Commit 52d33f5a authored by Remi  PLANEL's avatar Remi PLANEL
Browse files

Display homologue's gene name and organism infos

parent 9baa6300
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
</fields> </fields>
</class> </class>
<class className="org.intermine.model.bio.Location"> <class className="org.intermine.model.bio.Location">
<fields> <fields>
<fieldconfig fieldExpr="feature.primaryIdentifier"/> <fieldconfig fieldExpr="feature.primaryIdentifier"/>
<fieldconfig fieldExpr="start"/> <fieldconfig fieldExpr="start"/>
...@@ -92,7 +92,7 @@ ...@@ -92,7 +92,7 @@
<class className="org.intermine.model.bio.OntologyTerm"> <class className="org.intermine.model.bio.OntologyTerm">
<headerconfig> <headerconfig>
<titles> <titles>
<title mainTitles="identifier|name" subTitles="ontology.name" /> <title mainTitles="identifier|name" subTitles="ontology.name" />
</titles> </titles>
</headerconfig> </headerconfig>
<fields> <fields>
...@@ -120,7 +120,7 @@ ...@@ -120,7 +120,7 @@
<class className="org.intermine.model.bio.Organism"> <class className="org.intermine.model.bio.Organism">
<headerconfig> <headerconfig>
<titles> <titles>
<title mainTitles="name"/> <title mainTitles="name"/>
</titles> </titles>
</headerconfig> </headerconfig>
<fields> <fields>
...@@ -143,9 +143,9 @@ ...@@ -143,9 +143,9 @@
<class className="org.intermine.model.bio.Publication"> <class className="org.intermine.model.bio.Publication">
<headerconfig> <headerconfig>
<titles> <titles>
<title mainTitles="title" /> <title mainTitles="title" />
</titles> </titles>
</headerconfig> </headerconfig>
<inlinelist> <inlinelist>
<table path="authors.name" showLinksToObjects="true" /> <table path="authors.name" showLinksToObjects="true" />
...@@ -163,9 +163,7 @@ ...@@ -163,9 +163,7 @@
<class className="org.intermine.model.bio.Sequence"> <class className="org.intermine.model.bio.Sequence">
<fields> <fields>
<fieldconfig fieldExpr="residues" fieldExporter="org.intermine.bio.web.export.ResidueFieldExporter" <fieldconfig fieldExpr="residues" fieldExporter="org.intermine.bio.web.export.ResidueFieldExporter" sectionOnRight="true" sectionTitle="Residues" openByDefault="true" showInSummary="false" showInResults="false" showInInlineCollection="false"/>
sectionOnRight="true" sectionTitle="Residues" openByDefault="true"
showInSummary="false" showInResults="false" showInInlineCollection="false"/>
<fieldconfig fieldExpr="length"/> <fieldconfig fieldExpr="length"/>
</fields> </fields>
<tabledisplayer src="/model/sequenceShortDisplayer.jsp"/> <tabledisplayer src="/model/sequenceShortDisplayer.jsp"/>
...@@ -188,57 +186,39 @@ ...@@ -188,57 +186,39 @@
</fields> </fields>
</class> </class>
<!-- exporters --> <class className="org.intermine.model.bio.Homologue">
<fields>
<fieldconfig fieldExpr="type"/>
<fieldconfig fieldExpr="homologue.primaryIdentifier" label="DB identifier"/>
<fieldconfig fieldExpr="homologue.symbol" label="Symbol"/>
<fieldconfig fieldExpr="homologue.length" label="Length"/>
<fieldconfig fieldExpr="homologue.chromosome.primaryIdentifier" label="DB identifier"/>
<fieldconfig fieldExpr="homologue.organism.shortName" label="Short Name"/>
</fields>
</class>
<!-- exporters -->
<tableExportConfig id="sequence" className="org.intermine.bio.web.export.SequenceHttpExporter"/> <tableExportConfig id="sequence" className="org.intermine.bio.web.export.SequenceHttpExporter"/>
<tableExportConfig id="gff3" className="org.intermine.bio.web.export.GFF3HttpExporter"/> <tableExportConfig id="gff3" className="org.intermine.bio.web.export.GFF3HttpExporter"/>
<tableExportConfig id="bed" className="org.intermine.bio.web.export.BEDHttpExporter"/> <tableExportConfig id="bed" className="org.intermine.bio.web.export.BEDHttpExporter"/>
