2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
3 * Copyright (C) 2015 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.bin.Cache;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.AlignmentView;
29 import jalview.datamodel.ColumnSelection;
30 import jalview.datamodel.SequenceI;
31 import jalview.gui.AlignFrame;
32 import jalview.gui.Desktop;
33 import jalview.gui.WebserviceInfo;
34 import jalview.io.FormatAdapter;
35 import jalview.util.Comparison;
36 import jalview.util.MessageManager;
37 import jalview.ws.AWsJob;
38 import jalview.ws.JobStateSummary;
39 import jalview.ws.WSClientI;
41 import java.util.Hashtable;
42 import java.util.List;
44 import vamsas.objects.simple.JpredResult;
46 class JPredThread extends JWS1Thread implements WSClientI
48 // TODO: put mapping between JPredJob input and input data here -
49 // JNetAnnotation adding is done after result parsing.
50 class JPredJob extends WSJob
52 // TODO: make JPredJob deal only with what was sent to and received from a
54 int[] predMap = null; // mapping from sequence(i) to the original
56 // sequence(predMap[i]) being predicted on
58 vamsas.objects.simple.Sequence sequence;
60 vamsas.objects.simple.Msfalignment msa;
62 java.util.Hashtable SequenceInfo = null;
64 int msaIndex = 0; // the position of the original sequence in the array of
66 // Sequences in the input object that this job holds a
71 * @return true if getResultSet will return a valid alignment and prediction
74 public boolean hasResults()
76 if (subjobComplete && result != null && result.isFinished()
77 && ((JpredResult) result).getPredfile() != null
78 && ((JpredResult) result).getAligfile() != null)
85 public boolean hasValidInput()
96 * @return null or Object[] { annotated alignment for this prediction,
97 * ColumnSelection for this prediction} or null if no results
101 public Object[] getResultSet() throws Exception
103 if (result == null || !result.isFinished())
107 AlignmentI al = null;
108 ColumnSelection alcsel = null;
109 int FirstSeq = -1; // the position of the query sequence in Alignment al
111 JpredResult result = (JpredResult) this.result;
113 jalview.bin.Cache.log.debug("Parsing output from JNet job.");
114 // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
116 jalview.io.JPredFile prediction = new jalview.io.JPredFile(
117 result.getPredfile(), "Paste");
118 SequenceI[] preds = prediction.getSeqsAsArray();
119 jalview.bin.Cache.log.debug("Got prediction profile.");
121 if ((this.msa != null) && (result.getAligfile() != null))
123 jalview.bin.Cache.log.debug("Getting associated alignment.");
124 // we ignore the returned alignment if we only predicted on a single
126 String format = new jalview.io.IdentifyFile().Identify(
127 result.getAligfile(), "Paste");
129 if (jalview.io.FormatAdapter.isValidFormat(format))
134 Object[] alandcolsel = input
135 .getAlignmentAndColumnSelection(getGapChar());
136 sqs = (SequenceI[]) alandcolsel[0];
137 al = new Alignment(sqs);
138 alcsel = (ColumnSelection) alandcolsel[1];
142 al = new FormatAdapter().readFile(result.getAligfile(),
144 sqs = new SequenceI[al.getHeight()];
146 for (int i = 0, j = al.getHeight(); i < j; i++)
148 sqs[i] = al.getSequenceAt(i);
150 if (!jalview.analysis.SeqsetUtils.deuniquify(SequenceInfo, sqs))
152 throw (new Exception(
154 .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
158 if (currentView.getDataset() != null)
160 al.setDataset(currentView.getDataset());
167 jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
168 FirstSeq, false, predMap);
173 throw (new Exception(MessageManager.formatMessage(
174 "exception.unknown_format_for_file", new String[] {
175 format, result.getAligfile() })));
180 al = new Alignment(preds);
181 FirstSeq = prediction.getQuerySeqPosition();
184 char gc = getGapChar();
185 SequenceI[] sqs = (SequenceI[]) input
186 .getAlignmentAndColumnSelection(gc)[0];
187 if (this.msaIndex >= sqs.length)
191 .getString("error.implementation_error_invalid_msa_index_for_job"));
195 // Uses RemoveGapsCommand
197 new jalview.commands.RemoveGapsCommand(
198 MessageManager.getString("label.remove_gaps"),
199 new SequenceI[] { sqs[msaIndex] }, currentView);
201 SequenceI profileseq = al.getSequenceAt(FirstSeq);
202 profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
205 if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
206 al.getSequenceAt(FirstSeq), SequenceInfo))
208 throw (new Exception(
210 .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
214 if (currentView.getDataset() != null)
216 al.setDataset(currentView.getDataset());
223 jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
224 FirstSeq, true, predMap);
225 SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
226 alignToProfileSeq(al, profileseq);
229 // Adjust input view for gaps
230 // propagate insertions into profile
231 alcsel = ColumnSelection.propagateInsertions(profileseq, al,
236 // transfer to dataset
