seqarray[i] = new vamsas.objects.simple.Sequence();
seqarray[i].setId(newname);
seqarray[i].setSeq((submitGaps) ? msa[i].getSequence()
- : AlignSeq.extractGaps("-. ", msa[i].getSequence()));
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars, msa[i].getSequence()));
}
this.seqs = new vamsas.objects.simple.SequenceSet();