
+ about.ShowModal()
+
+ def resetDefaults(self):
+ """Just to reset the fonts back to the PlotCanvas defaults"""
+ self.plotcanvas.SetFont(wx.Font(10,wx.SWISS,wx.NORMAL,wx.NORMAL))
+ self.plotcanvas.SetFontSizeAxis(10)
+ self.plotcanvas.SetFontSizeLegend(7)
+ self.plotcanvas.SetXSpec('auto')
+ self.plotcanvas.SetYSpec('auto')
+ self.plotcanvas.SetEnableZoom(1)
+
+#######################################################
+#######################################################
+################ PepListCtrlPanel ###############
+################ and PepListCtrl classes###############
+#######################################################
+#######################################################
+#######################################################
+#----------------------------------------------------------------------------
+# Name: ListCtrl.py
+# Purpose: Testing lots of stuff, controls, window types, etc.
+#
+# Author: Robin Dunn & Gary Dumer
+#
+# Created:
+# RCS-ID: $Id: ListCtrl.py,v 1.3 2004/03/05 00:06:32 RD Exp $
+# Copyright: (c) 1998 by Total Control Software
+# Licence: wxWindows license
+#
+# Modified by Cosmin Saveanu, IP, September 2004
+# to be able to deal with peptide entries for SILAC
+#----------------------------------------------------------------------------
+def getSmallUpArrowData():
+ return \
+'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00<IDATx\x9ccddbf\xa0\x040Q\xa4{h\x18\xf0\xff\xdf\xdf\xffd\x1b\x00\xd3\
+\x8c\xcf\x10\x9c\x06\xa0k\xc2e\x08m\xc2\x00\x97m\xd8\xc41\x0c \x14h\xe8\xf2\
+\x8c\xa3)q\x10\x18\x00\x00R\xd8#\xec\x95{\xc4\x11\x00\x00\x00\x00IEND\xaeB`\
+\x82'
+
+def getSmallUpArrowBitmap():
+ return BitmapFromImage(getSmallUpArrowImage())
+def getSmallUpArrowImage():
+ stream = cStringIO.StringIO(getSmallUpArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+
+def getSmallDnArrowData():
+ return \
+"\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00HIDATx\x9ccddbf\xa0\x040Q\xa4{\xd4\x00\x06\x06\x06\x06\x06\x16t\x81\
+\xff\xff\xfe\xfe'\xa4\x89\x91\x89\x99\x11\xa7\x0b\x90%\ti\xc6j\x00>C\xb0\x89\
+\xd3.\x10\xd1m\xc3\xe5*\xbc.\x80i\xc2\x17.\x8c\xa3y\x81\x01\x00\xa1\x0e\x04e\
+\x1d\xc4;\xb7\x00\x00\x00\x00IEND\xaeB`\x82"
+def getSmallDnArrowBitmap():
+ return BitmapFromImage(getSmallDnArrowImage())
+
+def getSmallDnArrowImage():
+ stream = cStringIO.StringIO(getSmallDnArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+class PepListCtrl(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin):
+
+ def __init__(self, parent, ID, pos=wx.DefaultPosition,
+ size=wx.DefaultSize, style=0):
+ wx.ListCtrl.__init__(self, parent, ID, pos, size, style)
+ listmix.ListCtrlAutoWidthMixin.__init__(self)
+
+class PepListCtrlPanel(wx.Panel, listmix.ColumnSorterMixin):
+
+ def __init__(self, parent, dictwithdata={}):
+ wx.Panel.__init__(self, parent, -1, style=wx.WANTS_CHARS)
+ tID = wx.NewId()
+ self.il = wx.ImageList(16, 16)
+ self.sm_up = self.il.Add(getSmallUpArrowBitmap())
+ self.sm_dn = self.il.Add(getSmallDnArrowBitmap())
+ self.list = PepListCtrl(self, tID,
+ style=wx.LC_REPORT
+ | wx.SUNKEN_BORDER
+ | wx.LC_SINGLE_SEL
+ #| wx.LC_HRULES
+ #| wx.LC_EDIT_LABELS
+ #| wxLC_NO_HEADER
+ #| wxLC_VRULES
+ )
+ self.list.SetImageList(self.il, wx.IMAGE_LIST_SMALL)
+ self.PopulateList(dictwithdata)
+ # Now that the list exists we can init the other base class,
+ # see wxPython/lib/mixins/listctrl.py
+
+ listmix.ColumnSorterMixin.__init__(self, 10)
+ #self.SortListItems(0, True)
+ self.Bind(wx.EVT_SIZE, self.OnSize)
+ #self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.list)
+ self.Bind(wx.EVT_LIST_COL_CLICK, self.OnColClick, self.list)
+
+ def PopulateList(self, externaldict):
+ """
+ Constructs the headings of the list control
+ and populates it with data
+ """
+
+ self.itemDataMap = externaldict
+ self.list.ClearAll()
+ if 0:
+ # for normal, simple columns, you can add them like this:
+ self.list.InsertColumn(0, "Peptide")
+ self.list.InsertColumn(1, "Leucines", wx.LIST_FORMAT_RIGHT)
+ self.list.InsertColumn(2, "m/z measured")
+ #etc...
+ else:
+ # but since we want images on the column header we have to do it the hard way:
+ info = wx.ListItem()
+ info.m_mask = wx.LIST_MASK_TEXT | wx.LIST_MASK_IMAGE | wx.LIST_MASK_FORMAT
+ info.m_image = -1
+ info.m_format = 0
+ info.m_text = "Peptide"
+ self.list.InsertColumnInfo(0, info)
+ #info.m_format = wx.LIST_FORMAT_RIGHT
+ info.m_format = 0
+ info.m_text = "Leucines"
+ self.list.InsertColumnInfo(1, info)
+ info.m_format = 0
+ info.m_text = "m/z meas."
+ self.list.InsertColumnInfo(2, info)
+
+ info.m_format = 0
+ info.m_text = "m/z calc."
+ self.list.InsertColumnInfo(3, info)
+
+ info.m_format = 0
+ info.m_text = "Base_int."
+ self.list.InsertColumnInfo(4, info)
+
+ info.m_format = 0
+ info.m_text = "Deut_int."
+ self.list.InsertColumnInfo(5, info)
+
+ info.m_format = 0
+ info.m_text = "Ratio"
+ self.list.InsertColumnInfo(6, info)
+
+ info.m_format = 0
+ info.m_text = "Corr_ratio"
+ self.list.InsertColumnInfo(7, info)
+
+ info.m_format = 0
+ info.m_text = "Local_bg"
+ self.list.InsertColumnInfo(8, info)
+
+ info.m_format = 0
+ info.m_text = "Valid."
+ self.list.InsertColumnInfo(9, info)
+ #Now put inside the data from the dictionary
+ items = externaldict.items()
+ for x in range(len(items)):
+ key, data = items[x]
+ self.list.InsertStringItem(x, data[0])
+ #self.list.InsertImageStringItem(x, data[0], self.sm_up)
+ self.list.SetStringItem(x, 1, data[1])
+ self.list.SetStringItem(x, 2, data[2])
+ self.list.SetStringItem(x, 3, data[3])
+ self.list.SetStringItem(x, 4, data[4])
+ self.list.SetStringItem(x, 5, data[5])
+ self.list.SetStringItem(x, 6, data[6])
+ self.list.SetStringItem(x, 7, data[7])
+ self.list.SetStringItem(x, 8, data[8])
+ self.list.SetStringItem(x, 9, data[9])
+ self.list.SetItemData(x, key) #why is that necessary ?
+ #Set colors for the adnotation - is light grey if
+ #no leucine exists in the peptide sequence
+ if data[9] == "YES":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if data[9] == "NO":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+ if data[1] == "0":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.LIGHT_GREY)
+ self.list.SetItem(item)
+
+ for i in range(9):
+ self.list.SetColumnWidth(i, 60)
+ #self.list.SetColumnWidth(i, wx.LIST_AUTOSIZE)
+ self.list.SetColumnWidth(9, 100)
+ # show how to select an item
+ #self.list.SetItemState(5, wx.LIST_STATE_SELECTED, wx.LIST_STATE_SELECTED)
+ self.currentItem = 0
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetListCtrl(self):
+ return self.list
+
+ def SetValidated(self, where, what):
+ """
+ Called when the OnValidate or OnInvalidate are activated
+ Changes the 9th element in the current list item to "YES"
+ or "NO"
+ """
+ self.list.SetStringItem(where, 9, what)
+ if what == "YES":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if what == "NO":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+
+ def SetBg(self, where, bg, ratio):
+ """
+ Shows local background value in the list and
+ the updated value of corrected ratio
+ """
+ self.list.SetStringItem(where, 8, "%.0f"%bg)
+ self.list.SetStringItem(where, 7, "%.2f"%ratio)
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetSortImages(self):
+ return (self.sm_dn, self.sm_up)
+
+ def getColumnText(self, index, col):
+ item = self.list.GetItem(index, col)
+ return item.GetText()
+
+ def OnItemSelected(self, event):
+ """
+ Overwritten by its equivalent in MainFrame
+ """
+ ##print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.list.GetItemText(self.currentItem)+\
+ self.getColumnText(self.currentItem, 1)
+ #print self.uniquekey
+ event.Skip()
+
+ def OnColClick(self, event):
+ #print ("OnColClick: %d\n" % event.GetColumn())
+ event.Skip()
+
+ def OnSize(self, event):
+ w,h = self.GetClientSizeTuple()
+ self.list.SetDimensions(0, 0, w, h)
+
+#######################################################
+#the equivalent of a main function.
+app = wx.PySimpleApp()
+frame = MainFrame(None, -1, "SILAC validator v. 0.2")
+app.SetTopWindow(frame)
+app.MainLoop()
+#######################################################
diff --git a/src/Silacvalidator_20080201.py~ b/src/Silacvalidator_20080201.py~
new file mode 100644
index 0000000000000000000000000000000000000000..f600396f8e76949f295ce7c84b4bf5936573d3c8
--- /dev/null
+++ b/src/Silacvalidator_20080201.py~
@@ -0,0 +1,1088 @@
+"""
+SILAC validator v. 0.2
+
+INSTRUCTIONS:
+
+This application recognizes XML files, as generated by lilamsXML. These files are
+obtained from a spectrum (in text format) and a MsFit3.2 results file (in html for-
+mat). Only the first entry in the file is quantified and generates an xml file.
+After opening an XML file, the first peptide-associated spectrum is displayed in
+the interactive plot window. You can zoom by drawing a rectangle with the left
+mouse click and unzoom with the menu >Plot>Full Unzoom. When clicking anywhere
+on the plot, the m/z value and intensity are shown in the status bar.
+To associate a local background to a spectrum double-click on the maximum and
+minimum of the peak considered as background. The difference of the two values
+is shown in the status bar. By clicking on the <Set Bgrnd.> button the last va-
+lue of the local background is inserted in the peptide table and the corrected
+ratio is automatically calculated. To validate the peptide quantification click
+on the <Validate> button.
+
+Clicking on the column titles allows sorting of the peptide list by any criteria.
+A visualisation program for XML files generated by lilamsxml. Allows validation
+of SILAC experiments, peptide by peptide.
+
+Written using wxPython, numarray, ElementTree et al., in Python, September 2004.
+Modified in January 2008, to be able to save in text format individual spectra
+regions. Several ergonomy amelioration also done and debugged the Next/Previous
+commands!
+
+Cosmin Saveanu in Alain Jacquier's laboratory, Institut Pasteur, CNRS-URA2171.
+
+Many thanks to all the people contributing to the development of tools like wxPython,
+Python itself, ElementTree, and wx.lib.plot and the wonderful examples to get
+inspiration (and sometimes copy/paste) from.
+
+This program may be freely distributed as long as correct references to it are
+provided, with this included note.
+"""
+import wx
+#import pdb
+import os, string
+from wx.lib.plot import *
+#the required plot module to draw spectra
+from elementtree import ElementTree as ET
+#elementtree is an excellent package written by Fredrik Lundh (effbot.org)
+#to deal with simple XML structures.
+
+#Imports for the ListCtrl class, copied from the wxPython documentation
+import wx.lib.mixins.listctrl as listmix
+from wx import ImageFromStream, BitmapFromImage
+
+import cStringIO
+
+try:
+ import Numeric
+except:
+ try:
+ import numarray as Numeric
+ except:
+ msg = """This program requires the Numeric or numarray
+ module to function - in fact is a requirement for the
+ wx.lib.plot module. Please install either Numeric or
+ numarray.
+ """
+ raise ImportError, "Numeric or numarray not found.\n"+msg
+
+#first - define unique identifiers for the different graphical elements
+[ID_OPEN,
+ID_OPENX,
+ID_CLOSE,
+ID_SAVEP,
+ID_SAVESP,
+ID_SAVEDATA,
+ID_EXIT,
+ID_ABOUT,
+ID_ENGRID,
+ID_UNZOOM,
+ID_NEXTF,
+ID_PREVF,
+ID_SETBGN,
+ID_INVALIDATE,
+ID_BTN1,
+ID_BTN2,
+ID_BTN3
+] = map(lambda init_ctrls: wx.NewId(), range(17))
+
+def get_flist_xml(dirname):
+ """get all .xml file names from dirname, not recursive
+ return only the file name, not the path
+
+ Needed by the OnPrevFile and OnNextFile functions
+ but called by <XMLOpen> to set the self.filelist list
+ of xml files from the current folder.
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".xml",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def get_flist_txt(dirname):
+ """get all .txt file names from dirname, not recursive
+ return only the file name, not the path
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".txt",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def map_pos_inlist(flist, fname):
+ """
+ Obtain the index of a file name in a file list
+ If file name not found return 0 as the position
+ Used in XMLOpen, generated a value for <self.where>
+ about the current position of a file in the file
+ list obtained with <get_flist_xml>.
+ """
+ for i in range(len(flist)):
+ if flist[i] == fname:
+ res = i
+ break
+ else:
+ res = 0
+ return res
+
+def ReadFromFileArray(file, skip=0):
+ """
+ Obtain floats from a tab delimited file into a numarray array
+ The <skip> parameter indicate the number of lines not
+ read.
+
+ This function is only used to directly open a complete spectrum
+ or a text delimited file with two columns - mz and intensity
+ """
+ data = []
+ err = 0
+ errmsg = ""
+ f=file
+ for i in range(skip):
+ f.readline()
+ #simple test to see if the file look like a float coercible text file
+ try:
+ for line in f:
+ data.append(map(float, line.strip().split("\t")))
+ data_array = Numeric.array(data)
+ except ValueError:
+ data = [[1, 1]]
+ data_array = Numeric.array(data)
+ err = 1
+ errmsg = "The file you are trying to open does not look like a tab delimited one"
+ return (data_array, err, errmsg)
+ #the returned data is a tuple with an array of floats, error and errmsg
+
+
+############################################
+# INTERFACE ############################
+############################################
+class MainFrame(wx.Frame):
+ """
+ The application main frame. Contains the following
+ graphic elements:
+ self.panel |---- self.lb - the text list control
+ |---- self.btnpanel1 - the panel containing
+ three buttons (Validate, Invalidate
+ and LocalBackground
+
+ self.panelplot - containing self.plotcanvas
+ to allow drawing of spectra files
+
+ self.log - a TextCtrl panel with information
+ on the analysed xml file
+ ______________________
+ --------------- ------
+ | || | self.lb and self.btnpanel1
+ -----------------------
+ | |
+ | | self.panelplot with self.plotcanvas
+ | |
+ -----------------------
+ | | self.log
+ -----------------------
+ """
+ def __init__(self, parent, id, title):
+ wx.Frame.__init__(self, parent, id, title,
+ wx.DefaultPosition, (800, 700))
+ self.defaultdirname = "."
+ #default directory for opening files, will be modified after first open
+ self.filelist = []
+ #list with all the xml files in a folder
+ self.where = 0
+ #position in the list of files
+ self.previousclick_y = 0.0
+ self.actualclick_y = 0.0
+ #local background is calculated by substracting
+ #self.previousclick_y from self.actualclick_y
+ #absolute value is returned anyway
+ self.localbg = 0.0
+
+ self.XMLdict = {'pepseq': 0, 'mzh':1, 'calc_mzh':2, 'leucines':3,
+ 'mono_iso_int':4, 'deuterated_intensity':5,
+ 'ratio':6, 'validated':7,
+ 'local_bg':8, 'corrected_ratio':9}
+ #the mapping of tags to numbers to allow easy orientation in the ElementTree
+ #Element object obtained by parsing a SILAC XML file. If the lilams XML format
+ #changes you should change accordingly these numbers
+ self.pdatapos = 5
+ #in the XML tree the pepdata values are in this position
+
+ ###################################################################
+ # Create the menu bar and items
+ self.menubar = wx.MenuBar()
+
+ filemenu = wx.Menu()
+ filemenu.Append(ID_OPENX, '&Open XML SILAC file...\tCtrl+O', 'Open XML file with SILAC data')
+ filemenu.Append(ID_SAVEDATA, 'Save XML &modifications\tCtrl+S', 'Save modifications with (validation/local background)')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_OPEN, 'O&pen text file...\tCtrl+T', 'Open tab delimited file for plotting')
+ filemenu.Append(ID_CLOSE, '&Close text file\tCtrl+W', 'Close text file')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVEP, '&Save plot image\tCtrl+U', 'Save plot image in a bmp, png or jpg format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVESP, 'Sa&ve plot data\tCtrl+D', 'Save the data corresponding to the plotted spectrum in text format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_EXIT, '&Quit\tCtrl+Q', 'Exit program')
+
+ navmenu = wx.Menu()
+ navmenu.Append(ID_NEXTF, '&Next XML file\tCtrl+N', 'Open next xml file in the current folder')
+ navmenu.Append(ID_PREVF, '&Previous XML file\tCtrl+P', 'Open previous xml file in the current folder')
+
+ plotmenu = wx.Menu()
+ plotmenu.Append(ID_UNZOOM, 'Full &Unzoom\tCtrl+U', 'Full unzoom for the current plot')
+ plotmenu.AppendSeparator()
+ plotmenu.Append(ID_ENGRID, 'Grid &enabled', 'Enable or disable grid when drawing', wx.ITEM_CHECK)
+
+ valmenu = wx.Menu()
+ valmenu.Append(ID_SETBGN, 'Set &Background\tCtrl+B', 'Set background, validate and go to next')
+ valmenu.Append(ID_INVALIDATE, '&Invalidate current\tCtrl+I', 'Invalidate current peptide and select next')
+ helpmenu = wx.Menu()
+ helpmenu.Append(ID_ABOUT, '&About...\tCtrl+E', 'About this program')
+
+ ###################################################################
+ # Bind the events to methods
+ wx.EVT_MENU(self, ID_OPENX, self.OnXMLOpen)
+ wx.EVT_MENU(self, ID_SAVEDATA, self.OnXMLSave)
+ wx.EVT_MENU(self, ID_OPEN, self.OnFileOpen)
+ wx.EVT_MENU(self, ID_CLOSE, self.OnFileClose)
+ wx.EVT_MENU(self, ID_SAVEP, self.OnSaveImage)
+ wx.EVT_MENU(self, ID_SAVESP, self.OnSpectrumSave)
+ wx.EVT_MENU(self, ID_EXIT, self.OnFileExit)
+ wx.EVT_MENU(self, ID_NEXTF, self.OnNextFile)
+ wx.EVT_MENU(self, ID_PREVF, self.OnPrevFile)
+ wx.EVT_MENU(self, ID_ENGRID, self.OnEnableGrid)
+ wx.EVT_MENU(self, ID_UNZOOM, self.OnFullUnzoom)
+ wx.EVT_MENU(self, ID_SETBGN, self.OnBackground)
+ wx.EVT_MENU(self, ID_INVALIDATE, self.OnInvalidate)
+ wx.EVT_MENU(self, ID_ABOUT, self.OnHelpAbout)
+
+ ###################################################################
+ # Attach menus to the menubar
+ self.menubar.Append(filemenu, '&File')
+ self.menubar.Append(navmenu, '&Next/Previous')
+ self.menubar.Append(plotmenu, '&Plot')
+ self.menubar.Append(valmenu, '&Mark')
+ self.menubar.Append(helpmenu, '&Help')
+
+ self.SetMenuBar(self.menubar)
+
+ ###################################################################
+ #Disable by default some menus and buttons
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 0)
+ self.menubar.Enable(ID_SAVEP, 0)
+ self.menubar.Enable(ID_SAVESP, 0)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ # A status bar to tell people what's happening
+ self.CreateStatusBar(1)
+
+ self.SetAutoLayout(True)
+
+ ###################################################################
+ self.panel = wx.Panel(self, -1, style=wx.SIMPLE_BORDER)
+ #in this case and all the others we use layout constraints
+ #I couldn't understand easily the sizers, while layout constraints seem
+ #quite easy to set up and they work very well.
+ #self.panel will contain the listctrl and button panel
+
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self, wx.Top, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 30)
+ self.panel.SetConstraints(lc)
+
+ ###################################################################
+ #the peplistctrlpanel - with the list of peptides and interesting data
+ self.smalldict = {1:("pepseq", "0", "mzh", "mzhcalc", "mono", "deuter", "ratio", "corr",
+ "localbg", "valid")}
+ #we need this to fill up the listctrl at program initialization
+ self.lb = PepListCtrlPanel(self.panel, dictwithdata=self.smalldict)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.PercentOf(self.panel, wx.Right, 80) #it will take up 80% of the panel
+ lc.left.SameAs(self.panel, wx.Left, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.lb.SetConstraints(lc)
+ ###################################################################
+ self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.lb.list)
+ ###################################################################
+ #the panel to hold the three buttons
+ self.btnpanel1 = wx.Panel(self.panel, -1, style=wx.SIMPLE_BORDER)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.SameAs(self.panel, wx.Right, 10)
+ lc.left.SameAs(self.lb, wx.Right, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.btnpanel1.SetConstraints(lc)
+ ###################################################################
+ #set up the buttons and bind to the corresponding functions
+ self.btn1 = wx.Button(self.btnpanel1, ID_BTN1, " Validate ", wx.DefaultPosition)
+ self.btn2 = wx.Button(self.btnpanel1, ID_BTN2, "INvalidate", wx.DefaultPosition)
+ self.btn3 = wx.Button(self.btnpanel1, ID_BTN3, "Set Bgrnd.", wx.DefaultPosition)
+ wx.EVT_BUTTON(self, ID_BTN1, self.OnValidate)
+ wx.EVT_BUTTON(self, ID_BTN2, self.OnInvalidate)
+ wx.EVT_BUTTON(self, ID_BTN3, self.OnSetLocalBg)
+
+ #Disable by default the three buttons
+ self.btn1.Enable(False)
+ self.btn2.Enable(False)
+ self.btn3.Enable(False)
+ ###################################################################
+ #layout the buttons on the btnpanel1
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btnpanel1, wx.CentreX)
+ lc.top.SameAs(self.btnpanel1, wx.Top, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn1.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.centreY.SameAs(self.btnpanel1, wx.CentreY)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn2.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.bottom.SameAs(self.btnpanel1, wx.Bottom, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn3.SetConstraints(lc)
+
+ ###################################################################
+ #A black panel to give contrast to the plot
+ self.panelplot = wx.Window(self, -1)
+ self.panelplot.SetBackgroundColour(wx.BLACK)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panel, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 85)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.panelplot.SetConstraints(lc)
+ ###################################################################
+ #The plot itself in self.panelplot
+ self.plotcanvas = PlotCanvas(self.panelplot, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panelplot, wx.Top, 2)
+ lc.left.SameAs(self.panelplot, wx.Left, 2)
+ lc.bottom.SameAs(self.panelplot, wx.Bottom, 2)
+ lc.right.SameAs(self.panelplot, wx.Right, 2)
+ self.plotcanvas.SetConstraints(lc)
+ ###################################################################
+ #A panel to hold the TextCtrl called self.log
+ self.logpanel = wx.Window(self, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panelplot, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.SameAs(self, wx.Bottom, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.logpanel.SetConstraints(lc)
+ ###################################################################
+ #The text control that will hold informations on the protein and file used
+ self.log = wx.TextCtrl(self.logpanel, -1,
+ style = wx.TE_MULTILINE|wx.TE_READONLY|wx.HSCROLL)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.logpanel, wx.Top, 2)
+ lc.left.SameAs(self.logpanel, wx.Left, 0)
+ lc.bottom.SameAs(self.logpanel, wx.Bottom, 2)
+ lc.right.SameAs(self.logpanel, wx.Right, 0)
+ self.log.SetConstraints(lc)
+ self.log.AppendText("> Hello. Load a LILAMS XML file from the File> menu (or Cmd+O).")
+ ###################################################################
+ # Create mouse event for showing cursor coords in status bar
+ self.plotcanvas.Bind(wx.EVT_LEFT_DOWN, self.OnMouseLeftDown)
+ self.plotcanvas.Bind(wx.EVT_LEFT_DCLICK, self.OnMouseDClick)
+ self.plotcanvas.SetEnableZoom(1) #to ensure zoom by default
+
+ self.Show(True)
+
+ ###################################################################
+ ## Main Frame function definitions ################################
+ ###################################################################
+
+ def OnXMLOpen(self, event):
+ """
+ Opens a XML file with SILAC data and generates
+ an ElementTree instance containing the data
+ in the variable self.data
+ """
+ self.resetDefaults()
+ wildcard = "XML file (*.xml)|*.xml|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a SILAC XML file:",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ try:
+ if not self.XMLOpen(dirname, filename):
+ msg = """
+ The file you wanted to open does not
+ contain valid SILAC XML data. Try opening it with
+ a text editor to see what is the problem."""
+ dlg = wx.MessageDialog(self, msg, 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ finally:
+ dlg.Destroy()
+
+ def XMLOpen(self, dirname, filename):
+ """
+ Will allow calls for XMLOpen from Previous
+ and Next calls. Returns True if everything OK.
+
+ -uses get_flist_xml to set up the file list
+ -uses map_pos_inlist to set up self.where
+ -uses self.PlotSpectrumXML to plot the first peptide
+ in file
+ -uses self.PopulateList to populate the self.lb list
+ control with data
+ -uses self.GenerateListDict to generate the dictionary
+ used to describe the data in the self.lb control
+ """
+ filename=filename
+ dirname=dirname
+ self.defaultdirname = dirname
+ fname = os.path.join(dirname, filename)
+ #self.fnameout = fname+"x"
+ #we write in the same xml file, overwriting previous file
+ self.fnameout = fname
+ self.filelist = get_flist_xml(dirname)
+ self.where = map_pos_inlist(self.filelist, filename)
+ try:
+ tree = ET.parse(fname)
+ self.data = tree.getroot()
+ #the root is a <protdata> entry
+ self.PlotSpectrumXML(0, title="peptide 1")
+ self.PopulateList(self.GenerateListDict(self.data))
+ #Clear the log, write text to it about the opened file
+ self.log.Remove(0, self.log.GetLastPosition())
+ self.log.AppendText("\n> Opened %s xml file.\n"%filename)
+ self.log.AppendText("> Mowse score: %s, database: %s, ppm tolerance: %s.\n"%(self.data[0][3].text,
+ self.data[0][1].text, self.data[0][2].text))
+ self.log.AppendText("> Spot identification: %s.\n"%self.data[0][0].text)
+ self.log.AppendText("> Identified protein: %s, accesion number: %s.\n"%(self.data[2].text, self.data[1].text))
+ self.log.AppendText("> Peptide coverage: %s percent, matched peptides: %s.\n"%(self.data[0][4].text[:-1], self.data[0][5].text))
+ self.menubar.Enable(ID_NEXTF, 1)
+ self.menubar.Enable(ID_PREVF, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.btn1.Enable(True)
+ self.btn2.Enable(True)
+ self.btn3.Enable(True)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVESP, 0)
+ return True
+ except:
+ return False
+
+ def PlotSpectrumXML(self, index=0, title=""):
+ """
+ Recover and plot data for the record that has <index>
+ It is found in self.data[5] - that is pepdata,
+ the subnode is 10 for <spectrum> and 0, 1 for
+ the two lists mz and int. "5 "is contained in self.pdatapos
+
+ -uses self.PlotArray - a function to do the plotting
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+ self.PlotArray(dataforarray, "blue", title)
+
+ def PlotArray(self, data_array, color, title):
+ """
+ Used to plot on the plotcanvas the points of a data_array
+ Default is autoscale, used by PlotSpectrumXML
+ """
+ self.line = PolyLine(data_array, colour = color)
+ self.plotcanvas.Draw(PlotGraphics([self.line, ], title, "m/z", ""))
+ #self.plotcanvas.Redraw()
+
+ def GenerateListDict(self, xmldata):
+ """
+ forms a dictionary {1:["a", "b", "c"], 2:...}
+ for the PepListCtrlPanel widget - to populate
+ with XML data
+ """
+ self.entriesdict = {}
+ for i in range(len(xmldata[self.pdatapos])):
+ self.entriesdict[i] = (self.GetValXML(i, 'pepseq'),
+ self.GetValXML(i, 'leucines'),
+ self.GetValXML(i, 'mzh'),
+ self.GetValXML(i, 'calc_mzh'),
+ self.GetValXML(i, 'mono_iso_int'),
+ self.GetValXML(i, 'deuterated_intensity'),
+ self.GetValXML(i, 'ratio'),
+ self.GetValXML(i, 'corrected_ratio'),
+ self.GetValXML(i, 'local_bg'),
+ self.GetValXML(i, 'validated'))
+ return self.entriesdict
+
+ def PopulateList(self, externaldict):
+ """
+ a wrapper to the function with the same name in self.lb
+ """
+ self.lb.PopulateList(externaldict)
+
+ def OnItemSelected(self, event):
+ """
+ Activated when one item in the self.lb list control
+ is selected. Determines the generation of a unique key
+ that will allow a correspondence between the list
+ elements and the underlying ElementTree Element
+ - uses MapUniqueKey function
+ """
+ #print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.lb.list.GetItemText(self.currentItem)+self.lb.getColumnText(self.currentItem, 2)
+ self.index = self.MapUniqueKey(self.uniquekey)
+ #print self.index, "self.index"
+ self.PlotSpectrumXML(self.index, title = self.GetValXML(self.index, 'pepseq')+\
+ " / "+self.GetValXML(self.index, 'mzh'))
+ self.menubar.Enable(ID_SAVEDATA, 1)
+ self.menubar.Enable(ID_SAVESP, 1)
+ event.Skip()
+ #the self.index variable allows us to recover and change the data if validation occurs
+
+ def MapUniqueKey(self, uniquekey):
+ """
+ Used by <OnItemSelected> to allow a correspondence between
+ self.currentItem - in the list and self.index in the ElementTree
+ Element representing data read from the XML SILAC file
+ """
+ result = 0
+ for i in range(len(self.data[self.pdatapos])):
+ #testing [0] is peptide sequence [1] is submitted m/z+h mass
+ if uniquekey == self.data[self.pdatapos][i][0].text+\
+ self.data[self.pdatapos][i][1].text:
+ #the index of the correspoinding key was found
+ result = i
+ break
+ return result
+
+ def OnValidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "YES")
+ self.SetXMLValidated(self.index, "YES")
+
+ def OnInvalidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "NO")
+ self.SetXMLValidated(self.index, "NO")
+
+ def SetXMLValidated(self, index, what):
+ """
+ 7 is the actual position of the <validated> field
+ in the self.data - coming from the SILAC XML tree
+ """
+ self.data[self.pdatapos][index][7].text = what
+
+ def GetValXML(self, index=0, what='pepseq'):
+ """
+ Returns the text attribute of an entry in an Element
+ object based on the self.XMLdict dictionary that maps
+ numbers to tags - definition in the init of the main
+ frame. By default it returns the peptide sequence of
+ the first record.
+
+ self.pdatapos - indicates the position of the <pepdata> in
+ the root of the pepdata xml entry
+ """
+ return self.data[self.pdatapos][index][self.XMLdict[what]].text
+
+ def OnXMLSave(self, event):
+ """
+ Writes the contents of self.data to the self.fnameout
+ (established when the actual file was opened)
+ """
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ def OnSpectrumSave(self, event):
+ self.SpectrumSave(self.index)
+
+ def SpectrumSave(self, index=0):
+ """
+ Writes the contents of the actual selected spectrum
+ to a given file name, in tab delimited format
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(
+ self, message="Save plot data to ...", defaultDir = self.defaultdirname,
+ defaultFile="pepspecdata.txt", wildcard=wildcard, style=wx.SAVE
+ )
+ dlg.SetFilterIndex(0)
+ if dlg.ShowModal() == wx.ID_OK:
+ path = dlg.GetPath()
+ try:
+ fout = open(path, "w")
+ for line in dataforarray:
+ fout.write('%.3f\t%d\n'%(line[0], line[1]))
+ fout.close()
+
+ self.SetStatusText("Data saved to file %s"%path)
+ except IOError:
+ dlg = wx.MessageDialog(self, "Error. Maybe the output file is in use...", 'Problem saving data',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ dlg.Destroy()
+
+ def OnNextFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO| wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+ #debugging here
+ #pdb.set_trace()
+ if len(self.filelist) > 0:
+ #print self.filelist
+ #print self.where
+ if self.where < len(self.filelist)-1:
+ #fname = os.path.split(self.filelist[self.where+1]
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where+1])
+ #self.where += 1 there is a risk in using global variables
+ #this one is already modified by XMLOpen to the correct value
+ else:
+ #we are at the end of the list, going on from the beginning
+ self.where = 0
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+ #self.where += 1
+
+ def OnPrevFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO | wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ if len(self.filelist) > 0:
+ if self.where > 0:
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where-1])
+ #self.where -= 1
+ else:
+ #we are at the beginning of the list
+ self.where = len(self.filelist)-1
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+ #self.where -= 1
+
+ def OnFullUnzoom(self, event):
+ self.plotcanvas.Reset()
+
+ def OnFileOpen(self, event):
+ """
+ Opens and plots a tab delimited text file
+ If not a recognized file, a message is displayed
+ Sets also the actual directory name: self.defaultdirname
+ """
+ self.resetDefaults()
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a tab delimited text file",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ self.filename=dlg.GetFilename()
+ self.dirname=dlg.GetDirectory()
+ self.defaultdirname = self.dirname
+ self.filelist = get_flist_txt(self.dirname)
+ fname = os.path.join(self.dirname, self.filename)
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ dlg.Destroy()
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", self.filename)
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ def PlotFile(self, fname):
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", os.path.split(fname)[1])
+
+ def OnFileClose(self, event):
+ self.plotcanvas.Clear()
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+
+ def OnMouseLeftDown(self,event):
+ self.localbg = abs(self.actualclick_y - self.previousclick_y)
+ s= "(m/z : %.2f, Intensity : %.2f)"%self.plotcanvas.GetXY(event)+\
+ " Local background : %.0f"%self.localbg
+ self.SetStatusText(s)
+ event.Skip()
+
+ def OnMouseDClick(self, event):
+ self.previousclick_y = self.actualclick_y
+ self.actualclick_y = self.plotcanvas.GetXY(event)[1]
+
+ def OnSetLocalBg(self, event):
+ """
+ Updates the local background data both in the shown list
+ and in self.data. Recalculated the corrected ratio
+ """
+ self.data[self.pdatapos][self.index][8].text = "%0.f"%self.localbg
+ deut = float(self.GetValXML(self.index, 'deuterated_intensity'))-self.localbg
+ monoiso = float(self.GetValXML(self.index, 'mono_iso_int'))-self.localbg
+ self.data[self.pdatapos][self.index][9].text = "%.2f"%(deut/monoiso)
+ self.lb.SetBg(self.currentItem, self.localbg, (deut/monoiso))
+
+ def OnSaveImage(self, event):
+ self.plotcanvas.SaveFile()
+
+ def OnFileExit(self, event):
+ self.Close()
+
+ def OnPlotRedraw(self,event):
+ self.plotcanvas.Redraw()
+
+ def OnPlotClear(self,event):
+ self.plotcanvas.Clear()
+
+ def OnPlotScale(self, event):
+ if self.plotcanvas.last_draw != None:
+ graphics, xAxis, yAxis= self.plotcanvas.last_draw
+ self.plotcanvas.Draw(graphics,(1,3.05),(0,1))
+
+ def OnEnableZoom(self, event):
+ self.plotcanvas.SetEnableZoom(event.IsChecked())
+
+ def OnEnableGrid(self, event):
+ self.plotcanvas.SetEnableGrid(event.IsChecked())
+
+ def OnEnableLegend(self, event):
+ self.plotcanvas.SetEnableLegend(event.IsChecked())
+ def OnReset(self,event):
+ self.plotcanvas.Reset()
+
+ def OnHelpAbout(self, event):
+ from wx.lib.dialogs import ScrolledMessageDialog
+ about = ScrolledMessageDialog(self, __doc__, "About...")
+ about.ShowModal()
+
+ def resetDefaults(self):
+ """Just to reset the fonts back to the PlotCanvas defaults"""
+ self.plotcanvas.SetFont(wx.Font(10,wx.SWISS,wx.NORMAL,wx.NORMAL))
+ self.plotcanvas.SetFontSizeAxis(10)
+ self.plotcanvas.SetFontSizeLegend(7)
+ self.plotcanvas.SetXSpec('auto')
+ self.plotcanvas.SetYSpec('auto')
+ self.plotcanvas.SetEnableZoom(1)
+
+#######################################################
+#######################################################
+################ PepListCtrlPanel ###############
+################ and PepListCtrl classes###############
+#######################################################
+#######################################################
+#######################################################
+#----------------------------------------------------------------------------
+# Name: ListCtrl.py
+# Purpose: Testing lots of stuff, controls, window types, etc.
+#
+# Author: Robin Dunn & Gary Dumer
+#
+# Created:
+# RCS-ID: $Id: ListCtrl.py,v 1.3 2004/03/05 00:06:32 RD Exp $
+# Copyright: (c) 1998 by Total Control Software
+# Licence: wxWindows license
+#
+# Modified by Cosmin Saveanu, IP, September 2004
+# to be able to deal with peptide entries for SILAC
+#----------------------------------------------------------------------------
+def getSmallUpArrowData():
+ return \
+'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00<IDATx\x9ccddbf\xa0\x040Q\xa4{h\x18\xf0\xff\xdf\xdf\xffd\x1b\x00\xd3\
+\x8c\xcf\x10\x9c\x06\xa0k\xc2e\x08m\xc2\x00\x97m\xd8\xc41\x0c \x14h\xe8\xf2\
+\x8c\xa3)q\x10\x18\x00\x00R\xd8#\xec\x95{\xc4\x11\x00\x00\x00\x00IEND\xaeB`\
+\x82'
+
+def getSmallUpArrowBitmap():
+ return BitmapFromImage(getSmallUpArrowImage())
+def getSmallUpArrowImage():
+ stream = cStringIO.StringIO(getSmallUpArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+
+def getSmallDnArrowData():
+ return \
+"\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00HIDATx\x9ccddbf\xa0\x040Q\xa4{\xd4\x00\x06\x06\x06\x06\x06\x16t\x81\
+\xff\xff\xfe\xfe'\xa4\x89\x91\x89\x99\x11\xa7\x0b\x90%\ti\xc6j\x00>C\xb0\x89\
+\xd3.\x10\xd1m\xc3\xe5*\xbc.\x80i\xc2\x17.\x8c\xa3y\x81\x01\x00\xa1\x0e\x04e\
+\x1d\xc4;\xb7\x00\x00\x00\x00IEND\xaeB`\x82"
+def getSmallDnArrowBitmap():
+ return BitmapFromImage(getSmallDnArrowImage())
+
+def getSmallDnArrowImage():
+ stream = cStringIO.StringIO(getSmallDnArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+class PepListCtrl(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin):
+
+ def __init__(self, parent, ID, pos=wx.DefaultPosition,
+ size=wx.DefaultSize, style=0):
+ wx.ListCtrl.__init__(self, parent, ID, pos, size, style)
+ listmix.ListCtrlAutoWidthMixin.__init__(self)
+
+class PepListCtrlPanel(wx.Panel, listmix.ColumnSorterMixin):
+
+ def __init__(self, parent, dictwithdata={}):
+ wx.Panel.__init__(self, parent, -1, style=wx.WANTS_CHARS)
+ tID = wx.NewId()
+ self.il = wx.ImageList(16, 16)
+ self.sm_up = self.il.Add(getSmallUpArrowBitmap())
+ self.sm_dn = self.il.Add(getSmallDnArrowBitmap())
+ self.list = PepListCtrl(self, tID,
+ style=wx.LC_REPORT
+ | wx.SUNKEN_BORDER
+ | wx.LC_SINGLE_SEL
+ #| wx.LC_HRULES
+ #| wx.LC_EDIT_LABELS
+ #| wxLC_NO_HEADER
+ #| wxLC_VRULES
+ )
+ self.list.SetImageList(self.il, wx.IMAGE_LIST_SMALL)
+ self.PopulateList(dictwithdata)
+ # Now that the list exists we can init the other base class,
+ # see wxPython/lib/mixins/listctrl.py
+
+ listmix.ColumnSorterMixin.__init__(self, 10)
+ #self.SortListItems(0, True)
+ self.Bind(wx.EVT_SIZE, self.OnSize)
+ #self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.list)
+ self.Bind(wx.EVT_LIST_COL_CLICK, self.OnColClick, self.list)
+
+ def PopulateList(self, externaldict):
+ """
+ Constructs the headings of the list control
+ and populates it with data
+ """
+
+ self.itemDataMap = externaldict
+ self.list.ClearAll()
+ if 0:
+ # for normal, simple columns, you can add them like this:
+ self.list.InsertColumn(0, "Peptide")
+ self.list.InsertColumn(1, "Leucines", wx.LIST_FORMAT_RIGHT)
+ self.list.InsertColumn(2, "m/z measured")
+ #etc...
+ else:
+ # but since we want images on the column header we have to do it the hard way:
+ info = wx.ListItem()
+ info.m_mask = wx.LIST_MASK_TEXT | wx.LIST_MASK_IMAGE | wx.LIST_MASK_FORMAT
+ info.m_image = -1
+ info.m_format = 0
+ info.m_text = "Peptide"
+ self.list.InsertColumnInfo(0, info)
+ #info.m_format = wx.LIST_FORMAT_RIGHT
+ info.m_format = 0
+ info.m_text = "Leucines"
+ self.list.InsertColumnInfo(1, info)
+ info.m_format = 0
+ info.m_text = "m/z meas."
+ self.list.InsertColumnInfo(2, info)
+
+ info.m_format = 0
+ info.m_text = "m/z calc."
+ self.list.InsertColumnInfo(3, info)
+
+ info.m_format = 0
+ info.m_text = "Base_int."
+ self.list.InsertColumnInfo(4, info)
+
+ info.m_format = 0
+ info.m_text = "Deut_int."
+ self.list.InsertColumnInfo(5, info)
+
+ info.m_format = 0
+ info.m_text = "Ratio"
+ self.list.InsertColumnInfo(6, info)
+
+ info.m_format = 0
+ info.m_text = "Corr_ratio"
+ self.list.InsertColumnInfo(7, info)
+
+ info.m_format = 0
+ info.m_text = "Local_bg"
+ self.list.InsertColumnInfo(8, info)
+
+ info.m_format = 0
+ info.m_text = "Valid."
+ self.list.InsertColumnInfo(9, info)
+ #Now put inside the data from the dictionary
+ items = externaldict.items()
+ for x in range(len(items)):
+ key, data = items[x]
+ self.list.InsertStringItem(x, data[0])
+ #self.list.InsertImageStringItem(x, data[0], self.sm_up)
+ self.list.SetStringItem(x, 1, data[1])
+ self.list.SetStringItem(x, 2, data[2])
+ self.list.SetStringItem(x, 3, data[3])
+ self.list.SetStringItem(x, 4, data[4])
+ self.list.SetStringItem(x, 5, data[5])
+ self.list.SetStringItem(x, 6, data[6])
+ self.list.SetStringItem(x, 7, data[7])
+ self.list.SetStringItem(x, 8, data[8])
+ self.list.SetStringItem(x, 9, data[9])
+ self.list.SetItemData(x, key) #why is that necessary ?
