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;
238 calcMan.workerComplete(this);
242 long progressId = -1;
244 int serverErrorsLeft = 3;
245 final boolean cancellable = CancellableI.class
246 .isAssignableFrom(annotService.getClass());
247 StringBuffer msg = new StringBuffer();
248 JobStateSummary job = new JobStateSummary();
249 WebserviceInfo info = new WebserviceInfo("foo", "bar", false);
252 List<SequenceI> seqs = getInputSequences(
253 alignViewport.getAlignment(),
254 bySequence ? alignViewport.getSelectionGroup() : null);
256 if (seqs == null || !checkValidInputSeqs(seqs))
258 jalview.bin.Cache.log.debug(
259 "Sequences for analysis service were null or not valid");
260 calcMan.workerComplete(this);
264 if (guiProgress != null)
266 guiProgress.setProgressBar(service.getActionText(),
267 progressId = System.currentTimeMillis());
269 jalview.bin.Cache.log.debug("submitted " + seqs.size()
270 + " sequences to " + service.getActionText());
272 rslt = annotService.submitToService(seqs, getPreset(),
278 // TODO: handle job submission error reporting here.
279 Cache.log.debug("Service " + service.getUri() + "\nSubmitted job ID: "
283 // otherwise, construct WsJob and any UI handlers
284 running = new AnnotationWsJob();
285 running.setJobHandle(rslt);
286 running.setSeqNames(seqNames);
287 running.setStartPos(start);
288 running.setSeqs(seqs);
289 job.updateJobPanelState(info, "", running);
290 if (guiProgress != null)
292 guiProgress.registerHandler(progressId,
293 new IProgressIndicatorHandler()
297 public boolean cancelActivity(long id)
299 ((CancellableI) annotService).cancel(running);
304 public boolean canCancel()
312 // and poll for updates until job finishes, fails or becomes stale
314 boolean finished = false;
317 Cache.log.debug("Updating status for annotation service.");
318 annotService.updateStatus(running);
319 job.updateJobPanelState(info, "", running);
320 if (running.isSubjobComplete())
323 "Finished polling analysis service job: status reported is "
324 + running.getState());
329 Cache.log.debug("Status now " + running.getState());
332 if (calcMan.isPending(this) && isInteractiveUpdate())
334 Cache.log.debug("Analysis service job is stale. aborting.");
335 // job has become stale.
338 // cancel this job and yield to the new job
342 && ((CancellableI) annotService).cancel(running))
344 System.err.println("Cancelled job: " + rslt);
348 System.err.println("FAILED TO CANCEL job: " + rslt);
351 } catch (Exception x)
356 rslt = running.getJobHandle();
360 // pull any stats - some services need to flush log output before
361 // results are available
362 Cache.log.debug("Updating progress log for annotation service.");
366 annotService.updateJobProgress(running);
367 } catch (Throwable thr)
369 Cache.log.debug("Ignoring exception during progress update.",
372 Cache.log.trace("Result of poll: " + running.getStatus());
374 if (!finished && !running.isFailed())
378 Cache.log.debug("Analysis service job thread sleeping.");
380 Cache.log.debug("Analysis service job thread woke.");
381 } catch (InterruptedException x)
388 Cache.log.debug("Job poll loop exited. Job is " + running.getState());
389 // TODO: need to poll/retry
390 if (serverErrorsLeft > 0)
395 } catch (InterruptedException x)
399 if (running.isFinished())
401 // expect there to be results to collect
402 // configure job with the associated view's feature renderer, if one
404 // TODO: here one would also grab the 'master feature renderer' in order
406 // features automatically according to user preferences
407 running.setFeatureRenderer(
408 ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer());
409 Cache.log.debug("retrieving job results.");
410 final Map<String, FeatureColourI> featureColours = new HashMap<>();
