package jalview.datamodel;
+
+
/**
* <p>Title: </p>
*
{
return contigs;
}
+ /**
+ * get the full alignment and a columnselection object marking the hidden regions
+ * @param gapCharacter char
+ * @return Object[] { SequenceI[], ColumnSelection}
+ */
public Object[] getAlignmentAndColumnSelection(char gapCharacter) {
ColumnSelection colsel = new ColumnSelection();
return seqs;
}
/**
- *
+ *
* @return visible number of columns in alignment view
*/
public int getWidth() {
protected void setWidth(int width) {
this.width = width;
}
-
+ /**
+ * get the contiguous subalignments in an alignment view.
+ * @param gapCharacter char
+ * @return SequenceI[][]
+ */
+ public SequenceI[][] getVisibleContigs(char gapCharacter) {
+ SequenceI[][] smsa;
+ int njobs = 1;
+ if (sequences==null || width<=0)
+ return null;
+ if (contigs != null && contigs.length > 0)
+ {
+ int start = 0;
+ njobs = 0;
+ int fwidth = width;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
+ if ( (contigs[contig + 1] - start) > 0)
+ {
+ njobs++;
+ }
+ fwidth += contigs[contig + 2]; // end up with full region width (including hidden regions)
+ start = contigs[contig + 1] + contigs[contig + 2];
+ }
+ if (start < fwidth)
+ {
+ njobs++;
+ }
+ smsa = new SequenceI[njobs][];
+ start = 0;
+ int j = 0;
+ for (int contig = 0; contig < contigs.length; contig += 3)
+ {
+ if (contigs[contig + 1] - start > 0)
+ {
+ SequenceI mseq[] = new SequenceI[sequences.length];
+ for (int s = 0; s < mseq.length; s++)
+ {
+ mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+ contigs[contig + 1]);
+ }
+ smsa[j] = mseq;
+ j++;
+ }
+ start = contigs[contig + 1] + contigs[contig + 2];
+ }
+ if (start < fwidth)
+ {
+ SequenceI mseq[] = new SequenceI[sequences.length];
+ for (int s = 0; s < mseq.length; s++)
+ {
+ mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+ fwidth + 1);
+ }
+ smsa[j] = mseq;
+ j++;
+ }
+ }
+ else
+ {
+ smsa = new SequenceI[1][];
+ smsa[0] = new SequenceI[sequences.length];
+ for (int s = 0; s < sequences.length; s++)
+ {
+ smsa[0][s] = sequences[s].getSeq(gapCharacter);
+ }
+ }
+ return smsa;
+ }
+ /**
+ * return full msa and hidden regions with visible blocks replaced with new sub alignments
+ * @param nvismsa SequenceI[][]
+ * @param orders AlignmentOrder[] corresponding to each SequenceI[] block.
+ * @return Object[]
+ */
+ public Object[] getUpdatedView(SequenceI[][] nvismsa, AlignmentOrder[] orders, char gapCharacter) {
+ if (sequences == null || width <= 0)
+ {
+ throw new Error("empty view cannot be updated.");
+ }
+ if (nvismsa == null)
+ throw new Error(
+ "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
+ if (contigs != null && contigs.length > 0)
+ {
+ SequenceI[] alignment = new SequenceI[sequences.length];
+ ColumnSelection columnselection = new ColumnSelection();
+ if (contigs != null && contigs.length > 0)
+ {
+ int start = 0;
+ int nwidth = 0;
+ int owidth = width;
+ 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 swidth = 0; // subalignment width
+ if (nvismsa[j] != null)
+ {
+ SequenceI mseq[] = nvismsa[j];
+ AlignmentOrder order=(orders==null) ? null : orders[j];
+ j++;
+ if (mseq.length!=sequences.length)
+ throw new Error("Mismatch between number of sequences in block "+j+" ("+mseq.length+") and the original view ("+sequences.length+")");
+ swidth = mseq[0].getLength(); // JBPNote: could ensure padded here.
+ 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());
+ }
+ if (order!=null) {
+ order.updateSequence(mseq[s], alignment[s]);
+ }
+ }
+ }
+ }
+ else
+ {
+ // recover original alignment block or place gaps
+ if (true)
+ {
+ // recover input data
+ for (int s = 0; s < sequences.length; s++)
+ {
+ SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+ contigs[contig + 1]);
+ if (swidth < oseq.getLength())
+ {
+ swidth = 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 += swidth;
+ }
+ // 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 < sequences.length; s++)
+ {
+ SequenceI hseq = sequences[s].getSeq(gapCharacter).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 segment - if it exists
+ if (j < nvismsa.length)
+ {
+ int swidth = 0;
+ if (nvismsa[j] != null)
+ {
+ SequenceI mseq[] = nvismsa[j];
+ AlignmentOrder order = (orders!=null) ? orders[j] : null;
+ swidth = 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());
+ }
+ if (order!=null) {
+ order.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 < sequences.length; s++)
+ {
+ SequenceI oseq = sequences[s].getSeq(gapCharacter).getSubSequence(start,
+ owidth + 1);
+ if (swidth < oseq.getLength())
+ {
+ swidth = 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 += swidth;
+ }
+ else
+ {
+ // place gaps.
