{
SequenceI seq = inorder[i];
- seqs[i] = new Sequence(seq.getName(),
- seq.getSequence(startRes, endRes + 1),
- seq.findPosition(startRes),
- findEndRes(seq));
+ seqs[i] = seq.getSubSequence(startRes, endRes+1);
seqs[i].setDescription(seq.getDescription());
seqs[i].setDBRef(seq.getDBRef());
{
for (int a = 0; a < seq.getAnnotation().length; a++)
{
- seqs[i].addAlignmentAnnotation(new AlignmentAnnotation(seq.getAnnotation()[a]));
+ AlignmentAnnotation newannot = new AlignmentAnnotation(seq.getAnnotation()[a]);
+ newannot.restrict(startRes, endRes);
+ newannot.setSequenceRef(seqs[i]);
+ newannot.adjustForAlignment();
+ seqs[i].addAlignmentAnnotation(newannot);
}
}
}