source: trunk/bio/tutorial/malariamine/webapp/resources/webapp/WEB-INF/webconfig-model.xml @ 27560

<webconfig>
  <class className="org.intermine.model.bio.Author">
    <fields>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.BioEntity">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Chromosome">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="organism.name"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Comment">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="text"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.DataSet">
    <fields>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.DataSource">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
    <tabledisplayer src="/model/dataSourceShort.jsp"/>
  </class>

  <class className="org.intermine.model.bio.Gene">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="chromosome.primaryIdentifier" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.start" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.end" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="organism.shortName" />
    </fields>
    <bagdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </bagdisplayers>
  </class>

  <class className="org.intermine.model.bio.GOAnnotation">
    <fields>
      <fieldconfig fieldExpr="subject.primaryIdentifier" showInInlineCollection="false" showInResults="true"/>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="property[GOTerm].namespace" showInSummary="false" />
      <fieldconfig fieldExpr="qualifier"/>
      <fieldconfig fieldExpr="isPrimaryAssignment"/>
    </fields>
  </class>

   <class className="org.intermine.model.bio.GOTerm">
    <fields>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

 <class className="org.intermine.model.bio.Location">
    <fields>
      <fieldconfig fieldExpr="object.primaryIdentifier"/>
      <fieldconfig fieldExpr="start"/>
      <fieldconfig fieldExpr="end"/>
      <fieldconfig fieldExpr="strand"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.SequenceFeature">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="chromosome.primaryIdentifier" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.start" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.end" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="organism.name"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.OntologyTerm">
    <fields>
      <fieldconfig fieldExpr="identifier"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="description" doNotTruncate="true" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.OntologyRelation">
    <fields>
      <fieldconfig fieldExpr="relationship"/>
      <fieldconfig fieldExpr="parentTerm.identifier"/>
      <fieldconfig fieldExpr="childTerm.identifier"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.OntologyTermSynonym">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="type"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Organism">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="taxonId" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Protein">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="primaryAccession"/>
      <fieldconfig fieldExpr="organism.name"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.Publication">
    <fields>
      <fieldconfig fieldExpr="firstAuthor"/>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="year"/>
      <fieldconfig fieldExpr="journal"/>
      <fieldconfig fieldExpr="volume"/>
      <fieldconfig fieldExpr="pages"/>
      <fieldconfig fieldExpr="pubMedId"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Sequence">
    <fields>
      <fieldconfig fieldExpr="residues" fieldExporter="org.intermine.bio.web.export.ResidueFieldExporter"
                   sectionOnRight="true" sectionTitle="Residues" openByDefault="true"
                   showInSummary="false" showInResults="false" showInInlineCollection="false"/>
      <fieldconfig fieldExpr="length"/>
    </fields>
    <tabledisplayer src="/model/sequenceShortDisplayer.jsp"/>
  </class>

  <class className="org.intermine.model.bio.Synonym">
    <fields>
      <fieldconfig fieldExpr="value"/>
      <fieldconfig fieldExpr="type"/>
    </fields>
  </class>

  <class className="org.intermine.model.bio.Transcript">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false"/>
      <fieldconfig fieldExpr="chromosome.primaryIdentifier" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.start" showInInlineCollection="false" showInSummary="false" />
      <fieldconfig fieldExpr="chromosomeLocation.end" showInInlineCollection="false" showInSummary="false" />
    </fields>
  </class>

  <class className="org.intermine.model.bio.UniProtFeature">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="description"/>
      <fieldconfig fieldExpr="begin"/>
      <fieldconfig fieldExpr="end"/>
    </fields>
  </class>

<!-- exporters -->
  <tableExportConfig id="sequence" className="org.intermine.bio.web.export.SequenceHttpExporter"/>
  <tableExportConfig id="gff3" className="org.intermine.bio.web.export.GFF3HttpExporter"/>

<!-- widgets -->
<widgets>
      <graphdisplayer id="chromosome_distribution" title="Chromosome Distribution"
        domainLabel="Chromosome"
        rangeLabel="Count"
        dataSetLoader="org.intermine.bio.web.widget.ChromosomeDistributionDataSetLdr"
        link="org.intermine.bio.web.widget.ChromosomeDistributionGraphURLGenerator"
        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="BarChart"
        extraAttributeClass="org.intermine.bio.util.BioUtil"
        typeClass="org.intermine.model.bio.Gene,org.intermine.model.bio.SequenceFeature"
       />

      <enrichmentwidgetdisplayer id="protein_features" title="UniProt Features"
                                 link="org.intermine.bio.web.widget.UniProtFeaturesURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.UniProtFeaturesLdr"
                                 label="Feature"
                                 description="UniProt features enriched for proteins in this list."
                                 typeClass="org.intermine.model.bio.Protein" />

      <enrichmentwidgetdisplayer id="uniprot_keywords" title="UniProt Keywords"
                                 link="org.intermine.bio.web.widget.UniProtKeywordsURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.UniProtKeywordsLdr"
                                 label="Keyword"
                                 description="UniProt keywords enriched for proteins in this list."
                                 typeClass="org.intermine.model.bio.Protein" />


      <enrichmentwidgetdisplayer id="go_enrichment" title="Gene Ontology Enrichment"
                                 link="org.intermine.bio.web.widget.GoStatURLQuery"
                                 dataSetLoader="org.intermine.bio.web.widget.GoStatLdr"
                                 description="GO terms enriched for items in this list."
                                 label="GO Term"
                                 filters="biological_process,cellular_component,molecular_function"
                                 filterLabel="Ontology"
                                 typeClass="org.intermine.model.bio.Gene,org.intermine.model.bio.Protein"
                                 externalLink="http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=" />
</widgets>
</webconfig>