OutputHeader = wsInfo.getProgressText();
alTitle = title;
dataset = seqset;
- SeqCigar[] msa = _msa.getSequences();
- int[] contigs = _msa.getContigs();
- int njobs = 1;
- if (contigs != null && contigs.length > 0)
+ SequenceI[][] conmsa = _msa.getVisibleContigs('-');
+ if (conmsa != null)
{
- int start = 0;
- njobs = 0;
- int width = _msa.getWidth();
- for (int contig = 0; contig < contigs.length; contig += 3)
- {
- if ( (contigs[contig + 1] - start) > 0)
- {
- njobs++;
- }
- width += contigs[contig + 2]; // end up with full region width (including hidden regions)
- start = contigs[contig + 1] + contigs[contig + 2];
- }
- if (start < width)
- {
- njobs++;
- }
+ int njobs = conmsa.length;
jobs = new MsaWSJob[njobs];
- start = 0;
- int j = 0;
- for (int contig = 0; contig < contigs.length; contig += 3)
+ for (int j = 0; j < njobs; j++)
{
- if (contigs[contig + 1] - start > 0)
- {
- SequenceI mseq[] = new SequenceI[msa.length];
- for (int s = 0; s < mseq.length; s++)
- {
- mseq[s] = msa[s].getSeq('-').getSubSequence(start,
- contigs[contig + 1]);
- }
- if (j != 0)
- {
- jobs[j] = new MsaWSJob(wsinfo.addJobPane(), mseq);
- }
- else
- {
- jobs[j] = new MsaWSJob(0, mseq);
- }
- wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
- wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
- j++;
- }
- start = contigs[contig + 1] + contigs[contig + 2];
- }
- if (start < width)
- {
- SequenceI mseq[] = new SequenceI[msa.length];
- for (int s = 0; s < mseq.length; s++)
- {
- mseq[s] = msa[s].getSeq('-').getSubSequence(start,
- width + 1);
- }
if (j != 0)
{
- jobs[j] = new MsaWSJob(wsinfo.addJobPane(), mseq);
+ jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
}
else
{
- jobs[j] = new MsaWSJob(0, mseq);
+ jobs[j] = new MsaWSJob(0, conmsa[j]);
}
- wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
+ if (njobs > 0)
+ wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
- j++;
- }
- }
- else
- {
- SequenceI mseq[] = new SequenceI[msa.length];
- for (int s = 0; s < mseq.length; s++)
- {
- mseq[s] = msa[s].getSeq('-');
}
- jobs = new MsaWSJob[1];
- wsinfo.setProgressText(OutputHeader); // ensures default text
- jobs[0] = new MsaWSJob(0, mseq);
}
}
-
public boolean isCancellable()
{
return true;
void displayResults(boolean newFrame)
{
// view input or result data for each block
- // warn user if a block is input rather than aligned data ?
-
- int contigs[] = input.getContigs();
- SeqCigar[] seqs = input.getSequences();
- SequenceI[] alignment = new SequenceI[seqs.length];
- ColumnSelection columnselection = new ColumnSelection();
Vector alorders = new Vector();
- if (contigs != null && contigs.length > 0)
- {
- int start = 0;
- int nwidth = 0;
- int owidth = input.getWidth();
- int j = 0;
- for (int contig = 0; contig < contigs.length; contig += 3)
- {
- owidth += contigs[contig + 2]; // recover final column width
- if (contigs[contig + 1] - start > 0)
- {
- int width = 0; // subalignment width
- 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].getStart() <= mseq[s].getEnd())
- {
- alignment[s].setEnd(mseq[s].getEnd());
- }
- ( (AlignmentOrder) subalg[1]).updateSequence(mseq[s],
- alignment[s]);
- }
- }
- }
- else
- {
- // 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,
- contigs[contig + 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());
- }
- }
- }
-
- }
- 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.");
- }
- }
- }
+ SequenceI[][] results=new SequenceI[jobs.length][];
+ AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
+ SequenceI[] first=null;
+ for (int j=0; j<jobs.length; j++) {
+ if (jobs[j].hasResults()) {
+ Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
+ alorders.add(res[1]);
+ results[j] = (SequenceI[]) res[0];
+ orders[j] = (AlignmentOrder) res[1];
+// SequenceI[] alignment = input.getUpdated
+ } else {
+ results[j]=null;
}
}
- else
- {
- if (jobs[0].hasResults())
- {
- Object[] alg = ((MsaWSJob) jobs[0]).getAlignment();
- alignment = (SequenceI[]) alg[0];
- alorders.add(alg[1]);
- }
- else
- {
- alignment = SeqCigar.createAlignmentSequences(seqs, '-',
- columnselection, null);
- }
+ Object[] newview = input.getUpdatedView(results, orders, '-');
+ // trash references to original result data
+ for (int j=0; j<jobs.length; j++) {
+ results[j] = null;
+ orders[j] = null;
}
+ SequenceI[] alignment = (SequenceI[]) newview[0];
+ ColumnSelection columnselection = (ColumnSelection) newview[1];
Alignment al = new Alignment(alignment);
if (dataset != null)
{
al.setDataset(dataset);
}
+ // JBNote- TODO: warn user if a block is input rather than aligned data ?
+
if (newFrame)
{
AlignFrame af = new AlignFrame(al, columnselection);
// found!!<<<
af.getFeatureRenderer().transferSettings(
alignFrame.getFeatureRenderer());
+ // update orders
if (alorders.size() > 0)
{
if (alorders.size() == 1)
}
}
+
+ public boolean canMergeResults()
+ {
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff