-package jalview.ws;
-
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.ColumnSelection;
-import jalview.gui.WebserviceInfo;
-import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
-import jalview.gui.AlignFrame;
-import javax.swing.JOptionPane;
-
-import vamsas.objects.simple.MsaResult;
-import vamsas.objects.simple.Result;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.SeqCigar;
-import jalview.gui.Desktop;
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
-import java.util.Vector;
-
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
-class MsaWSThread extends Thread implements WSClientI {
- jalview.gui.AlignFrame alignFrame;
-
- WebserviceInfo wsInfo = null;
-
- String WebServiceName = null;
-
- String OutputHeader;
- AlignmentView input;
- boolean submitGaps = false; // pass sequences including gaps to alignment
-
- // service
-
- boolean preserveOrder = true; // and always store and recover sequence
-
- // order
-
- class MsaWSJob {
- int jobnum = 0; // WebServiceInfo pane for this job
-
- String jobId; // ws job ticket
-
- vamsas.objects.simple.MsaResult result = null;
-
- vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
-
- /**
- * MsaWSJob
- *
- * @param jobNum
- * int
- * @param jobId
- * String
- */
- public MsaWSJob(int jobNum, SequenceI[] inSeqs) {
- this.jobnum = jobNum;
- prepareInput(inSeqs);
- }
-
- int allowedServerExceptions = 3; // thread dies if too many
-
- // exceptions.
- boolean submitted=false;
- boolean subjobComplete = false;
-
- Hashtable SeqNames = new Hashtable();
- Vector emptySeqs = new Vector();
- private void prepareInput(SequenceI[] seqs) {
- int nseqs = 0;
- for (int i = 0; i < seqs.length; i++) {
- if (seqs[i].getStart() < seqs[i].getEnd()) {
- nseqs++;
- }
- }
- vamsas.objects.simple.Sequence[] seqarray =
- (nseqs>0)
- ? new vamsas.objects.simple.Sequence[nseqs]
- :null;
- for (int i = 0, n = 0; i < seqs.length; i++) {
-
- String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
- // for
- // any
- // subjob
- SeqNames.put(newname, jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seqs[i]));
- if (seqs[i].getStart() < seqs[i].getEnd()) {
- seqarray[n] = new vamsas.objects.simple.Sequence();
- seqarray[n].setId(newname);
- seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequence()
- : AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, seqs[i]
- .getSequence()));
- } else {
- emptySeqs.add(newname);
- }
- }
- this.seqs = new vamsas.objects.simple.SequenceSet();
- this.seqs.setSeqs(seqarray);
- }
- public Object[] getAlignment() {
-
- if (result!=null) {
- SequenceI[] alseqs=null;
- char alseq_gapchar='-';
- int alseq_l=0;
- if (result.getMsa() != null) {
- alseqs = getVamsasAlignment(result.getMsa());
- alseq_gapchar=result.getMsa().getGapchar().charAt(0);
- alseq_l = alseqs.length;
- }
- if (emptySeqs.size()>0) {
- SequenceI[] t_alseqs = new SequenceI[alseq_l+emptySeqs.size()];
- // get width
- int i,w=0;
- if (alseq_l>0) {
- for (i=0,w=alseqs[0].getLength(); i<alseq_l; i++) {
- if (w<alseqs[i].getLength())
- w=alseqs[i].getLength();
- t_alseqs[i] = alseqs[i];
- alseqs[i] = null;
- }
- }
- // make a gapped string.
- StringBuffer insbuff=new StringBuffer(w);
- for (i=0; i<w; i++)
- insbuff.append(alseq_gapchar);
- for (i=0, w=emptySeqs.size(); i<w; i++) {
- t_alseqs[i+alseqs.length] = new jalview.datamodel.Sequence((String)emptySeqs.get(i), insbuff.toString());
- }
- alseqs = t_alseqs;
- }
- AlignmentOrder msaorder = new AlignmentOrder(alseqs);
- // always recover the order - makes parseResult()'s life easier.
- jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
- // account for any missing sequences
- jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
- return new Object[] { alseqs, msaorder};
- }
- return null;
- }
- }
- MsaWSJob jobs[] = null;
-
- String alTitle; // name which will be used to form new alignment window.
-
- boolean jobComplete = false;
-
- Alignment dataset; // dataset to which the new alignment will be
-
- // associated.
