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.SeqsetUtils;
25 import jalview.api.AlignViewportI;
26 import jalview.api.AlignmentViewPanel;
27 import jalview.bin.Console;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AnnotatedCollectionI;
31 import jalview.datamodel.SequenceI;
32 import jalview.gui.AlignFrame;
33 import jalview.gui.IProgressIndicator;
34 import jalview.gui.IProgressIndicatorHandler;
35 import jalview.schemes.ResidueProperties;
36 import jalview.workers.AlignCalcWorker;
37 import jalview.ws.jws2.dm.AAConSettings;
38 import jalview.ws.jws2.dm.JabaWsParamSet;
39 import jalview.ws.jws2.jabaws2.Jws2Instance;
40 import jalview.ws.params.WsParamSetI;
42 import java.util.ArrayList;
43 import java.util.HashMap;
44 import java.util.List;
47 import compbio.data.sequence.FastaSequence;
48 import compbio.metadata.Argument;
49 import compbio.metadata.ChunkHolder;
50 import compbio.metadata.JobStatus;
51 import compbio.metadata.JobSubmissionException;
52 import compbio.metadata.Option;
53 import compbio.metadata.ResultNotAvailableException;
55 public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
58 protected Jws2Instance service;
60 protected WsParamSetI preset;
62 protected List<Argument> arguments;
64 protected IProgressIndicator guiProgress;
66 protected boolean submitGaps = true;
69 * by default, we filter out non-standard residues before submission
71 protected boolean filterNonStandardResidues = true;
74 * Recover any existing parameters for this service
76 protected void initViewportParams()
78 if (getCalcId() != null)
80 ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
82 new AAConSettings(true, service, this.preset,
84 ? JabaParamStore.getJwsArgsfromJaba(arguments)
92 * @return null or a string used to recover all annotation generated by this
95 public abstract String getCalcId();
97 public WsParamSetI getPreset()
102 public List<Argument> getArguments()
108 * reconfigure and restart the AAConClient. This method will spawn a new
109 * thread that will wait until any current jobs are finished, modify the
110 * parameters and restart the conservation calculation with the new values.
113 * @param newarguments
115 public void updateParameters(final WsParamSetI newpreset,
116 final List<Argument> newarguments)
119 arguments = newarguments;
120 calcMan.startWorker(this);
121 initViewportParams();
124 public List<Option> getJabaArguments()
126 List<Option> newargs = new ArrayList<>();
127 if (preset != null && preset instanceof JabaWsParamSet)
129 newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
131 if (arguments != null && arguments.size() > 0)
133 for (Argument rg : arguments)
135 if (Option.class.isAssignableFrom(rg.getClass()))
137 newargs.add((Option) rg);
144 protected boolean alignedSeqs = true;
146 protected boolean nucleotidesAllowed = false;
148 protected boolean proteinAllowed = false;
151 * record sequences for mapping result back to afterwards
153 protected boolean bySequence = false;
155 protected Map<String, SequenceI> seqNames;
157 protected boolean[] gapMap;
165 public AbstractJabaCalcWorker(AlignViewportI alignViewport,
166 AlignmentViewPanel alignPanel)
168 super(alignViewport, alignPanel);
171 public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
172 WsParamSetI preset, List<Argument> paramset)
174 this(alignFrame.getCurrentView(), alignFrame.alignPanel);
175 this.guiProgress = alignFrame;
176 this.preset = preset;
177 this.arguments = paramset;
178 this.service = service;
183 * @return true if the submission thread should attempt to submit data
185 abstract boolean hasService();
187 volatile String rslt = "JOB NOT DEFINED";
196 long progressId = -1;
198 int serverErrorsLeft = 3;
200 StringBuffer msg = new StringBuffer();
207 List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(
208 alignViewport.getAlignment(),
209 bySequence ? alignViewport.getSelectionGroup() : null);
211 if (seqs == null || !checkValidInputSeqs(true, seqs))
213 calcMan.workerComplete(this);
217 AlignmentAnnotation[] aa = alignViewport.getAlignment()
218 .getAlignmentAnnotation();
219 if (guiProgress != null)
221 guiProgress.setProgressBar("JABA " + getServiceActionText(),
222 progressId = System.currentTimeMillis());
224 rslt = submitToService(seqs);
225 if (guiProgress != null)
227 guiProgress.registerHandler(progressId,
228 new IProgressIndicatorHandler()
232 public boolean cancelActivity(long id)
239 public boolean canCancel()
245 boolean finished = false;
249 JobStatus status = getJobStatus(rslt);
250 if (status.equals(JobStatus.FINISHED))
254 if (calcMan.isPending(this) && isInteractiveUpdate())
257 // cancel this job and yield to the new job
263 .errPrintln("Cancelled AACon job: " + rslt);
268 .errPrintln("FAILED TO CANCEL AACon job: " + rslt);
271 } catch (Exception x)
275 rslt = "CANCELLED JOB";
279 ChunkHolder stats = null;
283 boolean retry = false;
288 stats = pullExecStatistics(rslt, rpos);
289 } catch (Exception x)
292 if (x.getMessage().contains(
293 "Position in a file could not be negative!"))