+ #Set colors for the adnotation - is light grey if
+ #no leucine exists in the peptide sequence
+ if data[9] == "YES":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if data[9] == "NO":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+ if data[1] == "0":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.LIGHT_GREY)
+ self.list.SetItem(item)
+
+ for i in range(9):
+ self.list.SetColumnWidth(i, 60)
+ #self.list.SetColumnWidth(i, wx.LIST_AUTOSIZE)
+ self.list.SetColumnWidth(9, 100)
+ # show how to select an item
+ #self.list.SetItemState(5, wx.LIST_STATE_SELECTED, wx.LIST_STATE_SELECTED)
+ self.currentItem = 0
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetListCtrl(self):
+ return self.list
+
+ def SetValidated(self, where, what):
+ """
+ Called when the OnValidate or OnInvalidate are activated
+ Changes the 9th element in the current list item to "YES"
+ or "NO"
+ """
+ self.list.SetStringItem(where, 9, what)
+ if what == "YES":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if what == "NO":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+
+ def SetBg(self, where, bg, ratio):
+ """
+ Shows local background value in the list and
+ the updated value of corrected ratio
+ """
+ self.list.SetStringItem(where, 8, "%.0f"%bg)
+ self.list.SetStringItem(where, 7, "%.2f"%ratio)
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetSortImages(self):
+ return (self.sm_dn, self.sm_up)
+
+ def getColumnText(self, index, col):
+ item = self.list.GetItem(index, col)
+ return item.GetText()
+
+ def OnItemSelected(self, event):
+ """
+ Overwritten by its equivalent in MainFrame
+ """
+ ##print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.list.GetItemText(self.currentItem)+\
+ self.getColumnText(self.currentItem, 1)
+ #print self.uniquekey
+ event.Skip()
+
+ def OnColClick(self, event):
+ #print ("OnColClick: %d\n" % event.GetColumn())
+ event.Skip()
+
+ def OnSize(self, event):
+ w,h = self.GetClientSizeTuple()
+ self.list.SetDimensions(0, 0, w, h)
+
+#######################################################
+#the equivalent of a main function.
+app = wx.PySimpleApp()
+frame = MainFrame(None, -1, "SILAC validator v. 0.2")
+app.SetTopWindow(frame)
+app.MainLoop()
+#######################################################
diff --git a/src/lilamslaunchGUI.py b/src/lilamslaunchGUI.py
new file mode 100644
index 0000000000000000000000000000000000000000..b4a453d23fc4f0a874da7bf92c5034de06fd4c00
--- /dev/null
+++ b/src/lilamslaunchGUI.py
@@ -0,0 +1,254 @@
+#!/usr/bin/env pythonw
+"""
+LilamslaunchGUI.py is a GUI for the lilamsxml.py script
+Allows interactive choosing of a file containing
+pairs of Spectrum/MSfit file names (complete path)
+and of a file containing ORF names of interest
+
+The output consists of xml files with the same name
+as the msfit html files used for quantitation.
+
+Cosmin, IP - September 2004
+Modified in Jan 2008 to be able to locate the
+lilamsxml script and the ipc executable path
+Updated the import of the ElementTree XML module
+to use the one integrated in Python 2.5
+"""
+
+import os, string, sys, re, wx
+from string import lstrip, rstrip
+#from elementtree import ElementTree as ET
+#import cElementTree as ET
+import xml.etree.cElementTree as ET
+#works with Python 2.5 and higher
+
+def ReadFromFile(filename, skip=0):
+ """
+ Obtain data from a tab delimited file into a list
+
+ Needs the import string statement
+ The <skip> parameter indicate the number of lines not
+ read.
+
+ """
+ data = []
+ f=open(filename, 'r')
+ for i in range(skip):
+ f.readline()
+ while (1):
+ line = f.readline()
+ if line == "": break
+ data.append(line.strip().split('\t'))
+ f.close()
+ return data
+ #the returned data will be in string format
+
+
+#generate IDs for the interface
+[ID_GO, ID_EXIT, ID_ABOUT, ID_PAIRS, ID_ORFS, ID_IPC, ID_LILAMS] = map(lambda init_ctrls: wx.NewId(), range(7))
+
+class MainFrame(wx.Frame):
+
+ def __init__(self, parent, id, title):
+ wx.Frame.__init__(self, parent, id, title,
+ wx.DefaultPosition, (600, 200))
+
+ #default directory for saving, will be modified after first save
+ self.defaultdirname = "."
+
+ self.orffilename_ok = False
+ self.pairsfilename_ok = False
+ self.ipc_path = ""
+ self.lilams_path = ""
+
+ # Create the menu bar and items
+ self.menubar = wx.MenuBar()
+
+ filemenu = wx.Menu()
+ filemenu.Append(ID_PAIRS, '&Open file with pairs...', 'Open a file that contains pairs of complete file names separated by tabs - spectrum file .. Msfit identification file')
+ filemenu.Append(ID_ORFS, 'Open f&ile with ORFs...', 'Open a list of ORFs to be considered for calculations')
+ filemenu.Append(ID_IPC, 'Choose &IPC location...', 'Choose the ipc program path.')
+ filemenu.Append(ID_LILAMS, 'Choose Li&lams.py location...', 'Choose the lilamsxml script.')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_GO, '&Run...\tCtrl+R', 'Run: perform calculations on the dataset')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_EXIT, '&Quit\tCtrl+Q', 'Exit program')
+
+ helpmenu = wx.Menu()
+ helpmenu.Append(ID_ABOUT, 'About...\tCtrl+E', 'About this program')
+
+ # Bind the events to methods
+ wx.EVT_MENU(self, ID_PAIRS, self.OnFileOpenPairs)
+ wx.EVT_MENU(self, ID_ORFS, self.OnFileOpenORFs)
+ wx.EVT_MENU(self, ID_IPC, self.OnIPCChoose)
+ wx.EVT_MENU(self, ID_LILAMS, self.OnLilamsChoose)
+ wx.EVT_MENU(self, ID_GO, self.OnGo)
+ wx.EVT_MENU(self, ID_EXIT, self.OnFileExit)
+ wx.EVT_MENU(self, ID_ABOUT, self.OnHelpAbout)
+
+ # Attach menus to the menubar
+ self.menubar.Append(filemenu, '&File')
+ self.menubar.Append(helpmenu, '&Help')
+
+ self.SetMenuBar(self.menubar)
+ #disable by default the Run menu
+ self.menubar.Enable(ID_GO, 0)
+
+ # A status bar to tell people what's happening
+ self.CreateStatusBar(1)
+ self.Show(True)
+
+ def OnFileOpenORFs(self, event):
+ """
+ Obtain the name of the file with the ORFs list
+ Set the self.orfname_ok to True
+ """
+ wildcard = "Text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose the interesting ORFs list text file",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.defaultdirname = dirname
+ self.orffilename = os.path.join(dirname, filename)
+ dlg.Destroy()
+ self.orffilename_ok = True
+ else:
+ self.orffilename_ok = False
+ if self.orffilename_ok == True and self.pairsfilename_ok == True:
+ self.menubar.Enable(ID_GO, 1)
+ else:
+ self.menubar.Enable(ID_GO, 0)
+
+ def OnFileOpenPairs(self, event):
+ """
+ Obtain the name of the file with the pairs
+ spectrum files/msfit files - complete paths
+ """
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose the tab delimited text file with spectra/msfit",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.defaultdirname = dirname
+ self.pairsfilename = os.path.join(dirname, filename)
+ dlg.Destroy()
+ #self.menubar.Enable(ID_SAVEDATA, 0)
+ self.pairsfilename_ok = True
+ else:
+ self.pairsfilename_ok = False
+
+ if self.orffilename_ok == True and self.pairsfilename_ok == True:
+ self.menubar.Enable(ID_GO, 1)
+ else:
+ self.menubar.Enable(ID_GO, 0)
+
+ def OnIPCChoose(self, event):
+ """
+ Obtain the path to the IPC executable with a dialog
+ Set the self.ipc_path
+ """
+ wildcard = "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose the interesting ORFs list text file",
+ "/usr/local/", "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.ipc_path = os.path.join(dirname, filename)
+ dlg.Destroy()
+ #self.menubar.Enable(ID_SAVEDATA, 0)
+
+ def OnLilamsChoose(self, event):
+ """
+ Obtain the path to the python program used for calculations with a dialog
+ Set the self.lilams_path
+ """
+ wildcard = "Python files (*.py)|*.py"
+ dlg = wx.FileDialog(self, "Choose the lilams xml python script to run",
+ ".", "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.lilams_path = os.path.join(dirname, filename)
+ dlg.Destroy()
+ #self.menubar.Enable(ID_SAVEDATA, 0)
+
+ def OnGo(self, event):
+ #scriptname = r"python lilamsxml.py"
+ scriptname = "python " + self.lilams_path
+ ipccommand = "-c " + self.ipc_path
+
+ if "" not in [self.ipc_path, self.lilams_path]:
+ #HTMLbasepath = "/Volumes/Fire/CosminF/200409September/SILAC_Rlp24/Msfit/"
+ #SPECTRAbasepath = "/Volumes/Fire/CosminF/200409September/SILAC_Rlp24/Spectra/"
+ #datalist = ReadFromFile(HTMLbasepath+"Results/pairsspectmsfitOK.txt")
+ datalist = ReadFromFile(self.pairsfilename)
+
+ #orffilename = HTMLbasepath+"Results/listeORFpreriboetcontam.tab"
+ orffilecomm = "-p " + self.orffilename
+
+ print len(datalist), "pairs of files to be analysed"
+ #print datalist
+ #print datalist
+ paircounter = 0
+ dlg = wx.ProgressDialog("Quantitating peptides...", "Working...", maximum = len(datalist), parent = self,
+ style = wx.PD_CAN_ABORT| wx.PD_APP_MODAL)
+
+ for pair in datalist:
+ #generate as many xml files as html files are present
+
+ #the pair contains the name of the spectrum file and the name of the msfit file
+ spectrumname = "-s " + pair[0]
+ identifname = "-i " + pair[1]
+
+ tailspecfile = os.path.split(pair[0])[1]
+ splittedid = os.path.splitext(tailspecfile)
+ splittedpath = os.path.split(pair[1])
+ splittedfname = os.path.splitext(splittedpath[1])
+ xmlfname = splittedfname[0] + "_" +splittedid[0] + ".xml"
+ resultfname = os.path.join(splittedpath[0], xmlfname)
+
+ try:
+ pipe_s = os.popen("%s %s %s %s %s" % (scriptname, spectrumname, identifname,
+ ipccommand, orffilecomm))
+ result = pipe_s.read()
+ #the result is an xml formatted string
+ if result <> "nodata":
+ fileout = open(resultfname, "w")
+ fileout.write(result)
+ fileout.close()
+ paircounter+=1
+ print paircounter, pair[0], pair[1], "done..."
+ dlg.Update(paircounter, "Done "+ xmlfname +".")
+ except:
+ print pair, "didn't work"
+ dlg.Destroy()
+
+ else:
+ dlg = wx.MessageDialog(self, 'IPC path and lilams script must be specified',
+ 'Alert', wx.OK | wx.ICON_INFORMATION)
+ try:
+ result = dlg.ShowModal()
+ if result == wx.ID_OK:
+ dlg.Destroy()
+ finally:
+ dlg.Destroy()
+
+ def OnHelpAbout(self, event):
+ from wx.lib.dialogs import ScrolledMessageDialog
+ about = ScrolledMessageDialog(self, __doc__, "About...")
+ about.ShowModal()
+
+ def OnFileExit(self, event):
+ self.Close()
+
+
+
+app = wx.PySimpleApp()
+frame = MainFrame(None, -1, "LilamsXML launcher v. 0.2")
+app.SetTopWindow(frame)
+app.MainLoop()
+
diff --git a/src/lilamslauncher_gui_20080130.py~ b/src/lilamslauncher_gui_20080130.py~
new file mode 100644
index 0000000000000000000000000000000000000000..fc1cc02ac42e0a89187bb71ff8ebff6fbaa68674
--- /dev/null
+++ b/src/lilamslauncher_gui_20080130.py~
@@ -0,0 +1,258 @@
+#!/usr/bin/env python
+"""
+Lilamslauncher is a GUI for the lilams script
+Allows interactive choosing of a file containing
+pairs of Spectrum/MSfit file names (complete path)
+and of a file containing ORF names of interest
+
+The output consists of xml files with the same name
+as the msfit html files used for quantitation.
+
+Cosmin, IP - September 2004
+Modified in Jan 2008 to be able to locate the
+lilamsxml script and the ipc executable path
+"""
+
+import os, string, sys, re, wx
+from string import lstrip, rstrip
+#from elementtree import ElementTree as ET
+import cElementTree as ET
+
+def ReadFromFile(filename, skip=0):
+ """
+ Obtain data from a tab delimited file into a list
+
+ Needs the import string statement
+ The <skip> parameter indicate the number of lines not
+ read.
+
+ """
+ data = []
+ f=open(filename, 'r')
+ for i in range(skip):
+ f.readline()
+ while (1):
+ line = f.readline()
+ if line == "": break
+ data.append(line.strip().split('\t'))
+ f.close()
+ return data
+ #the returned data will be in string format
+
+
+#generate IDs for the interface
+[ID_GO, ID_EXIT, ID_ABOUT, ID_PAIRS, ID_ORFS, ID_IPC, ID_LILAMS] = map(lambda init_ctrls: wx.NewId(), range(7))
+
+class MainFrame(wx.Frame):
+
+ def __init__(self, parent, id, title):
+ wx.Frame.__init__(self, parent, id, title,
+ wx.DefaultPosition, (600, 200))
+
+ #default directory for saving, will be modified after first save
+ self.defaultdirname = "."
+
+ self.orffilename_ok = False
+ self.pairsfilename_ok = False
+ self.ipc_path = ""
+ self.lilams_path = ""
+
+ # Create the menu bar and items
+ self.menubar = wx.MenuBar()
+
+ filemenu = wx.Menu()
+ filemenu.Append(ID_PAIRS, '&Open file with pairs...', 'Open a file that contains pairs of complete file names separated by tabs - spectrum file .. Msfit identification file')
+ filemenu.Append(ID_ORFS, 'Open f&ile with ORFs...', 'Open a list of ORFs to be considered for calculations')
+ filemenu.Append(ID_IPC, 'Choose &IPC location...', 'Choose the ipc program path.')
+ filemenu.Append(ID_LILAMS, 'Choose Li&lams.py location...', 'Choose the lilamsxml script.')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_GO, '&Run...\tCtrl+R', 'Run: perform calculations on the dataset')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_EXIT, '&Quit\tCtrl+Q', 'Exit program')
+
+ helpmenu = wx.Menu()
+ helpmenu.Append(ID_ABOUT, 'About...\tCtrl+E', 'About this program')
+
+ # Bind the events to methods
+ wx.EVT_MENU(self, ID_PAIRS, self.OnFileOpenPairs)
+ wx.EVT_MENU(self, ID_ORFS, self.OnFileOpenORFs)
+ wx.EVT_MENU(self, ID_IPC, self.OnIPCChoose)
+ wx.EVT_MENU(self, ID_LILAMS, self.OnLilamsChoose)
+ wx.EVT_MENU(self, ID_GO, self.OnGo)
+ wx.EVT_MENU(self, ID_EXIT, self.OnFileExit)
+ wx.EVT_MENU(self, ID_ABOUT, self.OnHelpAbout)
+
+ # Attach menus to the menubar
+ self.menubar.Append(filemenu, '&File')
+ self.menubar.Append(helpmenu, '&Help')
+
+ self.SetMenuBar(self.menubar)
+ #disable by default the Run menu
+ self.menubar.Enable(ID_GO, 0)
+
+ # A status bar to tell people what's happening
+ self.CreateStatusBar(1)
+ self.Show(True)
+
+ def OnFileOpenORFs(self, event):
+ """
+ Obtain the name of the file with the ORFs list
+ Set the self.orfname_ok to True
+ """
+ wildcard = "Text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose the interesting ORFs list text file",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.defaultdirname = dirname
+ self.orffilename = os.path.join(dirname, filename)
+ dlg.Destroy()
+ #self.menubar.Enable(ID_SAVEDATA, 0)
+ self.orffilename_ok = True
+ else:
+ self.orffilename_ok = False
+ if self.orffilename_ok == True and self.pairsfilename_ok == True:
+ self.menubar.Enable(ID_GO, 1)
+ else:
+ self.menubar.Enable(ID_GO, 0)
+
+ def OnFileOpenPairs(self, event):
+ """
+ Obtain the name of the file with the pairs
+ spectrum files/msfit files - complete paths
+ """
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose the tab delimited text file with spectra/msfit",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.defaultdirname = dirname
+ self.pairsfilename = os.path.join(dirname, filename)
+ dlg.Destroy()
+ #self.menubar.Enable(ID_SAVEDATA, 0)
+ self.pairsfilename_ok = True
+ else:
+ self.pairsfilename_ok = False
+
+ if self.orffilename_ok == True and self.pairsfilename_ok == True:
+ self.menubar.Enable(ID_GO, 1)
+ else:
+ self.menubar.Enable(ID_GO, 0)
+
+ def OnIPCChoose(self, event):
+ """
+ Obtain the path to the IPC executable with a dialog
+ Set the self.ipc_path
+ """
+ wildcard = "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose the interesting ORFs list text file",
+ "/usr/local/", "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.ipc_path = os.path.join(dirname, filename)
+ dlg.Destroy()
+ #self.menubar.Enable(ID_SAVEDATA, 0)
+ else:
+ self.ipc_path = ""
+
+ def OnLilamsChoose(self, event):
+ """
+ Obtain the path to the python program used for calculations with a dialog
+ Set the self.lilams_path
+ """
+ wildcard = "Python files (*.py)|*.py"
+ dlg = wx.FileDialog(self, "Choose the lilams xml python script to run",
+ ".", "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ self.lilams_path = os.path.join(dirname, filename)
+ dlg.Destroy()
+ #self.menubar.Enable(ID_SAVEDATA, 0)
+ else:
+ self.lilams_path = ""
+
+
+
+ def OnGo(self, event):
+ #scriptname = r"python lilamsxml.py"
+ scriptname = "python " + self.lilams_path
+ ipccommand = "-c " + self.ipc_path
+ dlg = wx.MessageDialog(self, 'IPC path and lilams script must be specified',
+ 'Alert', wx.OK | wx.ICON_INFORMATION)
+ try:
+ result = dlg.ShowModal()
+ if result == wx.ID_OK:
+ dlg.Destroy()
+ finally:
+ dlg.Destroy()
+ if "" not in [self.ipc_path, self.lilams_path]:
+ #HTMLbasepath = "/Volumes/Fire/CosminF/200409September/SILAC_Rlp24/Msfit/"
+ #SPECTRAbasepath = "/Volumes/Fire/CosminF/200409September/SILAC_Rlp24/Spectra/"
+ #datalist = ReadFromFile(HTMLbasepath+"Results/pairsspectmsfitOK.txt")
+ datalist = ReadFromFile(self.pairsfilename)
+
+ #orffilename = HTMLbasepath+"Results/listeORFpreriboetcontam.tab"
+ orffilecomm = "-p " + self.orffilename
+
+ print len(datalist), "pairs of files to be analysed"
+ #print datalist
+ #print datalist
+ paircounter = 0
+ dlg = wx.ProgressDialog("Quantitating peptides...", "Working...", maximum = len(datalist), parent = self,
+ style = wx.PD_CAN_ABORT| wx.PD_APP_MODAL)
+
+ for pair in datalist:
+ #generate as many xml files as html files are present
+
+ #the pair contains the name of the spectrum file and the name of the msfit file
+ spectrumname = "-s " + pair[0]
+ #spectrumname = "-s " + SPECTRAbasepath + pair[0]
+ identifname = "-i " + pair[1]
+
+ tailspecfile = os.path.split(pair[0])[1]
+ splittedid = os.path.splitext(tailspecfile)
+ #identifname = "-i " + HTMLbasepath + pair[1]
+ splittedpath = os.path.split(pair[1])
+ splittedfname = os.path.splitext(splittedpath[1])
+ xmlfname = splittedfname[0] + "_" +splittedid[0] + ".xml"
+ resultfname = os.path.join(splittedpath[0], xmlfname)
+
+ try:
+ pipe_s = os.popen("%s %s %s %s %s" % (scriptname, spectrumname, identifname,
+ ipccommand, orffilecomm))
+ #print "%s %s %s %s" % (scriptname, spectrumname, identifname, orffilecomm)
+ result = pipe_s.read()
+ #the result is an xml formatted string
+ if result <> "nodata":
+ fileout = open(resultfname, "w")
+ fileout.write(result)
+ fileout.close()
+ paircounter+=1
+ print paircounter, pair[0], pair[1], "done..."
+ dlg.Update(paircounter, "Done "+ xmlfname +".")
+ except:
+ print pair, "didn't work"
+ dlg.Destroy()
+
+ def OnHelpAbout(self, event):
+ from wx.lib.dialogs import ScrolledMessageDialog
+ about = ScrolledMessageDialog(self, __doc__, "About...")
+ about.ShowModal()
+
+ def OnFileExit(self, event):
+ self.Close()
+
+
+
+app = wx.PySimpleApp()
+frame = MainFrame(None, -1, "LilamsXML launcher v. 0.2")
+app.SetTopWindow(frame)
+app.MainLoop()
+
+
diff --git a/src/lilamsxml.py b/src/lilamsxml.py
new file mode 100644
index 0000000000000000000000000000000000000000..881850546d6e6958a8ed10aea90cc79fd0582e8c
--- /dev/null
+++ b/src/lilamsxml.py
@@ -0,0 +1,962 @@
+#!/usr/bin/env python
+"""
+lilamsxml.py - python script for the analysis
+of SILAC experiments with MALDI spectra
+and MSFit protein identifications
+
+first version - September 2003
+this version - September 2004
+slightly revised in oct 2005 and jan 2008
+
+Allows generation of XML output containing
+the whole information used for quantitations
+As a result, the output of this script is an
+XML-like string with <pepdata>...</pepdata>
+as delimiters.
+
+Uses HTMLparser to parse the MSFit files. While much
+slower, this method is much more flexible
+
+GIM - Institut Pasteur
+first argument - spectrum (text format) (--spectrum, -s)
+second argument - Msfit file (html format) (--msfithtml, -i)
+third argument - a list of ORFs that will be quantified (--orflist, -p)
+fourth argument - the path to the ipc, Isotope Pattern Calculator
+executable (--ipc_path, -c) as it may vary in localization
+
+Returns the results to the stdout with the peptide sequence and differences
+between observed peak intensities and their theoretical intensities.
