/**
* 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);
}
@Override
public int convertSourceCoordinateToLocalCoordinate(int sourceCoordinate) {
List<Exon> exons = BioObjectUtil.createSortedFeatureListByLocation(getExons());
int localCoordinate = -1;
if (exons.size() == 0) {
return super.convertSourceCoordinateToLocalCoordinate(sourceCoordinate);
}
int currentCoordinate = 0;
for (Exon exon : exons) {
if (exon.getFeatureLocation().getFmin() <= sourceCoordinate
&& exon.getFeatureLocation().getFmax() >= sourceCoordinate) {
if (getFeatureLocation().getStrand() == -1) {
localCoordinate =
currentCoordinate + (exon.getFeatureLocation().getFmax() - sourceCoordinate) - 1;
} else {
localCoordinate =
currentCoordinate + (sourceCoordinate - exon.getFeatureLocation().getFmin());
}
}
currentCoordinate += exon.getLength();
}
return localCoordinate;
}
@Override
public int convertLocalCoordinateToSourceCoordinate(int localCoordinate) {
List<Exon> exons = BioObjectUtil.createSortedFeatureListByLocation(getExons());
int sourceCoordinate = -1;
if (exons.size() == 0) {
return super.convertLocalCoordinateToSourceCoordinate(localCoordinate);
}
int currentLength = 0;
int currentCoordinate = localCoordinate;
for (Exon exon : exons) {
int exonLength = exon.getLength();
if (currentLength + exonLength >= localCoordinate) {
if (getFeatureLocation().getStrand() == -1) {
sourceCoordinate = exon.getFeatureLocation().getFmax() - currentCoordinate - 1;
} else {
sourceCoordinate = exon.getFeatureLocation().getFmin() + currentCoordinate;
}
break;
}
currentLength += exonLength;
currentCoordinate -= exonLength;
}
return sourceCoordinate;
}