237 for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
239 if (alant.sequenceRef != null)
241 replaceAnnotationOnAlignmentWith(alant, alant.label,
242 "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
246 return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
250 * copied from JabawsCalcWorker
257 protected void replaceAnnotationOnAlignmentWith(
258 AlignmentAnnotation newAnnot, String typeName, String calcId,
261 SequenceI dsseq = aSeq.getDatasetSequence();
262 while (dsseq.getDatasetSequence() != null)
264 dsseq = dsseq.getDatasetSequence();
266 // look for same annotation on dataset and lift this one over
267 List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(
269 if (dsan != null && dsan.size() > 0)
271 for (AlignmentAnnotation dssan : dsan)
273 dsseq.removeAlignmentAnnotation(dssan);
276 AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
277 dsseq.addAlignmentAnnotation(dssan);
278 dssan.adjustForAlignment();
282 * Given an alignment where all other sequences except profileseq are
283 * aligned to the ungapped profileseq, insert gaps in the other sequences to
284 * realign them with the residues in profileseq
289 private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
291 char gc = al.getGapCharacter();
292 int[] gapMap = profileseq.gapMap();
293 // insert gaps into profile
294 for (int lp = 0, r = 0; r < gapMap.length; r++)
296 if (gapMap[r] - lp > 1)
298 StringBuffer sb = new StringBuffer();
299 for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
303 for (int s = 1, ns = al.getHeight(); s < ns; s++)
305 String sq = al.getSequenceAt(s).getSequenceAsString();
306 int diff = gapMap[r] - sq.length();
311 while ((diff = gapMap[r] - sq.length()) > 0)
314 + ((diff >= sb.length()) ? sb.toString() : sb
315 .substring(0, diff));
317 al.getSequenceAt(s).setSequence(sq);
321 al.getSequenceAt(s).setSequence(
322 sq.substring(0, gapMap[r]) + sb.toString()
323 + sq.substring(gapMap[r]));
331 public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
334 this.predMap = delMap;
335 String sq = AlignSeq.extractGaps(Comparison.GapChars,
336 seq.getSequenceAsString());
337 if (sq.length() >= 20)
339 this.SequenceInfo = SequenceInfo;
340 sequence = new vamsas.objects.simple.Sequence();
341 sequence.setId(seq.getName());
346 errorMessage = "Sequence is too short to predict with JPred - need at least 20 amino acids.";
350 public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
352 this(SequenceInfo, msf[0], delMap);
353 if (sequence != null)
357 msa = new vamsas.objects.simple.Msfalignment();
358 jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
359 msa.setMsf(pileup.print(msf));
364 String errorMessage = "";
366 public String getValidationMessages()
368 return errorMessage + "\n";
372 ext.vamsas.Jpred server;
376 JPredThread(WebserviceInfo wsinfo, String altitle,
377 ext.vamsas.Jpred server, String wsurl, AlignmentView alview,
380 super(alframe, wsinfo, alview, wsurl);
381 this.altitle = altitle;
382 this.server = server;
385 JPredThread(WebserviceInfo wsinfo, String altitle,
386 ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
387 SequenceI seq, int[] delMap, AlignmentView alview,
390 this(wsinfo, altitle, server, wsurl, alview, alframe);
391 JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
392 if (job.hasValidInput())
394 OutputHeader = wsInfo.getProgressText();
395 jobs = new WSJob[] { job };
400 wsInfo.appendProgressText(job.getValidationMessages());
404 JPredThread(WebserviceInfo wsinfo, String altitle,
405 ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
406 int[] delMap, AlignmentView alview, AlignFrame alframe,
409 this(wsinfo, altitle, server, wsurl, alview, alframe);
410 JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
411 if (job.hasValidInput())
413 jobs = new WSJob[] { job };
414 OutputHeader = wsInfo.getProgressText();
419 wsInfo.appendProgressText(job.getValidationMessages());
423 public void StartJob(AWsJob j)
425 if (!(j instanceof JPredJob))
427 throw new Error(MessageManager.formatMessage(
428 "error.implementation_error_startjob_called",
429 new String[] { j.getClass().toString() }));
433 JPredJob job = (JPredJob) j;
436 job.setJobId(server.predictOnMsa(job.msa));
438 else if (job.sequence != null)
440 job.setJobId(server.predict(job.sequence)); // debug like : job.jobId =
441 // "/jobs/www-jpred/jp_Yatat29";//
444 if (job.getJobId() != null)
446 if (job.getJobId().startsWith("Broken"))
448 job.result = new JpredResult();
449 job.result.setInvalid(true);
450 job.result.setStatus(MessageManager.formatMessage(
451 "label.submission_params", new String[] { job.getJobId()
453 throw new Exception(job.getJobId());
457 job.setSubmitted(true);
458 job.setSubjobComplete(false);
459 Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
466 .getString("exception.server_timeout_try_later"));
468 } catch (Exception e)
470 // kill the whole job.