+By default 10 peak differences from a family of peaks are returned
+this takes in account 0, 1, 2 or 3 leucines
+Makes use of the external IPC program for calculating
+peak mass distributions. The program should be installed locally.
+
+Modified on 20080130 to handle the absence of a mowse score
+Will report 1, if a Mowse score is present. April 2008, integrated the
+HTML parser in the script
+
+Cosmin SAVEANU, Genetique des Interactions Macromoleculaires
+Alain Jacquier's lab, Institut Pasteur, CNRS-URA 2171
+
+"""
+import sys, re, os, string, copy, math, getopt
+from HTMLParser import HTMLParser
+#import cElementTree as ET
+import xml.etree.cElementTree as ET #latest version integrated in Python 2.5
+
+#############################################
+####### MSFit html file parser #########
+#############################################
+# regular expressions used to isolate the elements of
+# parsed HTML files when extracting peptide and protein
+# information from MSFit files
+pepseqRE = r"sequence=([A-Z]+)\*?\\"
+peplinePATT = re.compile(pepseqRE)
+pepseqmodRE = r"\)([A-Z]+)\*?\("
+peplinePATTmod = re.compile(pepseqmodRE)
+
+class MSFit32Parser(HTMLParser):
+ """
+ A parser for MSFit HTML (version 3.2) results to obtain a
+ dictionary of data corresponding to the page, first entry only
+
+ Regular expression needed to extract sequences
+ of peptides from MSFit lines are compiled outside
+ functions to avoid repetition of re compilations
+ """
+ def reset(self):
+ HTMLParser.reset(self)
+ self.parsedlist =[]
+ #list of text chunks contained between tags
+ self.comments = []
+ #list of comment texts, this is
+ self.aftercomment = 0
+ #true if the text to be handled follows a comment
+ self.accesionRE = re.compile('> (.+)')
+ #allows extraction of ORF name from the first table
+
+ #two variables to allow start of scanning for peptide sequences in file
+ self.seeksequence = False
+ self.seeksequencemod = False
+
+ self.seqlist = []
+ #contains the list of sequences of all peptides
+
+ def handle_starttag(self, tag, attrs):
+ #print tag, attrs
+ if tag.lower() == "nobr":
+ self.seeksequencemod = True
+ elif tag.lower() == "script":
+ self.seeksequence = True
+ else:
+ self.seeksequencemod, self.seeksequence = False, False
+
+ def handle_comment(self, tag):
+ """
+ Overrides the handle_comment method
+ Builds a list of all the found comments
+ If a comment is found, the aftercomment
+ variable is set to True
+ """
+ self.comments.append(tag)
+ self.aftercomment = 1
+ #if tag == 'delta_mass':
+ #self.seeksequence = True
+
+
+ def handle_data(self, text):
+ """
+ Overrides the handle_data method
+ writes to a list the text following
+ any comment - modifies self.parsedlist
+ """
+ #print "text", text
+ if self.aftercomment:
+ cleantext = text.strip('\n\r ./')
+ self.parsedlist.append([self.comments[-1], cleantext])
+ #append the last comment and the text that follows
+ self.aftercomment = 0
+ #don't get any other value until the next comment appears
+ #however obtain the sequence of a peptide if we are in an in_mass tags
+ elif self.seeksequence:
+ pepmatch = peplinePATT.search(text)
+ if pepmatch:
+ self.seqlist.append(pepmatch.groups()[0])
+ elif self.seeksequencemod:
+ pepmatch = peplinePATTmod.search(text)
+ if pepmatch:
+ self.seqlist.append(pepmatch.groups()[0])
+ return 1
+
+
+ def get_dictionary(self):
+ """
+ Reorganizes data and treats some special cases
+ of data found after comment tags
+ Should be called after closing the parser
+ """
+ reccounter = 0
+ secreccounter = 0
+ list_out = []
+ list = self.parsedlist
+ details = 0
+ passedrank1 = 0
+ seq_counter = 0 #a counter for the list of sequences, append to matched masses
+
+ for i in range(len(list)):
+ if list[i][0] == 'rank':
+ passedrank1 = 1
+ if list[i+1][0] <> 'fraction_matched':
+ #we are not at the beginning of the details
+ #sometimes proteins have equal ranks
+ #we build the data dictionary for the identified proteins
+ reccounter+=1
+ list_out.append({'protdata':{'rank':list[i][1]}, \
+ 'pepdata':{'matched':[], 'unmatched':[]}})
+ details = 0
+ list_out[reccounter-1]['protdata']['comment'] = list[0][1]
+ list_out[reccounter-1]['protdata']['database'] = list[1][1]
+ list_out[reccounter-1]['protdata']['parent_mass_tolerance'] = list[3][1]
+
+ else:
+ #we are at the beginning of the details
+ details = 1
+ secreccounter+=1
+ else:
+ if details == 0 and passedrank1 == 1:
+ #not yet in details but passed the first rank tags
+ #take care first of the accesion numbers
+ if list[i][0] == 'accession_number':
+ matches = self.accesionRE.search(self.parsedlist[i][1])
+ if matches:
+ entries = matches.groups()
+ list[i][1]=entries[0]
+ list_out[reccounter-1]['protdata'][list[i][0]] = list[i][1]
+ elif details == 1:
+ #we are in the details, we may build the peptide masses lists
+ if list[i][0] == 'protein_coverage':
+ list_out[secreccounter-1]['protdata'][list[i][0]] = list[i][1]
+ elif list[i][0] == 'in_mass':
+ if list[i+1][0] == 'matched_mass':
+ #we are in the matched masses
+ list_out[secreccounter-1]['pepdata']['matched'].append([list[i][1], self.seqlist[seq_counter]])
+
+ seq_counter+=1
+ #print seq_counter
+ else:
+ list_out[secreccounter-1]['pepdata']['unmatched'].append(list[i][1])
+
+
+ return list_out
+
+def ParseMSFIT(msfitfilehandle):
+ """
+ Parses an MSFit generated html identification file
+
+ Returns a list of dictionaries with 2 entries:
+ dict key = protdata - with many subkeys
+ dict key = pepdata with subkeys 'matched' - a list
+ m/z - sequence, and 'unmatched' - a simple list
+
+ """
+ htmlpage = msfitfilehandle.read()
+ parser = MSFit32Parser()
+ parser.feed(htmlpage)
+ parser.close()
+ return parser.get_dictionary()
+
+#####################################################
+##### STATISTICAL AND COMPUTATIONAL FUNCTIONS ######
+#####################################################
+
+def CalcMonoMz(pepseq):
+ """
+ Returns the m/zH+ for a peptide
+
+ Using the monoisotopic masses of aminoacid residues calculates the
+ monoisotopic mass of a peptide with a given sequence. Variations
+ may be implemented by the use of modified aminoacid masses
+ """
+ Daamass = {"G":57.02147, "A":71.03712, "S":87.03203,
+ "P":97.05277, "V":99.06842, "T":101.04768,
+ "C":103.00919, "carbamidomethyl":57.02146,
+ "carboxymethyl":58.00547, "acrylamide":71.05511,
+ "I":113.08407, "L":113.08407, "N":114.04293,
+ "D":115.02695, "Q":128.05858, "K":128.09497,
+ "E":129.0426, "M":131.04049, "MOxidized":147.0354,
+ "H":137.05891, "F":147.06842, "R":156.10112,
+ "Y":163.06333, "W":186.07932, "water":18.01056, "Hplus":1.007825,
+ "Oxygen16":15.99491}
+ mass = 0.0
+ for aminoacid in pepseq:
+ mass+=Daamass[aminoacid]
+ mass+=Daamass["water"]+Daamass["Hplus"] #add the water and charged H+
+ return mass
+
+def Mean(inlist):
+ """
+ Obtain the mean of the values from a list
+ """
+ sum = 0
+ for item in inlist:
+ sum = sum + item
+ if len(inlist)>0:
+ return sum/float(len(inlist))
+ else:
+ return 0
+
+def SumSquares(inlist):
+ """
+ Squares each value in the passed list, adds up these squares and
+ returns the result.
+ """
+ ss = 0
+ for item in inlist:
+ ss = ss + item*item
+ return ss
+
+def Variance(inlist):
+ """
+ Calculates the variance for a sample
+ Returns 1 if less than 2 values are provided
+ """
+ n = len(inlist)
+ mn = Mean(inlist)
+ ssq = SumSquares(inlist)
+ if n >1:
+ vari = (ssq - n*mn*mn)/(n-1)
+ else:
+ vari = 1
+ return vari
+
+def StdDev(inlist):
+ """
+ Returns the standard deviation of the values in the passed list
+ using N-1 in the denominator (i.e., to estimate population stdev).
+ """
+ return math.sqrt(Variance(inlist))
+
+def Median(inlist):
+ """
+ Returns the median of the passed list.
+ Returns 0 or the element if less than 2 elements
+ are passed to the function
+ """
+ newlist = copy.deepcopy(inlist)
+ newlist.sort()
+ if len(newlist) == 0:
+ median = 0
+ elif len(newlist) == 1:
+ median = newlist[0]
+ elif len(newlist) % 2 == 0: # if even number, simple mean of middles
+ index = len(newlist)/2
+ median = float(newlist[index] + newlist[index-1]) /2
+ else:
+ index = len(newlist)/2
+ median = newlist[index]
+ return median
+
+#############################################
+####### I/O functions ####################
+#############################################
+def ReadFromFileFloats(fhandle, skip=0):
+ """
+ Obtain data from a tab delimited file into a list of floats
+
+ Needs the import string statement
+ The <skip> parameter indicate the number of lines not
+ read. This version uses a filehandle for calls
+ Entry file has the format (with or without a header):
+ 1000.0450 tab 158
+ 1000.0650 tab 190
+ ...
+ ...
+ """
+ data = []
+ for i in range(skip):
+ fhandle.readline()
+ for line in fhandle:
+ data.append(map(float, line.strip().split('\t')))
+ return data
+ #the returned data will be in float format
+
+
+def WriteMToFile(matrix, file_handle):
+ """
+ Writes the content of a matrix (list of lists) to a
+ tab delimited text file
+ """
+ for line in matrix:
+ for item in line:
+ file_handle.write(str(item))
+ file_handle.write('\t')
+ file_handle.write('\n')
+
+def WriteMToString(matrix):
+ """
+ Returns the content of a matrix to a tab delimited
+ string
+ """
+ res = ""
+ for line in matrix:
+ for item in line:
+ res = res + (str(item)) + '\t'
+ res = res + '\n'
+ return res
+
+def WriteListToString(list, format):
+ res = ""
+ for item in list:
+ res = res + format %(item) + " "
+ return res
+
+###############################################
+######### SPECTRA ANALYSIS functions ##########
+###############################################
+def GetPeak(data, peakx, lo=0, hi=41357):
+ """
+ Obtain the x y index for the pair most closely to the peak mass
+ in the list of data: mass-intensity
+
+ Uses a binary search algorithm since the list is sorted
+ 41357 is the number of datapoints from a typical exported spectrum
+ between 700 and 3000 Da
+
+ """
+ mindif = 0.037 #it depends on the minimal distance between values
+ #should be larger than half that minimal distance
+ #hi = len(data)
+ #lo = 0
+ dif = 10000.0
+
+ while (abs(dif) > mindif):
+ middle = int(round((hi-lo)/2 +lo))
+ dif = peakx - data[middle][0]
+ if dif == 0: break
+ if dif > 0:
+ lo = middle
+ else:
+ hi = middle
+ return middle
+
+def CrowlToMax(peakindex, howmuch, data):
+ """
+ Returns the most probable position of a maximum around a given index
+
+ Go around to see if the peak is really at the maximum value, otherwise
+ leave it as it was
+ <howmuch> the number of values tested around the actual value - 10 should be good
+ """
+ peak_int = data[peakindex][1]
+ newmax = peakindex
+ #initialize with the value of the peak index, will be changed later
+ for i in range(peakindex-howmuch, peakindex+howmuch):
+ if peak_int <= data[i][1]:
+ newmax = i
+ peak_int = data[i][1]
+ return newmax
+
+
+def GetBackground(monoindex, points, data, level=0.05):
+ """
+ Define the background as the average of the <level>% lowest
+ intensity values; uses function Mean
+
+ <monoindex> - position of the monoisotopic peak
+ <points> points considered
+ <data> list of floats m/z, intensity
+ <level> percent of points that might be considered in background
+ """
+ intensities = []
+ for i in range(monoindex, monoindex+points):
+ intensities.append(data[i][1])
+ intensities.sort()
+ smallestval_list = intensities[0:int(len(intensities)*level)]
+ return Mean(smallestval_list)
+
+def GetIsotopeSeries(monoindex, howmany, data):
+ """
+ Returns a list of intensities in a series of peaks
+
+ Starting from the monoisotopic peak obtain maximum peaks at 1 Da
+ distance intervals; uses function CrowlToMax to recenter on real peaks
+ <howmany> defines the number of peaks to be retrieved
+ <monoindex> the mass of the firs peak in the series
+ <data> a list containing floats in pairs: mass/intensity
+ """
+ # calculate average distance for a dalton in the range of monoindex, between
+ # 15 and 30 values/dalton normally
+ distforonedalton = abs(round(100/(data[monoindex][0] - data[(monoindex+100)][0])))
+
+ peaklist = []
+ for i in range(0, howmany):
+ peakindex = CrowlToMax(int(monoindex + i*distforonedalton), int(distforonedalton/3), data)
+ #we accept deviations of distforonedalton/3 - that is 0,33 Da - this can be modified
+ #in general, the peptides are singly charged
+ peakvalue = data[peakindex][1]
+ peakamu = data[peakindex][0]
+ peaklist.append([peakamu, peakvalue])
+ return peaklist
+
+
+def GetPeaksFromValue(monopeak, data, bground = 100, nbisotopes = 14, crowlnb = 5):
+ """
+ Generates the list (amu and intensities) from a peak amu value
+
+ returns the family of peaks (amu and intensities) starting
+ from a value of a peak measured in the spectra;
+ uses functions GetPeak, GetBackground, GetIsotopeSeries,
+ CrowlToMax
+ monopeak - the mass of the monoisotopic peak
+ bground - number of points around the peak to be considered
+ for calculating the background
+ nbisotopes - number of peaks returned for a family
+ crowlnb - number of points tested to see if a peak is a peak
+ """
+ resultlst = []
+ #see if we may find the peak around that value
+ peak_pos = GetPeak(data, monopeak, hi=len(data))
+ #test to see if there is no peak higher at 5 values around
+ real_peakpos = CrowlToMax(peak_pos, crowlnb, data)
+ background = GetBackground(real_peakpos, bground, data)
+ peak_list = GetIsotopeSeries(real_peakpos, nbisotopes, data)
+
+ for element in peak_list:
+ resultlst.append([element[0], element[1]-background])
+
+ return resultlst
+
+### INTERFACE WITH Isotope Pattern Calculator IPC ###
+def RunIPC(peptide, howmany, monoisoint, ipc_path):
+ """
+ Runs the external program IPC -> theoretical isotopic distribution
+
+ Returns a list of peptide masses+H and intensities at 1 Da distance,
+ normalized to the intensity of the monoisoint peak. Theoretical distribution
+ of the peak intensities is calculated by IPC, its path is indicated by <ipc_path>
+ needs os and string import.
+
+ How to test:
+ pep = "AADGGHGGHHILL"
+ hmany = 6
+ rlist = []
+ rlist = RunIPC(pep, hmany)
+ """
+ HMASS = 1.007825 #to be added to the peaks for m/z calculations
+ #ipccommand = r"/usr/local/ipc-1.1/ipc" #example of hardcoded path to ipc executable
+ ipccommand = ipc_path
+ ipciterations = "-f 500"
+ ipcresolution = "-d 1" #this will sum the intensities of peaks at less than 0.1 Da apart
+ ipcpeptide = "-a " + peptide
+
+ pipe_ipc = os.popen("%s %s %s %s" % (ipccommand, ipciterations, ipcresolution, ipcpeptide))
+ pipe_ipc.readline()
+ out_list = []
+ res_list = []
+ for i in range(howmany):
+ out_list.append(string.split(pipe_ipc.readline()))
+
+ for elm in out_list:
+ amustr = elm[1]
+ percentstr = elm[3]
+ res_list.append([float(amustr[0:-1])+HMASS, float(percentstr[0:-1])])
+ #the elements 1 and 3 are the amu and the relative abundance
+ #the [0:-1] chops the last character (comma)
+
+ norm_lst = [] #normalized list in function of the intensity of the first peak
+ for i in range(len(res_list)):
+ norm_lst.append([res_list[i][0], res_list[i][1]*monoisoint/res_list[0][1]])
+
+ return norm_lst
+
+def IsDifference(difference, dif, tolerated):
+ """
+ Returns 1 if the <difference> is in the tolerated range around <dif>
+ accepts an error, the <tolerated> parameter
+ """
+ if (difference>(dif-tolerated) and difference <(dif+tolerated)):
+ return 1
+ else:
+ return 0
+
+def PepCompare(pepmz, pepseq):
+ """
+ Evaluates the measured mass of a peptide to see if its deuterated or not
+
+ Returns a dictionary containing the corrected pepmz if deuterated,
+ the peptide sequence (unchanged), and two flags MODIFIED if MetOX or other
+ has been found and IGNORE if no known modification was found. It also calculates
+ the number of leucines and reports it as a fifth element NBLEU.
+ Uses CalcMonoMz and IsDifference.
+ """
+ HPLUS = 1.007825
+ tolerated = 0.3 #daltons
+ theor_mz = CalcMonoMz(pepseq)
+ modif_dict = {"MetOX":15.9949}
+ deut_dict = {"NotD": 0.0, "1LeuD3": 3.023, "2LeuD3" : 6.047, "3LeuD3": 9.07, "4LeuD3": 12.094}
+
+ #test if the peptide is the deuterated form (up to 4 Leu)
+ diff_mz = pepmz - theor_mz
+ MODIFIED = 0
+ IGNORE = 0
+ NBLEU = pepseq.count('L')
+
+ FOUND = 0
+ for mod in modif_dict.keys():
+ for dif in deut_dict.keys():
+ if IsDifference(diff_mz, deut_dict[dif], tolerated):
+ pepmz = pepmz - deut_dict[dif]
+ FOUND = 1
+ break
+ elif IsDifference(diff_mz, deut_dict[dif]+modif_dict[mod], tolerated):
+ pepmz = pepmz - deut_dict[dif]
+ MODIFIED = 1
+ FOUND = 1
+ break
+ if not FOUND:
+ #none of the tested modifications or deuteration accounted for the mass difference
+ IGNORE = 1
+ return {"pepmz":pepmz, "pepseq":pepseq, "MODIFIED":MODIFIED, "IGNORE":IGNORE, "NBLEU":NBLEU}
+
+def CorrectIsotopicSeries(pepmz, pepseq, data, peaks, ipc_path):
+ """
+ Calculates the theoretical intensities of the first 4 peaks
+ for peptides with 1 Leucine, the pepmz corresponds to the nondeuterated form.
+
+ This function is called only when the NBLEU of a peptide is 1
+ Otherwise, the differences in m/z between non-deuterated and deuterated
+ peptides are larger, the contribution of secondary peaks to the quantification
+ is less important (ignored)
+ Returns a list of differences between the measured and theoretical
+ intensities for the peaks normalized to the monoisotopic peak.
