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 java.util.*;
-import vamsas.objects.simple.MsaResult;
-import vamsas.objects.simple.Result;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
import jalview.datamodel.Alignment;
-import jalview.datamodel.SeqCigar;
-import jalview.gui.Desktop;
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
-import java.util.Vector;
+import jalview.gui.*;
+import vamsas.objects.simple.MsaResult;
/**
* <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 {
+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 {
+
+ 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();
-
+
+ vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
+ SequenceSet();
+
/**
* MsaWSJob
- *
+ *
* @param jobNum
* int
* @param jobId
* String
*/
- public MsaWSJob(int jobNum, SequenceI[] inSeqs) {
+ public MsaWSJob(int jobNum, SequenceI[] inSeqs)
+ {
this.jobnum = jobNum;
- if (!prepareInput(inSeqs,2)) {
- submitted=true;
- subjobComplete=true;
+ if (!prepareInput(inSeqs, 2))
+ {
+ submitted = true;
+ subjobComplete = true;
result = new MsaResult();
result.setFinished(true);
result.setStatus("Job never ran - input returned to user.");
}
-
+
}
-
+
int allowedServerExceptions = 3; // thread dies if too many
-
+
// exceptions.
- boolean submitted=false;
+ boolean submitted = false;
boolean subjobComplete = false;
-
+
Hashtable SeqNames = new Hashtable();
Vector emptySeqs = new Vector();
/**
* @param minlen minimum number of residues required for this MsaWS service
* @return true if seqs contains sequences to be submitted to service.
*/
- private boolean prepareInput(SequenceI[] seqs, int minlen) {
+ private boolean prepareInput(SequenceI[] seqs, int minlen)
+ {
int nseqs = 0;
- if (minlen<0)
+ if (minlen < 0)
+ {
throw new Error("Implementation error: minlen must be zero or more.");
- for (int i = 0; i < seqs.length; i++) {
- if (seqs[i].getEnd()-seqs[i].getStart()>minlen-1) {
+ }
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
nseqs++;
}
}
- boolean valid=nseqs>1; // need at least two seqs
- vamsas.objects.simple.Sequence[] seqarray =
- (valid)
- ? 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 (valid && seqs[i].getEnd()-seqs[i].getStart()>minlen-1) {
- seqarray[n] = new vamsas.objects.simple.Sequence();
- seqarray[n].setId(newname);
- seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequence()
+ boolean valid = nseqs > 1; // need at least two seqs
+ vamsas.objects.simple.Sequence[] seqarray =
+ (valid)
+ ? 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 (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+ {
+ 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
+ {
+ String empty = null;
+ if (seqs[i].getEnd() >= seqs[i].getStart())
+ {
+ empty = (submitGaps) ? seqs[i].getSequence()
: AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, seqs[i]
- .getSequence()));
- } else {
- String empty=null;
- if (seqs[i].getEnd()>=seqs[i].getStart()) {
- empty = (submitGaps) ? seqs[i].getSequence()
- : AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, seqs[i]
- .getSequence());
- }
- emptySeqs.add(new String[] { newname, empty});
+ .getSequence());
}
+ emptySeqs.add(new String[]
+ {newname, empty});
}
- this.seqs = new vamsas.objects.simple.SequenceSet();
- this.seqs.setSeqs(seqarray);
- return valid;
+ }
+ this.seqs = new vamsas.objects.simple.SequenceSet();
+ this.seqs.setSeqs(seqarray);
+ return valid;
}
+
/**
- *
+ *
* @return true if getAlignment will return a valid alignment result.
*/
- public boolean hasResults() {
- if (subjobComplete && result!=null && jobs[0].result.isFinished())
+ public boolean hasResults()
+ {
+ if (subjobComplete && result != null && result.isFinished()
+ && result.getMsa() != null && result.getMsa().getSeqs() != null)
+ {
return true;
+ }
return false;
}
- public Object[] getAlignment() {
-
- if (result!=null && result.isFinished()) {
- SequenceI[] alseqs=null;
- char alseq_gapchar='-';
- int alseq_l=0;
- if (result.getMsa() != null) {
+
+ public Object[] getAlignment()
+ {
+
+ if (result != null && result.isFinished())
+ {
+ 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_gapchar = result.getMsa().getGapchar().charAt(0);
alseq_l = alseqs.length;
}
- if (emptySeqs.size()>0) {
- SequenceI[] t_alseqs = new SequenceI[alseq_l+emptySeqs.size()];
+ 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();
+ 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;
}
}
// check that aligned width is at least as wide as emptySeqs width.
