endRes + 1);
if (seqipos != null)
{
- seqipos.setDescription(seq.getDescription());
- seqipos.setDBRefs(seq.getDBRefs());
- seqipos.setSequenceFeatures(seq.getSequenceFeatures());
- if (seq.getDatasetSequence() != null)
- {
- seqipos.setDatasetSequence(seq.getDatasetSequence());
- }
-
if (seq.getAnnotation() != null)
{
AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
newannot.restrict(startRes, endRes);
newannot.setSequenceRef(seqs[ipos]);
newannot.adjustForAlignment();
+ ContactMatrixI cm = seq.getContactMatrixFor(seq.getAnnotation()[a]);
+ if (cm!=null)
+ {
+ seqs[ipos].addContactListFor(newannot, cm);
+ }
seqipos.addAlignmentAnnotation(newannot);
}
}