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.jws2;
23 import jalview.analysis.AlignSeq;
24 import jalview.analysis.AlignmentAnnotationUtils;
25 import jalview.analysis.SeqsetUtils;
26 import jalview.api.AlignViewportI;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.api.FeatureColourI;
29 import jalview.bin.Cache;
30 import jalview.datamodel.AlignmentAnnotation;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.AnnotatedCollectionI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.ContiguousI;
35 import jalview.datamodel.Mapping;
36 import jalview.datamodel.SequenceI;
37 import jalview.datamodel.features.FeatureMatcherSetI;
38 import jalview.gui.AlignFrame;
39 import jalview.gui.Desktop;
40 import jalview.gui.IProgressIndicator;
41 import jalview.gui.IProgressIndicatorHandler;
42 import jalview.gui.JvOptionPane;
43 import jalview.gui.WebserviceInfo;
44 import jalview.schemes.FeatureSettingsAdapter;
45 import jalview.schemes.ResidueProperties;
46 import jalview.util.MapList;
47 import jalview.util.MessageManager;
48 import jalview.workers.AlignCalcWorker;
49 import jalview.ws.JobStateSummary;
50 import jalview.ws.api.CancellableI;
51 import jalview.ws.api.JalviewServiceEndpointProviderI;
52 import jalview.ws.api.JobId;
53 import jalview.ws.api.SequenceAnnotationServiceI;
54 import jalview.ws.api.ServiceWithParameters;
55 import jalview.ws.api.WSAnnotationCalcManagerI;
56 import jalview.ws.gui.AnnotationWsJob;
57 import jalview.ws.jws2.dm.AAConSettings;
58 import jalview.ws.params.ArgumentI;
59 import jalview.ws.params.WsParamSetI;
61 import java.util.ArrayList;
62 import java.util.HashMap;
63 import java.util.List;
66 public class SeqAnnotationServiceCalcWorker extends AlignCalcWorker
67 implements WSAnnotationCalcManagerI
70 protected ServiceWithParameters service;
72 protected WsParamSetI preset;
74 protected List<ArgumentI> arguments;
76 protected IProgressIndicator guiProgress;
78 protected boolean submitGaps = true;
81 * by default, we filter out non-standard residues before submission
83 protected boolean filterNonStandardResidues = true;
86 * Recover any existing parameters for this service
88 protected void initViewportParams()
90 if (getCalcId() != null)
92 ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
94 new AAConSettings(true, service, this.preset, arguments),
101 * @return null or a string used to recover all annotation generated by this
104 public String getCalcId()
106 return service.getAlignAnalysisUI() == null ? null
107 : service.getAlignAnalysisUI().getCalcId();
110 public WsParamSetI getPreset()
115 public List<ArgumentI> getArguments()
121 * reconfigure and restart the AAConClient. This method will spawn a new
122 * thread that will wait until any current jobs are finished, modify the
123 * parameters and restart the conservation calculation with the new values.
126 * @param newarguments
128 public void updateParameters(final WsParamSetI newpreset,
129 final List<ArgumentI> newarguments)
132 arguments = newarguments;
133 calcMan.startWorker(this);
134 initViewportParams();
136 protected boolean alignedSeqs = true;
138 protected boolean nucleotidesAllowed = false;
140 protected boolean proteinAllowed = false;
143 * record sequences for mapping result back to afterwards
145 protected boolean bySequence = false;
147 protected Map<String, SequenceI> seqNames;
149 // TODO: convert to bitset
150 protected boolean[] gapMap;
158 private AlignFrame alignFrame;
160 public boolean[] getGapMap()
165 public SeqAnnotationServiceCalcWorker(AlignViewportI alignViewport,
166 AlignmentViewPanel alignPanel)
168 super(alignViewport, alignPanel);
171 public SeqAnnotationServiceCalcWorker(ServiceWithParameters service,
172 AlignFrame alignFrame,
173 WsParamSetI preset, List<ArgumentI> paramset)
175 this(alignFrame.getCurrentView(), alignFrame.alignPanel);
176 // TODO: both these fields needed ?