- int ow=w,nw=w;
- for (i=0, w=emptySeqs.size(); i<w; i++) {
- String[] es=(String[]) emptySeqs.get(i);
- if (es!=null && es[1]!=null) {
- int sw=es[1].length();
- if (nw<sw)
- nw=sw;
+ int ow = w, nw = w;
+ for (i = 0, w = emptySeqs.size(); i < w; i++)
+ {
+ String[] es = (String[]) emptySeqs.get(i);
+ if (es != null && es[1] != null)
+ {
+ int sw = es[1].length();
+ if (nw < sw)
+ {
+ nw = sw;
+ }
}
}
// make a gapped string.
- StringBuffer insbuff=new StringBuffer(w);
- for (i=0; i<nw; i++)
+ StringBuffer insbuff = new StringBuffer(w);
+ for (i = 0; i < nw; i++)
+ {
insbuff.append(alseq_gapchar);
- if (ow<nw) {
- for (i=0; i<alseq_l; i++) {
- int sw=t_alseqs[i].getLength();
- if (nw>sw) {
+ }
+ if (ow < nw)
+ {
+ for (i = 0; i < alseq_l; i++)
+ {
+ int sw = t_alseqs[i].getLength();
+ if (nw > sw)
+ {
// pad at end
- alseqs[i].setSequence(t_alseqs[i].getSequence()+insbuff.substring(0,sw-nw));
+ alseqs[i].setSequence(t_alseqs[i].getSequence() +
+ insbuff.substring(0, sw - nw));
}
}
}
- for (i=0, w=emptySeqs.size(); i<w; i++) {
- String[] es=(String[]) emptySeqs.get(i);
- if (es[1]==null)
- t_alseqs[i+alseq_l] = new jalview.datamodel.Sequence(es[0], insbuff.toString(),1,0);
- else {
- if (es[1].length()<nw) {
- t_alseqs[i+alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]+insbuff.substring(0, nw-es[1].length()),1,1+es[1].length());
- } else {
- t_alseqs[i+alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
+ for (i = 0, w = emptySeqs.size(); i < w; i++)
+ {
+ String[] es = (String[]) emptySeqs.get(i);
+ if (es[1] == null)
+ {
+ t_alseqs[i +
+ alseq_l] = new jalview.datamodel.Sequence(es[0],
+ insbuff.toString(), 1, 0);
+ }
+ else
+ {
+ if (es[1].length() < nw)
+ {
+ t_alseqs[i +
+ alseq_l] = new jalview.datamodel.Sequence(es[0],
+ es[1] + insbuff.substring(0, nw - es[1].length()), 1,
+ 1 + es[1].length());
+ }
+ else
+ {
+ t_alseqs[i +
+ alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
}
}
}
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 new Object[]
+ {
+ alseqs, msaorder};
}
return null;
}
+
+ boolean cancelled = false;
+ /**
+ * mark subjob as cancelled and set result object appropriatly
+ */
+ void cancel() {
+ cancelled=true;
+ subjobComplete = true;
+ result = 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) {
+ WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+ AlignmentView alview,
+ String wsname, boolean subgaps, boolean presorder)
+ {
this.server = server;
this.WsUrl = wsUrl;
this.wsInfo = wsinfo;
this.preserveOrder = presorder;
this.alignFrame = alFrame;
}
-
+
/**
* create one or more Msa jobs to align visible seuqences in _msa
- *
+ *
* @param title
* String
* @param _msa
* 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) {
+ 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 njobs = 1;
+ if (contigs != null && contigs.length > 0)
+ {
int start = 0;
- njobs=0;
+ njobs = 0;
int width = _msa.getWidth();
- for (int contig = 0; contig < contigs.length; contig += 3) {
- if ((contigs[contig+1] - start) > 0) {
+ 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];
+ width += contigs[contig + 2]; // end up with full region width (including hidden regions)
+ start = contigs[contig + 1] + contigs[contig + 2];
}
- if (start<width) {
