2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.jws1;
23 import jalview.analysis.AlignSeq;
24 import jalview.analysis.SeqsetUtils;
25 import jalview.bin.Cache;
26 import jalview.datamodel.Alignment;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.AlignmentView;
30 import jalview.datamodel.HiddenColumns;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.AlignFrame;
33 import jalview.gui.Desktop;
34 import jalview.gui.WebserviceInfo;
35 import jalview.io.DataSourceType;
36 import jalview.io.FileFormatI;
37 import jalview.io.FormatAdapter;
38 import jalview.io.IdentifyFile;
39 import jalview.io.JPredFile;
40 import jalview.io.JnetAnnotationMaker;
41 import jalview.io.PileUpfile;
42 import jalview.util.Comparison;
43 import jalview.util.MessageManager;
44 import jalview.ws.AWsJob;
45 import jalview.ws.JobStateSummary;
46 import jalview.ws.WSClientI;
48 import java.util.Hashtable;
49 import java.util.List;
51 import vamsas.objects.simple.JpredResult;
53 class JPredThread extends JWS1Thread implements WSClientI
55 // TODO: put mapping between JPredJob input and input data here -
56 // JNetAnnotation adding is done after result parsing.
57 class JPredJob extends WSJob
59 // TODO: make JPredJob deal only with what was sent to and received from a
61 int[] predMap = null; // mapping from sequence(i) to the original
63 // sequence(predMap[i]) being predicted on
65 vamsas.objects.simple.Sequence sequence;
67 vamsas.objects.simple.Msfalignment msa;
69 java.util.Hashtable SequenceInfo = null;
71 int msaIndex = 0; // the position of the original sequence in the array of
73 // Sequences in the input object that this job holds a
78 * @return true if getResultSet will return a valid alignment and prediction
82 public boolean hasResults()
84 if (subjobComplete && result != null && result.isFinished()
85 && ((JpredResult) result).getPredfile() != null
86 && ((JpredResult) result).getAligfile() != null)
94 public boolean hasValidInput()
105 * @return null or Object[] { annotated alignment for this prediction,
106 * ColumnSelection for this prediction} or null if no results
110 public Object[] getResultSet() throws Exception
112 if (result == null || !result.isFinished())
116 AlignmentI al = null;
117 HiddenColumns alhidden = null;
118 int FirstSeq = -1; // the position of the query sequence in Alignment al
120 JpredResult result = (JpredResult) this.result;
122 Cache.log.debug("Parsing output from JNet job.");
123 // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
125 JPredFile prediction = new JPredFile(result.getPredfile(),
126 DataSourceType.PASTE);
127 SequenceI[] preds = prediction.getSeqsAsArray();
128 Cache.log.debug("Got prediction profile.");
130 if ((this.msa != null) && (result.getAligfile() != null))
132 Cache.log.debug("Getting associated alignment.");
133 // we ignore the returned alignment if we only predicted on a single
135 FileFormatI format = new IdentifyFile()
136 .identify(result.getAligfile(), DataSourceType.PASTE);
143 Object[] alandcolsel = input
144 .getAlignmentAndHiddenColumns(getGapChar());
145 sqs = (SequenceI[]) alandcolsel[0];
146 al = new Alignment(sqs);
147 alhidden = (HiddenColumns) alandcolsel[1];
151 al = new FormatAdapter().readFile(result.getAligfile(),
152 DataSourceType.PASTE, format);
153 sqs = new SequenceI[al.getHeight()];
155 for (int i = 0, j = al.getHeight(); i < j; i++)
157 sqs[i] = al.getSequenceAt(i);
159 if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
161 throw (new Exception(MessageManager.getString(
162 "exception.couldnt_recover_sequence_properties_for_alignment")));
166 if (currentView.getDataset() != null)
168 al.setDataset(currentView.getDataset());
175 JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
181 throw (new Exception(MessageManager.formatMessage(
182 "exception.unknown_format_for_file", new String[]
183 { "", result.getAligfile() })));
188 al = new Alignment(preds);
189 FirstSeq = prediction.getQuerySeqPosition();
192 char gc = getGapChar();
193 SequenceI[] sqs = (SequenceI[]) input
194 .getAlignmentAndHiddenColumns(gc)[0];
195 if (this.msaIndex >= sqs.length)
197 throw new Error(MessageManager.getString(
198 "error.implementation_error_invalid_msa_index_for_job"));
202 // Uses RemoveGapsCommand
204 new jalview.commands.RemoveGapsCommand(
205 MessageManager.getString("label.remove_gaps"),
207 { sqs[msaIndex] }, currentView);
209 SequenceI profileseq = al.getSequenceAt(FirstSeq);
210 profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
213 if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
214 al.getSequenceAt(FirstSeq), SequenceInfo))
216 throw (new Exception(MessageManager.getString(
217 "exception.couldnt_recover_sequence_props_for_jnet_query")));
221 if (currentView.getDataset() != null)
223 al.setDataset(currentView.getDataset());
230 jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
231 FirstSeq, true, predMap);
232 SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
233 alignToProfileSeq(al, profileseq);
236 // Adjust input view for gaps
237 // propagate insertions into profile
