ref.getStart() + alseqs[i].start+bounds[0],
ref.getStart() + alseqs[i].start+(bounds[2]==0 ? -1 : bounds[2]));
seqs[i].setDatasetSequence(ref);
+ seqs[i].setDescription(ref.getDescription());
}
if (segments!=null) {
for (int i=0; i<segments.length; i+=3) {