471 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
472 if (e.getMessage().indexOf("Exception") > -1)
474 wsInfo.setStatus(j.getJobnum(),
475 WebserviceInfo.STATE_STOPPED_SERVERERROR);
476 wsInfo.setProgressText(
478 "Failed to submit the prediction. (Just close the window)\n"
479 + "It is most likely that there is a problem with the server.\n");
481 .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
482 + e.getMessage() + "\n");
484 jalview.bin.Cache.log.warn("Server Exception", e);
488 wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
489 // JBPNote - this could be a popup informing the user of the problem.
490 wsInfo.appendProgressText(j.getJobnum(), MessageManager
492 "info.failed_to_submit_prediction",
493 new String[] { e.getMessage(),
494 wsInfo.getProgressText() }));
496 jalview.bin.Cache.log.debug(
497 "Failed Submission of job " + j.getJobnum(), e);
500 j.setAllowedServerExceptions(-1);
501 j.setSubjobComplete(true);
505 public void parseResult()
507 int results = 0; // number of result sets received
508 JobStateSummary finalState = new JobStateSummary();
511 for (int j = 0; j < jobs.length; j++)
513 finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
514 if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete()
515 && jobs[j].hasResults())
520 } catch (Exception ex)
523 Cache.log.error("Unexpected exception when processing results for "
525 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
529 wsInfo.showResultsNewFrame
530 .addActionListener(new java.awt.event.ActionListener()
532 public void actionPerformed(java.awt.event.ActionEvent evt)
534 displayResults(true);
538 .addActionListener(new java.awt.event.ActionListener()
540 public void actionPerformed(java.awt.event.ActionEvent evt)
542 displayResults(false);
545 wsInfo.setResultsReady();
549 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
550 wsInfo.appendInfoText("No jobs ran.");
551 wsInfo.setFinishedNoResults();
555 void displayResults(boolean newWindow)
557 // TODO: cope with multiple subjobs.
562 for (int jn = 0; jn < jobs.length; jn++)
564 Object[] jobres = null;
565 JPredJob j = (JPredJob) jobs[jn];
569 // hack - we only deal with all single seuqence predictions or all
570 // profile predictions
571 msa = (j.msa != null) ? true : msa;
574 jalview.bin.Cache.log.debug("Parsing output of job " + jn);
575 jobres = j.getResultSet();
576 jalview.bin.Cache.log.debug("Finished parsing output.");
577 if (jobs.length == 1)
583 // do merge with other job results
586 .getString("error.multiple_jnet_subjob_merge_not_implemented"));
588 } catch (Exception e)
590 jalview.bin.Cache.log.error(
591 "JNet Client: JPred Annotation Parse Error", e);
592 wsInfo.setStatus(j.getJobnum(),
593 WebserviceInfo.STATE_STOPPED_ERROR);
594 wsInfo.appendProgressText(j.getJobnum(), MessageManager
595 .formatMessage("info.invalid_jnet_job_result_data",
596 new String[] { OutputHeader.toString(),
597 j.result.getStatus(), e.getMessage() }));
598 j.result.setBroken(true);
608 ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0])
614 af = new AlignFrame((Alignment) res[0],
615 (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
616 AlignFrame.DEFAULT_HEIGHT);
620 af = new AlignFrame((Alignment) res[0],
621 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
627 * java.lang.Object[] alandcolsel =
628 * input.getAlignmentAndColumnSelection
629 * (alignFrame.getViewport().getGapCharacter()); if
630 * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
631 * if (msa) { throw new Error("Implementation Error! ColumnSelection
632 * from input alignment will not map to result alignment!"); } } if
633 * (!msa) { // update hidden regions to account for loss of gaps in
634 * profile. - if any // gapMap returns insert list, interpreted as
635 * delete list by pruneDeletions //((ColumnSelection)
636 * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])
637 * alandcolsel[0])[0].gapMap())); }
640 af = new AlignFrame((Alignment) res[0],
641 (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
642 AlignFrame.DEFAULT_HEIGHT);
644 Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
645 AlignFrame.DEFAULT_HEIGHT);
649 Cache.log.info("Append results onto existing alignment.");
655 public void pollJob(AWsJob job) throws Exception
657 ((JPredJob) job).result = server.getresult(job.getJobId());
660 public boolean isCancellable()
665 public void cancelJob()
667 throw new Error(MessageManager.getString("error.implementation_error"));
670 public boolean canMergeResults()