+ Uses most of the functions previously defined by calls to
+ GetPeaksFromValue and RunIPC. The first elements of the returned
+ list are the peptide sequence, mz and the intensity of the monoisotopic peak
+ """
+ theor_mz = CalcMonoMz(pepseq)
+ mz_difference = pepmz - theor_mz
+ measured_lst = GetPeaksFromValue(pepmz, data, nbisotopes=peaks)
+ #recover the peaks on a range of 6 daltons from the monoisotopic peak
+ monointensity = measured_lst[0][1]
+ if pepseq.count("L") == 1:
+ theor_lst = RunIPC(pepseq, 6, monointensity, ipc_path)
+ #obtain the calculated list of pairs (mz, Intensity) based on the monointensity value given
+
+ dif_lstint= [pepseq]
+ dif_lstint.append(pepmz)
+
+ for i in range(len(measured_lst)):
+ #we only substract from the measured values the peaks 4, 5, 6
+ if pepseq.count("L") == 1:
+ if i < 3 or i > 5:
+ dif_lstint.append(measured_lst[i][1])
+ else:
+ dif_lstint.append(measured_lst[i][1]-theor_lst[i][1])
+ else:
+ dif_lstint.append(measured_lst[i][1])
+
+ return dif_lstint
+
+def MzIntGet(data, pepmz, plusminus=15):
+ """
+ Obtain the list of mz-int pairs
+ from the spectrum data
+
+ Returns tuple of two lists
+ """
+ mzdata, intdata = [], []
+
+ peakindex = GetPeak(data, float(pepmz), hi=len(data))
+ distforonedalton = abs(round(100/(data[peakindex][0] - data[(peakindex+100)][0])))
+ minindex = int(peakindex - distforonedalton*plusminus)
+ maxindex = int(peakindex + distforonedalton*plusminus + 6*distforonedalton)
+ for i in range(minindex, maxindex):
+ mzdata.append(data[i][0])
+ intdata.append(data[i][1])
+ return(mzdata, intdata)
+
+##################################
+#### Processing data structure ###
+##################################
+class DataIntObj:
+ """
+ A data structure to handle SILAC
+ difference results and calculate
+ statistics
+ """
+ def __init__(self):
+ self.nmbentries = 0
+ self.data = {}
+ self.results = {}
+ self.statistics = {}
+ #dictionaries with unique keys formed by pepseq+mzh
+ self.deleted = []
+
+ def get_data(self , matrix):
+ """
+ transforms the matrix obtained by several
+ calls to DiffMeasTheor into internal data
+ """
+ for element in matrix:
+ listdiff = []
+ for i in range(2, len(element)-1):
+ #first element is pepseq, second element modif pepmz
+ listdiff.append(float(element[i]))
+ intdict = {"pepseq":element[0], "mzh":float(element[1]),
+ "calcmzh":CalcMonoMz(element[0]),
+ "int0":float(element[2]),
+ "BADPEAKS": 0,
+ "listdiff":listdiff}
+ intdict["massdiff"]=intdict["mzh"]-intdict["calcmzh"]
+ intdict["Lnumber"]=intdict["pepseq"].count('L')
+ self.data[element[0]+'_'+str(element[1])] = intdict
+ return self.data
+
+ def filter_peaks(self):
+ """
+ Eliminates from self.data the peaks for which
+ the peak 3 or multiple is higher than 2 or multiple
+ Decides whether to take the non-deuterated or the
+ deuterated form in function of the intensity of the
+ corresponding peaks
+ """
+ entrieslist = self.data.keys()
+ for entrykey in entrieslist:
+ #print self.data[entrykey]
+ peak2, peak3, peakdx2, peakdx3 = 0.0, 0.0, 0.0, 0.0
+ nbleu = self.data[entrykey]["Lnumber"]
+ if nbleu <= 4:
+ #treat maximum 4 leucines
+ if len(self.data[entrykey]["listdiff"]) > 13:
+ peak2 = self.data[entrykey]["listdiff"][1]
+ peak3 = self.data[entrykey]["listdiff"][2]
+ peakdx2 = self.data[entrykey]["listdiff"][nbleu*3+1]
+ peakdx3 = self.data[entrykey]["listdiff"][nbleu*3+2]
+ #print peak2, peak3, peakdx2, peakdx3, "peaks"
+ if (peak2+peak3) > (peakdx2+peakdx3):
+ #work only with the highest value pair
+ if peak3 > peak2:
+ del self.data[entrykey]
+ self.deleted.append(entrykey)
+ #"Considered unreliable", entrykey
+ else:
+ if peakdx3 > peakdx2:
+ del self.data[entrykey]
+ self.deleted.append(entrykey)
+ #"Considered unreliable", entrykey
+ else:
+ del self.data[entrykey]
+ #"List too short", entrykey
+ else:
+ del self.data[entrykey]
+ #"More than 4 leucines", entrykey
+ return self.data
+
+ def calc_ratios(self):
+ """
+ Calculates the ratios deut/nondeuterated peptides
+ in a mix based on peptide sequence (0, 1-4 leucines)
+ """
+ entrieslist = self.data.keys()
+
+ for key in entrieslist:
+ nbleu = self.data[key]["Lnumber"]
+ monoisoint = self.data[key]["listdiff"][0]
+ if nbleu <> 0 and monoisoint <> 0:
+ self.results[key] = self.data[key]["listdiff"][nbleu*3]/monoisoint
+ else:
+ self.results[key] = 0.0
+ return self.results
+
+ def calc_statistics(self):
+ """
+ Median, average and StdDev for the fractions calculated for
+ peptides with 1, 2, 3 or 4 leucines
+ """
+ frlist = []
+ entrieslist = self.data.keys()
+ for key in entrieslist:
+ nbleu = self.data[key]["Lnumber"]
+ if (nbleu > 0 and nbleu < 5):
+ frlist.append(self.results[key])
+ self.statistics["Median"]=Median(frlist)
+ self.statistics["Mean"]=Mean(frlist)
+ self.statistics["StdDev"]=StdDev(frlist)
+ self.statistics["Nbvalues"]=len(frlist)
+ #print self.statistics
+
+ return self.statistics
+
+ def return_resultsXML(self, spectr_dict, record):
+ """
+ The results are returned in very simple XML-like format
+ that should be compatible with Silacvalidator.py (interactive visualization
+ of the results)
+ """
+ #res = [["Pepseq", "mz", "mzcalc", "Leucines", "MonoisoIntensity", "DeuteratedIntensity",
+ #"Deuterated_fraction"]]
+ #Add primary data
+ root= ET.Element("protdata")
+ idroot = ET.SubElement(root, "id_parameters")
+ comm = ET.SubElement(idroot, "spot_id")
+ comm.text = record["protdata"]["comment"]
+ dbase = ET.SubElement(idroot, "database")
+ dbase.text = record["protdata"]["database"]
+ ppm = ET.SubElement(idroot, "ppm_tolerance")
+ ppm.text = record["protdata"]["parent_mass_tolerance"]
+ mowse = ET.SubElement(idroot, "mowse_score")
+ try:
+ mowse.text = record["protdata"]["mowse_score"]
+ except:
+ mowse.text = "1.0"
+ protcovg = ET.SubElement(idroot, "pep_coverage")
+ protcovg.text = record["protdata"]["protein_coverage"]
+ matchedpep = ET.SubElement(idroot, "no_matched_pept")
+ matchedpep.text = str(len(record["pepdata"]["matched"]))
+ accnb = ET.SubElement(root, "accession_number")
+ accnb.text = record["protdata"]["accession_number"]
+ enname = ET.SubElement(root, "entry_name")
+ enname.text = record["protdata"]["entry_name"]
+ protmw = ET.SubElement(root, "prot_mw")
+ protmw.text = record["protdata"]["protein_mw"]
+ protpi = ET.SubElement(root, "prot_pi")
+ protpi.text = record["protdata"]["protein_pI"]
+
+ pepdataroot = ET.SubElement(root, "pepdata")
+
+ for peprec in self.data.keys():
+ nbleu = self.data[peprec]["Lnumber"]
+ if nbleu in (1, 2, 3, 4):
+ deuterated = self.data[peprec]["listdiff"][nbleu*3]
+ else:
+ deuterated = 0.0
+
+ pepentry = ET.SubElement(pepdataroot, "measured")
+ pepseq = ET.SubElement(pepentry, "pepseq")
+ pepseq.text = self.data[peprec]["pepseq"]
+ mzh = ET.SubElement(pepentry, "mzh")
+ mzh.text = "%.4f" %(self.data[peprec]["mzh"])
+ calcmzh = ET.SubElement(pepentry, "calc_mzh")
+ calcmzh.text = "%.4f" %(self.data[peprec]["calcmzh"])
+ Lnumber = ET.SubElement(pepentry, "leucines")
+ Lnumber.text = str(self.data[peprec]["Lnumber"])
+ int0 = ET.SubElement(pepentry, "mono_iso_intensity")
+ int0.text = "%.0f" %(self.data[peprec]["int0"])
+ intd = ET.SubElement(pepentry, "deuterated_intensity")
+ intd.text = "%.0f" %(deuterated)
+ ratio = ET.SubElement(pepentry, "ratio")
+ ratio.text = "%.2f" %(self.results[peprec])
+ validated = ET.SubElement(pepentry, "validated")
+ validated.text = "UNKNOWN"
+ #lookedat = ET.SubElement(pepentry, "looked_at")
+ #lookedat.text = "NO"
+ local_bg = ET.SubElement(pepentry, "local_bg")
+ local_bg.text = "0.0000"
+ corr_ratio = ET.SubElement(pepentry, "corrected_ratio")
+ corr_ratio.text = "%.2f" %(self.results[peprec])
+ spec_piece = ET.SubElement(pepentry, "spectrum")
+ mzspec = ET.SubElement(spec_piece, "mz_list")
+ mzspec.text = WriteListToString(spectr_dict[self.data[peprec]["pepseq"]][0], "%.4f")
+ intspec = ET.SubElement(spec_piece, "int_list")
+ intspec.text = WriteListToString(spectr_dict[self.data[peprec]["pepseq"]][1], "%.4f")
+
+ return ET.tostring(root)
+
+
+ def return_results(self):
+ """
+ Return the results as as a list of lists
+ """
+ res = [["Pepseq", "mz", "mzcalc", "Leucines", "MonoisoIntensity", "DeuteratedIntensity",
+ "Deuterated_fraction"]]
+ #Add primary data
+ for peprec in self.data.keys():
+ nbleu = self.data[peprec]["Lnumber"]
+ if nbleu in (1, 2, 3):
+ deuterated = self.data[peprec]["listdiff"][nbleu*3]
+ else:
+ deuterated = 0.0
+ res.append([self.data[peprec]["pepseq"], "%.4f" %(self.data[peprec]["mzh"]),
+ "%.4f" %(self.data[peprec]["calcmzh"]), self.data[peprec]["Lnumber"],
+ "%.0f" %(self.data[peprec]["int0"]), "%.0f" %(deuterated),
+ "%.2f" %(self.results[peprec])])
+
+ res.append(["Nbofvalues", "Median", "Mean", "StdDev"])
+ res.append(["%s" %(self.statistics["Nbvalues"]),
+ "%.2f" %(self.statistics["Median"]),
+ "%.2f" %(self.statistics["Mean"]),
+ "%.4f" %(self.statistics["StdDev"])])
+ return res
+
+
+#######################
+#######################
+def ProcessSpectrum(spectrahandle, msfithandle, orflisthandle, ipc_path):
+ """
+ A function to simplify the aspect of Main
+ uses handles to file or file-like objects
+ Returns the results in list/string form
+ May also be used in a CGI
+ """
+ global calc_res
+ calc_res = ""
+ #insert data from the spectra in a list of floats
+ data_num = ReadFromFileFloats(spectrahandle, 2)
+ data_num_minmz = data_num[0][0]
+ data_num_maxmz = data_num[-1][0]
+ #parse the HTML file
+ parseddict = ParseMSFIT(msfithandle)
+ orflist = []
+
+ #the next lines are only necessary if the entries were not
+ #well formated in the database. To be modified otherwise.
+ ###############################################
+ for line in orflisthandle:
+ orflist.append(line.strip())
+ ###############################################
+
+ record = parseddict[0]
+ proteinrank = record['protdata']['rank']
+ if record['protdata']['accession_number'] in orflist:
+
+ peplist = record['pepdata']['matched']
+ #the list of pairs mzh/pepseq for a given protein
+ result_matrix = []
+ spectrum_dict = {}
+ PLUSMINUS = 25
+ #the number of daltons around the monoisotopic peak to be retrieved
+ for peptide in peplist:
+ difflist = []
+ peptidesequence = peptide[1]
+ inputpepmz = float(peptide[0])
+ decision_dict = PepCompare(inputpepmz, peptidesequence)
+ #if the peptide entry is a deuterated peptide or if its mass is already in the
+ #result_matrix (DUPLICATED = 1), no calculation is performed
+
+ if decision_dict["IGNORE"] == 0:
+ DUPLICATED = 0
+ for i in range(len(result_matrix)):
+ if abs(result_matrix[i][1]-decision_dict["pepmz"]) < 0.5:
+ #look for pepmz similar in the range +-0.5 Da to the one tested.
+ #If it exists do not run CorrectIsotopicSeries
+ DUPLICATED = 1
+ break
+ if DUPLICATED == 0:
+ #test also if the range of mass from the spectrum is OK, otherwise stop
+ if decision_dict["pepmz"] > data_num_minmz and\
+ decision_dict["pepmz"] < data_num_maxmz:
+ difflist = CorrectIsotopicSeries(decision_dict["pepmz"], \
+ decision_dict["pepseq"], data_num, 16, ipc_path)
+ result_matrix.append(difflist)
+ spectrum_dict[decision_dict["pepseq"]] = MzIntGet(data_num,
+ decision_dict["pepmz"], PLUSMINUS)
+
+ rawdiff= DataIntObj()
+ rawdiff.get_data(result_matrix)
+ rawdiff.filter_peaks()
+ rawdiff.calc_ratios()
+ pepresults = rawdiff.return_resultsXML(spectrum_dict, record)
+ else:
+ pepresults = "nodata"
+
+ return pepresults
+
+####################
+####### MAIN #######
+####################
+class Usage(Exception):
+ """
+ used for catching exceptions generated
+ during command line parameter parsing
+ """
+ def __init__(self, msg):
+ self.msg = msg
+
+def main(argv=None):
+ global fname_spectra, fname_msfit, fname_orflist, ipc_command_path
+ global spectrumhandle, msfithandle, orflisthandle
+ spectrumhandle, msfithandle, orflisthandle = sys.stdin, sys.stdin, sys.stdin
+
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "hs:i:p:c:", ["help", "spectrum=",
+ "msfithtml=", 'orflist=', "ipc_path="])
+ except getopt.error, msg:
+ raise Usage(msg)
+ # option processing
+
+ fname_spectra, fname_msfit = "", ""
+ for option, value in opts:
+ if option in ("-h", "--help"):
+ raise Usage(__doc__)
+ if option in ("-s", "--spectrum"):
+ fname_spectra = value
+ if option in ("-i", "--msfithtml"):
+ fname_msfit = value
+ if option in ("-p", "--orflist"):
+ fname_orflist = value
+ if option in ("-c", "--ipc_path"):
+ ipc_command_path = value
+
+ if (fname_spectra == "" or fname_msfit == "" or fname_orflist == ""):
+ raise Usage("no input filenames!")
+ sys.exit(2)
+ else:
+ try:
+ spectrumhandle = open(fname_spectra, "r")
+ msfithandle = open(fname_msfit, "r")
+ orflisthandle = open(fname_orflist, "r")
+ print ProcessSpectrum(spectrumhandle, msfithandle, orflisthandle, ipc_command_path)
+ finally:
+ spectrumhandle.close()
+ msfithandle.close()
+ orflisthandle.close()
+ except Usage, err:
+ print >>sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+ print >>sys.stderr, "\t for help use --help or -h"
+ return 2
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/src/lilamsxml_20080130.py~ b/src/lilamsxml_20080130.py~
new file mode 100644
index 0000000000000000000000000000000000000000..46903301560552f73fd5050e4912e39ad7776a0b
--- /dev/null
+++ b/src/lilamsxml_20080130.py~
@@ -0,0 +1,905 @@
+#!/usr/bin/python
+"""
+lilams - python script for the analysis
+of SILAC experiments with MALDI spectra
+and MSFit protein identifications
+
+first version - September 2003
+this version - September 2004
+slightly revised in oct 2005 and jan 2008
+
+Allows generation of XML output containing
+the whole information used for quantitations
+As a result, the output of this script is an
+XML-like string with <pepdata>...</pepdata>
+as delimiters.
+
+Uses HTMLparser to parse the MSFit files. While much
+slower, this method is much more flexible
+
+GIM - Institut Pasteur
+first argument - spectrum (text format) (--spectrum, -s)
+second argument - Msfit file (html format) (--msfithtml, -i)
+third argument - a list of ORFs that will be quantified (--orflist, -p)
+fourth argument - the path to the ipc, Isotope Pattern Calculator
+executable (--ipc_path, -c) as it may vary in localization
+
+Returns the results to the stdout with the peptide sequence and differences
+between observed peak intensities and their theoretical intensities.
+By default 10 peak differences from a family of peaks are returned
+this takes in account 0, 1, 2 or 3 leucines
+Makes use of the external IPC program for calculating
+peak mass distributions, if not on the system path, please modify
+the call in the RunIPC function
+
+Modified on 20080130 to handle the absence of a mowse score
+Will report 1, if a Mowse score is present
+"""
+import sys, re, os, string, copy, math, getopt
+from MsFitHTMLparse02 import MSFit32Parser
+#from elementtree import ElementTree as ET
+import cElementTree as ET
+def TEST(specfileh, msfith):
+ return specfileh.readline()
+#############################################
+####### MSFit html file parser #########
+#############################################
+def ParseMSFITold(msfitfilehandle):
+ """
+ Parses an MSFit generated html identification file
+
+ Returns a dictionary:
+ key = rank -> subdict key = protdata
+ -> subdict key = pepdata (mzh, pepseq)
+ needs the re module
+ """
+ data_dict = {}
+ #REGULAR expressions to parse an MS-FIT identification htm file
+ rankRE = r"\<A NAME=\"([0-9])\"\>\<\/A\>\<!--rank--\>[0-9].+"
+ accesionRE = r"--accession_number--\>(.+)\<\!--spe.+"
+ nameRE = r"--entry_name--\>\>(.+)"
+ entrylineRE = rankRE + accesionRE + nameRE
+ entrylinePATT = re.compile(entrylineRE)
+ pepinmassRE = r"--in_mass--\>([0-9\.]+)\<.+"
+ pepseqmodRE = r"\)([A-Z]+)\("
+ pepseqRE = r"sequence=([A-Z]+)\\"
+ peplineREmod = pepinmassRE + pepseqmodRE
+ peplineRE = pepinmassRE + pepseqRE
+ peplinePATT = re.compile(peplineRE)
+ peplinePATTmod = re.compile(peplineREmod)
+ try:
+ #infile = open(msfitfilename, 'r')
+ lines = msfitfilehandle.readlines()
+
+ for line in lines:
+ entry = entrylinePATT.search(line)
+ if entry:
+ efound = entry.groups()
+ data_dict[efound[0]] = {"protdata":(efound[1], efound[2][:-1]), "pepdata":[]}
+ #strip the last character from the entry name (efound[2])
+ #rank, accesion nb, entry name
+ else:
+ pepmatch = peplinePATT.search(line)
+ if pepmatch:
+ data_dict[efound[0]]["pepdata"].append([pepmatch.groups()[0],\
+ pepmatch.groups()[1]])
+ else:
+ pepmatch = peplinePATTmod.search(line)
+ if pepmatch:
+ data_dict[efound[0]]["pepdata"].append([pepmatch.groups()[0],\
+ pepmatch.groups()[1]])
+ finally:
+ #infile.close()
+ return data_dict
+
+def ParseMSFIT(msfitfilehandle):
+ """
+ Parses an MSFit generated html identification file
+
+ Returns a list of dictionaries with 2 entries:
+ dict key = protdata - with many subkeys
+ dict key = pepdata with subkeys 'matched' - a list
+ m/z - sequence, and 'unmatched' - a simple list
+
+ """
+ htmlpage = msfitfilehandle.read()
+ parser = MSFit32Parser()
+ parser.feed(htmlpage)
+ parser.close()
+ return parser.get_dictionary()
+
+######TESTING######
+###################
+#msfitfile = sys.argv[1]
+#resdict = {}
+#resdict = ParseMSFIT(msfitfile)
+#print resdict
+
+###################################################
+##### STATISTICAL FUNCTIONS #################
+###################################################
+
+def CalcMonoMz(pepseq):
+ """
+ Returns the m/zH+ for a peptide
+
+ Using the monoisotopic masses of aminoacid residues calculates the
+ monoisotopic mass of a peptide with a given sequence. Variations
+ may be implemented by the use of modified aminoacid masses
+ """
+ Daamass = {"G":57.02147, "A":71.03712,"S":87.03203,
+ "P":97.05277, "V":99.06842,"T":101.04768,
+ "C":103.00919, "carbamidomethyl":57.02146,
+ "carboxymethyl":58.00547, "acrylamide":71.05511,
+ "I":113.08407, "L":113.08407, "N":114.04293,
+ "D":115.02695, "Q":128.05858, "K":128.09497,
+ "E":129.0426, "M":131.04049, "MOxidized":147.0354,
+ "H":137.05891, "F":147.06842, "R":156.10112,
+ "Y":163.06333, "W":186.07932, "water":18.01056, "Hplus":1.007825,
+ "Oxygen16":15.99491}
+ mass = 0.0
+ for i in range(len(pepseq)):
+ mass+=Daamass[pepseq[i]]
+ mass+=Daamass["water"]+Daamass["Hplus"] #add the water and charged H+
+ return mass
+def Mean(inlist):
+ """
+ Obtain the mean of the values from a list
+
+ """
+ sum = 0
+ for item in inlist:
+ sum = sum + item
+ if len(inlist)>0:
+ return sum/float(len(inlist))
+ else:
+ return 0
+def SumSquares(inlist):
+ """
+ Squares each value in the passed list, adds up these squares and
+ returns the result.
+ """
+ ss = 0
+ for item in inlist:
+ ss = ss + item*item
+ return ss
+
+def Variance(inlist):
+ """
+ Calculates the variance for a sample
+ Returns 1 if less than 2 values are provided
+ """
+ n = len(inlist)
+ mn = Mean(inlist)
+ ssq = SumSquares(inlist)
+ if n >1:
+ vari = (ssq - n*mn*mn)/(n-1)
+ else:
+ vari = 1
+ return vari
+def StdDev(inlist):
+ """
+ Returns the standard deviation of the values in the passed list
+ using N-1 in the denominator (i.e., to estimate population stdev).
+ """
+ return math.sqrt(Variance(inlist))
+
+def Median(inlist):
+ """
+ Returns the median of the passed list.
+ Returns 0 or the element if less than 2 elements
+ are passed to the function
+ """
+ newlist = copy.deepcopy(inlist)
+ newlist.sort()
+ if len(newlist) == 0:
+ median = 0
+ elif len(newlist) == 1:
+ median = newlist[0]
+ elif len(newlist) % 2 == 0: # if even number, simple mean of middles
+ index = len(newlist)/2
+ median = float(newlist[index] + newlist[index-1]) /2
+ else:
+ index = len(newlist)/2
+ median = newlist[index]
+ return median
+
+#############################################
+####### IO functions #####################
+#############################################
+def ReadFromFile(fhandle, skip=0):
+ """
+ Obtain data from a tab delimited file into a list
+
+ Needs the import string statement
+ The <skip> parameter indicate the number of lines not
+ read. This version uses a filehandle for calls
+
+ """
+
+ #for line in file:
+ # data.append(map(float,line.strip().split("\t")))
+ # an iterator could be used.
