示例#1
0
 /**
  * Retrieve the gene that this transcript is associated with. Uses the configuration to determine
  * which parent is a gene. The gene object is generated on the fly. Returns <code>null</code> if
  * this transcript is not associated with any gene.
  *
  * @return Gene that this Transcript is associated with
  */
 public Gene getGene() {
   Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
   Collection<CVTerm> geneCvterms = conf.getDescendantCVTermsForClass("Gene");
   for (FeatureRelationship fr : feature.getParentFeatureRelationships()) {
     if (!partOfCvterms.contains(fr.getType())) {
       continue;
     }
     if (!geneCvterms.contains(fr.getObjectFeature().getType())) {
       continue;
     }
     return ((Gene) BioObjectUtil.createBioObject(fr.getObjectFeature(), conf));
   }
   return null;
 }
示例#2
0
  /**
   * Delete an exon. Deletes both the transcript -> exon and exon -> transcript relationships.
   *
   * @param exon - Exon to be deleted
   */
  public void deleteExon(Exon exon) {
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> exonCvterms = conf.getCVTermsForClass("Exon");
    Collection<CVTerm> transcriptCvterms = conf.getCVTermsForClass("Transcript");

    // delete transcript -> exon child relationship
    for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!exonCvterms.contains(fr.getSubjectFeature().getType())) {
        continue;
      }
      if (fr.getSubjectFeature().equals(exon.getFeature())) {
        boolean ok = feature.getChildFeatureRelationships().remove(fr);
        break;
      }
    }

    // delete transcript -> exon parent relationship
    for (FeatureRelationship fr : exon.getFeature().getParentFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!transcriptCvterms.contains(fr.getObjectFeature().getType())) {
        continue;
      }
      if (fr.getSubjectFeature().equals(exon.getFeature())) {
        boolean ok = exon.getFeature().getParentFeatureRelationships().remove(fr);
        break;
      }
    }
  }
示例#3
0
  /**
   * Delete an non canonical 3' splice site. Deletes both the transcript -> non canonical 3' splice
   * site and non canonical 3' splice site -> transcript relationships.
   *
   * @param nonCanonicalThreePrimeSpliceSite - NonCanonicalThreePrimeSpliceSite to be deleted
   */
  public void deleteNonCanonicalThreePrimeSpliceSite(
      NonCanonicalThreePrimeSpliceSite nonCanonicalThreePrimeSpliceSite) {
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> nonCanonicalThreePrimeSpliceSiteCvterms =
        conf.getCVTermsForClass("NonCanonicalThreePrimeSpliceSite");
    Collection<CVTerm> transcriptCvterms = conf.getCVTermsForClass("Transcript");

    // delete transcript -> non canonical 3' splice site child relationship
    for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!nonCanonicalThreePrimeSpliceSiteCvterms.contains(fr.getSubjectFeature().getType())) {
        continue;
      }
      if (fr.getSubjectFeature().equals(nonCanonicalThreePrimeSpliceSite.getFeature())) {
        boolean ok = feature.getChildFeatureRelationships().remove(fr);
        break;
      }
    }

    // delete transcript -> non canonical 3' splice site parent relationship
    for (FeatureRelationship fr :
        nonCanonicalThreePrimeSpliceSite.getFeature().getParentFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!transcriptCvterms.contains(fr.getObjectFeature().getType())) {
        continue;
      }
      if (fr.getSubjectFeature().equals(nonCanonicalThreePrimeSpliceSite.getFeature())) {
        boolean ok =
            nonCanonicalThreePrimeSpliceSite
                .getFeature()
                .getParentFeatureRelationships()
                .remove(fr);
        break;
      }
    }
  }
示例#4
0
  /**
   * Set the gene that this transcript is associated with. Uses the configuration to determine which
   * parent is a gene. If the transcript is already associated with a gene, updates that
   * association. Otherwise, it creates a new association.
   *
   * @param gene - Gene that this transcript will be associated with
   */
  public void setGene(Gene gene) {
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> geneCvterms = conf.getDescendantCVTermsForClass("Gene");
    for (FeatureRelationship fr : feature.getParentFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!geneCvterms.contains(fr.getObjectFeature().getType())) {
        continue;
      }
      fr.setObjectFeature(gene.getFeature());
      return;
    }

    FeatureRelationship fr =
        new FeatureRelationship(
            conf.getDefaultCVTermForClass("PartOf"),
            gene.getFeature(),
            this.feature,
            0 // TODO: Do we need to rank the order of any other transcripts?
            );
    feature.getParentFeatureRelationships().add(fr);
    gene.getFeature().getChildFeatureRelationships().add(fr);
  }