-
- ext.vamsas.MuscleWS server = null;
-
- String WsUrl = null;
-
- /**
- * set basic options for this (group) of Msa jobs
- *
- * @param subgaps
- * boolean
- * @param presorder
- * boolean
- */
- MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, AlignmentView alview,
- String wsname, boolean subgaps, boolean presorder) {
- this.server = server;
- this.WsUrl = wsUrl;
- this.wsInfo = wsinfo;
- this.WebServiceName = wsname;
- this.input = alview;
- this.submitGaps = subgaps;
- this.preserveOrder = presorder;
- this.alignFrame = alFrame;
- }
-
- /**
- * create one or more Msa jobs to align visible seuqences in _msa
- *
- * @param title
- * String
- * @param _msa
- * AlignmentView
- * @param subgaps
- * boolean
- * @param presorder
- * boolean
- * @param seqset
- * Alignment
- */
- MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
- String wsname, String title, AlignmentView _msa, boolean subgaps,
- boolean presorder, Alignment seqset) {
- this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
- OutputHeader = wsInfo.getProgressText();
- alTitle = title;
- dataset = seqset;
- SeqCigar[] msa = _msa.getSequences();
- int[] contigs = _msa.getContigs();
- int njobs=1;
- if (contigs != null && contigs.length > 0) {
- 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++;
- }
- jobs = new MsaWSJob[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[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);
- } else {
- jobs[j] = new MsaWSJob(0, mseq);
- }
- 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;
- }
-
- public void cancelJob() {
- if (!jobComplete && jobs != null) {
- boolean cancelled = true;
- for (int job = 0; job < jobs.length; job++) {
- if (jobs[job].submitted && !jobs[job].subjobComplete)
- {
- String cancelledMessage = "";
- try {
- vamsas.objects.simple.WsJobId cancelledJob = server
- .cancel(jobs[job].jobId);
- if (cancelledJob.getStatus() == 2) {
- // CANCELLED_JOB
- cancelledMessage = "Job cancelled.";
- jobs[job].subjobComplete = true;
- jobs[job].result = null;
- wsInfo.setStatus(jobs[job].jobnum, WebserviceInfo.STATE_CANCELLED_OK);
- } else if (cancelledJob.getStatus() == 3) {
- // VALID UNSTOPPABLE JOB
- cancelledMessage += "Server cannot cancel this job. just close the window.\n";
- cancelled = false;
- wsInfo.setStatus(jobs[job].jobnum, WebserviceInfo.STATE_CANCELLED_OK);
- }
-
- if (cancelledJob.getJobId() != null) {
- cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
- }
-
- cancelledMessage += "\n";
- } catch (Exception exc) {
- cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
- + exc + "\n");
- exc.printStackTrace();
- }
- wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
- + cancelledMessage + "\n");
- }
- }
- if (cancelled) {
- wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
- jobComplete = true;
- }
- } else {
- if (!jobComplete) {
- wsInfo
- .setProgressText(OutputHeader
- + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
- }
- }
- }
-
- public void run() {
-
- while (!jobComplete) {
- int running=0;
- int queuing=0;
- int finished=0;
- int error=0;
- int serror=0;
- for (int j=0; j<jobs.length; j++) {
-
- if (!jobs[j].submitted && jobs[j].seqs.getSeqs()!=null)
- StartJob(jobs[j]);
-
- if (jobs[j].submitted && !jobs[j].subjobComplete) {
- try {
- if ((jobs[j].result = server.getResult(jobs[j].jobId)) == null) {
- throw (new Exception(
- "Timed out when communicating with server\nTry again later.\n"));
- }
- jalview.bin.Cache.log.debug("Job "+j+" Result state " + jobs[j].result.getState()
- + "(ServerError=" + jobs[j].result.isServerError() + ")");
- } catch (Exception ex) {
- // Deal with Transaction exceptions
- wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
- + " Server exception!\n" + ex.getMessage());
- Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
- + ") Server exception: " + ex.getMessage());
-
- if (jobs[j].allowedServerExceptions > 0) {
- jobs[j].allowedServerExceptions--;
- Cache.log.debug("Sleeping after a server exception.");
- try {
- Thread.sleep(5000);
- }
- catch (InterruptedException ex1) {
- }
- } else {
- Cache.log.warn("Dropping job "+j+" "+jobs[j].jobId);
- jobs[j].subjobComplete=true;
- wsInfo.setStatus(jobs[j].jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
- catch (OutOfMemoryError er) {
- jobComplete = true;
- jobs[j].subjobComplete=true;
- jobs[j].result=null; // may contain out of date result object
- wsInfo.setStatus(jobs[j].jobnum,
- WebserviceInfo.STATE_STOPPED_ERROR);
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Out of memory handling result for job !!"