411 final Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
412 List<AlignmentAnnotation> returnedAnnot = annotService
413 .getAnnotationResult(running.getJobHandle(), seqs,
414 featureColours, featureFilters);
416 Cache.log.debug("Obtained " + (returnedAnnot == null ? "no rows"
417 : ("" + returnedAnnot.size())));
418 Cache.log.debug("There were " + featureColours.size()
419 + " feature colours and " + featureFilters.size()
420 + " filters defined.");
423 // copy over each annotation row reurned and also defined on each
424 // sequence, excluding regions not annotated due to gapMap/column
427 // update calcId if it is not already set on returned annotation
428 if (returnedAnnot != null)
430 for (AlignmentAnnotation aa : returnedAnnot)
432 // assume that any CalcIds already set
433 if (getCalcId() != null && aa.getCalcId() == null
434 || "".equals(aa.getCalcId()))
436 aa.setCalcId(getCalcId());
438 // autocalculated annotation are created by interactive alignment
440 aa.autoCalculated = service.isAlignmentAnalysis()
441 && service.isInteractiveUpdate();
445 running.setAnnotation(returnedAnnot);
447 if (running.hasResults())
449 jalview.bin.Cache.log.debug("Updating result annotation from Job "
450 + rslt + " at " + service.getUri());
451 updateResultAnnotation(true);
452 if (running.isTransferSequenceFeatures())
455 // look at each sequence and lift over any features, excluding
457 // not annotated due to gapMap/column visibility
459 jalview.bin.Cache.log.debug(
460 "Updating feature display settings and transferring features from Job "
461 + rslt + " at " + service.getUri());
462 // TODO: consider merge rather than apply here
463 alignViewport.applyFeaturesStyle(new FeatureSettingsAdapter()
466 public FeatureColourI getFeatureColour(String type)
468 return featureColours.get(type);
472 public FeatureMatcherSetI getFeatureFilters(String type)
474 return featureFilters.get(type);
478 public boolean isFeatureDisplayed(String type)
480 return featureColours.containsKey(type);
484 // TODO: JAL-1150 - create sequence feature settings API for
486 // styles and enabling/disabling feature overlay on alignment panel
488 if (alignFrame.alignPanel == ap)
490 alignViewport.setShowSequenceFeatures(true);
491 alignFrame.setMenusForViewport();
494 ap.adjustAnnotationHeight();
497 Cache.log.debug("Annotation Service Worker thread finished.");
499 // TODO: use service specitic exception handlers
500 // catch (JobSubmissionException x)
503 // System.err.println(
504 // "submission error with " + getServiceActionText() + " :");
505 // x.printStackTrace();
506 // calcMan.disableWorker(this);
507 // } catch (ResultNotAvailableException x)
509 // System.err.println("collection error:\nJob ID: " + rslt);
510 // x.printStackTrace();
511 // calcMan.disableWorker(this);
513 // } catch (OutOfMemoryError error)
515 // calcMan.disableWorker(this);
517 // ap.raiseOOMWarning(getServiceActionText(), error);
521 calcMan.disableWorker(this);
524 .println("Blacklisting worker due to unexpected exception:");
529 calcMan.workerComplete(this);
532 if (guiProgress != null && progressId != -1)
534 guiProgress.setProgressBar("", progressId);
536 // TODO: may not need to paintAlignment again !
537 ap.paintAlignment(false, false);
539 if (msg.length() > 0)
541 // TODO: stash message somewhere in annotation or alignment view.
542 // code below shows result in a text box popup
544 * jalview.gui.CutAndPasteTransfer cap = new
545 * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
546 * jalview.gui.Desktop.addInternalFrame(cap,
547 * "Job Status for "+getServiceActionText(), 600, 400);
555 * validate input for dynamic/non-dynamic update context TODO: move to
556 * analysis interface ?
559 * @return true if input is valid
561 boolean checkValidInputSeqs(List<SequenceI> seqs)
564 for (SequenceI sq : seqs)
566 if (sq.getStart() <= sq.getEnd()
567 && (sq.isProtein() ? proteinAllowed : nucleotidesAllowed))
570 || sq.getLength() == (sq.getEnd() - sq.getStart() + 1))
576 return nvalid >= min_valid_seqs;
579 public void cancelCurrentJob()
583 String id = running.getJobId();
584 if (((CancellableI) annotService).cancel(running))
586 System.err.println("Cancelled job " + id);
590 System.err.println("Job " + id + " couldn't be cancelled.");
592 } catch (Exception q)
599 * Interactive updating. Analysis calculations that work on the currently
600 * displayed alignment data should cancel existing jobs when the input data
603 * @return true if a running job should be cancelled because new input data is
604 * available for analysis
606 boolean isInteractiveUpdate()
608 return service.isInteractiveUpdate();
612 * decide what sequences will be analysed TODO: refactor to generate
613 * List<SequenceI> for submission to service interface
619 public List<SequenceI> getInputSequences(AlignmentI alignment,
620 AnnotatedCollectionI inputSeqs)
622 if (alignment == null || alignment.getWidth() <= 0
623 || alignment.getSequences() == null || alignment.isNucleotide()
624 ? !nucleotidesAllowed
629 if (inputSeqs == null || inputSeqs.getWidth() <= 0
630 || inputSeqs.getSequences() == null
631 || inputSeqs.getSequences().size() < 1)
633 inputSeqs = alignment;
636 List<SequenceI> seqs = new ArrayList<>();
642 seqNames = new HashMap<>();
644 gapMap = new boolean[0];
645 start = inputSeqs.getStartRes();
646 end = inputSeqs.getEndRes();
647 // TODO: URGENT! unify with JPred / MSA code to handle hidden regions
649 // TODO: push attributes into WsJob instance (so they can be safely
650 // persisted/restored
651 for (SequenceI sq : (inputSeqs.getSequences()))
654 ? sq.findPosition(end + 1)
655 - sq.findPosition(start + 1) > minlen - 1
656 : sq.getEnd() - sq.getStart() > minlen - 1)
658 String newname = SeqsetUtils.unique_name(seqs.size() + 1);
659 // make new input sequence with or without gaps
660 if (seqNames != null)
662 seqNames.put(newname, sq);
667 seqs.add(seq = new jalview.datamodel.Sequence(newname,
668 sq.getSequenceAsString()));
669 if (gapMap == null || gapMap.length < seq.getLength())
671 boolean[] tg = gapMap;
672 gapMap = new boolean[seq.getLength()];
673 System.arraycopy(tg, 0, gapMap, 0, tg.length);
674 for (int p = tg.length; p < gapMap.length; p++)
676 gapMap[p] = false; // init as a gap
679 for (int apos : sq.gapMap())
681 char sqc = sq.getCharAt(apos);
682 if (!filterNonStandardResidues
683 || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
684 : ResidueProperties.nucleotideIndex[sqc] < 5))
686 gapMap[apos] = true; // aligned and real amino acid residue
693 // TODO: add ability to exclude hidden regions
694 seqs.add(seq = new jalview.datamodel.Sequence(newname,
695 AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
696 sq.getSequenceAsString(start, end + 1))));
697 // for annotation need to also record map to sequence start/end
699 // then transfer back to original sequence on return.
701 if (seq.getLength() > ln)
703 ln = seq.getLength();
707 if (alignedSeqs && submitGaps)
710 for (int i = 0; i < gapMap.length; i++)
717 // try real hard to return something submittable
718 // TODO: some of AAcon measures need a minimum of two or three amino
719 // acids at each position, and AAcon doesn't gracefully degrade.
720 for (int p = 0; p < seqs.size(); p++)
722 SequenceI sq = seqs.get(p);
723 // strip gapped columns
724 char[] padded = new char[realw],
725 orig = sq.getSequence();
726 for (int i = 0, pp = 0; i < realw; pp++)
730 if (orig.length > pp)
732 padded[i++] = orig[pp];
740 seqs.set(p, new jalview.datamodel.Sequence(sq.getName(),
741 new String(padded)));
748 public void updateAnnotation()
750 updateResultAnnotation(false);
753 public void updateResultAnnotation(boolean immediate)
755 if ((immediate || !calcMan.isWorking(this)) && running != null
756 && running.hasResults())
758 List<AlignmentAnnotation> ourAnnot = running.getAnnotation(),
759 newAnnots = new ArrayList<>();
761 // update graphGroup for all annotation
764 * find a graphGroup greater than any existing ones this could be a method
765 * provided by alignment Alignment.getNewGraphGroup() - returns next
769 if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
771 for (AlignmentAnnotation ala : alignViewport.getAlignment()
772 .getAlignmentAnnotation())
774 if (ala.graphGroup > graphGroup)
776 graphGroup = ala.graphGroup;
781 * update graphGroup in the annotation rows returned from service
783 // TODO: look at sequence annotation rows and update graph groups in the
784 // case of reference annotation.
785 for (AlignmentAnnotation ala : ourAnnot)
787 if (ala.graphGroup > 0)
789 ala.graphGroup += graphGroup;
791 SequenceI aseq = null;
794 * transfer sequence refs and adjust gapmap
796 if (ala.sequenceRef != null)
798 SequenceI seq = running.getSeqNames()
799 .get(ala.sequenceRef.getName());
801 while (seq.getDatasetSequence() != null)
803 seq = seq.getDatasetSequence();
806 Annotation[] resAnnot = ala.annotations,
807 gappedAnnot = new Annotation[Math.max(
808 alignViewport.getAlignment().getWidth(),
810 for (int p = 0, ap = start; ap < gappedAnnot.length; ap++)
812 if (gapMap != null && gapMap.length > ap && !gapMap[ap])
814 gappedAnnot[ap] = new Annotation("", "", ' ', Float.NaN);
816 else if (p < resAnnot.length)
818 gappedAnnot[ap] = resAnnot[p++];
821 ala.sequenceRef = aseq;
822 ala.annotations = gappedAnnot;
823 AlignmentAnnotation newAnnot = getAlignViewport().getAlignment()
824 .updateFromOrCopyAnnotation(ala);
828 aseq.addAlignmentAnnotation(newAnnot);
829 newAnnot.adjustForAlignment();
831 AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(
832 newAnnot, newAnnot.label, newAnnot.getCalcId());
834 newAnnots.add(newAnnot);
837 for (SequenceI sq : running.getSeqs())
839 if (!sq.getFeatures().hasFeatures()
840 && (sq.getDBRefs() == null || sq.getDBRefs().length == 0))
844 running.setTransferSequenceFeatures(true);
845 SequenceI seq = running.getSeqNames().get(sq.getName());
847 ContiguousI seqRange = seq.findPositions(start, end);
849 while ((dseq = seq).getDatasetSequence() != null)
851 seq = seq.getDatasetSequence();
853 List<ContiguousI> sourceRange = new ArrayList();
854 if (gapMap != null && gapMap.length >= end)
856 int lastcol = start, col = start;
859 if (col == end || !gapMap[col])
861 if (lastcol <= (col - 1))
863 seqRange = seq.findPositions(lastcol, col);
864 sourceRange.add(seqRange);
868 } while (++col <= end);
872 sourceRange.add(seq.findPositions(start, end));
875 int source_startend[] = new int[sourceRange.size() * 2];
877 for (ContiguousI range : sourceRange)
879 source_startend[i++] = range.getBegin();
880 source_startend[i++] = range.getEnd();
882 Mapping mp = new Mapping(
883 new MapList(source_startend, new int[]
884 { seq.getStart(), seq.getEnd() }, 1, 1));
885 dseq.transferAnnotation(sq, mp);
888 updateOurAnnots(newAnnots);
893 * notify manager that we have started, and wait for a free calculation slot
895 * @return true if slot is obtained and work still valid, false if another
896 * thread has done our work for us.
898 protected boolean checkDone()
900 calcMan.notifyStart(this);
901 ap.paintAlignment(false, false);
902 while (!calcMan.notifyWorking(this))
904 if (calcMan.isWorking(this))
912 ap.paintAlignment(false, false);
916 } catch (Exception ex)
918 ex.printStackTrace();
921 if (alignViewport.isClosed())
929 protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
931 List<AlignmentAnnotation> our = ourAnnots;
932 ourAnnots = ourAnnot;
933 AlignmentI alignment = alignViewport.getAlignment();
938 for (AlignmentAnnotation an : our)
940 if (!ourAnnots.contains(an))
942 // remove the old annotation
943 alignment.deleteAnnotation(an);
950 // validate rows and update Alignmment state
951 for (AlignmentAnnotation an : ourAnnots)
953 alignViewport.getAlignment().validateAnnotation(an);
955 // TODO: may need a menu refresh after this
956 // af.setMenusForViewport();
957 ap.adjustAnnotationHeight();
961 public SequenceAnnotationServiceI getService()