source: trunk/bio/core/genomic_additions.xml @ 25778

<?xml version="1.0"?>
<classes>

    <class name="CDS" is-interface="true">
      <reference name="gene" referenced-type="Gene" reverse-reference="CDSs"/>
      <reference name="protein" referenced-type="Protein" reverse-reference="CDSs"/>
    </class>

    <class name="Exon" is-interface="true">
      <reference name="gene" referenced-type="Gene" reverse-reference="exons"/>
    </class>

    <class name="Gene" is-interface="true">
      <reference name="upstreamIntergenicRegion" referenced-type="IntergenicRegion"/>
      <reference name="downstreamIntergenicRegion" referenced-type="IntergenicRegion"/>  
      <collection name="UTRs" referenced-type="UTR" reverse-reference="gene"/>
      <collection name="exons" referenced-type="Exon" reverse-reference="gene"/>
      <collection name="CDSs" referenced-type="CDS" reverse-reference="gene"/>
      <collection name="flankingRegions" referenced-type="GeneFlankingRegion" reverse-reference="gene"/>
      <collection name="introns" referenced-type="Intron" reverse-reference="genes"/>
    </class>

    <class name="GeneFlankingRegion" extends="SequenceFeature" is-interface="true">
      <attribute name="distance" type="java.lang.String"/>
      <attribute name="direction" type="java.lang.String"/>
      <attribute name="includeGene" type="java.lang.Boolean"/>
      <reference name="gene" referenced-type="Gene" reverse-reference="flankingRegions"/>
    </class>

    <class name="IntergenicRegion" is-interface="true">
      <collection name="adjacentGenes" referenced-type="Gene"/>
     </class>

    <class name="Intron" is-interface="true">
      <collection name="genes" referenced-type="Gene" reverse-reference="introns"/>
    </class>

    <class name="Protein" is-interface="true">
      <collection name="CDSs" referenced-type="CDS" reverse-reference="protein"/>
      <collection name="transcripts" referenced-type="Transcript" reverse-reference="protein"/>
    </class>

    <class name="SequenceVariant" is-interface="true">
      <collection name="genes" referenced-type="Gene"/>
    </class>
        
    <class name="Transcript" is-interface="true">
      <reference name="protein" referenced-type="Protein" reverse-reference="transcripts"/>
    </class>
    
    <class name="UTR" is-interface="true">
      <reference name="gene" referenced-type="Gene" reverse-reference="UTRs"/>
    </class>
</classes>