- int[] delMap = viewOnly ?
- view.getVisibleContigMapFor(seq.gapMap()) : null;
- var sequenceInfo = SeqsetUtils.uniquify(aln, true);
+ var sequenceInfo = msf.length > 1 ? SeqsetUtils.uniquify(aln, true)
+ : SeqsetUtils.SeqCharacterHash(seq);
+ if (viewOnly)
+ {
+ String seqs[] = view.getSequenceStrings('-');
+ for (int i = 0; i < msf.length; i++)
+ aln[i].setSequence(seqs[i]);
+ seq.setSequence(seqs[0]);
+ }