177 this.alignFrame = alignFrame;
178 this.guiProgress = alignFrame;
179 this.preset = preset;
180 this.arguments = paramset;
181 this.service = service;
184 annotService = (jalview.ws.api.SequenceAnnotationServiceI) ((JalviewServiceEndpointProviderI) service)
186 } catch (ClassCastException cce)
188 JvOptionPane.showMessageDialog(Desktop.desktop,
189 MessageManager.formatMessage(
190 "label.service_called_is_not_an_annotation_service",
192 { service.getName() }),
193 MessageManager.getString("label.internal_jalview_error"),
194 JvOptionPane.WARNING_MESSAGE);
197 // configure submission flags
198 proteinAllowed = service.isProteinService();
199 nucleotidesAllowed = service.isNucleotideService();
200 alignedSeqs = service.isNeedsAlignedSequences();
201 bySequence = !service.isAlignmentAnalysis();
202 filterNonStandardResidues = service.isFilterSymbols();
203 min_valid_seqs = service.getMinimumInputSequences();
204 submitGaps = service.isAlignmentAnalysis();
206 if (service.isInteractiveUpdate())
208 initViewportParams();
214 * @return true if the submission thread should attempt to submit data
216 public boolean hasService()
218 return annotService != null;
221 protected jalview.ws.api.SequenceAnnotationServiceI annotService = null;
223 volatile JobId rslt = null;
225 AnnotationWsJob running = null;
227 private int min_valid_seqs;
237 long progressId = -1;
239 int serverErrorsLeft = 3;
240 final boolean cancellable = CancellableI.class
241 .isAssignableFrom(annotService.getClass());
242 StringBuffer msg = new StringBuffer();
243 JobStateSummary job = new JobStateSummary();
244 WebserviceInfo info = new WebserviceInfo("foo", "bar", false);
251 List<SequenceI> seqs = getInputSequences(
252 alignViewport.getAlignment(),
253 bySequence ? alignViewport.getSelectionGroup() : null);
255 if (seqs == null || !checkValidInputSeqs(seqs))
257 jalview.bin.Cache.log.debug(
258 "Sequences for analysis service were null or not valid");
259 calcMan.workerComplete(this);
263 if (guiProgress != null)
265 guiProgress.setProgressBar(service.getActionText(),
266 progressId = System.currentTimeMillis());
268 jalview.bin.Cache.log.debug("submitted " + seqs.size()
269 + " sequences to " + service.getActionText());
271 rslt = annotService.submitToService(seqs, getPreset(),
277 // TODO: handle job submission error reporting here.
280 // otherwise, construct WsJob and any UI handlers
281 running = new AnnotationWsJob();
282 running.setJobHandle(rslt);
283 running.setSeqNames(seqNames);
284 running.setStartPos(start);
285 running.setSeqs(seqs);
286 job.updateJobPanelState(info, "", running);
287 if (guiProgress != null)
289 guiProgress.registerHandler(progressId,
290 new IProgressIndicatorHandler()
294 public boolean cancelActivity(long id)
296 ((CancellableI) annotService).cancel(running);
301 public boolean canCancel()
309 // and poll for updates until job finishes, fails or becomes stale
311 boolean finished = false;
314 Cache.log.debug("Updating status for annotation service.");
315 annotService.updateStatus(running);
316 job.updateJobPanelState(info, "", running);
317 if (running.isSubjobComplete())
320 "Finished polling analysis service job: status reported is "
321 + running.getState());
326 Cache.log.debug("Status now " + running.getState());
329 if (calcMan.isPending(this) && isInteractiveUpdate())
331 Cache.log.debug("Analysis service job is stale. aborting.");
332 // job has become stale.