+
+ data = []
+ #f=open(filename, 'r')
+ for i in range(skip):
+ fhandle.readline()
+ while (1):
+ line = fhandle.readline()
+ if line == "": break
+ #line = line[:-1] #strip the last character (the newline usually)
+ data.append(map(float,line.strip().split('\t')))
+ #f.close()
+ return data
+ #the returned data will be in float format
+
+
+def WriteMToFile(matrix, file_handle):
+ """
+ Writes the content of a matrix (list of lists) to a
+ tab delimited text file
+ """
+ for line in matrix:
+ for item in line:
+ file_handle.write(str(item))
+ file_handle.write('\t')
+ file_handle.write('\n')
+
+def WriteMToString(matrix):
+ """
+ Returns the content of a matrix to a tab delimited
+ string
+ """
+ res = ""
+ for line in matrix:
+ for item in line:
+ res = res + (str(item)) + '\t'
+ res = res + '\n'
+ return res
+
+def WriteListToString(list, format):
+ res = ""
+ for item in list:
+ res = res + format %(item) + " "
+ return res
+
+###############################################
+######### SPECTRA ANALYSIS functions ##########
+###############################################
+def GetPeak(data, peakx, lo=0, hi=41357):
+ """
+ Obtain the x y values for the pair most closely to the peak mass
+
+ Uses a binary search algorithm since the list is sorted
+ 41357 is the number of datapoints from an exported spectrum between
+ 700 and 3000 Da
+
+ """
+ mindif = 0.037 #it depends on the minimal distance between values
+ #should be larger than half that minimal distance
+ #hi = len(data)
+ #lo = 0
+ dif = 10000.0
+
+ while (abs(dif) > mindif):
+ middle = int(round((hi-lo)/2 +lo))
+ dif = peakx - data[middle][0]
+ if dif == 0: break
+ if dif > 0:
+ lo = middle
+ else:
+ hi = middle
+ return middle
+
+def CrowlToMax(peakindex, howmuch, data):
+ """
+ Returns the real position of a maximum
+
+ Go around to see if the peak is really at the maximum value, otherwise
+ leave it as it was
+ <howmuch> the number of values around the actual value - 10 is a good value
+ """
+ peak_int = data[peakindex][1]
+ newmax = peakindex
+ #initialize with the value of the peak index, will be changed later
+ for i in range(peakindex-howmuch, peakindex+howmuch):
+ if peak_int <= data[i][1]:
+ newmax = i
+ peak_int = data[i][1]
+ return newmax
+
+
+def GetBackground(monoindex, points, data, level=0.05):
+ """
+ Define the background as the average of the <level>% lowest
+ intensity values; uses function Mean
+
+ <monoindex> - position of the monoisotopic peak
+ <points> points considered
+ <data> list of floats m/z, intensity
+ <level> percent of points that might be considered in background
+ """
+ #obtain the values
+ intensities = []
+ for i in range(monoindex, monoindex+points):
+ intensities.append(data[i][1])
+ #sort the list
+ intensities.sort()
+ smallestval_list = intensities[0:int(len(intensities)*level)]
+ return Mean(smallestval_list)
+
+def GetIsotopeSeries(monoindex, howmany, data):
+ """
+ Returns a list of intensities in a series of peaks
+
+ Starting from the monoisotopic peak obtain maximum peaks at 1 Da
+ distance intervals; uses function CrowlToMax
+ <howmany> defines the number of peaks to be retrieved
+ <monoindex> the mass of the firs peak in the series
+ <data> a list containing floats in pairs: mass/intensity
+ """
+ # calculate average distance for a dalton in the range of monoindex, between15 and 30 values/dalton normally
+ distforonedalton = abs(round(100/(data[monoindex][0] - data[(monoindex+100)][0])))
+
+ peaklist = []
+ for i in range(0, howmany):
+ peakindex = CrowlToMax(int(monoindex + i*distforonedalton), int(distforonedalton/3), data)
+ #we accept deviations of distforonedalton/3 - that is 0,33 Da - this can be modified
+ peakvalue = data[peakindex][1]
+ peakamu = data[peakindex][0]
+ peaklist.append([peakamu, peakvalue])
+ return peaklist
+
+
+def GetPeaksFromValue(monopeak, data, bground = 100, nbisotopes = 14, crowlnb = 5):
+ """
+ Generates the list (amu and intensities) from a peak amu value
+
+ returns the family of peaks (amu and intensities) starting
+ from a value of a peak measured in the spectra;
+ uses functions GetPeak, GetBackground, GetIsotopeSeries,
+ CrowlToMax
+ monopeak - the mass of the monoisotopic peak
+ bground - number of points around the peak to be considered
+ for calculating the background
+ nbisotopes - number of peaks returned for a family
+ crowlnb - number of points tested to see if a peak is a peak
+
+ """
+ resultlst = []
+ #see if we may find the peak around that value
+ peak_pos = GetPeak(data, monopeak, hi=len(data))
+ #test to see if there is no peak higher at 5 values around
+ real_peakpos = CrowlToMax(peak_pos, crowlnb, data)
+ background = GetBackground(real_peakpos, bground, data)
+ #print "background", background
+ peak_list = GetIsotopeSeries(real_peakpos, nbisotopes, data)
+
+ for element in peak_list:
+ resultlst.append([element[0], element[1]-background])
+
+ return resultlst
+
+### INTERFACE WITH Isotope Pattern Calculator IPC ###
+def RunIPC(peptide, howmany, monoisoint, ipc_path):
+ """
+ Runs the external program IPC -> theoretical isotopic distribution
+
+ Returns a list of peptide masses+H and intensities at 1 Da distance,
+ normalized to the intensity of the monoisoint peak.
+ the ipc program must be available on the shell path; needs os and
+ string import.
+
+ How to test:
+ pep = "AADGGHGGHHILL"
+ hmany = 6
+ rlist = []
+ rlist = RunIPC(pep, hmany)
+ """
+ HMASS = 1.007825 #to be added to the peaks for m/z calculations
+ #ipccommand = r"/usr/local/ipc-1.1/ipc" #correct for agathe, modify if on other machine
+ ipccommand = ipc_path
+ ipciterations = "-f 500"
+ ipcresolution = "-d 1" #this will sum the intensities of peaks at less than 0.1 Da apart
+ ipcpeptide = "-a " + peptide
+
+ pipe_ipc = os.popen("%s %s %s %s" % (ipccommand, ipciterations, ipcresolution, ipcpeptide))
+ pipe_ipc.readline()
+ out_list = []
+ res_list = []
+ for i in range(howmany):
+ out_list.append(string.split(pipe_ipc.readline()))
+
+ #print out_list
+ for elm in out_list:
+ amustr = elm[1]
+ percentstr = elm[3]
+ res_list.append([float(amustr[0:-1])+HMASS, float(percentstr[0:-1])])
+ #the elements 1 and 3 are the amu and the relative abundance
+ #the [0:-1] chops the last character (comma)
+
+ norm_lst = [] #normalized list in function of the intensity of the first peak
+ for i in range(len(res_list)):
+ norm_lst.append([res_list[i][0], res_list[i][1]*monoisoint/res_list[0][1]])
+
+ return norm_lst
+
+def IsDifference(difference, dif, tolerated):
+ """
+ Returns 1 if the difference is in the tolerated range around dif
+
+ accepts an error, the "tolerated" parameter
+ """
+ if (difference>(dif-tolerated) and difference <(dif+tolerated)):
+ return 1
+ else:
+ return 0
+
+def PepCompare(pepmz, pepseq):
+ """
+ Evaluates the measured mass of a peptide to see if its deuterated or not
+
+ Returns a dictionary containing the corrected pepmz if deuterated,
+ the peptide sequence (unchanged), and two flags MODIFIED if MetOX or other
+ has been found and IGNORE if no known modification was found. It also calculates
+ the number of leucines and reports it as a fifth element NBLEU.
+ Uses CalcMonoMz and IsDifference.
+ """
+ HPLUS = 1.007825
+ tolerated = 0.3 #daltons
+ theor_mz = CalcMonoMz(pepseq)
+ modif_dict = {"MetOX":15.9949}
+ deut_dict = {"NotD": 0.0, "1LeuD3": 3.023, "2LeuD3" : 6.047, "3LeuD3": 9.07, "4LeuD3": 12.094}
+
+ #test if the peptide is the deuterated form (up to 4 Leu)
+ diff_mz = pepmz - theor_mz
+ MODIFIED = 0
+ IGNORE = 0
+ NBLEU = pepseq.count('L')
+
+ FOUND = 0
+ for mod in modif_dict.keys():
+ #print mod, modif_dict[mod], "modif"
+ #print deut_dict.keys()
+ for dif in deut_dict.keys():
+ #print dif, deut_dict[dif], "dif"
+ if IsDifference(diff_mz, deut_dict[dif], tolerated):
+ #print dif, "found"
+ pepmz = pepmz - deut_dict[dif]
+ FOUND = 1
+ break
+ elif IsDifference(diff_mz, deut_dict[dif]+modif_dict[mod], tolerated):
+ #print dif, "found and modification", mod
+ pepmz = pepmz - deut_dict[dif]
+ MODIFIED = 1
+ FOUND = 1
+ break
+ if not FOUND:
+ #none of the tested modifications or deuteration accounted for the mass difference
+ IGNORE = 1
+ #print pepseq, "ignored"
+ return {"pepmz":pepmz, "pepseq":pepseq, "MODIFIED":MODIFIED, "IGNORE":IGNORE, "NBLEU":NBLEU}
+
+def CalcAndGet(pepmz, pepseq, data, peaks, ipc_path):
+ """
+ Calculates the theoretical intensities of the first 4 peaks
+ for peptides with 1 Leucine, the pepmz corresponds to the nondeuterated form.
+
+ This function is called only when the NBLEU of a peptide is 1
+ Returns a list of differences between the measured and theoretical
+ intensities for the peaks normalized to the monoisotopic peak.
+ Uses most of the functions previously defined by calls to
+ GetPeaksFromValue and RunIPC. The first elements of the returned
+ list are the peptide sequence, mz and the intensity of the monoisotopic peak
+ """
+ theor_mz = CalcMonoMz(pepseq)
+ mz_difference = pepmz - theor_mz
+ measured_lst = GetPeaksFromValue(pepmz, data, nbisotopes=peaks)
+ #print measured_lst, "measured_lst"
+ #recover the peaks on a range of 6 daltons from the monoisotopic peak
+ monointensity = measured_lst[0][1]
+ if pepseq.count("L") == 1:
+ theor_lst = RunIPC(pepseq, 6, monointensity, ipc_path)
+ #obtain the calculated list of pairs (mz, Intensity) based on the monointensity value given
+
+ dif_lstint= [pepseq]
+ dif_lstint.append(pepmz)
+ #dif_lstint.append(monointensity)
+
+ for i in range(len(measured_lst)):
+ #we only substract from the measured values the peaks 4, 5, 6
+ if pepseq.count("L") == 1:
+ if i < 3 or i > 5:
+ dif_lstint.append(measured_lst[i][1])
+ else:
+ dif_lstint.append(measured_lst[i][1]-theor_lst[i][1])
+ else:
+ dif_lstint.append(measured_lst[i][1])
+
+ #print dif_lstint, "dif_lstint"
+
+ return dif_lstint
+
+def MzIntGet(data, pepmz, plusminus=15):
+ """
+ Obtain the list of mz-int pairs
+ from the spectrum data
+
+ Returns tuple of two lists
+ """
+ mzdata, intdata = [], []
+
+ peakindex = GetPeak(data, float(pepmz), hi=len(data))
+ distforonedalton = abs(round(100/(data[peakindex][0] - data[(peakindex+100)][0])))
+ minindex = int(peakindex - distforonedalton*plusminus)
+ maxindex = int(peakindex + distforonedalton*plusminus + 6*distforonedalton)
+ for i in range(minindex, maxindex):
+ mzdata.append(data[i][0])
+ intdata.append(data[i][1])
+ return(mzdata, intdata)
+
+##################################
+#### Processing data structure ###
+##################################
+class DataIntObj:
+ """
+ A data structure to handle silac
+ difference results and calculate
+ statistics on them
+
+ """
+ def __init__(self):
+ self.nmbentries = 0
+ self.data = {}
+ self.results = {}
+ self.statistics = {}
+ #dictionaries with unique keys formed by pepseq+mzh
+ self.deleted = []
+
+
+ def get_data(self , matrix):
+ """
+ transforms the matrix obtained by several
+ calls to DiffMeasTheor into internal data
+ """
+ for element in matrix:
+ listdiff = []
+ for i in range(2, len(element)-1):
+ #first element is pepseq, second element modif pepmz
+ listdiff.append(float(element[i]))
+ intdict = {"pepseq":element[0], "mzh":float(element[1]),
+ "calcmzh":CalcMonoMz(element[0]),
+ "int0":float(element[2]),
+ "BADPEAKS": 0,
+ "listdiff":listdiff}
+ intdict["massdiff"]=intdict["mzh"]-intdict["calcmzh"]
+ intdict["Lnumber"]=intdict["pepseq"].count('L')
+ self.data[element[0]+'_'+str(element[1])] = intdict
+ return self.data
+
+ def filter_peaks(self):
+ """
+ Eliminates from self.data the peaks for which
+ the peak 3 or multiple is higher than 2 or multiple
+ Decides whether to take the non-deuterated or the
+ deuterated form in function of the intensity of the
+ corresponding peaks
+ """
+ entrieslist = self.data.keys()
+ for entrykey in entrieslist:
+ #print self.data[entrykey]
+ peak2, peak3, peakdx2, peakdx3 = 0.0, 0.0, 0.0, 0.0
+ nbleu = self.data[entrykey]["Lnumber"]
+ if nbleu <= 4:
+ #treat maximum 4 leucines
+ if len(self.data[entrykey]["listdiff"]) > 13:
+ peak2 = self.data[entrykey]["listdiff"][1]
+ peak3 = self.data[entrykey]["listdiff"][2]
+ peakdx2 = self.data[entrykey]["listdiff"][nbleu*3+1]
+ peakdx3 = self.data[entrykey]["listdiff"][nbleu*3+2]
+ #print peak2, peak3, peakdx2, peakdx3, "peaks"
+ if (peak2+peak3) > (peakdx2+peakdx3):
+ #work only with the highest value pair
+ if peak3 > peak2:
+ del self.data[entrykey]
+ self.deleted.append(entrykey)
+ #print " <br> Considered unreliable", entrykey
+ else:
+ if peakdx3 > peakdx2:
+ del self.data[entrykey]
+ self.deleted.append(entrykey)
+ #print " <br> Considered unreliable", entrykey
+ else:
+ del self.data[entrykey]
+ #print " <br> List too short", entrykey
+ else:
+ del self.data[entrykey]
+ #print " <br> More than 4 leucines", entrykey
+ return self.data
+
+ def calc_ratios(self):
+ """
+ Calculates the ratios deut/nondeuterated peptides
+ in a mix based on peptide sequence (0, 1-4 leucines)
+ """
+ entrieslist = self.data.keys()
+
+ for key in entrieslist:
+ nbleu = self.data[key]["Lnumber"]
+ monoisoint = self.data[key]["listdiff"][0]
+ if nbleu <> 0 and monoisoint <> 0:
+ self.results[key] = self.data[key]["listdiff"][nbleu*3]/monoisoint
+ else:
+ self.results[key] = 0.0
+ return self.results
+
+
+ def calc_statistics(self):
+ """
+ Median, average and StdDev for the fractions calculated for
+ peptides with 1, 2, 3 or 4 leucines
+ """
+ frlist = []
+ entrieslist = self.data.keys()
+ for key in entrieslist:
+ nbleu = self.data[key]["Lnumber"]
+ if (nbleu > 0 and nbleu < 5):
+ frlist.append(self.results[key])
+ self.statistics["Median"]=Median(frlist)
+ self.statistics["Mean"]=Mean(frlist)
+ self.statistics["StdDev"]=StdDev(frlist)
+ self.statistics["Nbvalues"]=len(frlist)
+ #print self.statistics
+
+ return self.statistics
+
+
+ def return_resultsXML(self, spectr_dict, record):
+ """
+ The object contains all the required information
+ the results are returned in very simple XML-like format
+ """
+ #res = [["Pepseq", "mz", "mzcalc", "Leucines", "MonoisoIntensity", "DeuteratedIntensity",
+ #"Deuterated_fraction"]]
+ #Add primary data
+ root= ET.Element("protdata")
+ idroot = ET.SubElement(root, "id_parameters")
+ comm = ET.SubElement(idroot, "spot_id")
+ comm.text = record["protdata"]["comment"]
+ dbase = ET.SubElement(idroot, "database")
+ dbase.text = record["protdata"]["database"]
+ ppm = ET.SubElement(idroot, "ppm_tolerance")
+ ppm.text = record["protdata"]["parent_mass_tolerance"]
+ mowse = ET.SubElement(idroot, "mowse_score")
+ try:
+ mowse.text = record["protdata"]["mowse_score"]
+ except:
+ mowse.text = "1.0"
+ protcovg = ET.SubElement(idroot, "pep_coverage")
+ protcovg.text = record["protdata"]["protein_coverage"]
+ matchedpep = ET.SubElement(idroot, "no_matched_pept")
+ matchedpep.text = str(len(record["pepdata"]["matched"]))
+ accnb = ET.SubElement(root, "accession_number")
+ accnb.text = record["protdata"]["accession_number"]
+ enname = ET.SubElement(root, "entry_name")
+ enname.text = record["protdata"]["entry_name"]
+ protmw = ET.SubElement(root, "prot_mw")
+ protmw.text = record["protdata"]["protein_mw"]
+ protpi = ET.SubElement(root, "prot_pi")
+ protpi.text = record["protdata"]["protein_pI"]
+
+ pepdataroot = ET.SubElement(root, "pepdata")
+
+ for peprec in self.data.keys():
+ nbleu = self.data[peprec]["Lnumber"]
+ if nbleu in (1,2,3,4):
+ deuterated = self.data[peprec]["listdiff"][nbleu*3]
+ else:
+ deuterated = 0.0
+
+ pepentry = ET.SubElement(pepdataroot, "measured")
+ pepseq = ET.SubElement(pepentry, "pepseq")
+ pepseq.text = self.data[peprec]["pepseq"]
+ mzh = ET.SubElement(pepentry, "mzh")
+ mzh.text = "%.4f" %(self.data[peprec]["mzh"])
+ calcmzh = ET.SubElement(pepentry, "calc_mzh")
+ calcmzh.text = "%.4f" %(self.data[peprec]["calcmzh"])
+ Lnumber = ET.SubElement(pepentry, "leucines")
+ Lnumber.text = str(self.data[peprec]["Lnumber"])
+ int0 = ET.SubElement(pepentry, "mono_iso_intensity")
+ int0.text = "%.0f" %(self.data[peprec]["int0"])
+ intd = ET.SubElement(pepentry, "deuterated_intensity")
+ intd.text = "%.0f" %(deuterated)
+ ratio = ET.SubElement(pepentry, "ratio")
+ ratio.text = "%.2f" %(self.results[peprec])
+ validated = ET.SubElement(pepentry, "validated")
+ validated.text = "UNKNOWN"
+ #lookedat = ET.SubElement(pepentry, "looked_at")
+ #lookedat.text = "NO"
+ local_bg = ET.SubElement(pepentry, "local_bg")
+ local_bg.text = "0.0000"
+ corr_ratio = ET.SubElement(pepentry, "corrected_ratio")
+ corr_ratio.text = "%.2f" %(self.results[peprec])
+ spec_piece = ET.SubElement(pepentry, "spectrum")
+ mzspec = ET.SubElement(spec_piece, "mz_list")
+ mzspec.text = WriteListToString(spectr_dict[self.data[peprec]["pepseq"]][0], "%.4f")
+ intspec = ET.SubElement(spec_piece, "int_list")
+ intspec.text = WriteListToString(spectr_dict[self.data[peprec]["pepseq"]][1], "%.4f")
+
+ #~ res.append([self.data[peprec]["pepseq"], "%.4f" %(self.data[peprec]["mzh"]),
+ #~ "%.4f" %(self.data[peprec]["calcmzh"]), self.data[peprec]["Lnumber"],
+ #~ "%.0f" %(self.data[peprec]["int0"]), "%.0f" %(deuterated),
+ #~ "%.2f" %(self.results[peprec])])
+
+ return ET.tostring(root)
+
+
+ def return_results(self):
+ """
+ The object contains all the required information
+ it is returned as a list of lists
+ """
+ res = [["Pepseq", "mz", "mzcalc", "Leucines", "MonoisoIntensity", "DeuteratedIntensity",
+ "Deuterated_fraction"]]
+ #Add primary data
+ for peprec in self.data.keys():
+ nbleu = self.data[peprec]["Lnumber"]
+ if nbleu in (1,2,3):
+ deuterated = self.data[peprec]["listdiff"][nbleu*3]
+ else:
+ deuterated = 0.0
+ res.append([self.data[peprec]["pepseq"], "%.4f" %(self.data[peprec]["mzh"]),
+ "%.4f" %(self.data[peprec]["calcmzh"]), self.data[peprec]["Lnumber"],
+ "%.0f" %(self.data[peprec]["int0"]), "%.0f" %(deuterated),
+ "%.2f" %(self.results[peprec])])
+
+ res.append(["Nbofvalues", "Median", "Mean", "StdDev"])
+ res.append(["%s" %(self.statistics["Nbvalues"]),
+ "%.2f" %(self.statistics["Median"]),
+ "%.2f" %(self.statistics["Mean"]),
+ "%.4f" %(self.statistics["StdDev"])])
+ return res
+
+
+#######################
+#####calls from CGI####
+#######################
+def ProcessSpectrum(spectrahandle, msfithandle, orflisthandle, ipc_path):
+ """
+ A function to simplify the aspect of Main
+ uses handles to file or file-like objects
+ Returns the results in list/string form
+ """
+ global calc_res
+ calc_res = ""
+ #insert data from the spectra in a list of floats
+ data_num = ReadFromFile(spectrahandle, 2)
+ data_num_minmz = data_num[0][0]
+ data_num_maxmz = data_num[-1][0]
+ #parse the HTML file
+ parseddict = ParseMSFIT(msfithandle)
+ #print "Parsing done"
+ #parseddictkeys = parseddict.keys() #####modified
+ #parseddictkeys.sort() #####modified
+ #pay attention - sorted by string not by integer value
+
+ #parse the orflist, the list of interesting things to be quantified
+ orflist = []
+ #the next lines are only necessary if the entries were not
+ #well formated in the database. To be modified otherwise.
+ ###############################################
+ for line in orflisthandle:
+ orflist.append(line.strip())
+ #print 'orflist 0', orflist[0]
+ ###############################################
+
+ record = parseddict[0] #take only the first record
+ proteinrank = record['protdata']['rank']
+ if record['protdata']['accession_number'] in orflist:
+
+ peplist = record['pepdata']['matched']
+ #the list of pairs mzh/pepseq for a given protein
+ result_matrix = []
+ spectrum_dict = {}
+ plusminus = 25
+ #the number of daltons around the monoisotopic peak to be retrieved
+ for peptide in peplist:
+ #print "Working on ", peptide[1]
+ difflist = []
+ peptidesequence = peptide[1]
+ inputpepmz = float(peptide[0])
+ decision_dict = PepCompare(inputpepmz, peptidesequence)
+ #if the peptide entry is a deuterated peptide or if its mass is already in the
+ #result_matrix (DUPLICATED = 1), no calculation is performed
+
+ if decision_dict["IGNORE"] == 0:
+ DUPLICATED = 0
+ for i in range(len(result_matrix)):
+ if abs(result_matrix[i][1]-decision_dict["pepmz"]) < 0.5:
+ #look for pepmz similar in the range +-0.5 Da to the one tested.
+ #If it exists do not run CalcAndGet
+ DUPLICATED = 1
+ break
+ if DUPLICATED == 0:
+ #test also if the range of mass from the spectrum is OK, otherwise stop
+ if decision_dict["pepmz"] > data_num_minmz and\
+ decision_dict["pepmz"] < data_num_maxmz:
+ difflist = CalcAndGet(decision_dict["pepmz"], \
+ decision_dict["pepseq"], data_num, 16, ipc_path)
+ result_matrix.append(difflist)
+ spectrum_dict[decision_dict["pepseq"]] = MzIntGet(data_num,
+ decision_dict["pepmz"], plusminus)
+
+ rawdiff= DataIntObj()
+ rawdiff.get_data(result_matrix)
+ rawdiff.filter_peaks()
+ rawdiff.calc_ratios()
+ pepresults = rawdiff.return_resultsXML(spectrum_dict, record)
+ else:
+ pepresults = "nodata"
+ #~ res = ET.Element("pepdata")
+ #~ ET.SubElement(res, "nodata")
+ #~ pepresults = ET.tostring(res)
+
+ return pepresults
+
+####################
+####### MAIN #######
+####################
+class Usage(Exception):
+ """
+ used for catching exceptions generated
+ during command line parameter parsing
+ """
+ def __init__(self, msg):
+ self.msg = msg
+def main(argv=None):
+ global fname_spectra, fname_msfit, fname_orflist, ipc_command_path
+ global spectrumhandle, msfithandle, orflisthandle
+ spectrumhandle, msfithandle, orflisthandle = sys.stdin, sys.stdin, sys.stdin
+
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "hs:i:p:c:", ["help", "spectrum=",
+ "msfithtml=", 'orflist=', "ipc_path="])
+ except getopt.error, msg:
+ raise Usage(msg)
+ # option processing
+
+ fname_spectra, fname_msfit = "", ""
+ for option, value in opts:
+ if option in ("-h", "--help"):
+ raise Usage(__doc__)
+ if option in ("-s", "--spectrum"):
+ fname_spectra = value
+ if option in ("-i", "--msfithtml"):
+ fname_msfit = value
+ if option in ("-p", "--orflist"):
+ fname_orflist = value
+ if option in ("-c", "--ipc_path"):
+ ipc_command_path = value
+
+ if (fname_spectra == "" or fname_msfit == "" or fname_orflist == ""):
+ raise Usage("no input filenames!")
+ sys.exit(2)
+ else:
+ try:
+ spectrumhandle = open(fname_spectra, "r")
+ msfithandle = open(fname_msfit, "r")
+ orflisthandle = open(fname_orflist, "r")
+ #print "OK", fname_spectra, fname_msfit, fname_orflist
+ print ProcessSpectrum(spectrumhandle, msfithandle, orflisthandle)
+ finally:
+ spectrumhandle.close()
+ msfithandle.close()
+ orflisthandle.close()
+ except Usage, err:
+ print >>sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+ print >>sys.stderr, "\t for help use --help or -h"
+ return 2
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/src/silacvalidator.py b/src/silacvalidator.py
new file mode 100644
index 0000000000000000000000000000000000000000..0b92184a27982aff6640f6af5608623f96d47960
--- /dev/null
+++ b/src/silacvalidator.py
@@ -0,0 +1,1087 @@
+#!/usr/bin/env pythonw
+"""
+SILAC validator v. 0.2, silacvalidator.py
+requires Python (2.5 or higher), wxPython and numpy (Numeric or numarray)
+(ElementTree is now included in Python 2.5)
+
+INSTRUCTIONS:
+
+This application recognizes XML files, as generated by lilamsXML. These files are
+obtained from a spectrum (in text format) and a MsFit3.2 results file (in html for-
+mat). Only the first entry in the file is quantified and generates an xml file.
+After opening an XML file, the first peptide-associated spectrum is displayed in
+the interactive plot window. You can zoom by drawing a rectangle with the left
+mouse click and unzoom with the menu >Plot>Full Unzoom. When clicking anywhere
+on the plot, the m/z value and intensity are shown in the status bar.
+To associate a local background to a spectrum double-click on the maximum and
+minimum of the peak considered as background. The difference of the two values
+is shown in the status bar. By clicking on the <Set Bgrnd.> button the last va-
+lue of the local background is inserted in the peptide table and the corrected
+ratio is automatically calculated. To validate the peptide quantification click
+on the <Validate> button.
+
+Clicking on the column titles allows sorting of the peptide list by any criteria.
+A visualisation program for XML files generated by lilamsxml. Allows validation
+of SILAC experiments, peptide by peptide.
+
+Written using wxPython, numarray, ElementTree et al., in Python, September 2004.
+Modified in January 2008, to be able to save in text format individual spectra
+regions. Several ergonomy amelioration also done and debugged the Next/Previous
+commands. THIS PROGRAM CONTAINS BUGS, SOME OF THEM IN THE UPSTREAM LIBRARIES!
+
+Cosmin Saveanu in Alain Jacquier's laboratory, Institut Pasteur, CNRS-URA2171.
+
+Many thanks to all the people contributing to the development of tools like wxPython,
+Python itself, ElementTree, and wx.lib.plot and the wonderful examples to get
+inspiration (and sometimes copy/paste) from.
+
+This program may be freely distributed as long as correct references to it are
+provided, with this included note.
+"""
+import wx
+import os, string
+from wx.lib.plot import *
+#the required plot module to draw spectra
+#from elementtree import ElementTree as ET
+#elementtree is an excellent package written by Fredrik Lundh (effbot.org)
+#to deal with simple XML structures.
+import xml.etree.cElementTree as ET #latest version integrated in Python 2.5
+
+#Imports for the ListCtrl class, copied from the wxPython documentation
+import wx.lib.mixins.listctrl as listmix
+from wx import ImageFromStream, BitmapFromImage
+
+import cStringIO
+
+try:
+ import Numeric
+except:
+ try:
+ import numarray as Numeric
+ except:
+ try:
+ import numpy as Numeric
+ except:
+ msg = """This program requires the Numeric or numarray
+ module to function - in fact is a requirement for the
+ wx.lib.plot module. Please install either Numeric or
+ numarray.
+ """
+ raise ImportError, "Numeric, numpy or numarray not found.\n"+msg
+
+#first - define unique identifiers for the different graphical elements
+[ID_OPEN,
+ID_OPENX,
+ID_CLOSE,
+ID_SAVEP,
+ID_SAVESP,
+ID_SAVEDATA,
+ID_EXIT,
+ID_ABOUT,
+ID_ENGRID,
+ID_UNZOOM,
+ID_NEXTF,
+ID_PREVF,
+ID_BTN1,
+ID_BTN2,
+ID_BTN3
+] = map(lambda init_ctrls: wx.NewId(), range(15))
+
+def get_flist_xml(dirname):
+ """get all .xml file names from dirname, not recursive
+ return only the file name, not the path
+
+ Needed by the OnPrevFile and OnNextFile functions
+ but called by <XMLOpen> to set the self.filelist list
+ of xml files from the current folder.
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".xml",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def get_flist_txt(dirname):
+ """get all .txt file names from dirname, not recursive
+ return only the file name, not the path
+ """
+ outlist = []
+ for f in os.listdir(dirname):
+ file = dirname + os.sep + f
+ if os.path.isdir(file):
+ pass
+ #we do nothing with the subfolders
+ else:
+ extension = os.path.splitext(f)[1]
+ if extension in (".txt",):
+ try:
+ outlist.append(f)
+ except:
+ pass
+ return outlist
+
+def map_pos_inlist(flist, fname):
+ """
+ Obtain the index of a file name in a file list
+ If file name not found return 0 as the position
+ Used in XMLOpen, generated a value for <self.where>
+ about the current position of a file in the file
+ list obtained with <get_flist_xml>.
+ """
+ for i in range(len(flist)):
+ if flist[i] == fname:
+ res = i
+ break
+ else:
+ res = 0
+ return res
+
+def ReadFromFileArray(file, skip=0):
+ """
+ Obtain floats from a tab delimited file into a numarray array
+ The <skip> parameter indicate the number of lines not
+ read.
+
+ This function is only used to directly open a complete spectrum
+ or a text delimited file with two columns - mz and intensity
+ """
+ data = []
+ err = 0
+ errmsg = ""
+ f=file
+ for i in range(skip):
+ f.readline()
+ #simple test to see if the file look like a float coercible text file
+ try:
+ for line in f:
+ data.append(map(float, line.strip().split("\t")))
+ data_array = Numeric.array(data)
+ except ValueError:
+ data = [[1, 1]]
+ data_array = Numeric.array(data)
+ err = 1
+ errmsg = "The file you are trying to open does not look like a tab delimited one"
+ return (data_array, err, errmsg)
+ #the returned data is a tuple with an array of floats, error and errmsg
+
+
+############################################
+# INTERFACE ############################
+############################################
+class MainFrame(wx.Frame):
+ """
+ The application main frame. Contains the following
+ graphic elements:
+ self.panel |---- self.lb - the text list control
+ |---- self.btnpanel1 - the panel containing
+ three buttons (Validate, Invalidate
+ and LocalBackground
+
+ self.panelplot - containing self.plotcanvas
+ to allow drawing of spectra files
+
+ self.log - a TextCtrl panel with information
+ on the analysed xml file
+ ______________________
+ --------------- ------
+ | || | self.lb and self.btnpanel1
+ -----------------------
+ | |
+ | | self.panelplot with self.plotcanvas
+ | |
+ -----------------------
+ | | self.log
+ -----------------------
+ """
+ def __init__(self, parent, id, title):
+ wx.Frame.__init__(self, parent, id, title,
+ wx.DefaultPosition, (800, 700))
+ self.defaultdirname = "."
+ #default directory for opening files, will be modified after first open
+ self.filelist = []
+ #list with all the xml files in a folder
+ self.where = 0
+ #position in the list of files
+ self.previousclick_y = 0.0
+ self.actualclick_y = 0.0
+ #local background is calculated by substracting
+ #self.previousclick_y from self.actualclick_y
+ #absolute value is returned anyway
+ self.localbg = 0.0
+
+ self.XMLdict = {'pepseq': 0, 'mzh':1, 'calc_mzh':2, 'leucines':3,
+ 'mono_iso_int':4, 'deuterated_intensity':5,
+ 'ratio':6, 'validated':7,
+ 'local_bg':8, 'corrected_ratio':9}
+ #the mapping of tags to numbers to allow easy orientation in the ElementTree
+ #Element object obtained by parsing a SILAC XML file. If the lilams XML format
+ #changes you should change accordingly these numbers
+ self.pdatapos = 5
+ #in the XML tree the pepdata values are in this position
+
+ ###################################################################
+ # Create the menu bar and items
+ self.menubar = wx.MenuBar()
+
+ filemenu = wx.Menu()
+ filemenu.Append(ID_OPENX, '&Open XML SILAC file...\tCtrl+O', 'Open XML file with SILAC data')
+ filemenu.Append(ID_SAVEDATA, 'Save XML &modifications\tCtrl+S', 'Save modifications with (validation/local background)')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_OPEN, 'O&pen text file...\tCtrl+T', 'Open tab delimited file for plotting')
+ filemenu.Append(ID_CLOSE, '&Close text file\tCtrl+W', 'Close text file')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVEP, '&Save plot image\tCtrl+I', 'Save plot image in a bmp, png or jpg format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_SAVESP, 'Sa&ve plot data\tCtrl+D', 'Save the data corresponding to the plotted spectrum in text format')
+ filemenu.AppendSeparator()
+ filemenu.Append(ID_EXIT, '&Quit\tCtrl+Q', 'Exit program')
+
+ navmenu = wx.Menu()
+ navmenu.Append(ID_NEXTF, '&Next XML file\tCtrl+N', 'Open next xml file in the current folder')
+ navmenu.Append(ID_PREVF, '&Previous XML file\tCtrl+P', 'Open previous xml file in the current folder')
+
+ plotmenu = wx.Menu()
+ plotmenu.Append(ID_UNZOOM, 'Full &Unzoom\tCtrl+U', 'Full unzoom for the current plot')
+ plotmenu.AppendSeparator()
+ plotmenu.Append(ID_ENGRID, 'Grid &enabled', 'Enable or disable grid when drawing', wx.ITEM_CHECK)
+
+ helpmenu = wx.Menu()
+ helpmenu.Append(ID_ABOUT, '&About...\tCtrl+E', 'About this program')
+
+ ###################################################################
+ # Bind the events to methods
+ wx.EVT_MENU(self, ID_OPENX, self.OnXMLOpen)
+ wx.EVT_MENU(self, ID_SAVEDATA, self.OnXMLSave)
+ wx.EVT_MENU(self, ID_OPEN, self.OnFileOpen)
+ wx.EVT_MENU(self, ID_CLOSE, self.OnFileClose)
+ wx.EVT_MENU(self, ID_SAVEP, self.OnSaveImage)
+ wx.EVT_MENU(self, ID_SAVESP, self.OnSpectrumSave)
+ wx.EVT_MENU(self, ID_EXIT, self.OnFileExit)
+ wx.EVT_MENU(self, ID_NEXTF, self.OnNextFile)
+ wx.EVT_MENU(self, ID_PREVF, self.OnPrevFile)
+ wx.EVT_MENU(self, ID_ENGRID, self.OnEnableGrid)
+ wx.EVT_MENU(self, ID_UNZOOM, self.OnFullUnzoom)
+ wx.EVT_MENU(self, ID_ABOUT, self.OnHelpAbout)
+
+ ###################################################################
+ # Attach menus to the menubar
+ self.menubar.Append(filemenu, '&File')
+ self.menubar.Append(navmenu, '&Next/Previous')
+ self.menubar.Append(plotmenu, '&Plot')
+ self.menubar.Append(helpmenu, '&Help')
+
+ self.SetMenuBar(self.menubar)
+
+ ###################################################################
+ #Disable by default some menus and buttons
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 0)
+ self.menubar.Enable(ID_SAVEP, 0)
+ self.menubar.Enable(ID_SAVESP, 0)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ # A status bar to tell people what's happening
+ self.CreateStatusBar(1)
+
+ self.SetAutoLayout(True)
+
+ ###################################################################
+ self.panel = wx.Panel(self, -1, style=wx.SIMPLE_BORDER)
+ #in this case and all the others we use layout constraints
+ #I couldn't understand easily the sizers, while layout constraints seem
+ #quite easy to set up and they work very well.
+ #self.panel will contain the listctrl and button panel
+
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self, wx.Top, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 30)
+ self.panel.SetConstraints(lc)
+
+ ###################################################################
+ #the peplistctrlpanel - with the list of peptides and interesting data
+ self.smalldict = {1:("pepseq", "0", "mzh", "mzhcalc", "mono", "deuter", "ratio", "corr",
+ "localbg", "valid")}
+ #we need this to fill up the listctrl at program initialization
+ self.lb = PepListCtrlPanel(self.panel, dictwithdata=self.smalldict)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.PercentOf(self.panel, wx.Right, 80) #it will take up 80% of the panel
+ lc.left.SameAs(self.panel, wx.Left, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.lb.SetConstraints(lc)
+ ###################################################################
+ self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.lb.list)
+ ###################################################################
+ #the panel to hold the three buttons
+ self.btnpanel1 = wx.Panel(self.panel, -1, style=wx.SIMPLE_BORDER)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panel, wx.Top, 10)
+ lc.right.SameAs(self.panel, wx.Right, 10)
+ lc.left.SameAs(self.lb, wx.Right, 10)
+ lc.bottom.SameAs(self.panel, wx.Bottom, 10)
+ self.btnpanel1.SetConstraints(lc)
+ ###################################################################
+ #set up the buttons and bind to the corresponding functions
+ self.btn1 = wx.Button(self.btnpanel1, ID_BTN1, " Validate ", wx.DefaultPosition)
+ self.btn2 = wx.Button(self.btnpanel1, ID_BTN2, "INvalidate", wx.DefaultPosition)
+ self.btn3 = wx.Button(self.btnpanel1, ID_BTN3, "Set Bgrnd.", wx.DefaultPosition)
+ wx.EVT_BUTTON(self, ID_BTN1, self.OnValidate)
+ wx.EVT_BUTTON(self, ID_BTN2, self.OnInvalidate)
+ wx.EVT_BUTTON(self, ID_BTN3, self.OnSetLocalBg)
+
+ #Disable by default the three buttons
+ self.btn1.Enable(False)
+ self.btn2.Enable(False)
+ self.btn3.Enable(False)
+ ###################################################################
+ #layout the buttons on the btnpanel1
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btnpanel1, wx.CentreX)
+ lc.top.SameAs(self.btnpanel1, wx.Top, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn1.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.centreY.SameAs(self.btnpanel1, wx.CentreY)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn2.SetConstraints(lc)
+
+ lc = wx.LayoutConstraints()
+ lc.centreX.SameAs(self.btn1, wx.CentreX)
+ lc.bottom.SameAs(self.btnpanel1, wx.Bottom, 10)
+ lc.width.AsIs()
+ lc.height.AsIs()
+ self.btn3.SetConstraints(lc)
+
+ ###################################################################
+ #A black panel to give contrast to the plot
+ self.panelplot = wx.Window(self, -1)
+ self.panelplot.SetBackgroundColour(wx.BLACK)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panel, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.PercentOf(self, wx.Bottom, 85)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.panelplot.SetConstraints(lc)
+ ###################################################################
+ #The plot itself in self.panelplot
+ self.plotcanvas = PlotCanvas(self.panelplot, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.panelplot, wx.Top, 2)
+ lc.left.SameAs(self.panelplot, wx.Left, 2)
+ lc.bottom.SameAs(self.panelplot, wx.Bottom, 2)
+ lc.right.SameAs(self.panelplot, wx.Right, 2)
+ self.plotcanvas.SetConstraints(lc)
+ ###################################################################
+ #A panel to hold the TextCtrl called self.log
+ self.logpanel = wx.Window(self, -1)
+ lc = wx.LayoutConstraints()
+ lc.top.Below(self.panelplot, 5)
+ lc.left.SameAs(self, wx.Left, 5)
+ lc.bottom.SameAs(self, wx.Bottom, 5)
+ lc.right.SameAs(self, wx.Right, 5)
+ self.logpanel.SetConstraints(lc)
+ ###################################################################
+ #The text control that will hold informations on the protein and file used
+ self.log = wx.TextCtrl(self.logpanel, -1,
+ style = wx.TE_MULTILINE|wx.TE_READONLY|wx.HSCROLL)
+ lc = wx.LayoutConstraints()
+ lc.top.SameAs(self.logpanel, wx.Top, 2)
+ lc.left.SameAs(self.logpanel, wx.Left, 0)
+ lc.bottom.SameAs(self.logpanel, wx.Bottom, 2)
+ lc.right.SameAs(self.logpanel, wx.Right, 0)
+ self.log.SetConstraints(lc)
+ self.log.AppendText("> Hello. Load a LILAMS XML file from the File> menu (or Cmd+O).")
+ ###################################################################
+ # Create mouse event for showing cursor coords in status bar
+ self.plotcanvas.canvas.Bind(wx.EVT_LEFT_DOWN, self.OnMLeftDown)
+ self.plotcanvas.canvas.Bind(wx.EVT_LEFT_DCLICK, self.OnMDoubleClick)
+ self.plotcanvas.SetEnableZoom(1) #to ensure zoom by default
+ self.plotcanvas.canvas.SetCursor(wx.StockCursor(wx.CURSOR_CROSS)) #by default it is a "loupe"
+
+ self.Show(True)
+
+ ###################################################################
+ ## Main Frame function definitions ################################
+ ###################################################################
+
+ def OnXMLOpen(self, event):
+ """
+ Opens a XML file with SILAC data and generates
+ an ElementTree instance containing the data
+ in the variable self.data
+ """
+ self.resetDefaults()
+ wildcard = "XML file (*.xml)|*.xml|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a SILAC XML file:",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ filename=dlg.GetFilename()
+ dirname=dlg.GetDirectory()
+ try:
+ if not self.XMLOpen(dirname, filename):
+ msg = """
+ The file you wanted to open does not
+ contain valid SILAC XML data. Try opening it with
+ a text editor to see what is the problem."""
+ dlg = wx.MessageDialog(self, msg, 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ finally:
+ dlg.Destroy()
+
+ def XMLOpen(self, dirname, filename):
+ """
+ Will allow calls for XMLOpen from Previous
+ and Next calls. Returns True if everything OK.