- + "\nSee help files for increasing Java Virtual Machine memory.",
- "Out of memory", JOptionPane.WARNING_MESSAGE);
- Cache.log.error("Out of memory when retrieving Job "+j+" id:" + WsUrl+"/"+jobs[j].jobId, er);
- System.gc();
- }
- }
- if (jobs[j].result!=null) {
- String progheader="";
- // Parse state of job[j]
- if (jobs[j].result.isRunning()) {
- running++;
- wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_RUNNING);
- } else if (jobs[j].result.isQueued()) {
- queuing++;
- wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_QUEUING);
- } else if (jobs[j].result.isFinished()) {
- finished++;
- jobs[j].subjobComplete = true;
- wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_OK);
- } else if (jobs[j].result.isFailed()) {
- progheader += "Job failed.\n";
- jobs[j].subjobComplete=true;
- wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_ERROR);
- error++;
- } else if (jobs[j].result.isServerError()) {
- serror++;
- jobs[j].subjobComplete = true;
- wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_SERVERERROR);
- } else if (jobs[j].result.isBroken() || jobs[j].result.isFailed()) {
- error++;
- jobs[j].subjobComplete=true;
- wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_ERROR);
- }
- // and pass on any sub-job messages to the user
- wsInfo.setProgressText(jobs[j].jobnum, OutputHeader);
- wsInfo.appendProgressText(jobs[j].jobnum, progheader);
- if (jobs[j].result.getStatus() != null) {
- wsInfo.appendProgressText(jobs[j].jobnum, jobs[j].result.getStatus());
- }
- } else {
- if (jobs[j].submitted && jobs[j].subjobComplete) {
- if (jobs[j].allowedServerExceptions==0) {
- serror++;
- } else if (jobs[j].result==null) {
- error++;
- }
- }
- }
- }
- // Decide on overall state based on collected jobs[] states
- if (running>0) {
- wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- } else if (queuing>0) {
- wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
- } else {
- jobComplete=true;
- if (finished>0) {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- } else if (error>0) {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- } else if (serror>0) {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- }
- }
- if (!jobComplete) {
- try {
- Thread.sleep(5000);
- }
- catch (InterruptedException e) {
- Cache.log.debug("Interrupted sleep waiting for next job poll.",e);
- }
- // System.out.println("I'm alive "+alTitle);
- }
- }
- if (jobComplete) {
- parseResult(); // tidy up and make results available to user
- }
- }
-
- void StartJob(MsaWSJob j) {
- if (j.submitted) {
- if (Cache.log.isDebugEnabled()) {
- Cache.log.debug("Tried to submit an already submitted job "+j.jobId);
- }
- return;
- }
- if (j.seqs.getSeqs()==null) {
- // special case - selection consisted entirely of empty sequences...
- j.submitted=true;
- j.result=new MsaResult();
- j.result.setFinished(true);
- j.result.setStatus("Empty Alignment Job");
- j.result.setMsa(null);
- }
- try {
- vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
-
- if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {
- j.jobId = jobsubmit.getJobId();
- j.submitted=true;
- j.subjobComplete = false;
- // System.out.println(WsURL + " Job Id '" + jobId + "'");
- } else {
- if (jobsubmit == null) {
- throw new Exception(
- "Server at "
- + WsUrl
- + " returned null object, it probably cannot be contacted. Try again later ?");
- }
-
- throw new Exception(jobsubmit.getJobId());
- }
- } catch (Exception e) {
- // TODO: JBPNote catch timeout or other fault types explicitly
- // For unexpected errors
- System.err
- .println(WebServiceName
- + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n"
- + e.toString() + "\n");
- j.allowedServerExceptions = 0;
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo
- .appendProgressText(
- j.jobnum,
- "Failed to submit sequences for alignment.\n"
- + "It is most likely that there is a problem with the server.\n"
- + "Just close the window\n");
-
- // e.printStackTrace(); // TODO: JBPNote DEBUG
- }
- }
-
- private jalview.datamodel.Sequence[] getVamsasAlignment(
- vamsas.objects.simple.Alignment valign) {
- vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
- jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