335 // cancel this job and yield to the new job
339 && ((CancellableI) annotService).cancel(running))
341 System.err.println("Cancelled job: " + rslt);
345 System.err.println("FAILED TO CANCEL job: " + rslt);
348 } catch (Exception x)
353 rslt = running.getJobHandle();
357 // pull any stats - some services need to flush log output before
358 // results are available
359 Cache.log.debug("Updating progress log for annotation service.");
363 annotService.updateJobProgress(running);
364 } catch (Throwable thr)
366 Cache.log.debug("Ignoring exception during progress update.",
369 Cache.log.trace("Result of poll: " + running.getStatus());
371 if (!finished && !running.isFailed())
375 Cache.log.debug("Analysis service job thread sleeping.");
377 Cache.log.debug("Analysis service job thread woke.");
378 } catch (InterruptedException x)
385 Cache.log.debug("Job poll loop exited. Job is " + running.getState());
386 // TODO: need to poll/retry
387 if (serverErrorsLeft > 0)
392 } catch (InterruptedException x)
396 if (running.isFinished())
398 // expect there to be results to collect
399 // configure job with the associated view's feature renderer, if one
401 // TODO: here one would also grab the 'master feature renderer' in order
403 // features automatically according to user preferences
404 running.setFeatureRenderer(
405 ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
406 Cache.log.debug("retrieving job results.");
407 final Map<String, FeatureColourI> featureColours = new HashMap<>();
408 final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
409 List<AlignmentAnnotation> returnedAnnot = annotService
410 .getAnnotationResult(running.getJobHandle(), seqs,
411 featureColours, featureFilters);
413 Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
414 : ("" + returnedAnnot.size())));
415 Cache.log.debug("There were " + featureColours.size()
416 + " feature colours and " + featureFilters.size()
417 + " filters defined.");
420 // copy over each annotation row reurned and also defined on each
421 // sequence, excluding regions not annotated due to gapMap/column
424 running.setAnnotation(returnedAnnot);
426 if (running.hasResults())
428 jalview.bin.Cache.log.debug("Updating result annotation from Job "
429 + rslt + " at " + service.getUri());
430 updateResultAnnotation(true);
431 if (running.isTransferSequenceFeatures())
434 // look at each sequence and lift over any features, excluding
436 // not annotated due to gapMap/column visibility
438 jalview.bin.Cache.log.debug(
439 "Updating feature display settings and transferring features from Job "
440 + rslt + " at " + service.getUri());
441 // TODO: consider merge rather than apply here
442 alignViewport.applyFeaturesStyle(new FeatureSettingsAdapter()
445 public FeatureColourI getFeatureColour(String type)
447 return featureColours.get(type);
451 public FeatureMatcherSetI getFeatureFilters(String type)
453 return featureFilters.get(type);
457 public boolean isFeatureDisplayed(String type)
459 return featureColours.containsKey(type);
463 // TODO: JAL-1150 - create sequence feature settings API for
465 // styles and enabling/disabling feature overlay on alignment panel
467 if (alignFrame.alignPanel == ap)
469 alignViewport.setShowSequenceFeatures(true);
470 alignFrame.setMenusForViewport();
473 ap.adjustAnnotationHeight();
476 Cache.log.debug("Annotation Service Worker thread finished.");
478 // TODO: use service specitic exception handlers
479 // catch (JobSubmissionException x)
482 // System.err.println(
483 // "submission error with " + getServiceActionText() + " :");
484 // x.printStackTrace();
485 // calcMan.disableWorker(this);
486 // } catch (ResultNotAvailableException x)
488 // System.err.println("collection error:\nJob ID: " + rslt);
489 // x.printStackTrace();
490 // calcMan.disableWorker(this);
492 // } catch (OutOfMemoryError error)
494 // calcMan.disableWorker(this);
496 // ap.raiseOOMWarning(getServiceActionText(), error);
500 calcMan.disableWorker(this);
503 .println("Blacklisting worker due to unexpected exception:");
508 calcMan.workerComplete(this);
511 calcMan.workerComplete(this);
512 if (guiProgress != null && progressId != -1)
514 guiProgress.setProgressBar("", progressId);
516 // TODO: may not need to paintAlignment again !
517 ap.paintAlignment(false, false);
519 if (msg.length() > 0)
521 // TODO: stash message somewhere in annotation or alignment view.
522 // code below shows result in a text box popup
524 * jalview.gui.CutAndPasteTransfer cap = new
525 * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
526 * jalview.gui.Desktop.addInternalFrame(cap,
527 * "Job Status for "+getServiceActionText(), 600, 400);
535 * validate input for dynamic/non-dynamic update context TODO: move to
536 * analysis interface ?
