/**
* Add a non canonical 5' splice site. Sets the splice site's transcript to this transcript
* object.
*
* @param nonCanonicalFivePrimeSpliceSite - Non canonical 5' splice site to be added
*/
public void addNonCanonicalFivePrimeSpliceSite(
NonCanonicalFivePrimeSpliceSite nonCanonicalFivePrimeSpliceSite) {
CVTerm partOfCvterm = conf.getDefaultCVTermForClass("PartOf");
// add non canonical 5' splice site
FeatureRelationship fr =
new FeatureRelationship(
conf.getDefaultCVTermForClass("PartOf"),
this.feature,
nonCanonicalFivePrimeSpliceSite.getFeature(),
0 // TODO: Do we need to rank the order of any other transcripts?
);
feature.getChildFeatureRelationships().add(fr);
nonCanonicalFivePrimeSpliceSite.getFeature().getParentFeatureRelationships().add(fr);
}
/**
* Delete an non canonical 5' splice site. Deletes both the transcript -> non canonical 5' splice
* site and non canonical 5' splice site -> transcript relationships.
*
* @param nonCanonicalFivePrimeSpliceSite - NonCanonicalFivePrimeSpliceSite to be deleted
*/
public void deleteNonCanonicalFivePrimeSpliceSite(
NonCanonicalFivePrimeSpliceSite nonCanonicalFivePrimeSpliceSite) {
Collection<CVTerm> partOfCvterms = conf.getCVTermsForClass("PartOf");
Collection<CVTerm> nonCanonicalFivePrimeSpliceSiteCvterms =
conf.getCVTermsForClass("NonCanonicalFivePrimeSpliceSite");
Collection<CVTerm> transcriptCvterms = conf.getCVTermsForClass("Transcript");
// delete transcript -> non canonical 5' splice site child relationship
for (FeatureRelationship fr : feature.getChildFeatureRelationships()) {
if (!partOfCvterms.contains(fr.getType())) {
continue;
}
if (!nonCanonicalFivePrimeSpliceSiteCvterms.contains(fr.getSubjectFeature().getType())) {
continue;
}
if (fr.getSubjectFeature().equals(nonCanonicalFivePrimeSpliceSite.getFeature())) {
boolean ok = feature.getChildFeatureRelationships().remove(fr);
break;
}
}
// delete transcript -> non canonical 5' splice site parent relationship
for (FeatureRelationship fr :
nonCanonicalFivePrimeSpliceSite.getFeature().getParentFeatureRelationships()) {
if (!partOfCvterms.contains(fr.getType())) {
continue;
}
if (!transcriptCvterms.contains(fr.getObjectFeature().getType())) {
continue;
}
if (fr.getSubjectFeature().equals(nonCanonicalFivePrimeSpliceSite.getFeature())) {
boolean ok =
nonCanonicalFivePrimeSpliceSite.getFeature().getParentFeatureRelationships().remove(fr);
break;
}
}
}
