- }
- j++;
- }
- nwidth += width;
- }
- // advance to begining of visible region
- start = contigs[contig + 1] + contigs[contig + 2];
- // add hidden segment to right of next region
- for (int s = 0; s < seqs.length; s++)
- {
- SequenceI hseq = seqs[s].getSeq('-').getSubSequence(contigs[contig +
- 1], start);
- if (alignment[s] == null)
- {
- alignment[s] = hseq;
- }
- else
- {
- alignment[s].setSequence(alignment[s].getSequence() +
- hseq.getSequence());
- if (hseq.getEnd() >= hseq.getStart())
- {
- alignment[s].setEnd(hseq.getEnd());
- }
- }
- }
- // mark hidden segment as hidden in the new alignment
- columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
- nwidth += contigs[contig + 2];
- }
- // Do final job - if it exists
- if (j < jobs.length)
- {
- int width = 0;
- if (jobs[j].hasResults())
- {
- Object[] subalg = ((MsaWSJob) jobs[j]).getAlignment();
- alorders.add(subalg[1]);
- SequenceI mseq[] = (SequenceI[]) subalg[0];
- width = mseq[0].getLength();
- for (int s = 0; s < mseq.length; s++)
- {
- if (alignment[s] == null)
- {
- alignment[s] = mseq[s];
- }
- else
- {
- alignment[s].setSequence(alignment[s].getSequence() +
- mseq[s].getSequence());
- if (mseq[s].getEnd() >= mseq[s].getStart())
- {
- alignment[s].setEnd(mseq[s].getEnd());
- }
- ( (AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
- }
- }
- }
- else
- {
- if (start < owidth)
- {
- // recover input data or place gaps
- if (true)
- {
- // recover input data
- for (int s = 0; s < seqs.length; s++)
- {
- SequenceI oseq = seqs[s].getSeq('-').getSubSequence(start,
- owidth + 1);
- if (width < oseq.getLength())
- {
- width = oseq.getLength();
- }
- if (alignment[s] == null)
- {
- alignment[s] = oseq;
- }
- else
- {
- alignment[s].setSequence(alignment[s].getSequence() +
- oseq.getSequence());
- if (oseq.getEnd() >= oseq.getStart())
- {
- alignment[s].setEnd(oseq.getEnd());
- }
- }
- }
- nwidth += width;
- }
- else
- {
- // place gaps.
- throw new Error("Padding not yet implemented.");
- }
- }
- }
- }
- }
- else