-
- for (int i = 0, j = seqs.length; i < j; i++) {
- msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]
- .getSeq());
- }
-
- return msa;
- }
-
- void parseResult() {
- try {
- for (int j=0; j<jobs.length; j++) {
- if (jobs[j].submitted && jobs[j].subjobComplete) {
- if (jobs[j].result!=null) {
- vamsas.objects.simple.Alignment valign = jobs[j].result.getMsa();
- if (valign!= null) {
- wsInfo.appendProgressText(jobs[j].jobnum,"\nAlignment Object Method Notes\n");
- String[] lines = valign.getMethod();
- for (int line = 0; line < lines.length; line++) {
- wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");
- }
- // JBPNote The returned files from a webservice could be
- // hidden behind icons in the monitor window that,
- // when clicked, pop up their corresponding data
- }
- }
- }
- }
- }
- catch (Exception ex) {
-
- Cache.log.error("Unexpected exception when processing results for "+alTitle,ex);
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- }
-
- wsInfo.showResultsNewFrame
- .addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(
- java.awt.event.ActionEvent evt) {
- displayResults(true);
- }
- });
- wsInfo.mergeResults
- .addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(
- java.awt.event.ActionEvent evt) {
- displayResults(false);
- }
- });
- wsInfo.setResultsReady();
- }
- void displayResults(boolean newFrame) {
- 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 cshift=0;
- int start = 0;
- int nwidth = 0;
- int j=0;
- for (int contig = 0; contig < contigs.length; contig += 3) {
- if (cshift+contigs[contig] - start > 0) {
- Object[] subalg = jobs[j++].getAlignment();
- alorders.add(subalg[1]);
- SequenceI mseq[] = (SequenceI[]) subalg[0];
- int 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 (alignment[s].getEnd()<mseq[s].getEnd())
- alignment[s].setEnd(mseq[s].getEnd());
- ((AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
- }
- }
- nwidth+=width;
- }
- // advance to begining of visible region
- start = cshift+contigs[contig] + 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(cshift+contigs[contig], start);
- if (alignment[s]==null) {
- alignment[s] = hseq;
- } else {
- alignment[s].setSequence(alignment[s].getSequence()+hseq.getSequence());
- 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];
- cshift+=contigs[contig+2];
- }
- // Do final job - if it exists
- if (j<jobs.length) {
- Object[] subalg = jobs[j].getAlignment();
- alorders.add(subalg[1]);
- SequenceI mseq[] = (SequenceI[]) subalg[0];
- int 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());
- alignment[s].setEnd(mseq[s].getEnd());
- ((AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
- }
- }
- nwidth+=width;
- }
- } else {
- if (jobs[0].subjobComplete && jobs[0].result!=null) {
- Object[] alg = jobs[0].getAlignment();
- alignment = (SequenceI[]) alg[0];
- alorders.add(alg[1]);
- } else {
- alignment = SeqCigar.createAlignmentSequences(seqs, '-', columnselection,null);
- }
- }
- Alignment al = new Alignment(alignment);
- if (dataset != null) {
- al.setDataset(dataset);
- }
-
- if (newFrame) {
- // TODO: JBPNote Should also rename the query sequence
- // sometime...
- AlignFrame af = new AlignFrame(al,columnselection);
-
- // >>>This is a fix for the moment, until a better solution is
- // found!!<<<
- af.getFeatureRenderer().transferSettings(
- alignFrame.getFeatureRenderer());
- if (alorders.size()>0) {
- if (alorders.size()==1) {
- af.addSortByOrderMenuItem(WebServiceName + " Ordering",
- (AlignmentOrder) alorders.get(0));
- } else {
- for (int i=0,l=alorders.size(); i<l; i++) {
- af.addSortByOrderMenuItem(WebServiceName + " Region "+i+" Ordering",
- (AlignmentOrder) alorders.get(i));
- }
- }
- }
-
- Desktop.addInternalFrame(af, alTitle,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
-
- } else {
- System.out.println("MERGE WITH OLD FRAME");
-
- }
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
+package jalview.ws;\r
+\r
+import java.util.*;\r
+\r
+import jalview.analysis.*;\r
+import jalview.bin.*;\r
+import jalview.datamodel.*;\r
+import jalview.datamodel.Alignment;\r
+import jalview.gui.*;\r
+import vamsas.objects.simple.MsaResult;\r
+\r
+/**\r
+ * <p>\r