539 * @return true if input is valid
541 boolean checkValidInputSeqs(List<SequenceI> seqs)
544 for (SequenceI sq : seqs)
546 if (sq.getStart() <= sq.getEnd()
547 && (sq.isProtein() ? proteinAllowed : nucleotidesAllowed))
550 || sq.getLength() == (sq.getEnd() - sq.getStart() + 1))
556 return nvalid >= min_valid_seqs;
559 public void cancelCurrentJob()
563 String id = running.getJobId();
564 if (((CancellableI) annotService).cancel(running))
566 System.err.println("Cancelled job " + id);
570 System.err.println("Job " + id + " couldn't be cancelled.");
572 } catch (Exception q)
579 * Interactive updating. Analysis calculations that work on the currently
580 * displayed alignment data should cancel existing jobs when the input data
583 * @return true if a running job should be cancelled because new input data is
584 * available for analysis
586 boolean isInteractiveUpdate()
588 return service.isInteractiveUpdate();
592 * decide what sequences will be analysed TODO: refactor to generate
593 * List<SequenceI> for submission to service interface
599 public List<SequenceI> getInputSequences(AlignmentI alignment,
600 AnnotatedCollectionI inputSeqs)
602 if (alignment == null || alignment.getWidth() <= 0
603 || alignment.getSequences() == null || alignment.isNucleotide()
604 ? !nucleotidesAllowed
609 if (inputSeqs == null || inputSeqs.getWidth() <= 0
610 || inputSeqs.getSequences() == null
611 || inputSeqs.getSequences().size() < 1)
613 inputSeqs = alignment;
616 List<SequenceI> seqs = new ArrayList<>();
622 seqNames = new HashMap<>();
624 gapMap = new boolean[0];
625 start = inputSeqs.getStartRes();
626 end = inputSeqs.getEndRes();
627 // TODO: URGENT! unify with JPred / MSA code to handle hidden regions
629 // TODO: push attributes into WsJob instance (so they can be safely
630 // persisted/restored
631 for (SequenceI sq : (inputSeqs.getSequences()))
634 ? sq.findPosition(end + 1)
635 - sq.findPosition(start + 1) > minlen - 1
636 : sq.getEnd() - sq.getStart() > minlen - 1)
638 String newname = SeqsetUtils.unique_name(seqs.size() + 1);
639 // make new input sequence with or without gaps
640 if (seqNames != null)
642 seqNames.put(newname, sq);
647 seqs.add(seq = new jalview.datamodel.Sequence(newname,
648 sq.getSequenceAsString()));
649 if (gapMap == null || gapMap.length < seq.getLength())
651 boolean[] tg = gapMap;
652 gapMap = new boolean[seq.getLength()];
653 System.arraycopy(tg, 0, gapMap, 0, tg.length);
654 for (int p = tg.length; p < gapMap.length; p++)
656 gapMap[p] = false; // init as a gap
659 for (int apos : sq.gapMap())
661 char sqc = sq.getCharAt(apos);
662 if (!filterNonStandardResidues
663 || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
664 : ResidueProperties.nucleotideIndex[sqc] < 5))
666 gapMap[apos] = true; // aligned and real amino acid residue
673 // TODO: add ability to exclude hidden regions
674 seqs.add(seq = new jalview.datamodel.Sequence(newname,
675 AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
676 sq.getSequenceAsString(start, end + 1))));
677 // for annotation need to also record map to sequence start/end
679 // then transfer back to original sequence on return.
681 if (seq.getLength() > ln)
683 ln = seq.getLength();
687 if (alignedSeqs && submitGaps)
690 for (int i = 0; i < gapMap.length; i++)
697 // try real hard to return something submittable
698 // TODO: some of AAcon measures need a minimum of two or three amino
699 // acids at each position, and AAcon doesn't gracefully degrade.
700 for (int p = 0; p < seqs.size(); p++)
702 SequenceI sq = seqs.get(p);
703 // strip gapped columns
704 char[] padded = new char[realw],
705 orig = sq.getSequence();
706 for (int i = 0, pp = 0; i < realw; pp++)
710 if (orig.length > pp)
712 padded[i++] = orig[pp];
720 seqs.set(p, new jalview.datamodel.Sequence(sq.getName(),
721 new String(padded)));
728 public void updateAnnotation()
730 updateResultAnnotation(false);
733 public void updateResultAnnotation(boolean immediate)
735 if ((immediate || !calcMan.isWorking(this)) && running != null
736 && running.hasResults())
738 List<AlignmentAnnotation> ourAnnot = running.getAnnotation(),
739 newAnnots = new ArrayList<>();
741 // update graphGroup for all annotation
744 * find a graphGroup greater than any existing ones this could be a method
745 * provided by alignment Alignment.getNewGraphGroup() - returns next
749 if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
751 for (AlignmentAnnotation ala : alignViewport.getAlignment()
752 .getAlignmentAnnotation())
754 if (ala.graphGroup > graphGroup)
756 graphGroup = ala.graphGroup;
761 * update graphGroup in the annotation rows returned from service
763 // TODO: look at sequence annotation rows and update graph groups in the
764 // case of reference annotation.