+ throw new Error("Padding not yet implemented.");
+ }
+ }
+ }
+ }
+ }
+ return new Object[] { alignment, columnselection};
+ } else {
+ if (nvismsa.length!=1)
+ throw new Error("Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="+nvismsa.length);
+ if (nvismsa[0]!=null)
+ return new Object[] { nvismsa[0], new ColumnSelection()};
+ else
+ return getAlignmentAndColumnSelection(gapCharacter);
+ }
+ }
+
}
if (msa.length == 1)\r
{\r
// Single Sequence prediction\r
- new jalview.ws.JPredClient(sh,title, msa[0]);\r
+ new jalview.ws.JPredClient(sh, title, msa[0], null);\r
}\r
else\r
{\r
{\r
// Single Sequence prediction\r
jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
- title, msa);\r
+ title, msa, null);\r
}\r
}\r
}\r
JInternalFrame frame;
JTabbedPane subjobs=null;
java.util.Vector jobPanes = null;
- // tabbed or not
+ private boolean serviceCanMergeResults = false;
+ private boolean viewResultsImmediatly = true;
+ // tabbed or not
public synchronized int addJobPane() {
JScrollPane jobpane = new JScrollPane();
JTextArea progressText = new JTextArea();
thisService = newservice;
serviceIsCancellable = newservice.isCancellable();
frame.setClosable(!serviceIsCancellable);
+ serviceCanMergeResults = newservice.canMergeResults();
}
/**
}
frame.setClosable(true);
}
-
+ /**
+ * Set up GUI for user to get at results - and possibly automatically display
+ * them if viewResultsImmediatly is set.
+ */
public void setResultsReady()
{
frame.setClosable(true);
buttonPanel.remove(cancel);
buttonPanel.add(showResultsNewFrame);
- buttonPanel.add(mergeResults);
+ if (serviceCanMergeResults)
+ buttonPanel.add(mergeResults);
buttonPanel.setLayout(new GridLayout(2,1,5,5));
buttonPanel.validate();
validate();
+ if (viewResultsImmediatly)
+ showResultsNewFrame.doClick();
}
/**
import jalview.bin.*;\r
import jalview.datamodel.*;\r
import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentView;\r
import jalview.gui.*;\r
import jalview.io.*;\r
+import jalview.util.*;\r
import jalview.ws.WSThread.*;\r
import vamsas.objects.simple.*;\r
-import jalview.util.Comparison;\r
\r
public class JPredClient\r
extends WSClient\r
{\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq)\r
+ AlignFrame parentFrame=null;\r
+ /**\r
+ * crate a new GUI JPred Job\r
+ * @param sh ServiceHandle\r
+ * @param title String\r
+ * @param msa boolean - true - submit alignment as a sequence profile\r
+ * @param alview AlignmentView\r
+ */\r
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {\r
+ wsInfo=setWebService(sh);\r
+ this.parentFrame=parentFrame;\r
+ startJPredClient(title, msa, alview);\r
+\r
+ }\r
+\r
+ /**\r
+ * startJPredClient\r
+ *\r
+ * @param title String\r
+ * @param msa boolean\r
+ * @param alview AlignmentView\r
+ */\r
+ private void startJPredClient(String title, boolean msa,\r
+ jalview.datamodel.AlignmentView alview)\r
+ {\r
+ }\r
+\r
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq, AlignFrame parentFrame)\r
{\r
wsInfo = setWebService(sh);\r
+ this.parentFrame=parentFrame;\r
startJPredClient(title, seq);\r
}\r
\r
- public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa)\r
+ public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa, AlignFrame parentFrame)\r
{\r
wsInfo = setWebService(sh);\r
+ this.parentFrame=parentFrame;\r
startJPredClient(title, msa);\r
}\r
\r
}\r
}\r
}\r
-\r
void pollJob(WSJob job)\r
throws Exception\r
{\r
throw new Error("Implementation error!");\r
}\r
\r
+ public boolean canMergeResults()\r
+ {\r
+ return false;\r
+ }\r
+\r
}\r
}\r
\r
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;
+ }
}
public interface WSClientI
{
- boolean isCancellable();
-
+ /**
+ *
+ * @return boolean true if job is cancellable
+ */
+ boolean isCancellable();
+ /**
+ *
+ * @return boolean true if results can be merged into the source of input data
+ */
+ boolean canMergeResults();
void cancelJob();
}
git://source.jalview.org / jalview.git / commitdiff