+
+ -uses get_flist_xml to set up the file list
+ -uses map_pos_inlist to set up self.where
+ -uses self.PlotSpectrumXML to plot the first peptide
+ in file
+ -uses self.PopulateList to populate the self.lb list
+ control with data
+ -uses self.GenerateListDict to generate the dictionary
+ used to describe the data in the self.lb control
+ """
+ filename=filename
+ dirname=dirname
+ self.defaultdirname = dirname
+ fname = os.path.join(dirname, filename)
+ #self.fnameout = fname+"x"
+ #we write in the same xml file, overwriting previous file
+ self.fnameout = fname
+ self.filelist = get_flist_xml(dirname)
+ self.where = map_pos_inlist(self.filelist, filename)
+ try:
+ tree = ET.parse(fname)
+ self.data = tree.getroot()
+ #the root is a <protdata> entry
+ self.PlotSpectrumXML(0, title="peptide 1")
+ self.PopulateList(self.GenerateListDict(self.data))
+ #Clear the log, write text to it about the opened file
+ self.log.Remove(0, self.log.GetLastPosition())
+ self.log.AppendText("\n> Opened %s xml file.\n"%filename)
+ self.log.AppendText("> Mowse score: %s, database: %s, ppm tolerance: %s.\n"%(self.data[0][3].text,
+ self.data[0][1].text, self.data[0][2].text))
+ self.log.AppendText("> Spot identification: %s.\n"%self.data[0][0].text)
+ self.log.AppendText("> Identified protein: %s, accesion number: %s.\n"%(self.data[2].text, self.data[1].text))
+ self.log.AppendText("> Peptide coverage: %s percent, matched peptides: %s.\n"%(self.data[0][4].text[:-1], self.data[0][5].text))
+ self.menubar.Enable(ID_NEXTF, 1)
+ self.menubar.Enable(ID_PREVF, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.btn1.Enable(True)
+ self.btn2.Enable(True)
+ self.btn3.Enable(True)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVESP, 0)
+ return True
+ except:
+ return False
+
+ def PlotSpectrumXML(self, index=0, title=""):
+ """
+ Recover and plot data for the record that has <index>
+ It is found in self.data[5] - that is pepdata,
+ the subnode is 10 for <spectrum> and 0, 1 for
+ the two lists mz and int. "5 "is contained in self.pdatapos
+
+ -uses self.PlotArray - a function to do the plotting
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+ self.PlotArray(dataforarray, "blue", title)
+
+ def PlotArray(self, data_array, color, title):
+ """
+ Used to plot on the plotcanvas the points of a data_array
+ Default is autoscale, used by PlotSpectrumXML
+ """
+ self.line = PolyLine(data_array, colour = color)
+ self.plotcanvas.Draw(PlotGraphics([self.line, ], title, "m/z", ""))
+ #self.plotcanvas.Redraw()
+
+ def GenerateListDict(self, xmldata):
+ """
+ forms a dictionary {1:["a", "b", "c"], 2:...}
+ for the PepListCtrlPanel widget - to populate
+ with XML data
+ """
+ self.entriesdict = {}
+ for i in range(len(xmldata[self.pdatapos])):
+ self.entriesdict[i] = (self.GetValXML(i, 'pepseq'),
+ self.GetValXML(i, 'leucines'),
+ self.GetValXML(i, 'mzh'),
+ self.GetValXML(i, 'calc_mzh'),
+ self.GetValXML(i, 'mono_iso_int'),
+ self.GetValXML(i, 'deuterated_intensity'),
+ self.GetValXML(i, 'ratio'),
+ self.GetValXML(i, 'corrected_ratio'),
+ self.GetValXML(i, 'local_bg'),
+ self.GetValXML(i, 'validated'))
+ return self.entriesdict
+
+ def PopulateList(self, externaldict):
+ """
+ a wrapper to the function with the same name in self.lb
+ """
+ self.lb.PopulateList(externaldict)
+
+ def OnItemSelected(self, event):
+ """
+ Activated when one item in the self.lb list control
+ is selected. Determines the generation of a unique key
+ that will allow a correspondence between the list
+ elements and the underlying ElementTree Element
+ - uses MapUniqueKey function
+ """
+ #print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.lb.list.GetItemText(self.currentItem)+self.lb.getColumnText(self.currentItem, 2)
+ self.index = self.MapUniqueKey(self.uniquekey)
+ #print self.index, "self.index"
+ self.PlotSpectrumXML(self.index, title = self.GetValXML(self.index, 'pepseq')+\
+ " / "+self.GetValXML(self.index, 'mzh'))
+ self.menubar.Enable(ID_SAVEDATA, 1)
+ self.menubar.Enable(ID_SAVESP, 1)
+ event.Skip()
+ #the self.index variable allows us to recover and change the data if validation occurs
+
+ def MapUniqueKey(self, uniquekey):
+ """
+ Used by <OnItemSelected> to allow a correspondence between
+ self.currentItem - in the list and self.index in the ElementTree
+ Element representing data read from the XML SILAC file
+ """
+ result = 0
+ for i in range(len(self.data[self.pdatapos])):
+ #testing [0] is peptide sequence [1] is submitted m/z+h mass
+ if uniquekey == self.data[self.pdatapos][i][0].text+\
+ self.data[self.pdatapos][i][1].text:
+ #the index of the correspoinding key was found
+ result = i
+ break
+ return result
+
+ def OnValidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "YES")
+ self.SetXMLValidated(self.index, "YES")
+
+ def OnInvalidate(self, event):
+ """
+ changes both the entry in the list control
+ -- see SetValidated function --- and the
+ same entry in the self.data (to be written)
+ """
+ self.lb.SetValidated(self.currentItem, "NO")
+ self.SetXMLValidated(self.index, "NO")
+
+ def SetXMLValidated(self, index, what):
+ """
+ 7 is the actual position of the <validated> field
+ in the self.data - coming from the SILAC XML tree
+ """
+ self.data[self.pdatapos][index][7].text = what
+
+ def GetValXML(self, index=0, what='pepseq'):
+ """
+ Returns the text attribute of an entry in an Element
+ object based on the self.XMLdict dictionary that maps
+ numbers to tags - definition in the init of the main
+ frame. By default it returns the peptide sequence of
+ the first record.
+
+ self.pdatapos - indicates the position of the <pepdata> in
+ the root of the pepdata xml entry
+ """
+ return self.data[self.pdatapos][index][self.XMLdict[what]].text
+
+ def OnXMLSave(self, event):
+ """
+ Writes the contents of self.data to the self.fnameout
+ (established when the actual file was opened)
+ """
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ def OnSpectrumSave(self, event):
+ self.SpectrumSave(self.index)
+
+ def SpectrumSave(self, index=0):
+ """
+ Writes the contents of the actual selected spectrum
+ to a given file name, in tab delimited format
+ """
+ mzdata = self.data[self.pdatapos][index][10][0].text.split()
+ intdata = self.data[self.pdatapos][index][10][1].text.split()
+ dataforarray = []
+ for i in range(len(mzdata)):
+ dataforarray.append([float(mzdata[i]), float(intdata[i])])
+
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(
+ self, message="Save plot data to ...", defaultDir = self.defaultdirname,
+ defaultFile="pepspecdata.txt", wildcard=wildcard, style=wx.SAVE
+ )
+ dlg.SetFilterIndex(0)
+ if dlg.ShowModal() == wx.ID_OK:
+ path = dlg.GetPath()
+ try:
+ fout = open(path, "w")
+ for line in dataforarray:
+ fout.write('%.3f\t%d\n'%(line[0], line[1]))
+ fout.close()
+
+ self.SetStatusText("Data saved to file %s"%path)
+ except IOError:
+ dlg = wx.MessageDialog(self, "Error. Maybe the output file is in use...", 'Problem saving data',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ dlg.Destroy()
+
+ def OnNextFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO| wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ if len(self.filelist) > 0:
+ #print self.filelist
+ #print self.where
+ if self.where < len(self.filelist)-1:
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where+1])
+ #self.where += 1 there is a risk in using global variables
+ #this one is already modified by XMLOpen to the correct value
+ else:
+ #we are at the end of the list, going on from the beginning
+ self.where = 0
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+
+ def OnPrevFile(self, event):
+ """
+ Allows navigation between the xml files
+ in a folder. Calls the self.XMLOpen function
+ exactly like the self.OnXMLOpen.
+ """
+ msg = "Save changes to the actual file ?"
+ dlg = wx.MessageDialog(self, msg, 'Save changes...',
+ wx.YES_NO | wx.ICON_QUESTION)
+ response = dlg.ShowModal()
+ dlg.Destroy()
+ if response == wx.ID_YES:
+ ET.ElementTree(self.data).write(self.fnameout)
+
+ if len(self.filelist) > 0:
+ if self.where > 0:
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where-1])
+ else:
+ #we are at the beginning of the list
+ self.where = len(self.filelist)-1
+ self.XMLOpen(self.defaultdirname, self.filelist[self.where])
+
+ def OnFullUnzoom(self, event):
+ self.plotcanvas.Reset()
+
+ def OnFileOpen(self, event):
+ """
+ Opens and plots a tab delimited text file
+ If not a recognized file, a message is displayed
+ Sets also the actual directory name: self.defaultdirname
+ """
+ self.resetDefaults()
+ wildcard = "Tab delimited text file (*.txt)|*.txt|"\
+ "All files (*.*)|*.*"
+ dlg = wx.FileDialog(self, "Choose a tab delimited text file",
+ self.defaultdirname, "", wildcard, wx.OPEN)
+ if dlg.ShowModal() == wx.ID_OK:
+ self.filename=dlg.GetFilename()
+ self.dirname=dlg.GetDirectory()
+ self.defaultdirname = self.dirname
+ self.filelist = get_flist_txt(self.dirname)
+ fname = os.path.join(self.dirname, self.filename)
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ dlg.Destroy()
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", self.filename)
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+ self.menubar.Enable(ID_UNZOOM, 1)
+ self.menubar.Enable(ID_SAVEP, 1)
+ self.menubar.Enable(ID_SAVEDATA, 0)
+ self.menubar.Enable(ID_CLOSE, 0)
+
+ def PlotFile(self, fname):
+ file = open(fname, "r")
+ readed = ReadFromFileArray(file, 5)
+ file.close()
+ self.array = readed[0]
+ if readed[1] == 1: #error
+ dlg = wx.MessageDialog(self, readed[2], 'Problem opening file',
+ wx.OK | wx.ICON_INFORMATION)
+ dlg.ShowModal()
+ dlg.Destroy()
+ else:
+ self.PlotArray(self.array, "blue", os.path.split(fname)[1])
+
+ def OnFileClose(self, event):
+ self.plotcanvas.Clear()
+ self.menubar.Enable(ID_NEXTF, 0)
+ self.menubar.Enable(ID_PREVF, 0)
+
+ def OnMLeftDown(self, event):
+ self.localbg = abs(self.actualclick_y - self.previousclick_y)
+ #self.position = event.GetPosition()
+ #print self.position
+ s= "(m/z : %.2f, Intensity : %.2f)"%self.plotcanvas.GetXY(event)+\
+ " Local background : %.0f"%self.localbg
+ self.SetStatusText(s)
+ self.plotcanvas.canvas.SetCursor(wx.StockCursor(wx.CURSOR_CROSS))
+ #we have to update the cursor form, otherwise it gets reset to "lens"
+
+ event.Skip()
+
+ def OnMDoubleClick(self, event):
+ self.previousclick_y = self.actualclick_y
+ self.actualclick_y = self.plotcanvas.GetXY(event)[1]
+
+ def OnSetLocalBg(self, event):
+ """
+ Updates the local background data both in the shown list
+ and in self.data. Recalculated the corrected ratio
+ """
+ self.data[self.pdatapos][self.index][8].text = "%0.f"%self.localbg
+ deut = float(self.GetValXML(self.index, 'deuterated_intensity'))-self.localbg
+ monoiso = float(self.GetValXML(self.index, 'mono_iso_int'))-self.localbg
+ self.data[self.pdatapos][self.index][9].text = "%.2f"%(deut/monoiso)
+ self.lb.SetBg(self.currentItem, self.localbg, (deut/monoiso))
+
+ def OnSaveImage(self, event):
+ self.plotcanvas.SaveFile()
+
+ def OnFileExit(self, event):
+ self.Close()
+
+ def OnPlotRedraw(self, event):
+ self.plotcanvas.Redraw()
+
+ def OnPlotClear(self, event):
+ self.plotcanvas.Clear()
+
+ def OnPlotScale(self, event):
+ if self.plotcanvas.last_draw != None:
+ graphics, xAxis, yAxis= self.plotcanvas.last_draw
+ self.plotcanvas.Draw(graphics, (1, 3.05), (0, 1))
+
+ def OnEnableZoom(self, event):
+ self.plotcanvas.SetEnableZoom(event.IsChecked())
+
+ def OnEnableGrid(self, event):
+ self.plotcanvas.SetEnableGrid(event.IsChecked())
+
+ def OnEnableLegend(self, event):
+ self.plotcanvas.SetEnableLegend(event.IsChecked())
+ def OnReset(self, event):
+ self.plotcanvas.Reset()
+
+ def OnHelpAbout(self, event):
+ from wx.lib.dialogs import ScrolledMessageDialog
+ about = ScrolledMessageDialog(self, __doc__, "About...", size = (600, 400))
+ about.ShowModal()
+
+ def resetDefaults(self):
+ """Just to reset the fonts back to the PlotCanvas defaults"""
+ self.plotcanvas.SetFont(wx.Font(10, wx.SWISS, wx.NORMAL, wx.NORMAL))
+ self.plotcanvas.SetFontSizeAxis(10)
+ self.plotcanvas.SetFontSizeLegend(7)
+ self.plotcanvas.SetXSpec('auto')
+ self.plotcanvas.SetYSpec('auto')
+ self.plotcanvas.SetEnableZoom(1)
+
+#######################################################
+#######################################################
+################ PepListCtrlPanel ###############
+################ and PepListCtrl classes###############
+#######################################################
+#######################################################
+#######################################################
+#----------------------------------------------------------------------------
+# Name: ListCtrl.py
+# Purpose: Testing lots of stuff, controls, window types, etc.
+#
+# Author: Robin Dunn & Gary Dumer
+#
+# Created:
+# RCS-ID: $Id: ListCtrl.py,v 1.3 2004/03/05 00:06:32 RD Exp $
+# Copyright: (c) 1998 by Total Control Software
+# Licence: wxWindows license
+#
+# Modified by Cosmin Saveanu, IP, September 2004
+# to be able to deal with peptide entries for SILAC
+#----------------------------------------------------------------------------
+def getSmallUpArrowData():
+ return \
+'\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00<IDATx\x9ccddbf\xa0\x040Q\xa4{h\x18\xf0\xff\xdf\xdf\xffd\x1b\x00\xd3\
+\x8c\xcf\x10\x9c\x06\xa0k\xc2e\x08m\xc2\x00\x97m\xd8\xc41\x0c \x14h\xe8\xf2\
+\x8c\xa3)q\x10\x18\x00\x00R\xd8#\xec\x95{\xc4\x11\x00\x00\x00\x00IEND\xaeB`\
+\x82'
+
+def getSmallUpArrowBitmap():
+ return BitmapFromImage(getSmallUpArrowImage())
+def getSmallUpArrowImage():
+ stream = cStringIO.StringIO(getSmallUpArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+
+def getSmallDnArrowData():
+ return \
+"\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x10\x00\x00\x00\x10\x08\x06\
+\x00\x00\x00\x1f\xf3\xffa\x00\x00\x00\x04sBIT\x08\x08\x08\x08|\x08d\x88\x00\
+\x00\x00HIDATx\x9ccddbf\xa0\x040Q\xa4{\xd4\x00\x06\x06\x06\x06\x06\x16t\x81\
+\xff\xff\xfe\xfe'\xa4\x89\x91\x89\x99\x11\xa7\x0b\x90%\ti\xc6j\x00>C\xb0\x89\
+\xd3.\x10\xd1m\xc3\xe5*\xbc.\x80i\xc2\x17.\x8c\xa3y\x81\x01\x00\xa1\x0e\x04e\
+\x1d\xc4;\xb7\x00\x00\x00\x00IEND\xaeB`\x82"
+def getSmallDnArrowBitmap():
+ return BitmapFromImage(getSmallDnArrowImage())
+
+def getSmallDnArrowImage():
+ stream = cStringIO.StringIO(getSmallDnArrowData())
+ return ImageFromStream(stream)
+#----------------------------------------------------------------------
+class PepListCtrl(wx.ListCtrl, listmix.ListCtrlAutoWidthMixin):
+
+ def __init__(self, parent, ID, pos=wx.DefaultPosition,
+ size=wx.DefaultSize, style=0):
+ wx.ListCtrl.__init__(self, parent, ID, pos, size, style)
+ listmix.ListCtrlAutoWidthMixin.__init__(self)
+
+class PepListCtrlPanel(wx.Panel, listmix.ColumnSorterMixin):
+
+ def __init__(self, parent, dictwithdata={}):
+ wx.Panel.__init__(self, parent, -1, style=wx.WANTS_CHARS)
+ tID = wx.NewId()
+ self.il = wx.ImageList(16, 16)
+ self.sm_up = self.il.Add(getSmallUpArrowBitmap())
+ self.sm_dn = self.il.Add(getSmallDnArrowBitmap())
+ self.list = PepListCtrl(self, tID,
+ style=wx.LC_REPORT
+ | wx.SUNKEN_BORDER
+ | wx.LC_SINGLE_SEL
+ #| wx.LC_HRULES
+ #| wx.LC_EDIT_LABELS
+ #| wxLC_NO_HEADER
+ #| wxLC_VRULES
+ )
+ self.list.SetImageList(self.il, wx.IMAGE_LIST_SMALL)
+ self.PopulateList(dictwithdata)
+ # Now that the list exists we can init the other base class,
+ # see wxPython/lib/mixins/listctrl.py
+
+ listmix.ColumnSorterMixin.__init__(self, 10)
+ #self.SortListItems(0, True)
+ self.Bind(wx.EVT_SIZE, self.OnSize)
+ #self.Bind(wx.EVT_LIST_ITEM_SELECTED, self.OnItemSelected, self.list)
+ self.Bind(wx.EVT_LIST_COL_CLICK, self.OnColClick, self.list)
+
+ def PopulateList(self, externaldict):
+ """
+ Constructs the headings of the list control
+ and populates it with data
+ """
+
+ self.itemDataMap = externaldict
+ self.list.ClearAll()
+ if 0:
+ # for normal, simple columns, you can add them like this:
+ self.list.InsertColumn(0, "Peptide")
+ self.list.InsertColumn(1, "Leucines", wx.LIST_FORMAT_RIGHT)
+ self.list.InsertColumn(2, "m/z measured")
+ #etc...
+ else:
+ # but since we want images on the column header we have to do it the hard way:
+ info = wx.ListItem()
+ info.m_mask = wx.LIST_MASK_TEXT | wx.LIST_MASK_IMAGE | wx.LIST_MASK_FORMAT
+ info.m_image = -1
+ info.m_format = 0
+ info.m_text = "Peptide"
+ self.list.InsertColumnInfo(0, info)
+ #info.m_format = wx.LIST_FORMAT_RIGHT
+ info.m_format = 0
+ info.m_text = "Leucines"
+ self.list.InsertColumnInfo(1, info)
+ info.m_format = 0
+ info.m_text = "m/z meas."
+ self.list.InsertColumnInfo(2, info)
+
+ info.m_format = 0
+ info.m_text = "m/z calc."
+ self.list.InsertColumnInfo(3, info)
+
+ info.m_format = 0
+ info.m_text = "Base_int."
+ self.list.InsertColumnInfo(4, info)
+
+ info.m_format = 0
+ info.m_text = "Deut_int."
+ self.list.InsertColumnInfo(5, info)
+
+ info.m_format = 0
+ info.m_text = "Ratio"
+ self.list.InsertColumnInfo(6, info)
+
+ info.m_format = 0
+ info.m_text = "Corr_ratio"
+ self.list.InsertColumnInfo(7, info)
+
+ info.m_format = 0
+ info.m_text = "Local_bg"
+ self.list.InsertColumnInfo(8, info)
+
+ info.m_format = 0
+ info.m_text = "Valid."
+ self.list.InsertColumnInfo(9, info)
+ #Now put inside the data from the dictionary
+ items = externaldict.items()
+ for x in range(len(items)):
+ key, data = items[x]
+ self.list.InsertStringItem(x, data[0])
+ #self.list.InsertImageStringItem(x, data[0], self.sm_up)
+ self.list.SetStringItem(x, 1, data[1])
+ self.list.SetStringItem(x, 2, data[2])
+ self.list.SetStringItem(x, 3, data[3])
+ self.list.SetStringItem(x, 4, data[4])
+ self.list.SetStringItem(x, 5, data[5])
+ self.list.SetStringItem(x, 6, data[6])
+ self.list.SetStringItem(x, 7, data[7])
+ self.list.SetStringItem(x, 8, data[8])
+ self.list.SetStringItem(x, 9, data[9])
+ self.list.SetItemData(x, key) #why is that necessary ?
+ #Set colors for the adnotation - is light grey if
+ #no leucine exists in the peptide sequence
+ if data[9] == "YES":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if data[9] == "NO":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+ if data[1] == "0":
+ item = self.list.GetItem(x)
+ item.SetTextColour(wx.LIGHT_GREY)
+ self.list.SetItem(item)
+
+ for i in range(9):
+ self.list.SetColumnWidth(i, 60)
+ #self.list.SetColumnWidth(i, wx.LIST_AUTOSIZE)
+ self.list.SetColumnWidth(9, 100)
+ # show how to select an item
+ #self.list.SetItemState(5, wx.LIST_STATE_SELECTED, wx.LIST_STATE_SELECTED)
+ self.currentItem = 0
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetListCtrl(self):
+ return self.list
+
+ def SetValidated(self, where, what):
+ """
+ Called when the OnValidate or OnInvalidate are activated
+ Changes the 9th element in the current list item to "YES"
+ or "NO"
+ """
+ self.list.SetStringItem(where, 9, what)
+ if what == "YES":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.BLUE)
+ self.list.SetItem(item)
+ if what == "NO":
+ item = self.list.GetItem(where)
+ item.SetTextColour(wx.RED)
+ self.list.SetItem(item)
+
+ def SetBg(self, where, bg, ratio):
+ """
+ Shows local background value in the list and
+ the updated value of corrected ratio
+ """
+ self.list.SetStringItem(where, 8, "%.0f"%bg)
+ self.list.SetStringItem(where, 7, "%.2f"%ratio)
+
+ # Used by the ColumnSorterMixin, see wxPython/lib/mixins/listctrl.py
+ def GetSortImages(self):
+ return (self.sm_dn, self.sm_up)
+
+ def getColumnText(self, index, col):
+ item = self.list.GetItem(index, col)
+ return item.GetText()
+
+ def OnItemSelected(self, event):
+ """
+ Overwritten by its equivalent in MainFrame
+ """
+ ##print event.GetItem().GetTextColour()
+ self.currentItem = event.m_itemIndex
+ self.uniquekey = self.list.GetItemText(self.currentItem)+\
+ self.getColumnText(self.currentItem, 1)
+ #print self.uniquekey
+ event.Skip()
+
+ def OnColClick(self, event):
+ #print ("OnColClick: %d\n" % event.GetColumn())
+ event.Skip()
+
+ def OnSize(self, event):
+ w, h = self.GetClientSizeTuple()
+ self.list.SetDimensions(0, 0, w, h)
+
+#######################################################
+#the equivalent of a main function.
+app = wx.PySimpleApp()
+frame = MainFrame(None, -1, "SILAC validator v. 0.2")
+app.SetTopWindow(frame)
+app.MainLoop()
+#######################################################