+ 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) {
+ 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++) {
+ for (int s = 0; s < mseq.length; s++)
+ {
mseq[s] = msa[s].getSeq('-').getSubSequence(start,
- contigs[contig+1]);
+ contigs[contig + 1]);
}
- if (j!=0) {
+ if (j != 0)
+ {
jobs[j] = new MsaWSJob(wsinfo.addJobPane(), mseq);
- } else {
+ }
+ else
+ {
jobs[j] = new MsaWSJob(0, mseq);
}
- wsinfo.setProgressName("region "+jobs[j].jobnum,jobs[j].jobnum);
+ wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
j++;
}
- start = contigs[contig+1] + contigs[contig + 2];
+ start = contigs[contig + 1] + contigs[contig + 2];
}
- if (start<width) {
+ if (start < width)
+ {
SequenceI mseq[] = new SequenceI[msa.length];
- for (int s = 0; s < mseq.length; s++) {
+ for (int s = 0; s < mseq.length; s++)
+ {
mseq[s] = msa[s].getSeq('-').getSubSequence(start,
- width+1);
+ width + 1);
}
- if (j!=0) {
+ if (j != 0)
+ {
jobs[j] = new MsaWSJob(wsinfo.addJobPane(), mseq);
- } else {
+ }
+ else
+ {
jobs[j] = new MsaWSJob(0, mseq);
}
- wsinfo.setProgressName("region "+jobs[j].jobnum,jobs[j].jobnum);
+ wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
- j++;
+ j++;
}
- } else {
+ }
+ else
+ {
SequenceI mseq[] = new SequenceI[msa.length];
- for (int s = 0; s < mseq.length; s++) {
+ for (int s = 0; s < mseq.length; s++)
+ {
mseq[s] = msa[s].getSeq('-');
}
jobs = new MsaWSJob[1];
jobs[0] = new MsaWSJob(0, mseq);
}
}
-
- public boolean isCancellable() {
+
+ public boolean isCancellable()
+ {
return true;
}
-
- public void cancelJob() {
- if (!jobComplete && jobs != null) {
+
+ public void cancelJob()
+ {
+ if (!jobComplete && jobs != null)
+ {
boolean cancelled = true;
- for (int job = 0; job < jobs.length; job++) {
+ for (int job = 0; job < jobs.length; job++)
+ {
if (jobs[job].submitted && !jobs[job].subjobComplete)
- {
+ {
String cancelledMessage = "";
- try {
+ try
+ {
vamsas.objects.simple.WsJobId cancelledJob = server
- .cancel(jobs[job].jobId);
- if (cancelledJob.getStatus() == 2) {
+ .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) {
+ jobs[job].cancel();
+ 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";
+ cancelledMessage +=
+ "Server cannot cancel this job. just close the window.\n";
cancelled = false;
- wsInfo.setStatus(jobs[job].jobnum, WebserviceInfo.STATE_CANCELLED_OK);
+ // wsInfo.setStatus(jobs[job].jobnum,
+ // WebserviceInfo.STATE_RUNNING);
}
-
- if (cancelledJob.getJobId() != null) {
+
+ if (cancelledJob.getJobId() != null)
+ {
cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
}
-
+
cancelledMessage += "\n";
- } catch (Exception exc) {
- cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
- + exc + "\n");
- exc.printStackTrace();
+ }
+ catch (Exception exc)
+ {
+ cancelledMessage +=
+ ("\nProblems cancelling the job : Exception received...\n"
+ + exc + "\n");
+ Cache.log.warn("Exception whilst cancelling "+jobs[job].jobId,exc);
}
wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
- + cancelledMessage + "\n");
+ + cancelledMessage + "\n");
}
}
- if (cancelled) {
+ if (cancelled)
+ {
wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
jobComplete = true;
}
- } else {
- if (!jobComplete) {
+ this.interrupt(); // kick thread to update job states.
