1 package jalview.ws2.operations;
3 import static java.lang.String.format;
5 import java.awt.event.MouseAdapter;
6 import java.awt.event.MouseEvent;
7 import java.io.IOException;
8 import java.util.ArrayList;
9 import java.util.Collections;
10 import java.util.HashMap;
11 import java.util.Hashtable;
12 import java.util.LinkedHashMap;
13 import java.util.List;
15 import java.util.Objects;
16 import java.util.concurrent.CompletionStage;
18 import javax.swing.JMenu;
19 import javax.swing.JMenuItem;
20 import javax.swing.ToolTipManager;
22 import jalview.analysis.AlignSeq;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.SeqsetUtils;
25 import jalview.bin.Cache;
26 import jalview.datamodel.AlignedCodonFrame;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.AlignmentOrder;
30 import jalview.datamodel.AlignmentView;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.SequenceI;
33 import jalview.datamodel.Sequence;
34 import jalview.gui.AlignFrame;
35 import jalview.gui.AlignViewport;
36 import jalview.gui.Desktop;
37 import jalview.gui.JvSwingUtils;
38 import jalview.gui.WebserviceInfo;
39 import jalview.gui.WsJobParameters;
40 import jalview.util.MathUtils;
41 import jalview.util.MessageManager;
42 import jalview.ws.params.ArgumentI;
43 import jalview.ws.params.WsParamSetI;
44 import jalview.ws2.MenuEntryProviderI;
45 import jalview.ws2.ResultSupplier;
46 import jalview.ws2.WSJob;
47 import jalview.ws2.WSJobStatus;
48 import jalview.ws2.WebServiceExecutor;
49 import jalview.ws2.WebServiceI;
50 import jalview.ws2.WebServiceInfoUpdater;
51 import jalview.ws2.WebServiceWorkerI;
52 import jalview.ws2.utils.WSJobList;
59 public class AlignmentOperation implements Operation
61 final WebServiceI service;
63 final ResultSupplier<AlignmentI> supplier;
65 public AlignmentOperation(WebServiceI service,
66 ResultSupplier<AlignmentI> supplier)
68 this.service = service;
69 this.supplier = supplier;
73 public String getName()
75 return service.getName();
79 public String getTypeName()
81 return "Multiple Sequence Alignment";
85 public int getMinSequences()
91 public int getMaxSequences()
93 return Integer.MAX_VALUE;
97 public boolean isProteinOperation()
103 public boolean isNucleotideOperation()
109 public boolean canSubmitGaps()
111 // hack copied from original jabaws code, don't blame me
112 return service.getName().contains("lustal");
116 public MenuEntryProviderI getMenuBuilder()
118 return this::buildMenu;
121 protected void buildMenu(JMenu parent, AlignFrame frame)
125 var alignSubmenu = new JMenu(service.getName());
126 buildMenu(alignSubmenu, frame, false);
127 parent.add(alignSubmenu);
128 var realignSubmenu = new JMenu(MessageManager.formatMessage(
129 "label.realign_with_params", service.getName()));
130 realignSubmenu.setToolTipText(MessageManager
131 .getString("label.align_sequences_to_existing_alignment"));
132 buildMenu(realignSubmenu, frame, true);
133 parent.add(realignSubmenu);
137 buildMenu(parent, frame, false);
141 protected void buildMenu(JMenu parent, AlignFrame frame,
144 final String action = submitGaps ? "Align" : "Realign";
145 final var calcName = service.getName();
147 final AlignmentView msa = frame.gatherSequencesForAlignment();
148 final AlignViewport viewport = frame.getViewport();
149 final AlignmentI alignment = frame.getViewport().getAlignment();
150 String title = frame.getTitle();
151 WebServiceExecutor executor = frame.getViewport().getWSExecutor();
153 var item = new JMenuItem(MessageManager.formatMessage(
154 "label.calcname_with_default_settings", calcName));
155 item.setToolTipText(MessageManager
156 .formatMessage("label.action_with_default_settings", action));
157 item.addActionListener((event) -> {
160 WebServiceWorkerI worker = new AlignmentWorker(msa,
161 Collections.emptyList(), title, submitGaps, true,
162 alignment, viewport);
163 executor.submit(worker);
169 if (service.hasParameters())
171 var item = new JMenuItem(
172 MessageManager.getString("label.edit_settings_and_run"));
173 item.setToolTipText(MessageManager.getString(
174 "label.view_and_change_parameters_before_alignment"));
175 item.addActionListener((event) -> {
178 openEditParamsDialog(service, null, null)
179 .thenAcceptAsync((arguments) -> {
180 if (arguments != null)
182 WebServiceWorkerI worker = new AlignmentWorker(msa,
183 arguments, title, submitGaps, true, alignment,
185 executor.submit(worker);
193 var presets = service.getParamStore().getPresets();
194 if (presets != null && presets.size() > 0)
196 final var presetList = new JMenu(MessageManager
197 .formatMessage("label.run_with_preset_params", calcName));
198 final var showToolTipFor = ToolTipManager.sharedInstance()
200 for (final var preset : presets)
202 var item = new JMenuItem(preset.getName());
203 final int QUICK_TOOLTIP = 1500;
204 item.addMouseListener(new MouseAdapter()
207 public void mouseEntered(MouseEvent e)
209 ToolTipManager.sharedInstance().setDismissDelay(QUICK_TOOLTIP);
213 public void mouseExited(MouseEvent e)
215 ToolTipManager.sharedInstance().setDismissDelay(showToolTipFor);
218 String tooltip = JvSwingUtils.wrapTooltip(true,
219 format("<strong>%s</strong><br/>%s",
220 MessageManager.getString(
221 preset.isModifiable() ? "label.user_preset"
222 : "label.service_preset"),
223 preset.getDescription()));
224 item.setToolTipText(tooltip);
225 item.addActionListener((event) -> {
228 WebServiceWorkerI worker = new AlignmentWorker(msa,
229 preset.getArguments(), title, submitGaps, true,
230 alignment, viewport);
231 executor.submit(worker);
234 presetList.add(item);
236 parent.add(presetList);
240 private CompletionStage<List<ArgumentI>> openEditParamsDialog(
241 WebServiceI service, WsParamSetI preset,
242 List<ArgumentI> arguments)
244 WsJobParameters jobParams;
245 if (preset == null && arguments != null && arguments.size() > 0)
246 jobParams = new WsJobParameters(service.getParamStore(), preset,
249 jobParams = new WsJobParameters(service.getParamStore(), preset,
251 var stage = jobParams.showRunDialog();
252 return stage.thenApply((startJob) -> {
255 if (jobParams.getPreset() == null)
257 return jobParams.getJobParams();
261 return jobParams.getPreset().getArguments();
272 * Implementation of the web service worker performing multiple sequence
278 private class AlignmentWorker implements WebServiceWorkerI
281 private long uid = MathUtils.getUID();
283 private final AlignmentView msa;
285 private final AlignmentI dataset;
287 private final List<AlignedCodonFrame> codonFrame = new ArrayList<>();
289 private List<ArgumentI> args = Collections.emptyList();
291 private String alnTitle = "";
293 private boolean submitGaps = false;
295 private boolean preserveOrder = false;
297 private char gapCharacter;
299 private WSJobList jobs = new WSJobList();
301 private Map<Long, JobInput> inputs = new LinkedHashMap<>();
303 private WebserviceInfo wsInfo;
305 private Map<Long, Integer> exceptionCount = new HashMap<>();
307 private final int MAX_RETRY = 5;
309 AlignmentWorker(AlignmentView msa, List<ArgumentI> args,
310 String alnTitle, boolean submitGaps, boolean preserveOrder,
311 AlignmentI alignment, AlignViewport viewport)
314 this.dataset = alignment.getDataset();
315 List<AlignedCodonFrame> cf = Objects.requireNonNullElse(
316 alignment.getCodonFrames(), Collections.emptyList());
317 this.codonFrame.addAll(cf);
319 this.alnTitle = alnTitle;
320 this.submitGaps = submitGaps;
321 this.preserveOrder = preserveOrder;
322 this.gapCharacter = viewport.getGapCharacter();
324 String panelInfo = String.format("%s using service hosted at %s%n%s",
325 service.getName(), service.getHostName(),
326 Objects.requireNonNullElse(service.getDescription(), ""));
327 wsInfo = new WebserviceInfo(service.getName(), panelInfo, false);
337 public WebServiceI getWebService()
343 public List<WSJob> getJobs()
345 return Collections.unmodifiableList(jobs);
349 public void startJobs() throws IOException
351 String outputHeader = String.format("%s of %s%nJob details%n",
352 submitGaps ? "Re-alignment" : "Alignment", alnTitle);
353 SequenceI[][] conmsa = msa.getVisibleContigs('-');
358 WebServiceInfoUpdater updater = new WebServiceInfoUpdater(wsInfo);
359 updater.setOutputHeader(outputHeader);
361 for (int i = 0; i < conmsa.length; i++)
363 JobInput input = JobInput.create(conmsa[i], 2, submitGaps);
364 WSJob job = new WSJob(service.getProviderName(), service.getName(),
365 service.getHostName());
366 job.setJobNum(wsInfo.addJobPane());
367 if (conmsa.length > 0)
369 wsInfo.setProgressName(String.format("region %d", i),
372 wsInfo.setProgressText(job.getJobNum(), outputHeader);
373 job.addPropertyChangeListener(updater);
374 inputs.put(job.getUid(), input);
376 if (input.isInputValid())
382 count = exceptionCount.getOrDefault(job.getUid(), MAX_RETRY);
385 jobId = service.submit(input.inputSequences, args);
386 Cache.log.debug((format("Job %s submitted", job)));
387 exceptionCount.remove(job.getUid());
388 } catch (IOException e)
390 exceptionCount.put(job.getUid(), --count);
392 } while (jobId == null && count > 0);
396 job.setStatus(WSJobStatus.SUBMITTED);
401 job.setStatus(WSJobStatus.SERVER_ERROR);
406 job.setStatus(WSJobStatus.INVALID);
408 MessageManager.getString("label.empty_alignment_job"));
413 // wsInfo.setThisService() should happen here
414 wsInfo.setVisible(true);
418 wsInfo.setVisible(false);
419 // TODO show notification dialog.
420 // JvOptionPane.showMessageDialog(frame,
421 // MessageManager.getString("info.invalid_msa_input_mininfo"),
422 // MessageManager.getString("info.invalid_msa_notenough"),
423 // JvOptionPane.INFORMATION_MESSAGE);
428 public boolean pollJobs()
431 for (WSJob job : getJobs())
433 if (!job.getStatus().isDone())
435 Cache.log.debug(format("Polling job %s.", job));
438 service.updateProgress(job);
439 exceptionCount.remove(job.getUid());
440 } catch (IOException e)
442 Cache.log.error(format("Polling job %s failed.", job), e);
443 wsInfo.appendProgressText(job.getJobNum(),
444 MessageManager.formatMessage("info.server_exception",
445 service.getName(), e.getMessage()));
446 int count = exceptionCount.getOrDefault(job.getUid(),
450 job.setStatus(WSJobStatus.SERVER_ERROR);
451 Cache.log.warn(format(
452 "Attempts limit exceeded. Droping job %s.", job));
454 exceptionCount.put(job.getUid(), count);
455 } catch (OutOfMemoryError e)
457 job.setStatus(WSJobStatus.BROKEN);
459 format("Out of memory when retrieving job %s", job), e);
462 format("Job %s status is %s", job, job.getStatus()));
464 done &= job.getStatus().isDone();
466 updateWSInfoGlobalStatus();
470 private void updateWSInfoGlobalStatus()
472 if (jobs.countRunning() > 0)
474 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
476 else if (jobs.countQueuing() > 0
477 || jobs.countSubmitted() < jobs.size())
479 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
483 if (jobs.countSuccessful() > 0)
485 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
487 else if (jobs.countCancelled() > 0)
489 wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
491 else if (jobs.countFailed() > 0)
493 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
501 long progbarId = MathUtils.getUID();
502 wsInfo.setProgressBar(
503 MessageManager.getString("status.collecting_job_results"),
505 Map<Long, AlignmentI> results = new LinkedHashMap<>();
506 for (WSJob job : getJobs())
510 AlignmentI alignment = supplier.getResult(job);
511 if (alignment != null)
513 results.put(job.getUid(), alignment);
515 } catch (Exception e)
517 if (!service.handleCollectionError(job, e))
519 Cache.log.error("Couldn't get alignment for job.", e);
520 // TODO: Increment exception count and retry.
