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(
126 result.getPredfile(), 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().identify(
136 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(
163 .getString("exception.couldnt_recover_sequence_properties_for_alignment")));
167 if (currentView.getDataset() != null)
169 al.setDataset(currentView.getDataset());
176 JnetAnnotationMaker.add_annotation(prediction, al,
177 FirstSeq, false, predMap);
182 throw (new Exception(MessageManager.formatMessage(
183 "exception.unknown_format_for_file", new String[] { "",
184 result.getAligfile() })));
189 al = new Alignment(preds);
190 FirstSeq = prediction.getQuerySeqPosition();
193 char gc = getGapChar();
194 SequenceI[] sqs = (SequenceI[]) input
195 .getAlignmentAndHiddenColumns(gc)[0];
196 if (this.msaIndex >= sqs.length)
200 .getString("error.implementation_error_invalid_msa_index_for_job"));
204 // Uses RemoveGapsCommand
206 new jalview.commands.RemoveGapsCommand(
207 MessageManager.getString("label.remove_gaps"),
208 new SequenceI[] { sqs[msaIndex] }, currentView);
210 SequenceI profileseq = al.getSequenceAt(FirstSeq);
211 profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
214 if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
215 al.getSequenceAt(FirstSeq), SequenceInfo))
217 throw (new Exception(
219 .getString("exception.couldnt_recover_sequence_props_for_jnet_query")));
223 if (currentView.getDataset() != null)
225 al.setDataset(currentView.getDataset());
232 jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
233 FirstSeq, true, predMap);
234 SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
235 alignToProfileSeq(al, profileseq);
238 // Adjust input view for gaps
239 // propagate insertions into profile
240 alhidden = HiddenColumns.propagateInsertions(profileseq, al,
245 // transfer to dataset
246 for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
248 if (alant.sequenceRef != null)
250 replaceAnnotationOnAlignmentWith(alant, alant.label,
251 "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
255 return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
259 * copied from JabawsCalcWorker
266 protected void replaceAnnotationOnAlignmentWith(
267 AlignmentAnnotation newAnnot, String typeName, String calcId,
270 SequenceI dsseq = aSeq.getDatasetSequence();
271 while (dsseq.getDatasetSequence() != null)
273 dsseq = dsseq.getDatasetSequence();
275 // look for same annotation on dataset and lift this one over
276 List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(
278 if (dsan != null && dsan.size() > 0)
280 for (AlignmentAnnotation dssan : dsan)
282 dsseq.removeAlignmentAnnotation(dssan);
285 AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
286 dsseq.addAlignmentAnnotation(dssan);
287 dssan.adjustForAlignment();
291 * Given an alignment where all other sequences except profileseq are
292 * aligned to the ungapped profileseq, insert gaps in the other sequences to
293 * realign them with the residues in profileseq
298 private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
300 char gc = al.getGapCharacter();
301 int[] gapMap = profileseq.gapMap();
302 // insert gaps into profile
303 for (int lp = 0, r = 0; r < gapMap.length; r++)
305 if (gapMap[r] - lp > 1)
307 StringBuffer sb = new StringBuffer();
308 for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
312 for (int s = 1, ns = al.getHeight(); s < ns; s++)
314 String sq = al.getSequenceAt(s).getSequenceAsString();
315 int diff = gapMap[r] - sq.length();
320 while ((diff = gapMap[r] - sq.length()) > 0)
323 + ((diff >= sb.length()) ? sb.toString() : sb
324 .substring(0, diff));
326 al.getSequenceAt(s).setSequence(sq);
330 al.getSequenceAt(s).setSequence(
331 sq.substring(0, gapMap[r]) + sb.toString()
332 + sq.substring(gapMap[r]));
340 public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
343 this.predMap = delMap;
344 String sq = AlignSeq.extractGaps(Comparison.GapChars,
345 seq.getSequenceAsString());
346 if (sq.length() >= 20)
348 this.SequenceInfo = SequenceInfo;
349 sequence = new vamsas.objects.simple.Sequence();
350 sequence.setId(seq.getName());
355 errorMessage = "Sequence is too short to predict with JPred - need at least 20 amino acids.";
359 public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
361 this(SequenceInfo, msf[0], delMap);
362 if (sequence != null)
366 msa = new vamsas.objects.simple.Msfalignment();
367 PileUpfile pileup = new PileUpfile();
368 msa.setMsf(pileup.print(msf, true));
373 String errorMessage = "";
375 public String getValidationMessages()
377 return errorMessage + "\n";
381 ext.vamsas.Jpred server;
385 JPredThread(WebserviceInfo wsinfo, String altitle,
386 ext.vamsas.Jpred server, String wsurl, AlignmentView alview,
389 super(alframe, wsinfo, alview, wsurl);
390 this.altitle = altitle;
391 this.server = server;
394 JPredThread(WebserviceInfo wsinfo, String altitle,
395 ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
396 SequenceI seq, int[] delMap, AlignmentView alview,
399 this(wsinfo, altitle, server, wsurl, alview, alframe);
400 JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
401 if (job.hasValidInput())
403 OutputHeader = wsInfo.getProgressText();
404 jobs = new WSJob[] { job };
409 wsInfo.appendProgressText(job.getValidationMessages());
413 JPredThread(WebserviceInfo wsinfo, String altitle,
414 ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
415 int[] delMap, AlignmentView alview, AlignFrame alframe,
418 this(wsinfo, altitle, server, wsurl, alview, alframe);
419 JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
420 if (job.hasValidInput())
422 jobs = new WSJob[] { job };
423 OutputHeader = wsInfo.getProgressText();
428 wsInfo.appendProgressText(job.getValidationMessages());
433 public void StartJob(AWsJob j)
435 if (!(j instanceof JPredJob))
437 throw new Error(MessageManager.formatMessage(
438 "error.implementation_error_startjob_called",
439 new String[] { j.getClass().toString() }));
443 JPredJob job = (JPredJob) j;
446 job.setJobId(server.predictOnMsa(job.msa));
448 else if (job.sequence != null)
450 job.setJobId(server.predict(job.sequence)); // debug like : job.jobId =
451 // "/jobs/www-jpred/jp_Yatat29";//
454 if (job.getJobId() != null)
456 if (job.getJobId().startsWith("Broken"))
458 job.result = new JpredResult();
459 job.result.setInvalid(true);
460 job.result.setStatus(MessageManager.formatMessage(
461 "label.submission_params", new String[] { job.getJobId()
463 throw new Exception(job.getJobId());
467 job.setSubmitted(true);
468 job.setSubjobComplete(false);
469 Cache.log.info(WsUrl + " Job Id '" + job.getJobId() + "'");
476 .getString("exception.server_timeout_try_later"));
478 } catch (Exception e)
480 // kill the whole job.