765 for (AlignmentAnnotation ala : ourAnnot)
767 if (ala.graphGroup > 0)
769 ala.graphGroup += graphGroup;
771 SequenceI aseq = null;
774 * transfer sequence refs and adjust gapmap
776 if (ala.sequenceRef != null)
778 SequenceI seq = running.getSeqNames()
779 .get(ala.sequenceRef.getName());
781 while (seq.getDatasetSequence() != null)
783 seq = seq.getDatasetSequence();
786 Annotation[] resAnnot = ala.annotations,
787 gappedAnnot = new Annotation[Math.max(
788 alignViewport.getAlignment().getWidth(),
790 for (int p = 0, ap = start; ap < gappedAnnot.length; ap++)
792 if (gapMap != null && gapMap.length > ap && !gapMap[ap])
794 gappedAnnot[ap] = new Annotation("", "", ' ', Float.NaN);
796 else if (p < resAnnot.length)
798 gappedAnnot[ap] = resAnnot[p++];
801 ala.sequenceRef = aseq;
802 ala.annotations = gappedAnnot;
803 AlignmentAnnotation newAnnot = getAlignViewport().getAlignment()
804 .updateFromOrCopyAnnotation(ala);
808 aseq.addAlignmentAnnotation(newAnnot);
809 newAnnot.adjustForAlignment();
811 AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
812 newAnnot, newAnnot.label, newAnnot.getCalcId());
814 newAnnots.add(newAnnot);
817 for (SequenceI sq : running.getSeqs())
819 if (!sq.getFeatures().hasFeatures()
820 && (sq.getDBRefs() == null || sq.getDBRefs().length == 0))
824 running.setTransferSequenceFeatures(true);
825 SequenceI seq = running.getSeqNames().get(sq.getName());
827 ContiguousI seqRange = seq.findPositions(start, end);
829 while ((dseq = seq).getDatasetSequence() != null)
831 seq = seq.getDatasetSequence();
833 List<ContiguousI> sourceRange = new ArrayList();
834 if (gapMap != null && gapMap.length >= end)
836 int lastcol = start, col = start;
839 if (col == end || !gapMap[col])
841 if (lastcol <= (col - 1))
843 seqRange = seq.findPositions(lastcol, col);
844 sourceRange.add(seqRange);
848 } while (++col <= end);
852 sourceRange.add(seq.findPositions(start, end));
855 int source_startend[] = new int[sourceRange.size() * 2];
857 for (ContiguousI range : sourceRange)
859 source_startend[i++] = range.getBegin();
860 source_startend[i++] = range.getEnd();
862 Mapping mp = new Mapping(
863 new MapList(source_startend, new int[]
864 { seq.getStart(), seq.getEnd() }, 1, 1));
865 dseq.transferAnnotation(sq, mp);
868 updateOurAnnots(newAnnots);
873 * notify manager that we have started, and wait for a free calculation slot
875 * @return true if slot is obtained and work still valid, false if another
876 * thread has done our work for us.
878 protected boolean checkDone()
880 calcMan.notifyStart(this);
881 ap.paintAlignment(false, false);
882 while (!calcMan.notifyWorking(this))
884 if (calcMan.isWorking(this))
892 ap.paintAlignment(false, false);
896 } catch (Exception ex)
898 ex.printStackTrace();
901 if (alignViewport.isClosed())
909 protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
911 List<AlignmentAnnotation> our = ourAnnots;
912 ourAnnots = ourAnnot;
913 AlignmentI alignment = alignViewport.getAlignment();
918 for (AlignmentAnnotation an : our)
920 if (!ourAnnots.contains(an))
922 // remove the old annotation
923 alignment.deleteAnnotation(an);
930 // validate rows and update Alignmment state
931 for (AlignmentAnnotation an : ourAnnots)
933 alignViewport.getAlignment().validateAnnotation(an);
935 // TODO: may need a menu refresh after this
936 // af.setMenusForViewport();
937 ap.adjustAnnotationHeight();
941 public SequenceAnnotationServiceI getService()