295 // squash index out of bounds exception- seems to happen for
296 // disorder predictors which don't (apparently) produce any
297 // progress information and JABA server throws an exception
298 // because progress length is -1.
303 if (--serverErrorsLeft > 0)
309 } catch (InterruptedException q)
323 System.out.print(stats.getChunk());
325 rpos = stats.getNextPosition();
327 } while (stats != null && rpos > cpos);
329 if (!finished && status.equals(JobStatus.FAILED))
334 } catch (InterruptedException x)
340 if (serverErrorsLeft > 0)
345 } catch (InterruptedException x)
348 if (collectAnnotationResultsFor(rslt))
350 Console.debug("Updating result annotation from Job " + rslt
351 + " at " + service.getUri());
352 updateResultAnnotation(true);
353 ap.adjustAnnotationHeight();
358 catch (JobSubmissionException x)
361 jalview.bin.Console.errPrintln(
362 "submission error with " + getServiceActionText() + " :");
364 calcMan.disableWorker(this);
365 } catch (ResultNotAvailableException x)
367 jalview.bin.Console.errPrintln("collection error:\nJob ID: " + rslt);
369 calcMan.disableWorker(this);
371 } catch (OutOfMemoryError error)
373 calcMan.disableWorker(this);
376 // hconsensus = null;
377 ap.raiseOOMWarning(getServiceActionText(), error);
378 } catch (Exception x)
380 calcMan.disableWorker(this);
383 // hconsensus = null;
385 .println("Blacklisting worker due to unexpected exception:");
390 calcMan.workerComplete(this);
393 calcMan.workerComplete(this);
394 if (guiProgress != null && progressId != -1)
396 guiProgress.setProgressBar("", progressId);
398 // TODO: may not need to paintAlignment again !
399 ap.paintAlignment(false, false);
401 if (msg.length() > 0)
403 // TODO: stash message somewhere in annotation or alignment view.
404 // code below shows result in a text box popup
406 * jalview.gui.CutAndPasteTransfer cap = new
407 * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
408 * jalview.gui.Desktop.addInternalFrame(cap,
409 * "Job Status for "+getServiceActionText(), 600, 400);
417 * validate input for dynamic/non-dynamic update context
421 * @return true if input is valid
423 abstract boolean checkValidInputSeqs(boolean dynamic,
424 List<FastaSequence> seqs);
426 abstract String submitToService(
427 List<compbio.data.sequence.FastaSequence> seqs)
428 throws JobSubmissionException;
430 abstract boolean cancelJob(String rslt) throws Exception;
432 abstract JobStatus getJobStatus(String rslt) throws Exception;
434 abstract ChunkHolder pullExecStatistics(String rslt, long rpos);
436 abstract boolean collectAnnotationResultsFor(String rslt)
437 throws ResultNotAvailableException;
439 public void cancelCurrentJob()
446 jalview.bin.Console.errPrintln("Cancelled job " + id);
451 .errPrintln("Job " + id + " couldn't be cancelled.");
453 } catch (Exception q)
460 * Interactive updating. Analysis calculations that work on the currently
461 * displayed alignment data should cancel existing jobs when the input data
464 * @return true if a running job should be cancelled because new input data is
465 * available for analysis
467 abstract boolean isInteractiveUpdate();
469 public List<FastaSequence> getInputSequences(AlignmentI alignment,
470 AnnotatedCollectionI inputSeqs)
472 if (alignment == null || alignment.getWidth() <= 0
473 || alignment.getSequences() == null || alignment.isNucleotide()
474 ? !nucleotidesAllowed
479 if (inputSeqs == null || inputSeqs.getWidth() <= 0
480 || inputSeqs.getSequences() == null
481 || inputSeqs.getSequences().size() < 1)
483 inputSeqs = alignment;
486 List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
492 seqNames = new HashMap<>();
494 gapMap = new boolean[0];
495 start = inputSeqs.getStartRes();
496 end = inputSeqs.getEndRes();
498 for (SequenceI sq : (inputSeqs.getSequences()))
501 ? sq.findPosition(end + 1)
502 - sq.findPosition(start + 1) > minlen - 1
503 : sq.getEnd() - sq.getStart() > minlen - 1)
505 String newname = SeqsetUtils.unique_name(seqs.size() + 1);
506 // make new input sequence with or without gaps
507 if (seqNames != null)
509 seqNames.put(newname, sq);
514 seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
515 sq.getSequenceAsString()));
516 if (gapMap == null || gapMap.length < seq.getSequence().length())
518 boolean[] tg = gapMap;
519 gapMap = new boolean[seq.getLength()];
520 System.arraycopy(tg, 0, gapMap, 0, tg.length);
521 for (int p = tg.length; p < gapMap.length; p++)
523 gapMap[p] = false; // init as a gap
526 for (int apos : sq.gapMap())
528 char sqc = sq.getCharAt(apos);
529 if (!filterNonStandardResidues
530 || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
531 : ResidueProperties.nucleotideIndex[sqc] < 5))
533 gapMap[apos] = true; // aligned and real amino acid residue
540 seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
541 AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
542 sq.getSequenceAsString(start, end + 1))));
544 if (seq.getSequence().length() > ln)
546 ln = seq.getSequence().length();
550 if (alignedSeqs && submitGaps)
553 for (int i = 0; i < gapMap.length; i++)
560 // try real hard to return something submittable
561 // TODO: some of AAcon measures need a minimum of two or three amino
562 // acids at each position, and AAcon doesn't gracefully degrade.
563 for (int p = 0; p < seqs.size(); p++)
565 FastaSequence sq = seqs.get(p);
566 int l = sq.getSequence().length();
567 // strip gapped columns
568 char[] padded = new char[realw],
569 orig = sq.getSequence().toCharArray();
570 for (int i = 0, pp = 0; i < realw; pp++)
574 if (orig.length > pp)
576 padded[i++] = orig[pp];
584 seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
585 new String(padded)));
592 public void updateAnnotation()
594 updateResultAnnotation(false);
597 public abstract void updateResultAnnotation(boolean immediate);
599 public abstract String getServiceActionText();
602 * notify manager that we have started, and wait for a free calculation slot
604 * @return true if slot is obtained and work still valid, false if another
605 * thread has done our work for us.
607 protected boolean checkDone()
609 calcMan.notifyStart(this);
610 ap.paintAlignment(false, false);
611 while (!calcMan.notifyWorking(this))
613 if (calcMan.isWorking(this))
621 ap.paintAlignment(false, false);
625 } catch (Exception ex)
627 ex.printStackTrace();
630 if (alignViewport.isClosed())
638 protected void updateOurAnnots(List<AlignmentAnnotation> ourAnnot)
640 List<AlignmentAnnotation> our = ourAnnots;
641 ourAnnots = ourAnnot;
642 AlignmentI alignment = alignViewport.getAlignment();
647 for (AlignmentAnnotation an : our)
649 if (!ourAnnots.contains(an))
651 // remove the old annotation
652 alignment.deleteAnnotation(an);
658 ap.adjustAnnotationHeight();