Commit 109e3ec9 authored by Keith Jolley's avatar Keith Jolley
Browse files

Use parent instead of base.

parent afe9f9cb
#Written by Keith Jolley
#Copyright (c) 2010-2011, University of Oxford
#Copyright (c) 2010-2012, University of Oxford
#E-mail: keith.jolley@zoo.ox.ac.uk
#
#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
......@@ -19,7 +19,7 @@
package BIGSdb::AlleleSequencePage;
use strict;
use warnings;
use base qw(BIGSdb::IsolateInfoPage BIGSdb::ExtractedSequencePage);
use parent qw(BIGSdb::IsolateInfoPage BIGSdb::ExtractedSequencePage);
use Log::Log4perl qw(get_logger);
use Error qw(:try);
my $logger = get_logger('BIGSdb.Page');
......@@ -80,7 +80,7 @@ sub print_content {
$buffer .= "<tr class=\"td1\"><th>translation</th><td colspan=\"2\" style=\"text-align:left\">";
my @stops = @{$display->{'internal_stop'}};
if (@stops){
$"=', ';
local $"=', ';
$buffer .= "<span class=\"highlight\">Internal stop codon" . (@stops == 1 ? '' : 's') . " at position". (@stops == 1 ? '' : 's') . ": @stops (numbering includes upstream flanking sequence).</span>\n";
}
$buffer .= "<pre class=\"sixpack\">\n";
......@@ -98,6 +98,7 @@ sub print_content {
} else {
print "<div class=\"box\" id=\"statusbad\"><p>This isolate does not have a sequence defined for locus $display_locus.</p></div>\n";
}
return;
}
sub get_title {
......
#Written by Keith Jolley
#(c) 2010-2011, University of Oxford
#(c) 2010-2012, University of Oxford
#E-mail: keith.jolley@zoo.ox.ac.uk
#
#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
......@@ -20,7 +20,7 @@
package BIGSdb::BIGSException;
use strict;
use warnings;
use base qw(Error);
use parent qw(Error);
use overload ( '""' => 'stringify' );
no warnings 'redefine';
......@@ -29,61 +29,61 @@ sub new {
my @args = ();
local $Error::Depth = $Error::Depth + 1;
local $Error::Debug = 1; # Enables storing of stacktrace
$self->SUPER::new( -text => $text, @args );
return $self->SUPER::new( -text => $text, @args );
}
1;
#Database exceptions
package BIGSdb::DatabaseException;
use base qw(BIGSdb::BIGSException);
use parent qw(BIGSdb::BIGSException);
1;
package BIGSdb::DatabaseConnectionException;
use base qw(BIGSdb::DatabaseException);
use parent -norequire, qw(BIGSdb::DatabaseException);
1;
package BIGSdb::DatabaseConfigurationException;
use base qw(BIGSdb::DatabaseException);
use parent -norequire, qw(BIGSdb::DatabaseException);
1;
package BIGSdb::DatabaseNoRecordException;
use base qw(BIGSdb::DatabaseException);
use parent -norequire, qw(BIGSdb::DatabaseException);
1;
package BIGSdb::PrefstoreConfigurationException;
use base qw(BIGSdb::DatabaseException);
use parent -norequire, qw(BIGSdb::DatabaseException);
1;
#File exceptions
package BIGSdb::FileException;
use base qw(BIGSdb::BIGSException);
use parent qw(BIGSdb::BIGSException);
1;
package BIGSdb::FileDoesNotExistException;
use base qw(BIGSdb::FileException);
use parent -norequire, qw(BIGSdb::FileException);
1;
package BIGSdb::CannotOpenFileException;
use base qw(BIGSdb::FileException);
use parent -norequire, qw(BIGSdb::FileException);
1;
#Data exceptions
package BIGSdb::DataException;
use base qw(BIGSdb::BIGSException);
use parent qw(BIGSdb::BIGSException);
1;
#Authentication exceptions
package BIGSdb::AuthenticationException;
use base qw(BIGSdb::BIGSException);
use parent qw(BIGSdb::BIGSException);
1;
#Plugins
package BIGSdb::PluginException;
use base qw(BIGSdb::BIGSException);
use parent qw(BIGSdb::BIGSException);
1;
package BIGSdb::InvalidPluginException;
use base qw(BIGSdb::PluginException);
use parent -norequire, qw(BIGSdb::PluginException);
1;
......
#Written by Keith Jolley
#Copyright (c) 2010-2011, University of Oxford
#Copyright (c) 2010-2012, University of Oxford
#E-mail: keith.jolley@zoo.ox.ac.uk
#
#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
......@@ -19,7 +19,7 @@
package BIGSdb::BatchProfileQueryPage;
use strict;
use warnings;
use base qw(BIGSdb::Page);
use parent qw(BIGSdb::Page);
use Log::Log4perl qw(get_logger);
use Error qw(:try);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::BlastPage;
use strict;
use warnings;
use base qw(BIGSdb::Page);
use parent qw(BIGSdb::Page);
use File::Path;
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::BrowsePage;
use strict;
use warnings;
use base qw(BIGSdb::Page);
use parent qw(BIGSdb::Page);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::ChangePasswordPage;
use strict;
use warnings;
use base qw(BIGSdb::LoginMD5);
use parent qw(BIGSdb::LoginMD5);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
#Written by Keith Jolley
#Copyright (c) 2010-2011, University of Oxford
#Copyright (c) 2010-2012, University of Oxford
#E-mail: keith.jolley@zoo.ox.ac.uk
#
#This file is part of Bacterial Isolate Genome Sequence Database (BIGSdb).
......@@ -19,7 +19,7 @@
package BIGSdb::ConfigCheckPage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::ConfigRepairPage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::Curate;
use strict;
use warnings;
use base qw(BIGSdb::Application);
use parent qw(BIGSdb::Application);
use BIGSdb::ConfigCheckPage;
use BIGSdb::ConfigRepairPage;
use BIGSdb::CurateAddPage;
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateAddPage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage BIGSdb::BlastPage);
use parent qw(BIGSdb::CuratePage BIGSdb::BlastPage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
use List::MoreUtils qw(any);
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateAlleleUpdatePage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage BIGSdb::TreeViewPage);
use parent qw(BIGSdb::CuratePage BIGSdb::TreeViewPage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -20,7 +20,7 @@ package BIGSdb::CurateBatchAddPage;
use strict;
use warnings;
use List::MoreUtils qw(any none uniq);
use base qw(BIGSdb::CurateAddPage);
use parent qw(BIGSdb::CurateAddPage);
use Log::Log4perl qw(get_logger);
use Error qw(:try);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateBatchAddSeqbinPage;
use strict;
use warnings;
use base qw(BIGSdb::CurateAddPage);
use parent qw(BIGSdb::CurateAddPage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
use Error qw(:try);
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateBatchIsolateUpdatePage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateCompositeQueryPage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateCompositeUpdatePage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateDatabankScanPage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use Log::Log4perl qw(get_logger);
use Error qw(:try);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateDeleteAllPage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use Log::Log4perl qw(get_logger);
use Error qw(:try);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateDeletePage;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use List::MoreUtils qw(any);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
......@@ -19,7 +19,7 @@
package BIGSdb::CurateExportConfig;
use strict;
use warnings;
use base qw(BIGSdb::CuratePage);
use parent qw(BIGSdb::CuratePage);
use List::MoreUtils qw(any);
use Log::Log4perl qw(get_logger);
my $logger = get_logger('BIGSdb.Page');
......
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