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);
}
}
} catch (java.lang.OutOfMemoryError err)
{
// TODO: catch OOM
- System.out.println("Out of memory loading groups: " + err);
+ jalview.bin.Console.outPrintln("Out of memory loading groups: " + err);
}
return upd;
}