<reportdisplayers> <reportdisplayers>
<reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer" <reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneOntologyDisplayer" jspName="model/geneOntologyDisplayer.jsp" replacesFields="goAnnotation,ontologyAnnotations" placement="Genomics" types="Gene"/>
jspName="model/geneOntologyDisplayer.jsp"
replacesFields="goAnnotation,ontologyAnnotations" <reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneStructureDisplayer" jspName="model/geneStructureDisplayer.jsp" replacesFields="transcripts,exons,CDSs,introns,UTRs,fivePrimeUTR,threePrimeUTR" placement="Genomics" types="Gene,Transcript,Exon,Intron,UTR,CDS"/>
placement="Genomics"
types="Gene"/> <reportdisplayer javaClass="org.intermine.bio.web.displayer.SequenceFeatureDisplayer" jspName="model/sequenceFeatureDisplayer.jsp" replacesFields="chromosome,chromosomeLocation,sequence,length,sequenceOntologyTerm,locations,cytoLocation" placement="summary" types="SequenceFeature"/>
<reportdisplayer javaClass="org.intermine.bio.web.displayer.GeneStructureDisplayer" <reportdisplayer javaClass="org.intermine.bio.web.displayer.UniProtCommentsDisplayer" jspName="model/uniProtCommentsDisplayer.jsp" replacesFields="" placement="Proteins" types="Gene,Protein"/>
jspName="model/geneStructureDisplayer.jsp"
replacesFields="transcripts,exons,CDSs,introns,UTRs,fivePrimeUTR,threePrimeUTR"
placement="Genomics"
types="Gene,Transcript,Exon,Intron,UTR,CDS"/>
<reportdisplayer javaClass="org.intermine.bio.web.displayer.SequenceFeatureDisplayer"
jspName="model/sequenceFeatureDisplayer.jsp"
replacesFields="chromosome,chromosomeLocation,sequence,length,sequenceOntologyTerm,locations,cytoLocation"
placement="summary"
types="SequenceFeature"/>
<reportdisplayer javaClass="org.intermine.bio.web.displayer.UniProtCommentsDisplayer"
jspName="model/uniProtCommentsDisplayer.jsp"
replacesFields=""
placement="Proteins"
types="Gene,Protein"/>
</reportdisplayers> </reportdisplayers>
<!-- widgets --> <!-- widgets -->
<widgets> <widgets>
<graphdisplayer id="chromosome_distribution_for_gene" <graphdisplayer id="chromosome_distribution_for_gene" title="Chromosome Distribution" description="Actual: number of items in this list found on each chromosome. Expected: given the total number of items on the chromosome and the number of items in this list, the number of items expected to be found on each chromosome." graphType="ColumnChart" rangeLabel="Count" domainLabel="Chromosome" filterLabel="Organism" filters="organism.name=[list]" startClass="Gene" typeClass="Gene" categoryPath="chromosome.primaryIdentifier" seriesLabels="Actual,Expected" seriesPath="ActualExpectedCriteria" constraints="organism.name=[Organism]" views="primaryIdentifier, symbol, secondaryIdentifier, organism.name, chromosome.primaryIdentifier,
title="Chromosome Distribution"
description="Actual: number of items in this list found on each chromosome. Expected: given the total number of items on the chromosome and the number of items in this list, the number of items expected to be found on each chromosome."
graphType="ColumnChart"
rangeLabel="Count"
domainLabel="Chromosome"
filterLabel="Organism"
filters="organism.name=[list]"
startClass="Gene"
typeClass="Gene"
categoryPath="chromosome.primaryIdentifier"
seriesLabels="Actual,Expected"
seriesPath="ActualExpectedCriteria"
constraints="organism.name=[Organism]"
views="primaryIdentifier, symbol, secondaryIdentifier, organism.name, chromosome.primaryIdentifier,
chromosomeLocation.start, chromosomeLocation.end, chromosomeLocation.strand"/> chromosomeLocation.start, chromosomeLocation.end, chromosomeLocation.strand"/>
</widgets> </widgets>
</webconfig> </webconfig>
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