238 alhidden = HiddenColumns.propagateInsertions(profileseq, al,
243 // transfer to dataset
244 for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
246 if (alant.sequenceRef != null)
248 replaceAnnotationOnAlignmentWith(alant, alant.label,
249 "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
253 return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
257 * copied from JabawsCalcWorker
264 protected void replaceAnnotationOnAlignmentWith(
265 AlignmentAnnotation newAnnot, String typeName, String calcId,
268 SequenceI dsseq = aSeq.getDatasetSequence();
269 while (dsseq.getDatasetSequence() != null)
271 dsseq = dsseq.getDatasetSequence();
273 // look for same annotation on dataset and lift this one over
274 List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
276 if (dsan != null && dsan.size() > 0)
278 for (AlignmentAnnotation dssan : dsan)
280 dsseq.removeAlignmentAnnotation(dssan);
283 AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
284 dsseq.addAlignmentAnnotation(dssan);
285 dssan.adjustForAlignment();
289 * Given an alignment where all other sequences except profileseq are
290 * aligned to the ungapped profileseq, insert gaps in the other sequences to
291 * realign them with the residues in profileseq
296 private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
298 char gc = al.getGapCharacter();
299 int[] gapMap = profileseq.gapMap();
300 // insert gaps into profile
301 for (int lp = 0, r = 0; r < gapMap.length; r++)
303 if (gapMap[r] - lp > 1)
305 StringBuffer sb = new StringBuffer();
306 for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
310 for (int s = 1, ns = al.getHeight(); s < ns; s++)
312 String sq = al.getSequenceAt(s).getSequenceAsString();
313 int diff = gapMap[r] - sq.length();
318 while ((diff = gapMap[r] - sq.length()) > 0)
320 sq = sq + ((diff >= sb.length()) ? sb.toString()
321 : sb.substring(0, diff));
323 al.getSequenceAt(s).setSequence(sq);
327 al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r])
328 + sb.toString() + sq.substring(gapMap[r]));
336 public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
339 this.predMap = delMap;
340 String sq = AlignSeq.extractGaps(Comparison.GapChars,
341 seq.getSequenceAsString());
342 if (sq.length() >= 20)
344 this.SequenceInfo = SequenceInfo;
345 sequence = new vamsas.objects.simple.Sequence();
346 sequence.setId(seq.getName());
351 errorMessage = "Sequence is too short to predict with JPred - need at least 20 amino acids.";
355 public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
357 this(SequenceInfo, msf[0], delMap);
358 if (sequence != null)
362 msa = new vamsas.objects.simple.Msfalignment();
363 PileUpfile pileup = new PileUpfile();
364 msa.setMsf(pileup.print(msf, true));
369 String errorMessage = "";
371 public String getValidationMessages()
373 return errorMessage + "\n";
377 ext.vamsas.Jpred server;
381 JPredThread(WebserviceInfo wsinfo, String altitle,
382 ext.vamsas.Jpred server, String wsurl, AlignmentView alview,
385 super(alframe, wsinfo, alview, wsurl);
386 this.altitle = altitle;
387 this.server = server;
390 JPredThread(WebserviceInfo wsinfo, String altitle,
391 ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
392 SequenceI seq, int[] delMap, AlignmentView alview,
395 this(wsinfo, altitle, server, wsurl, alview, alframe);
396 JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
397 if (job.hasValidInput())
399 OutputHeader = wsInfo.getProgressText();
400 jobs = new WSJob[] { job };
405 wsInfo.appendProgressText(job.getValidationMessages());
409 JPredThread(WebserviceInfo wsinfo, String altitle,
410 ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
411 int[] delMap, AlignmentView alview, AlignFrame alframe,
414 this(wsinfo, altitle, server, wsurl, alview, alframe);
415 JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
416 if (job.hasValidInput())
418 jobs = new WSJob[] { job };
419 OutputHeader = wsInfo.getProgressText();
424 wsInfo.appendProgressText(job.getValidationMessages());
429 public void StartJob(AWsJob j)
431 if (!(j instanceof JPredJob))
433 throw new Error(MessageManager.formatMessage(
434 "error.implementation_error_startjob_called", new String[]
435 { j.getClass().toString() }));
439 JPredJob job = (JPredJob) j;
442 job.setJobId(server.predictOnMsa(job.msa));
444 else if (job.sequence != null)
446 job.setJobId(server.predict(job.sequence)); // debug like : job.jobId =
447 // "/jobs/www-jpred/jp_Yatat29";//
450 if (job.getJobId() != null)
452 if (job.getJobId().startsWith("Broken"))
454 job.result = new JpredResult();
455 job.result.setInvalid(true);
456 job.result.setStatus(MessageManager
457 .formatMessage("label.submission_params", new String[]
458 { job.getJobId().toString() }));
459 throw new Exception(job.getJobId());
463 job.setSubmitted(true);
464 job.setSubjobComplete(false);
465 Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
470 throw new Exception(MessageManager
471 .getString("exception.server_timeout_try_later"));
473 } catch (Exception e)
475 // kill the whole job.
