/**
* 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;
}
}
}
/**
* 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;
}
}
}
/**
* 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;
}
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;
}
}
/**
* 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;
}
/**
* 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;
}
/**
* 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;
}
/**
* 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;
}
/**
* 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);
}