521 job.setStatus(WSJobStatus.SERVER_ERROR);
525 updateWSInfoGlobalStatus();
526 if (results.size() > 0)
528 OutputWrapper out = prepareOutput(results);
529 wsInfo.showResultsNewFrame.addActionListener(evt -> displayNewFrame(
530 new Alignment(out.aln), out.alorders, out.hidden));
531 wsInfo.setResultsReady();
535 wsInfo.setFinishedNoResults();
537 wsInfo.removeProgressBar(progbarId);
540 private class OutputWrapper
544 List<AlignmentOrder> alorders;
546 HiddenColumns hidden;
548 OutputWrapper(AlignmentI aln, List<AlignmentOrder> alorders,
549 HiddenColumns hidden)
552 this.alorders = alorders;
553 this.hidden = hidden;
557 private OutputWrapper prepareOutput(Map<Long, AlignmentI> alignments)
559 List<AlignmentOrder> alorders = new ArrayList<>();
560 SequenceI[][] results = new SequenceI[jobs.size()][];
561 AlignmentOrder[] orders = new AlignmentOrder[jobs.size()];
562 for (int i = 0; i < jobs.size(); i++)
564 WSJob job = jobs.get(i);
565 AlignmentI aln = alignments.get(job.getUid());
566 if (aln != null) // equivalent of job.hasResults()
568 /* Get the alignment including any empty sequences in the original
569 * order with original ids. */
570 JobInput input = inputs.get(job.getUid());
571 char gapChar = aln.getGapCharacter();
572 List<SequenceI> emptySeqs = input.emptySequences;
573 List<SequenceI> alnSeqs = aln.getSequences();
574 // find the width of the longest sequence
576 for (var seq : alnSeqs)
577 width = Integer.max(width, seq.getLength());
578 for (var emptySeq : emptySeqs)
579 width = Integer.max(width, emptySeq.getLength());
580 // pad shorter sequences with gaps
581 String gapSeq = String.join("",
582 Collections.nCopies(width, Character.toString(gapChar)));
583 List<SequenceI> seqs = new ArrayList<>(
584 alnSeqs.size() + emptySeqs.size());
585 seqs.addAll(alnSeqs);
586 seqs.addAll(emptySeqs);
589 if (seq.getLength() < width)
590 seq.setSequence(seq.getSequenceAsString()
591 + gapSeq.substring(seq.getLength()));
593 SequenceI[] result = seqs.toArray(new SequenceI[0]);
594 AlignmentOrder msaOrder = new AlignmentOrder(result);
595 AlignmentSorter.recoverOrder(result);
596 // temporary workaround for deuniquify
597 @SuppressWarnings({ "rawtypes", "unchecked" })
598 Hashtable names = new Hashtable(input.sequenceNames);
599 // FIXME first call to deuniquify alters original alignment
600 SeqsetUtils.deuniquify(names, result);
601 alorders.add(msaOrder);
603 orders[i] = msaOrder;
611 Object[] newView = msa.getUpdatedView(results, orders, gapCharacter);
612 // free references to original data
613 for (int i = 0; i < jobs.size(); i++)
618 SequenceI[] alignment = (SequenceI[]) newView[0];
619 HiddenColumns hidden = (HiddenColumns) newView[1];
620 Alignment aln = new Alignment(alignment);
621 aln.setProperty("Alignment Program", service.getName());
623 aln.setDataset(dataset);
625 propagateDatasetMappings(aln);
626 return new OutputWrapper(aln, alorders, hidden);
627 // displayNewFrame(aln, alorders, hidden);
631 * conserves dataset references to sequence objects returned from web
632 * services. propagate codon frame data to alignment.
634 private void propagateDatasetMappings(Alignment aln)
636 if (codonFrame != null)
638 SequenceI[] alignment = aln.getSequencesArray();
639 for (SequenceI seq : alignment)
641 for (AlignedCodonFrame acf : codonFrame)
643 if (acf != null && acf.involvesSequence(seq))
645 aln.addCodonFrame(acf);
653 private void displayNewFrame(AlignmentI aln,
654 List<AlignmentOrder> alorders, HiddenColumns hidden)
656 AlignFrame frame = new AlignFrame(aln, hidden,
657 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
658 // TODO store feature renderer settings in worker object
659 // frame.getFeatureRenderer().transferSettings(featureSettings);
660 var regions = sortOrders(alorders);
661 if (alorders.size() == 1)
663 frame.addSortByOrderMenuItem(
664 format("%s Ordering", service.getName()), alorders.get(0));
668 for (int i = 0; i < alorders.size(); i++)
671 Iterable<String> iter = () -> regions.get(j).stream()
672 .map(it -> Integer.toString(it)).iterator();
673 var orderName = format("%s Region %s Ordering", service.getName(),
674 String.join(",", iter));
675 frame.addSortByOrderMenuItem(orderName, alorders.get(i));
680 * If alignment was requested from one half of a SplitFrame, show in a
681 * SplitFrame with the other pane similarly aligned.
684 Desktop.addInternalFrame(frame, alnTitle, AlignFrame.DEFAULT_WIDTH,
685 AlignFrame.DEFAULT_HEIGHT);
688 private List<List<Integer>> sortOrders(List<?> alorders)
690 List<List<Integer>> regions = new ArrayList<>();
691 for (int i = 0; i < alorders.size(); i++)
693 List<Integer> regs = new ArrayList<>();
696 while (j < alorders.size())
698 if (alorders.get(i).equals(alorders.get(j)))
714 private static class JobInput
716 final List<SequenceI> inputSequences;
718 final List<SequenceI> emptySequences;
720 @SuppressWarnings("rawtypes")
721 final Map<String, ? extends Map> sequenceNames;
723 private JobInput(int numSequences, List<SequenceI> inputSequences,
724 List<SequenceI> emptySequences,
725 @SuppressWarnings("rawtypes") Map<String, ? extends Map> names)
727 this.inputSequences = Collections.unmodifiableList(inputSequences);
728 this.emptySequences = Collections.unmodifiableList(emptySequences);
729 this.sequenceNames = names;
732 boolean isInputValid()
734 return inputSequences.size() >= 2;
737 static JobInput create(SequenceI[] sequences, int minLength,
740 assert minLength >= 0 : MessageManager.getString(
741 "error.implementation_error_minlen_must_be_greater_zero");
743 for (SequenceI seq : sequences)
745 if (seq.getEnd() - seq.getStart() >= minLength)
751 List<SequenceI> inputSequences = new ArrayList<>();
752 List<SequenceI> emptySequences = new ArrayList<>();
753 @SuppressWarnings("rawtypes")
754 Map<String, Hashtable> names = new LinkedHashMap<>();
755 for (int i = 0; i < sequences.length; i++)
757 SequenceI seq = sequences[i];
758 String newName = SeqsetUtils.unique_name(i);
759 @SuppressWarnings("rawtypes")
760 Hashtable hash = SeqsetUtils.SeqCharacterHash(seq);
761 names.put(newName, hash);
762 if (numSeq > 1 && seq.getEnd() - seq.getStart() >= minLength)
764 String seqString = seq.getSequenceAsString();
767 seqString = AlignSeq.extractGaps(
768 jalview.util.Comparison.GapChars, seqString);
770 inputSequences.add(new Sequence(newName, seqString));
774 String seqString = null;
775 if (seq.getEnd() >= seq.getStart()) // is it ever false?
777 seqString = seq.getSequenceAsString();
780 seqString = AlignSeq.extractGaps(
781 jalview.util.Comparison.GapChars, seqString);
784 emptySequences.add(new Sequence(newName, seqString));
788 return new JobInput(numSeq, inputSequences, emptySequences, names);