@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;
}
