SequenceI mapFromSequence = seq;
SequenceI mapToSequence = mappedSequence;
if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
- || (type == MappingType.PeptideToNucleotide && !featureIsOnTarget))
+ || (type == MappingType.PeptideToNucleotide
+ && !featureIsOnTarget))
{
mapFromSequence = mappedSequence;
mapToSequence = seq;
{
fromStart = alignToStart;
toStart = alignFromStart;
- toEnd = forwardStrand ? toStart + alignCount - 1 : toStart
- - (alignCount - 1);
+ toEnd = forwardStrand ? toStart + alignCount - 1
+ : toStart - (alignCount - 1);
int toLength = Math.abs(toEnd - toStart) + 1;
int fromLength = toLength * type.getFromRatio() / type.getToRatio();
fromEnd = fromStart + fromLength - 1;
return false;
}
+ /**
+ * An override to set feature group to "exonerate" instead of the default GFF
+ * source value (column 2)
+ */
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
Map<String, List<String>> set)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, set);
- sf.setFeatureGroup("exonerate");
+ SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+ "exonerate", set);
return sf;
}