481 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
482 if (e.getMessage().indexOf("Exception") > -1)
484 wsInfo.setStatus(j.getJobnum(),
485 WebserviceInfo.STATE_STOPPED_SERVERERROR);
486 wsInfo.setProgressText(
488 "Failed to submit the prediction. (Just close the window)\n"
489 + "It is most likely that there is a problem with the server.\n");
491 .println("JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
492 + e.getMessage() + "\n");
494 jalview.bin.Cache.log.warn("Server Exception", e);
498 wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
499 // JBPNote - this could be a popup informing the user of the problem.
500 wsInfo.appendProgressText(j.getJobnum(), MessageManager
502 "info.failed_to_submit_prediction",
503 new String[] { e.getMessage(),
504 wsInfo.getProgressText() }));
506 jalview.bin.Cache.log.debug(
507 "Failed Submission of job " + j.getJobnum(), e);
510 j.setAllowedServerExceptions(-1);
511 j.setSubjobComplete(true);
516 public void parseResult()
518 int results = 0; // number of result sets received
519 JobStateSummary finalState = new JobStateSummary();
522 for (int j = 0; j < jobs.length; j++)
524 finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
525 if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete()
526 && jobs[j].hasResults())
531 } catch (Exception ex)
534 Cache.log.error("Unexpected exception when processing results for "
536 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
540 wsInfo.showResultsNewFrame
541 .addActionListener(new java.awt.event.ActionListener()
544 public void actionPerformed(java.awt.event.ActionEvent evt)
546 displayResults(true);
550 .addActionListener(new java.awt.event.ActionListener()
553 public void actionPerformed(java.awt.event.ActionEvent evt)
555 displayResults(false);
558 wsInfo.setResultsReady();
562 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
563 wsInfo.appendInfoText("No jobs ran.");
564 wsInfo.setFinishedNoResults();
568 void displayResults(boolean newWindow)
570 // TODO: cope with multiple subjobs.
575 for (int jn = 0; jn < jobs.length; jn++)
577 Object[] jobres = null;
578 JPredJob j = (JPredJob) jobs[jn];
582 // hack - we only deal with all single seuqence predictions or all
583 // profile predictions
584 msa = (j.msa != null) ? true : msa;
587 jalview.bin.Cache.log.debug("Parsing output of job " + jn);
588 jobres = j.getResultSet();
589 jalview.bin.Cache.log.debug("Finished parsing output.");
590 if (jobs.length == 1)
596 // do merge with other job results
599 .getString("error.multiple_jnet_subjob_merge_not_implemented"));
601 } catch (Exception e)
603 jalview.bin.Cache.log.error(
604 "JNet Client: JPred Annotation Parse Error", e);
605 wsInfo.setStatus(j.getJobnum(),
606 WebserviceInfo.STATE_STOPPED_ERROR);
607 wsInfo.appendProgressText(j.getJobnum(), MessageManager
608 .formatMessage("info.invalid_jnet_job_result_data",
609 new String[] { OutputHeader.toString(),
610 j.result.getStatus(), e.getMessage() }));
611 j.result.setBroken(true);
621 ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0])
627 af = new AlignFrame((Alignment) res[0],
628 (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH,
629 AlignFrame.DEFAULT_HEIGHT);
633 af = new AlignFrame((Alignment) res[0],
634 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
640 * java.lang.Object[] alandcolsel =
641 * input.getAlignmentAndColumnSelection
642 * (alignFrame.getViewport().getGapCharacter()); if
643 * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
644 * if (msa) { throw new Error("Implementation Error! ColumnSelection
645 * from input alignment will not map to result alignment!"); } } if
646 * (!msa) { // update hidden regions to account for loss of gaps in
647 * profile. - if any // gapMap returns insert list, interpreted as
648 * delete list by pruneDeletions //((ColumnSelection)
649 * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])
650 * alandcolsel[0])[0].gapMap())); }
653 af = new AlignFrame((Alignment) res[0],
654 (HiddenColumns) res[1],
655 AlignFrame.DEFAULT_WIDTH,
656 AlignFrame.DEFAULT_HEIGHT);
658 Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
659 AlignFrame.DEFAULT_HEIGHT);
663 Cache.log.info("Append results onto existing alignment.");
670 public void pollJob(AWsJob job) throws Exception
672 ((JPredJob) job).result = server.getresult(job.getJobId());
676 public boolean isCancellable()
682 public void cancelJob()
684 throw new Error(MessageManager.getString("error.implementation_error"));
688 public boolean canMergeResults()