+ * Title:\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Description:\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Copyright: Copyright (c) 2004\r
+ * </p>\r
+ * \r
+ * <p>\r
+ * Company: Dundee University\r
+ * </p>\r
+ * \r
+ * @author not attributable\r
+ * @version 1.0\r
+ */\r
+class MsaWSThread extends WSThread implements WSClientI\r
+{\r
+ boolean submitGaps = false; // pass sequences including gaps to alignment\r
+\r
+ // service\r
+\r
+ boolean preserveOrder = true; // and always store and recover sequence\r
+\r
+ // order\r
+\r
+ class MsaWSJob extends WSThread.WSJob\r
+ {\r
+ // hold special input for this\r
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();\r
+\r
+ /**\r
+ * MsaWSJob\r
+ * \r
+ * @param jobNum\r
+ * int\r
+ * @param jobId\r
+ * String\r
+ */\r
+ public MsaWSJob(int jobNum, SequenceI[] inSeqs)\r
+ {\r
+ this.jobnum = jobNum;\r
+ if (!prepareInput(inSeqs, 2))\r
+ {\r
+ submitted = true;\r
+ subjobComplete = true;\r
+ result = new MsaResult();\r
+ result.setFinished(true);\r
+ result.setStatus("Job never ran - input returned to user.");\r
+ }\r
+\r
+ }\r
+\r
+ Hashtable SeqNames = new Hashtable();\r
+\r
+ Vector emptySeqs = new Vector();\r
+\r
+ /**\r
+ * prepare input sequences for MsaWS service\r
+ * \r
+ * @param seqs\r
+ * jalview sequences to be prepared\r
+ * @param minlen\r
+ * minimum number of residues required for this MsaWS service\r
+ * @return true if seqs contains sequences to be submitted to service.\r
+ */\r
+ private boolean prepareInput(SequenceI[] seqs, int minlen)\r
+ {\r
+ int nseqs = 0;\r
+ if (minlen < 0)\r
+ {\r
+ throw new Error(\r
+ "Implementation error: minlen must be zero or more.");\r
+ }\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
+ {\r
+ nseqs++;\r
+ }\r
+ }\r
+ boolean valid = nseqs > 1; // need at least two seqs\r
+ vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]\r
+ : null;\r
+ for (int i = 0, n = 0; i < seqs.length; i++)\r
+ {\r
+\r
+ String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same\r
+ // for\r
+ // any\r
+ // subjob\r
+ SeqNames.put(newname, jalview.analysis.SeqsetUtils\r
+ .SeqCharacterHash(seqs[i]));\r
+ if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)\r
+ {\r
+ seqarray[n] = new vamsas.objects.simple.Sequence();\r
+ seqarray[n].setId(newname);\r
+ seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()\r
+ : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,\r
+ seqs[i].getSequenceAsString()));\r
+ }\r
+ else\r
+ {\r
+ String empty = null;\r
+ if (seqs[i].getEnd() >= seqs[i].getStart())\r
+ {\r
+ empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq\r
+ .extractGaps(jalview.util.Comparison.GapChars, seqs[i]\r
+ .getSequenceAsString());\r
+ }\r
+ emptySeqs.add(new String[]\r
+ { newname, empty });\r
+ }\r
+ }\r
+ this.seqs = new vamsas.objects.simple.SequenceSet();\r
+ this.seqs.setSeqs(seqarray);\r
+ return valid;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return true if getAlignment will return a valid alignment result.\r
+ */\r
+ public boolean hasResults()\r
+ {\r
+ if (subjobComplete && result != null && result.isFinished()\r
+ && ((MsaResult) result).getMsa() != null\r
+ && ((MsaResult) result).getMsa().getSeqs() != null)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ public Object[] getAlignment()\r
+ {\r
+\r
+ if (result != null && result.isFinished())\r
+ {\r
+ SequenceI[] alseqs = null;\r
+ char alseq_gapchar = '-';\r
+ int alseq_l = 0;\r
+ if (((MsaResult) result).getMsa() != null)\r
+ {\r
+ alseqs = getVamsasAlignment(((MsaResult) result).getMsa());\r
+ alseq_gapchar = ((MsaResult) result).getMsa().getGapchar()\r
+ .charAt(0);\r
+ alseq_l = alseqs.length;\r
+ }\r
+ if (emptySeqs.size() > 0)\r
+ {\r
+ SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];\r
+ // get width\r
+ int i, w = 0;\r
+ if (alseq_l > 0)\r
+ {\r
+ for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)\r
+ {\r
+ if (w < alseqs[i].getLength())\r
+ {\r
+ w = alseqs[i].getLength();\r
+ }\r
+ t_alseqs[i] = alseqs[i];\r
+ alseqs[i] = null;\r
+ }\r
+ }\r
+ // check that aligned width is at least as wide as emptySeqs width.\r
+ int ow = w, nw = w;\r
+ for (i = 0, w = emptySeqs.size(); i < w; i++)\r