+ }
+ else
+ {
+ if (!jobComplete)
+ {
wsInfo
- .setProgressText(OutputHeader
- + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+ .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) {
+
+ class JobStateSummary {
+ int running = 0;
+ int queuing = 0;
+ int finished = 0;
+ int error = 0;
+ int serror = 0;
+ int cancelled=0;
+ int results=0;
+ void updateJobPanelState(WebserviceInfo wsInfo, MsaWSJob j) {
+ if (j.result != null)
+ {
+ String progheader = "";
+ // Parse state of job[j]
+ if (j.result.isRunning())
+ {
+ running++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+ }
+ else if (j.result.isQueued())
+ {
+ queuing++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+ }
+ else if (j.result.isFinished())
+ {
+ finished++;
+ j.subjobComplete = true;
+ if (j.hasResults())
+ results++;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+ }
+ else if (j.result.isFailed())
+ {
+ progheader += "Job failed.\n";
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ error++;
+ }
+ else if (j.result.isServerError())
+ {
+ serror++;
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum,
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ }
+ else if (j.result.isBroken() || j.result.isFailed())
+ {
+ error++;
+ j.subjobComplete = true;
+ wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ // and pass on any sub-job messages to the user
+ wsInfo.setProgressText(j.jobnum, OutputHeader);
+ wsInfo.appendProgressText(j.jobnum, progheader);
+ if (j.result.getStatus() != null)
+ {
+ wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+ }
+ }
+ else
+ {
+ if (j.submitted && j.subjobComplete)
+ {
+ if (j.allowedServerExceptions == 0)
+ {
+ serror++;
+ }
+ else if (j.result == null)
+ {
+ error++;
+ }
+ }
+ }
+ }
+ }
+ public void run()
+ {
+ JobStateSummary jstate=null;
+ while (!jobComplete)
+ {
+ jstate = new JobStateSummary();
+ 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"));
+ "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) {
+ 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());
+ + " Server exception!\n" + ex.getMessage());
Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
- + ") Server exception: " + ex.getMessage());
-
- if (jobs[j].allowedServerExceptions > 0) {
+ + ") Server exception: " + ex.getMessage());
+
+ if (jobs[j].allowedServerExceptions > 0)
+ {
jobs[j].allowedServerExceptions--;
Cache.log.debug("Sleeping after a server exception.");
- try {
+ try
+ {
Thread.sleep(5000);
}
- catch (InterruptedException ex1) {
+ 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);
+ }
+ 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) {
+ catch (OutOfMemoryError er)
+ {
jobComplete = true;
- jobs[j].subjobComplete=true;
- jobs[j].result=null; // may contain out of date result object
+ jobs[j].subjobComplete = true;
+ jobs[j].result = null; // may contain out of date result object
wsInfo.setStatus(jobs[j].jobnum,
- WebserviceInfo.STATE_STOPPED_ERROR);
+ 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);
+ .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++;
- }
- }
- }
+ jstate.updateJobPanelState(wsInfo, jobs[j]);
}
// Decide on overall state based on collected jobs[] states
- if (running>0) {
+ if (jstate.running > 0)
+ {
wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
- } else if (queuing>0) {
+ }
+ else if (jstate.queuing > 0)
+ {
wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
- } else {
- jobComplete=true;
- if (finished>0) {
+ }
+ else
+ {
+ jobComplete = true;
+ if (jstate.finished > 0)
+ {
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
- } else if (error>0) {
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
- } else if (serror>0) {
+ }
+ else if (jstate.error > 0)
+ {
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ }
+ else if (jstate.serror > 0)
+ {
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
}
}
- if (!jobComplete) {
- try {
+ if (!jobComplete)
+ {
+ try
+ {
Thread.sleep(5000);
}
- catch (InterruptedException e) {
- Cache.log.debug("Interrupted sleep waiting for next job poll.",e);
+ catch (InterruptedException e)
+ {
+ Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
}
// System.out.println("I'm alive "+alTitle);
}
}
- if (jobComplete) {
+ 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);
+
+ 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) {
+ if (j.seqs.getSeqs() == null)
+ {
// special case - selection consisted entirely of empty sequences...
- j.submitted=true;
- j.result=new MsaResult();
+ j.submitted = true;
+ j.result = new MsaResult();
j.result.setFinished(true);
j.result.setStatus("Empty Alignment Job");
j.result.setMsa(null);
}
- try {
+ try
+ {
vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
-
- if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {
+
+ if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
+ {
j.jobId = jobsubmit.getJobId();
- j.submitted=true;
+ j.submitted = true;
j.subjobComplete = false;
// System.out.println(WsURL + " Job Id '" + jobId + "'");
- } else {
- if (jobsubmit == null) {
+ }
+ else
+ {
+ if (jobsubmit == null)
+ {
throw new Exception(
"Server at "
+ WsUrl
- + " returned null object, it probably cannot be contacted. Try again later ?");
+ +
+ " returned null object, it probably cannot be contacted. Try again later ?");
}
-
+
throw new Exception(jobsubmit.getJobId());
}
- } catch (Exception e) {
+ }
+ 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");
+ .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");
-
+ .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.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++) {
+ 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());
+ .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
+
+ void parseResult()
+ {
+ int results = 0; // number of result sets received
+ JobStateSummary finalState = new JobStateSummary();
+ try
+ {
+ for (int j = 0; j < jobs.length; j++)
+ {
+ finalState.updateJobPanelState(wsInfo, jobs[j]);
+ if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+ {
+ results++;
+ 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);
+ 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();
+ if (results > 0)
+ {
+ 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) {
+
+ 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 cshift=0;
+ Vector alorders = new Vector();
+ if (contigs != null && contigs.length > 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 (mseq[s].getStart()<=mseq[s].getEnd())
- alignment[s].setEnd(mseq[s].getEnd());
- ((AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
+ 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 = 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;
+ nwidth += width;
}
// advance to begining of visible region
- start = cshift+contigs[contig] + contigs[contig + 2];
+ 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(cshift+contigs[contig], start);
- if (alignment[s]==null) {
+ 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())
+ }
+ 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];
- cshift+=contigs[contig+2];
+ columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
+ nwidth += contigs[contig + 2];
}
// Do final job - if it exists
- if (j<jobs.length && jobs[j].hasResults()) {
- 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 (mseq[s].getEnd()>=mseq[s].getStart())
- alignment[s].setEnd(mseq[s].getEnd());
- ((AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
+ if (j < jobs.length)
+ {
+ int width = 0;
+ if (jobs[j].hasResults())
+ {
+ Object[] subalg = 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.");
+ }
}
}
- nwidth+=width;
}
- } else {
- if (jobs[0].hasResults()) {
+ }
+ else
+ {
+ if (jobs[0].hasResults())
+ {
Object[] alg = jobs[0].getAlignment();
alignment = (SequenceI[]) alg[0];
alorders.add(alg[1]);
- } else {
- alignment = SeqCigar.createAlignmentSequences(seqs, '-', columnselection,null);
+ }
+ else
+ {
+ alignment = SeqCigar.createAlignmentSequences(seqs, '-',
+ columnselection, null);
}
}
Alignment al = new Alignment(alignment);
- if (dataset != null) {
+ if (dataset != null)
+ {
al.setDataset(dataset);
}
-
- if (newFrame) {
+
+ if (newFrame)
+ {
// TODO: JBPNote Should also rename the query sequence
// sometime...
- AlignFrame af = new AlignFrame(al,columnselection);
-
+ 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) {
+ if (alorders.size() > 0)
+ {
+ if (alorders.size() == 1)
+ {
af.addSortByOrderMenuItem(WebServiceName + " Ordering",
- (AlignmentOrder) alorders.get(0));
- } else {
+ (AlignmentOrder) alorders.get(0));
+ }
+ else
+ {
// construct a non-redundant ordering set
- Vector names=new Vector();
- for (int i=0,l=alorders.size(); i<l; i++) {
- String orderName = new String("Region "+i);
- int j=i+1;
- int r=l;
- while (j<l) {
- if (((AlignmentOrder) alorders.get(i)).equals(((AlignmentOrder) alorders.get(j)))) {
- alorders.remove(j); l--;
- orderName+=","+j;
- } else
+ Vector names = new Vector();
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ String orderName = new String("Region " + i);
+ int j = i + 1;
+ int r = l;
+ while (j < l)
+ {
+ if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
+ AlignmentOrder) alorders.get(j))))
+ {
+ alorders.remove(j);
+ l--;
+ orderName += "," + j;
+ }
+ else
+ {
j++;
+ }
}
-
- if (i==0 && j==1)
+
+ if (i == 0 && j == 1)
+ {
names.add(new String(""));
+ }
else
+ {
names.add(orderName);
+ }
}
- for (int i=0,l=alorders.size(); i<l; i++) {
- af.addSortByOrderMenuItem(WebServiceName + ((String) names.get(i))+" Ordering",
- (AlignmentOrder) alorders.get(i));
+ for (int i = 0, l = alorders.size(); i < l; i++)
+ {
+ af.addSortByOrderMenuItem(WebServiceName + ( (String) names.get(i)) +
+ " Ordering",
+ (AlignmentOrder) alorders.get(i));
}
}
}
-
+
Desktop.addInternalFrame(af, alTitle,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
-
- } else {
+ AlignFrame.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_HEIGHT);
+
+ }
+ else
+ {
System.out.println("MERGE WITH OLD FRAME");
-
+
}
}
}
git://source.jalview.org / jalview.git / commitdiff