476 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
477 if (e.getMessage().indexOf("Exception") > -1)
479 wsInfo.setStatus(j.getJobnum(),
480 WebserviceInfo.STATE_STOPPED_SERVERERROR);
481 wsInfo.setProgressText(j.getJobnum(),
482 "Failed to submit the prediction. (Just close the window)\n"
483 + "It is most likely that there is a problem with the server.\n");
485 "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
486 + e.getMessage() + "\n");
488 jalview.bin.Cache.log.warn("Server Exception", e);
492 wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
493 // JBPNote - this could be a popup informing the user of the problem.
494 wsInfo.appendProgressText(j.getJobnum(),
495 MessageManager.formatMessage(
496 "info.failed_to_submit_prediction", new String[]
497 { e.getMessage(), wsInfo.getProgressText() }));
499 jalview.bin.Cache.log
500 .debug("Failed Submission of job " + j.getJobnum(), e);
503 j.setAllowedServerExceptions(-1);
504 j.setSubjobComplete(true);
509 public void parseResult()
511 int results = 0; // number of result sets received
512 JobStateSummary finalState = new JobStateSummary();
515 for (int j = 0; j < jobs.length; j++)
517 finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
518 if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete()
519 && jobs[j].hasResults())
524 } catch (Exception ex)
528 "Unexpected exception when processing results for " + altitle,
530 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
534 wsInfo.showResultsNewFrame
535 .addActionListener(new java.awt.event.ActionListener()
538 public void actionPerformed(java.awt.event.ActionEvent evt)
540 displayResults(true);
544 .addActionListener(new java.awt.event.ActionListener()
547 public void actionPerformed(java.awt.event.ActionEvent evt)
549 displayResults(false);
552 wsInfo.setResultsReady();
556 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
557 wsInfo.appendInfoText("No jobs ran.");
558 wsInfo.setFinishedNoResults();
562 void displayResults(boolean newWindow)
564 // TODO: cope with multiple subjobs.
569 for (int jn = 0; jn < jobs.length; jn++)
571 Object[] jobres = null;
572 JPredJob j = (JPredJob) jobs[jn];
576 // hack - we only deal with all single seuqence predictions or all
577 // profile predictions
578 msa = (j.msa != null) ? true : msa;
581 jalview.bin.Cache.log.debug("Parsing output of job " + jn);
582 jobres = j.getResultSet();
583 jalview.bin.Cache.log.debug("Finished parsing output.");
584 if (jobs.length == 1)
590 // do merge with other job results
591 throw new Error(MessageManager.getString(
592 "error.multiple_jnet_subjob_merge_not_implemented"));
594 } catch (Exception e)
596 jalview.bin.Cache.log
597 .error("JNet Client: JPred Annotation Parse Error", e);
598 wsInfo.setStatus(j.getJobnum(),
599 WebserviceInfo.STATE_STOPPED_ERROR);
600 wsInfo.appendProgressText(j.getJobnum(),
601 MessageManager.formatMessage(
602 "info.invalid_jnet_job_result_data",
604 { OutputHeader.toString(), j.result.getStatus(),
606 j.result.setBroken(true);
616 ((AlignmentI) res[0])
617 .setSeqrep(((AlignmentI) res[0]).getSequenceAt(0));
622 af = new AlignFrame((Alignment) res[0],
623 (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH,
624 AlignFrame.DEFAULT_HEIGHT);
628 af = new AlignFrame((Alignment) res[0],
629 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
635 * java.lang.Object[] alandcolsel =
636 * input.getAlignmentAndColumnSelection
637 * (alignFrame.getViewport().getGapCharacter()); if
638 * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
639 * if (msa) { throw new Error("Implementation Error! ColumnSelection
640 * from input alignment will not map to result alignment!"); } } if
641 * (!msa) { // update hidden regions to account for loss of gaps in
642 * profile. - if any // gapMap returns insert list, interpreted as
643 * delete list by pruneDeletions //((ColumnSelection)
644 * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])
645 * alandcolsel[0])[0].gapMap())); }
648 af = new AlignFrame((Alignment) res[0], (HiddenColumns) res[1],
649 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
651 Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
652 AlignFrame.DEFAULT_HEIGHT);
656 Cache.log.info("Append results onto existing alignment.");
663 public void pollJob(AWsJob job) throws Exception
665 ((JPredJob) job).result = server.getresult(job.getJobId());
669 public boolean isCancellable()
675 public void cancelJob()
677 throw new Error(MessageManager.getString("error.implementation_error"));
681 public boolean canMergeResults()