+ {\r
+ String[] es = (String[]) emptySeqs.get(i);\r
+ if (es != null && es[1] != null)\r
+ {\r
+ int sw = es[1].length();\r
+ if (nw < sw)\r
+ {\r
+ nw = sw;\r
+ }\r
+ }\r
+ }\r
+ // make a gapped string.\r
+ StringBuffer insbuff = new StringBuffer(w);\r
+ for (i = 0; i < nw; i++)\r
+ {\r
+ insbuff.append(alseq_gapchar);\r
+ }\r
+ if (ow < nw)\r
+ {\r
+ for (i = 0; i < alseq_l; i++)\r
+ {\r
+ int sw = t_alseqs[i].getLength();\r
+ if (nw > sw)\r
+ {\r
+ // pad at end\r
+ alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()\r
+ + insbuff.substring(0, sw - nw));\r
+ }\r
+ }\r
+ }\r
+ for (i = 0, w = emptySeqs.size(); i < w; i++)\r
+ {\r
+ String[] es = (String[]) emptySeqs.get(i);\r
+ if (es[1] == null)\r
+ {\r
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],\r
+ insbuff.toString(), 1, 0);\r
+ }\r
+ else\r
+ {\r
+ if (es[1].length() < nw)\r
+ {\r
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(\r
+ es[0],\r
+ es[1] + insbuff.substring(0, nw - es[1].length()),\r
+ 1, 1 + es[1].length());\r
+ }\r
+ else\r
+ {\r
+ t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(\r
+ es[0], es[1]);\r
+ }\r
+ }\r
+ }\r
+ alseqs = t_alseqs;\r
+ }\r
+ AlignmentOrder msaorder = new AlignmentOrder(alseqs);\r
+ // always recover the order - makes parseResult()'s life easier.\r
+ jalview.analysis.AlignmentSorter.recoverOrder(alseqs);\r
+ // account for any missing sequences\r
+ jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);\r
+ return new Object[]\r
+ { alseqs, msaorder };\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * mark subjob as cancelled and set result object appropriatly\r
+ */\r
+ void cancel()\r
+ {\r
+ cancelled = true;\r
+ subjobComplete = true;\r
+ result = null;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return boolean true if job can be submitted.\r
+ */\r
+ boolean hasValidInput()\r
+ {\r
+ if (seqs.getSeqs() != null)\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+ }\r
+\r
+ String alTitle; // name which will be used to form new alignment window.\r
+\r
+ Alignment dataset; // dataset to which the new alignment will be\r
+\r
+ // associated.\r
+\r
+ ext.vamsas.MuscleWS server = null;\r
+\r
+ /**\r
+ * set basic options for this (group) of Msa jobs\r
+ * \r
+ * @param subgaps\r
+ * boolean\r
+ * @param presorder\r
+ * boolean\r
+ */\r
+ MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
+ AlignmentView alview, String wsname, boolean subgaps,\r
+ boolean presorder)\r
+ {\r
+ super(alFrame, wsinfo, alview, wsname, wsUrl);\r
+ this.server = server;\r
+ this.submitGaps = subgaps;\r
+ this.preserveOrder = presorder;\r
+ }\r
+\r
+ /**\r
+ * create one or more Msa jobs to align visible seuqences in _msa\r
+ * \r
+ * @param title\r
+ * String\r
+ * @param _msa\r
+ * AlignmentView\r
+ * @param subgaps\r
+ * boolean\r
+ * @param presorder\r
+ * boolean\r
+ * @param seqset\r
+ * Alignment\r
+ */\r
+ MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,\r
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
+ String wsname, String title, AlignmentView _msa, boolean subgaps,\r
+ boolean presorder, Alignment seqset)\r
+ {\r
+ this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);\r
+ OutputHeader = wsInfo.getProgressText();\r
+ alTitle = title;\r
+ dataset = seqset;\r
+\r
+ SequenceI[][] conmsa = _msa.getVisibleContigs('-');\r
+ if (conmsa != null)\r
+ {\r
+ int njobs = conmsa.length;\r
+ jobs = new MsaWSJob[njobs];\r
+ for (int j = 0; j < njobs; j++)\r
+ {\r
+ if (j != 0)\r
+ {\r
+ jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);\r
+ }\r
+ else\r
+ {\r
+ jobs[j] = new MsaWSJob(0, conmsa[j]);\r
+ }\r
+ if (njobs > 0)\r
+ {\r
+ wsinfo\r
+ .setProgressName("region " + jobs[j].jobnum,\r
+ jobs[j].jobnum);\r
+ }\r
+ wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);\r
+ }\r
+ }\r
+ }\r
+\r
+ public boolean isCancellable()\r
+ {\r
+ return true;\r
+ }\r
+\r
+ public void cancelJob()\r
+ {\r
+ if (!jobComplete && jobs != null)\r
+ {\r
+ boolean cancelled = true;\r
+ for (int job = 0; job < jobs.length; job++)\r
+ {\r
+ if (jobs[job].submitted && !jobs[job].subjobComplete)\r
+ {\r
+ String cancelledMessage = "";\r
+ try\r
+ {\r
+ vamsas.objects.simple.WsJobId cancelledJob = server\r
