/**
* 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;
}
}
}
/**
* Add an exon. If the exon's bounds are beyond the transcript's bounds, the transcript's bounds
* are adjusted accordingly. Sets the exon's transcript to this transcript object.
*
* @param exon - Exon to be added
*/
public void addExon(Exon exon) {
CVTerm partOfCvterm = conf.getDefaultCVTermForClass("PartOf");
// if the exon's bounds are beyond the transcript's bounds, need to adjust the transcript's
// bounds
if (exon.getFeatureLocation().getFmin() < getFeatureLocation().getFmin()) {
getFeatureLocation().setFmin(exon.getFeatureLocation().getFmin());
}
if (exon.getFeatureLocation().getFmax() > getFeatureLocation().getFmax()) {
getFeatureLocation().setFmax(exon.getFeatureLocation().getFmax());
}
// if the transcript's bounds are beyond the gene's bounds, need to adjust the gene's bounds
if (getGene() != null) {
if (getFmin() < getGene().getFmin()) {
getGene().setFmin(getFmin());
}
if (getFmax() > getGene().getFmax()) {
getGene().setFmax(getFmax());
}
}
// add exon
int rank = 0;
// TODO: do we need to figure out the rank?
feature
.getChildFeatureRelationships()
.add(new FeatureRelationship(partOfCvterm, feature, exon.getFeature(), rank));
exon.setTranscript(this);
}
