コード例 #1
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;
      }
    }
  }
コード例 #2
0
  /**
   * Retrieve the CDS associated with this transcript. Uses the configuration to determine which
   * child is a CDS. The CDS object is generated on the fly. Returns <code>null</code> if no CDS is
   * associated.
   *
   * @return CDS associated with this transcript
   */
  public CDS getCDS() {
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> cdsCvterms = conf.getCVTermsForClass("CDS");

    for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!cdsCvterms.contains(fr.getSubjectFeature().getType())) {
        continue;
      }
      return new CDS(fr.getSubjectFeature(), conf);
    }
    return null;
  }
コード例 #3
0
  /**
   * Retrieve all the exons associated with this transcript. Uses the configuration to determine
   * which children are exons. Exon objects are generated on the fly. The collection will be empty
   * if there are no exons associated with the transcript.
   *
   * @return Collection of exons associated with this transcript
   */
  public Collection<Exon> getExons() {
    Collection<Exon> exons = new ArrayList<Exon>();
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> exonCvterms = conf.getCVTermsForClass("Exon");

    for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!exonCvterms.contains(fr.getSubjectFeature().getType())) {
        continue;
      }
      exons.add(new Exon(fr.getSubjectFeature(), conf));
    }
    return exons;
  }
コード例 #4
0
  /**
   * Retrieve all the non canonical 3' splice sites associated with this transcript. Uses the
   * configuration to determine which children are non canonical 3' splice sites. Non canonical 3'
   * splice site objects are generated on the fly. The collection will be empty if there are no non
   * canonical 3' splice sites associated with the transcript.
   *
   * @return Collection of non canonical 3' splice sites associated with this transcript
   */
  public Collection<NonCanonicalThreePrimeSpliceSite> getNonCanonicalThreePrimeSpliceSites() {
    Collection<NonCanonicalThreePrimeSpliceSite> nonCanonicalThreePrimeSpliceSites =
        new ArrayList<NonCanonicalThreePrimeSpliceSite>();
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> nonCanonicalThreePrimeSpliceSiteCvterms =
        conf.getCVTermsForClass("NonCanonicalThreePrimeSpliceSite");

    for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!nonCanonicalThreePrimeSpliceSiteCvterms.contains(fr.getSubjectFeature().getType())) {
        continue;
      }
      nonCanonicalThreePrimeSpliceSites.add(
          new NonCanonicalThreePrimeSpliceSite(fr.getSubjectFeature(), conf));
    }
    return nonCanonicalThreePrimeSpliceSites;
  }
コード例 #5
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;
      }
    }
  }
コード例 #6
0
  public void deleteCDS() {
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> cdsCvterms = conf.getCVTermsForClass("CDS");

    for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!cdsCvterms.contains(fr.getSubjectFeature().getType())) {
        continue;
      }
      feature.getChildFeatureRelationships().remove(fr);
      break;
    }
  }
コード例 #7
0
  /**
   * Get the number of exons.
   *
   * @return Number of exons
   */
  public int getNumberOfExons() {
    Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
    Collection<CVTerm> exonCvterms = conf.getCVTermsForClass("Exon");
    int numExons = 0;

    for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
      if (!partOfCvterms.contains(fr.getType())) {
        continue;
      }
      if (!exonCvterms.contains(fr.getSubjectFeature().getType())) {
        continue;
      }
      ++numExons;
    }
    return numExons;
  }