+ .cancel(jobs[job].jobId);\r
+ if (cancelledJob.getStatus() == 2)\r
+ {\r
+ // CANCELLED_JOB\r
+ cancelledMessage = "Job cancelled.";\r
+ ((MsaWSJob) jobs[job]).cancel();\r
+ wsInfo.setStatus(jobs[job].jobnum,\r
+ WebserviceInfo.STATE_CANCELLED_OK);\r
+ }\r
+ else if (cancelledJob.getStatus() == 3)\r
+ {\r
+ // VALID UNSTOPPABLE JOB\r
+ cancelledMessage += "Server cannot cancel this job. just close the window.\n";\r
+ cancelled = false;\r
+ // wsInfo.setStatus(jobs[job].jobnum,\r
+ // WebserviceInfo.STATE_RUNNING);\r
+ }\r
+\r
+ if (cancelledJob.getJobId() != null)\r
+ {\r
+ cancelledMessage += ("[" + cancelledJob.getJobId() + "]");\r
+ }\r
+\r
+ cancelledMessage += "\n";\r
+ } catch (Exception exc)\r
+ {\r
+ cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"\r
+ + exc + "\n");\r
+ Cache.log.warn(\r
+ "Exception whilst cancelling " + jobs[job].jobId, exc);\r
+ }\r
+ wsInfo.setProgressText(jobs[job].jobnum, OutputHeader\r
+ + cancelledMessage + "\n");\r
+ }\r
+ }\r
+ if (cancelled)\r
+ {\r
+ wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);\r
+ jobComplete = true;\r
+ }\r
+ this.interrupt(); // kick thread to update job states.\r
+ }\r
+ else\r
+ {\r
+ if (!jobComplete)\r
+ {\r
+ wsInfo\r
+ .setProgressText(OutputHeader\r
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");\r
+ }\r
+ }\r
+ }\r
+\r
+ void pollJob(WSJob job) throws Exception\r
+ {\r
+ ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);\r
+ }\r
+\r
+ void StartJob(WSJob job)\r
+ {\r
+ if (!(job instanceof MsaWSJob))\r
+ {\r
+ throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "\r
+ + job.getClass());\r
+ }\r
+ MsaWSJob j = (MsaWSJob) job;\r
+ if (j.submitted)\r
+ {\r
+ if (Cache.log.isDebugEnabled())\r
+ {\r
+ Cache.log.debug("Tried to submit an already submitted job "\r
+ + j.jobId);\r
+ }\r
+ return;\r
+ }\r
+ if (j.seqs.getSeqs() == null)\r
+ {\r
+ // special case - selection consisted entirely of empty sequences...\r
+ j.submitted = true;\r
+ j.result = new MsaResult();\r
+ j.result.setFinished(true);\r
+ j.result.setStatus("Empty Alignment Job");\r
+ ((MsaResult) j.result).setMsa(null);\r
+ }\r
+ try\r
+ {\r
+ vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);\r
+\r
+ if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))\r
+ {\r
+ j.jobId = jobsubmit.getJobId();\r
+ j.submitted = true;\r
+ j.subjobComplete = false;\r
+ // System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+ }\r
+ else\r
+ {\r
+ if (jobsubmit == null)\r
+ {\r
+ throw new Exception(\r
+ "Server at "\r
+ + WsUrl\r
+ + " returned null object, it probably cannot be contacted. Try again later ?");\r
+ }\r
+\r
+ throw new Exception(jobsubmit.getJobId());\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ // TODO: JBPNote catch timeout or other fault types explicitly\r
+ // For unexpected errors\r
+ System.err\r
+ .println(WebServiceName\r
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"\r
+ + "When contacting Server:" + WsUrl + "\n"\r
+ + e.toString() + "\n");\r
+ j.allowedServerExceptions = 0;\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+ wsInfo\r
+ .appendProgressText(\r
+ j.jobnum,\r
+ "Failed to submit sequences for alignment.\n"\r
+ + "It is most likely that there is a problem with the server.\n"\r
+ + "Just close the window\n");\r
+\r
+ // e.printStackTrace(); // TODO: JBPNote DEBUG\r
+ }\r
+ }\r
+\r
+ private jalview.datamodel.Sequence[] getVamsasAlignment(\r
+ vamsas.objects.simple.Alignment valign)\r
+ {\r
+ // TODO: refactor to helper class for vamsas.objects.simple objects\r
+ vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();\r
+ jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];\r
+\r
+ for (int i = 0, j = seqs.length; i < j; i++)\r
+ {\r
+ msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i]\r
+ .getSeq());\r
+ }\r
+\r
+ return msa;\r
+ }\r
+\r
+ void parseResult()\r
+ {\r
+ int results = 0; // number of result sets received\r
+ JobStateSummary finalState = new JobStateSummary();\r
+ try\r
+ {\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+ finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);\r
+ if (jobs[j].submitted && jobs[j].subjobComplete\r
+ && jobs[j].hasResults())\r
+ {\r
+ results++;\r
+ vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result)\r
+ .getMsa();\r
+ if (valign != null)\r
+ {\r
+ wsInfo.appendProgressText(jobs[j].jobnum,\r
+ "\nAlignment Object Method Notes\n");\r
+ String[] lines = valign.getMethod();\r
+ for (int line = 0; line < lines.length; line++)\r
+ {\r
+ wsInfo.appendProgressText(jobs[j].jobnum, lines[line] + "\n");\r
+ }\r
+ // JBPNote The returned files from a webservice could be\r
+ // hidden behind icons in the monitor window that,\r
+ // when clicked, pop up their corresponding data\r
+ }\r
+ }\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+\r
+ Cache.log.error("Unexpected exception when processing results for "\r
+ + alTitle, ex);\r
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+ }\r
+ if (results > 0)\r
+ {\r
+ wsInfo.showResultsNewFrame\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(java.awt.event.ActionEvent evt)\r
+ {\r
+ displayResults(true);\r
+ }\r
+ });\r
+ wsInfo.mergeResults\r
+ .addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(java.awt.event.ActionEvent evt)\r
+ {\r
+ displayResults(false);\r
+ }\r
+ });\r
+ wsInfo.setResultsReady();\r
+ }\r
+ else\r
+ {\r
+ wsInfo.setFinishedNoResults();\r
+ }\r
+ }\r
+\r
+ void displayResults(boolean newFrame)\r
+ {\r
+ // view input or result data for each block\r
+ Vector alorders = new Vector();\r
+ SequenceI[][] results = new SequenceI[jobs.length][];\r
+ AlignmentOrder[] orders = new AlignmentOrder[jobs.length];\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+ if (jobs[j].hasResults())\r
+ {\r
+ Object[] res = ((MsaWSJob) jobs[j]).getAlignment();\r
+ alorders.add(res[1]);\r
+ results[j] = (SequenceI[]) res[0];\r
+ orders[j] = (AlignmentOrder) res[1];\r
+\r
+ // SequenceI[] alignment = input.getUpdated\r
+ }\r
+ else\r
+ {\r
+ results[j] = null;\r
+ }\r
+ }\r
+ Object[] newview = input.getUpdatedView(results, orders, getGapChar());\r
+ // trash references to original result data\r
+ for (int j = 0; j < jobs.length; j++)\r
+ {\r
+ results[j] = null;\r
+ orders[j] = null;\r
+ }\r
+ SequenceI[] alignment = (SequenceI[]) newview[0];\r
+ ColumnSelection columnselection = (ColumnSelection) newview[1];\r
+ Alignment al = new Alignment(alignment);\r
+ // TODO: add 'provenance' property to alignment from the method notes\r
+ // accompanying each subjob\r
+ if (dataset != null)\r
+ {\r
+ al.setDataset(dataset);\r
+ }\r
+\r
+ propagateDatasetMappings(al);\r
+ // JBNote- TODO: warn user if a block is input rather than aligned data ?\r
+\r
+ if (newFrame)\r
+ {\r
+ AlignFrame af = new AlignFrame(al, columnselection,\r
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);\r
+\r
+ // initialise with same renderer settings as in parent alignframe.\r
+ af.getFeatureRenderer().transferSettings(this.featureSettings);\r
+ // update orders\r
+ if (alorders.size() > 0)\r
+ {\r
+ if (alorders.size() == 1)\r
+ {\r
+ af.addSortByOrderMenuItem(WebServiceName + " Ordering",\r
+ (AlignmentOrder) alorders.get(0));\r
+ }\r
+ else\r
+ {\r
+ // construct a non-redundant ordering set\r
+ Vector names = new Vector();\r
+ for (int i = 0, l = alorders.size(); i < l; i++)\r
+ {\r
+ String orderName = new String(" Region " + i);\r
+ int j = i + 1;\r
+\r
+ while (j < l)\r
+ {\r
+ if (((AlignmentOrder) alorders.get(i))\r
+ .equals(((AlignmentOrder) alorders.get(j))))\r
+ {\r
+ alorders.remove(j);\r
+ l--;\r
+ orderName += "," + j;\r
+ }\r
+ else\r
+ {\r
+ j++;\r
+ }\r
+ }\r
+\r
+ if (i == 0 && j == 1)\r
+ {\r
+ names.add(new String(""));\r
+ }\r
+ else\r
+ {\r
+ names.add(orderName);\r
+ }\r
+ }\r
+ for (int i = 0, l = alorders.size(); i < l; i++)\r
+ {\r
+ af.addSortByOrderMenuItem(WebServiceName\r
+ + ((String) names.get(i)) + " Ordering",\r
+ (AlignmentOrder) alorders.get(i));\r
+ }\r
+ }\r
+ }\r
+\r
+ Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+\r
+ }\r
+ else\r
+ {\r
+ System.out.println("MERGE WITH OLD FRAME");\r
+ // TODO: modify alignment in original frame, replacing old for new\r
+ // alignment using the commands.EditCommand model to ensure the update can\r
+ // be undone\r
+ }\r
+ }\r
+\r
+ public boolean canMergeResults()\r
+ {\r
+ return false;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff