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Coverage Report

  1. Project Clover database Wed Nov 12 2025 09:00:47 GMT
  2. Package jalview.ws.jws2

File MsaWSThread.java

 

Coverage histogram

../../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

162
345
32
2
1,123
842
146
0.42
10.78
16
4.56

Classes

Class Line # Actions
MsaWSThread 57 240 85
0.00%
MsaWSThread.MsaWSJob 67 105 61
0.00%
 

Contributing tests

No tests hitting this source file were found.

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.ws.jws2;
22   
23    import jalview.analysis.AlignSeq;
24    import jalview.bin.Console;
25    import jalview.datamodel.Alignment;
26    import jalview.datamodel.AlignmentI;
27    import jalview.datamodel.AlignmentOrder;
28    import jalview.datamodel.AlignmentView;
29    import jalview.datamodel.HiddenColumns;
30    import jalview.datamodel.Sequence;
31    import jalview.datamodel.SequenceI;
32    import jalview.gui.AlignFrame;
33    import jalview.gui.Desktop;
34    import jalview.gui.SplitFrame;
35    import jalview.gui.WebserviceInfo;
36    import jalview.util.MessageManager;
37    import jalview.ws.AWsJob;
38    import jalview.ws.JobStateSummary;
39    import jalview.ws.WSClientI;
40    import jalview.ws.jws2.dm.JabaWsParamSet;
41    import jalview.ws.params.WsParamSetI;
42   
43    import java.util.ArrayList;
44    import java.util.Hashtable;
45    import java.util.List;
46    import java.util.Map;
47    import java.util.Vector;
48   
49    import javax.swing.JInternalFrame;
50   
51    import compbio.data.msa.MsaWS;
52    import compbio.metadata.Argument;
53    import compbio.metadata.ChunkHolder;
54    import compbio.metadata.JobStatus;
55    import compbio.metadata.Preset;
56   
 
57    class MsaWSThread extends AWS2Thread implements WSClientI
58    {
59    boolean submitGaps = false; // pass sequences including gaps to alignment
60   
61    // service
62   
63    boolean preserveOrder = true; // and always store and recover sequence
64   
65    // order
66   
 
67    class MsaWSJob extends JWs2Job
68    {
69    long lastChunk = 0;
70   
71    WsParamSetI preset = null;
72   
73    List<Argument> arguments = null;
74   
75    /**
76    * input
77    */
78    ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
79   
80    /**
81    * output
82    */
83    compbio.data.sequence.Alignment alignment;
84   
85    // set if the job didn't get run - then the input is simply returned to the
86    // user
87    private boolean returnInput = false;
88   
89    /**
90    * MsaWSJob
91    *
92    * @param jobNum
93    * int
94    * @param jobId
95    * String
96    */
 
97  0 toggle public MsaWSJob(int jobNum, SequenceI[] inSeqs)
98    {
99  0 this.jobnum = jobNum;
100  0 if (!prepareInput(inSeqs, 2))
101    {
102  0 submitted = true;
103  0 subjobComplete = true;
104  0 returnInput = true;
105    }
106   
107    }
108   
109    Hashtable<String, Map> SeqNames = new Hashtable();
110   
111    Vector<String[]> emptySeqs = new Vector();
112   
113    /**
114    * prepare input sequences for MsaWS service
115    *
116    * @param seqs
117    * jalview sequences to be prepared
118    * @param minlen
119    * minimum number of residues required for this MsaWS service
120    * @return true if seqs contains sequences to be submitted to service.
121    */
122    // TODO: return compbio.seqs list or nothing to indicate validity.
 
123  0 toggle private boolean prepareInput(SequenceI[] seqs, int minlen)
124    {
125  0 int nseqs = 0;
126  0 if (minlen < 0)
127    {
128  0 throw new Error(MessageManager.getString(
129    "error.implementation_error_minlen_must_be_greater_zero"));
130    }
131  0 for (int i = 0; i < seqs.length; i++)
132    {
133  0 if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
134    {
135  0 nseqs++;
136    }
137    }
138  0 boolean valid = nseqs > 1; // need at least two seqs
139  0 compbio.data.sequence.FastaSequence seq;
140  0 for (int i = 0, n = 0; i < seqs.length; i++)
141    {
142   
143  0 String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
144    // for
145    // any
146    // subjob
147  0 SeqNames.put(newname,
148    jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
149  0 if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
150    {
151    // make new input sequence with or without gaps
152  0 seq = new compbio.data.sequence.FastaSequence(newname,
153  0 (submitGaps) ? seqs[i].getSequenceAsString()
154    : AlignSeq.extractGaps(
155    jalview.util.Comparison.GapChars,
156    seqs[i].getSequenceAsString()));
157  0 this.seqs.add(seq);
158    }
159    else
160    {
161  0 String empty = null;
162  0 if (seqs[i].getEnd() >= seqs[i].getStart())
163    {
164  0 empty = (submitGaps) ? seqs[i].getSequenceAsString()
165    : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
166    seqs[i].getSequenceAsString());
167    }
168  0 emptySeqs.add(new String[] { newname, empty });
169    }
170    }
171  0 return valid;
172    }
173   
174    /**
175    *
176    * @return true if getAlignment will return a valid alignment result.
177    */
 
178  0 toggle @Override
179    public boolean hasResults()
180    {
181  0 if (subjobComplete && isFinished() && (alignment != null
182    || (emptySeqs != null && emptySeqs.size() > 0)))
183    {
184  0 return true;
185    }
186  0 return false;
187    }
188   
189    /**
190    *
191    * get the alignment including any empty sequences in the original order
192    * with original ids. Caller must access the alignment.getMetadata() object
193    * to annotate the final result passsed to the user.
194    *
195    * @return { SequenceI[], AlignmentOrder }
196    */
 
197  0 toggle public Object[] getAlignment()
198    {
199    // is this a generic subjob or a Jws2 specific Object[] return signature
200  0 if (hasResults())
201    {
202  0 SequenceI[] alseqs = null;
203  0 char alseq_gapchar = '-';
204  0 int alseq_l = 0;
205  0 if (alignment.getSequences().size() > 0)
206    {
207  0 alseqs = new SequenceI[alignment.getSequences().size()];
208  0 for (compbio.data.sequence.FastaSequence seq : alignment
209    .getSequences())
210    {
211  0 alseqs[alseq_l++] = new Sequence(seq.getId(),
212    seq.getSequence());
213    }
214  0 alseq_gapchar = alignment.getMetadata().getGapchar();
215   
216    }
217    // add in the empty seqs.
218  0 if (emptySeqs.size() > 0)
219    {
220  0 SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
221    // get width
222  0 int i, w = 0;
223  0 if (alseq_l > 0)
224    {
225  0 for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
226    {
227  0 if (w < alseqs[i].getLength())
228    {
229  0 w = alseqs[i].getLength();
230    }
231  0 t_alseqs[i] = alseqs[i];
232  0 alseqs[i] = null;
233    }
234    }
235    // check that aligned width is at least as wide as emptySeqs width.
236  0 int ow = w, nw = w;
237  0 for (i = 0, w = emptySeqs.size(); i < w; i++)
238    {
239  0 String[] es = emptySeqs.get(i);
240  0 if (es != null && es[1] != null)
241    {
242  0 int sw = es[1].length();
243  0 if (nw < sw)
244    {
245  0 nw = sw;
246    }
247    }
248    }
249    // make a gapped string.
250  0 StringBuffer insbuff = new StringBuffer(w);
251  0 for (i = 0; i < nw; i++)
252    {
253  0 insbuff.append(alseq_gapchar);
254    }
255  0 if (ow < nw)
256    {
257  0 for (i = 0; i < alseq_l; i++)
258    {
259  0 int sw = t_alseqs[i].getLength();
260  0 if (nw > sw)
261    {
262    // pad at end
263  0 alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()
264    + insbuff.substring(0, sw - nw));
265    }
266    }
267    }
268  0 for (i = 0, w = emptySeqs.size(); i < w; i++)
269    {
270  0 String[] es = emptySeqs.get(i);
271  0 if (es[1] == null)
272    {
273  0 t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
274    insbuff.toString(), 1, 0);
275    }
276    else
277    {
278  0 if (es[1].length() < nw)
279    {
280  0 t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
281    es[0],
282    es[1] + insbuff.substring(0, nw - es[1].length()),
283    1, 1 + es[1].length());
284    }
285    else
286    {
287  0 t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
288    es[0], es[1]);
289    }
290    }
291    }
292  0 alseqs = t_alseqs;
293    }
294  0 AlignmentOrder msaorder = new AlignmentOrder(alseqs);
295    // always recover the order - makes parseResult()'s life easier.
296  0 jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
297    // account for any missing sequences
298  0 jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
299  0 return new Object[] { alseqs, msaorder };
300    }
301  0 return null;
302    }
303   
304    /**
305    * mark subjob as cancelled and set result object appropriatly
306    */
 
307  0 toggle void cancel()
308    {
309  0 cancelled = true;
310  0 subjobComplete = true;
311  0 alignment = null;
312    }
313   
314    /**
315    *
316    * @return boolean true if job can be submitted.
317    */
 
318  0 toggle @Override
319    public boolean hasValidInput()
320    {
321    // TODO: get attributes for this MsaWS instance to check if it can do two
322    // sequence alignment.
323  0 if (seqs != null && seqs.size() >= 2) // two or more sequences is valid ?
324    {
325  0 return true;
326    }
327  0 return false;
328    }
329   
330    StringBuffer jobProgress = new StringBuffer();
331   
 
332  0 toggle public void setStatus(String string)
333    {
334  0 jobProgress.setLength(0);
335  0 jobProgress.append(string);
336    }
337   
 
338  0 toggle @Override
339    public String getStatus()
340    {
341  0 return jobProgress.toString();
342    }
343   
 
344  0 toggle @Override
345    public boolean hasStatus()
346    {
347  0 return jobProgress != null;
348    }
349   
350    /**
351    * @return the lastChunk
352    */
 
353  0 toggle public long getLastChunk()
354    {
355  0 return lastChunk;
356    }
357   
358    /**
359    * @param lastChunk
360    * the lastChunk to set
361    */
 
362  0 toggle public void setLastChunk(long lastChunk)
363    {
364  0 this.lastChunk = lastChunk;
365    }
366   
367    String alignmentProgram = null;
368   
 
369  0 toggle public String getAlignmentProgram()
370    {
371  0 return alignmentProgram;
372    }
373   
 
374  0 toggle public boolean hasArguments()
375    {
376  0 return (arguments != null && arguments.size() > 0)
377    || (preset != null && preset instanceof JabaWsParamSet);
378    }
379   
 
380  0 toggle public List<Argument> getJabaArguments()
381    {
382  0 List<Argument> newargs = new ArrayList<Argument>();
383  0 if (preset != null && preset instanceof JabaWsParamSet)
384    {
385  0 newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
386    }
387  0 if (arguments != null && arguments.size() > 0)
388    {
389  0 newargs.addAll(arguments);
390    }
391  0 return newargs;
392    }
393   
394    /**
395    * add a progess header to status string containing presets/args used
396    */
 
397  0 toggle public void addInitialStatus()
398    {
399  0 if (preset != null)
400    {
401  0 jobProgress.append("Using "
402  0 + (preset instanceof JabaPreset ? "Server" : "User")
403    + "Preset: " + preset.getName());
404  0 if (preset instanceof JabaWsParamSet)
405    {
406  0 for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
407    {
408  0 jobProgress.append(
409    opt.getName() + " " + opt.getDefaultValue() + "\n");
410    }
411    }
412    }
413  0 if (arguments != null && arguments.size() > 0)
414    {
415  0 jobProgress.append("With custom parameters : \n");
416    // merge arguments with preset's own arguments.
417  0 for (Argument opt : arguments)
418    {
419  0 jobProgress.append(
420    opt.getName() + " " + opt.getDefaultValue() + "\n");
421    }
422    }
423  0 jobProgress.append("\nJob Output:\n");
424    }
425   
 
426  0 toggle public boolean isPresetJob()
427    {
428  0 return preset != null && preset instanceof JabaPreset;
429    }
430   
 
431  0 toggle public Preset getServerPreset()
432    {
433  0 return (isPresetJob()) ? ((JabaPreset) preset).p : null;
434    }
435    }
436   
437    String alTitle; // name which will be used to form new alignment window.
438   
439    AlignmentI dataset; // dataset to which the new alignment will be
440   
441    // associated.
442   
443    @SuppressWarnings("unchecked")
444    MsaWS server = null;
445   
446    /**
447    * set basic options for this (group) of Msa jobs
448    *
449    * @param subgaps
450    * boolean
451    * @param presorder
452    * boolean
453    */
 
454  0 toggle private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
455    jalview.gui.AlignFrame alFrame, AlignmentView alview,
456    String wsname, boolean subgaps, boolean presorder)
457    {
458  0 super(alFrame, wsinfo, alview, wsname, wsUrl);
459  0 this.server = server;
460  0 this.submitGaps = subgaps;
461  0 this.preserveOrder = presorder;
462    }
463   
464    /**
465    * create one or more Msa jobs to align visible seuqences in _msa
466    *
467    * @param title
468    * String
469    * @param _msa
470    * AlignmentView
471    * @param subgaps
472    * boolean
473    * @param presorder
474    * boolean
475    * @param seqset
476    * Alignment
477    */
 
478  0 toggle MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
479    String wsUrl, WebserviceInfo wsinfo,
480    jalview.gui.AlignFrame alFrame, String wsname, String title,
481    AlignmentView _msa, boolean subgaps, boolean presorder,
482    AlignmentI seqset)
483    {
484  0 this(server2, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
485  0 OutputHeader = wsInfo.getProgressText();
486  0 alTitle = title;
487  0 dataset = seqset;
488   
489  0 SequenceI[][] conmsa = _msa.getVisibleContigs('-');
490  0 if (conmsa != null)
491    {
492  0 int nvalid = 0, njobs = conmsa.length;
493  0 jobs = new MsaWSJob[njobs];
494  0 for (int j = 0; j < njobs; j++)
495    {
496  0 if (j != 0)
497    {
498  0 jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
499    }
500    else
501    {
502  0 jobs[j] = new MsaWSJob(0, conmsa[j]);
503    }
504  0 if (((MsaWSJob) jobs[j]).hasValidInput())
505    {
506  0 nvalid++;
507    }
508  0 ((MsaWSJob) jobs[j]).preset = preset;
509  0 ((MsaWSJob) jobs[j]).arguments = paramset;
510  0 ((MsaWSJob) jobs[j]).alignmentProgram = wsname;
511  0 if (njobs > 0)
512    {
513  0 wsinfo.setProgressName("region " + jobs[j].getJobnum(),
514    jobs[j].getJobnum());
515    }
516  0 wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
517    }
518  0 validInput = nvalid > 0;
519    }
520    }
521   
522    boolean validInput = false;
523   
524    /**
525    *
526    * @return true if the thread will perform a calculation
527    */
 
528  0 toggle public boolean hasValidInput()
529    {
530  0 return validInput;
531    }
532   
 
533  0 toggle @Override
534    public boolean isCancellable()
535    {
536  0 return true;
537    }
538   
 
539  0 toggle @Override
540    public void cancelJob()
541    {
542  0 if (!jobComplete && jobs != null)
543    {
544  0 boolean cancelled = true;
545  0 for (int job = 0; job < jobs.length; job++)
546    {
547  0 if (jobs[job].isSubmitted() && !jobs[job].isSubjobComplete())
548    {
549  0 String cancelledMessage = "";
550  0 try
551    {
552  0 boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
553  0 if (true) // cancelledJob || true)
554    {
555    // CANCELLED_JOB
556    // if the Jaba server indicates the job can't be cancelled, its
557    // because its running on the server's local execution engine
558    // so we just close the window anyway.
559  0 cancelledMessage = "Job cancelled.";
560  0 ((MsaWSJob) jobs[job]).cancel(); // TODO: refactor to avoid this
561    // ugliness -
562  0 wsInfo.setStatus(jobs[job].getJobnum(),
563    WebserviceInfo.STATE_CANCELLED_OK);
564    }
565    else
566    {
567    // VALID UNSTOPPABLE JOB
568  0 cancelledMessage += "Server cannot cancel this job. just close the window.\n";
569  0 cancelled = false;
570    // wsInfo.setStatus(jobs[job].jobnum,
571    // WebserviceInfo.STATE_RUNNING);
572    }
573    } catch (Exception exc)
574    {
575  0 cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
576    + exc + "\n");
577  0 Console.warn(
578    "Exception whilst cancelling " + jobs[job].getJobId(),
579    exc);
580    }
581  0 wsInfo.setProgressText(jobs[job].getJobnum(),
582    OutputHeader + cancelledMessage + "\n");
583    }
584    else
585    {
586    // if we hadn't submitted then just mark the job as cancelled.
587  0 jobs[job].setSubjobComplete(true);
588  0 wsInfo.setStatus(jobs[job].getJobnum(),
589    WebserviceInfo.STATE_CANCELLED_OK);
590   
591    }
592    }
593  0 if (cancelled)
594    {
595  0 wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
596  0 jobComplete = true;
597    }
598  0 this.interrupt(); // kick thread to update job states.
599    }
600    else
601    {
602  0 if (!jobComplete)
603    {
604  0 wsInfo.setProgressText(OutputHeader
605    + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
606    }
607    }
608    }
609   
 
610  0 toggle @Override
611    public void pollJob(AWsJob job) throws Exception
612    {
613    // TODO: investigate if we still need to cast here in J1.6
614  0 MsaWSJob j = ((MsaWSJob) job);
615    // this is standard code, but since the interface doesn't comprise of a
616    // basic one that implements (getJobStatus, pullExecStatistics) we have to
617    // repeat the code for all jw2s services.
618  0 j.setjobStatus(server.getJobStatus(job.getJobId()));
619  0 updateJobProgress(j);
620    }
621   
622    /**
623    *
624    * @param j
625    * @return true if more job progress data was available
626    * @throws Exception
627    */
 
628  0 toggle protected boolean updateJobProgress(MsaWSJob j) throws Exception
629    {
630  0 StringBuffer response = j.jobProgress;
631  0 long lastchunk = j.getLastChunk();
632  0 boolean changed = false;
633  0 do
634    {
635  0 j.setLastChunk(lastchunk);
636  0 ChunkHolder chunk = server.pullExecStatistics(j.getJobId(),
637    lastchunk);
638  0 if (chunk != null)
639    {
640  0 changed |= chunk.getChunk().length() > 0;
641  0 response.append(chunk.getChunk());
642  0 lastchunk = chunk.getNextPosition();
643  0 try
644    {
645  0 Thread.sleep(50);
646    } catch (InterruptedException x)
647    {
648    }
649  0 ;
650    }
651  0 ;
652  0 } while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
653  0 return changed;
654    }
655   
 
656  0 toggle @Override
657    public void StartJob(AWsJob job)
658    {
659  0 Exception lex = null;
660    // boiler plate template
661  0 if (!(job instanceof MsaWSJob))
662    {
663  0 throw new Error(MessageManager.formatMessage(
664    "error.implementation_error_msawbjob_called", new String[]
665    { job.getClass().toString() }));
666    }
667  0 MsaWSJob j = (MsaWSJob) job;
668  0 if (j.isSubmitted())
669    {
670  0 if (Console.isDebugEnabled())
671    {
672  0 Console.debug(
673    "Tried to submit an already submitted job " + j.getJobId());
674    }
675  0 return;
676    }
677    // end boilerplate
678   
679  0 if (j.seqs == null || j.seqs.size() == 0)
680    {
681    // special case - selection consisted entirely of empty sequences...
682  0 j.setjobStatus(JobStatus.FINISHED);
683  0 j.setStatus(MessageManager.getString("label.empty_alignment_job"));
684    }
685  0 try
686    {
687  0 j.addInitialStatus(); // list the presets/parameters used for the job in
688    // status
689  0 if (j.isPresetJob())
690    {
691  0 j.setJobId(server.presetAlign(j.seqs, j.getServerPreset()));
692    }
693  0 else if (j.hasArguments())
694    {
695  0 j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
696    }
697    else
698    {
699  0 j.setJobId(server.align(j.seqs));
700    }
701   
702  0 if (j.getJobId() != null)
703    {
704  0 j.setSubmitted(true);
705  0 j.setSubjobComplete(false);
706    // jalview.bin.Console.outPrintln(WsURL + " Job Id '" + jobId + "'");
707  0 return;
708    }
709    else
710    {
711  0 throw new Exception(MessageManager.formatMessage(
712    "exception.web_service_returned_null_try_later",
713    new String[]
714    { WsUrl }));
715    }
716    } catch (compbio.metadata.UnsupportedRuntimeException _lex)
717    {
718  0 lex = _lex;
719  0 wsInfo.appendProgressText(MessageManager.formatMessage(
720    "info.job_couldnt_be_run_server_doesnt_support_program",
721    new String[]
722    { _lex.getMessage() }));
723  0 wsInfo.warnUser(_lex.getMessage(),
724    MessageManager.getString("warn.service_not_supported"));
725  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
726  0 wsInfo.setStatus(j.getJobnum(),
727    WebserviceInfo.STATE_STOPPED_SERVERERROR);
728    } catch (compbio.metadata.LimitExceededException _lex)
729    {
730  0 lex = _lex;
731  0 wsInfo.appendProgressText(MessageManager.formatMessage(
732    "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
733    { _lex.getMessage() }));
734  0 wsInfo.warnUser(_lex.getMessage(),
735    MessageManager.getString("warn.input_is_too_big"));
736  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
737  0 wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
738    } catch (compbio.metadata.WrongParameterException _lex)
739    {
740  0 lex = _lex;
741  0 wsInfo.warnUser(_lex.getMessage(),
742    MessageManager.getString("warn.invalid_job_param_set"));
743  0 wsInfo.appendProgressText(MessageManager.formatMessage(
744    "info.job_couldnt_be_run_incorrect_param_setting",
745    new String[]
746    { _lex.getMessage() }));
747  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
748  0 wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
749    } catch (Error e)
750    {
751    // For unexpected errors
752  0 jalview.bin.Console.errPrintln(WebServiceName
753    + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
754    + "When contacting Server:" + WsUrl + "\n");
755  0 e.printStackTrace(System.err);
756  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
757  0 wsInfo.setStatus(j.getJobnum(),
758    WebserviceInfo.STATE_STOPPED_SERVERERROR);
759    } catch (Exception e)
760    {
761    // For unexpected errors
762  0 jalview.bin.Console.errPrintln(WebServiceName
763    + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
764    + "When contacting Server:" + WsUrl + "\n");
765  0 e.printStackTrace(System.err);
766  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
767  0 wsInfo.setStatus(j.getJobnum(),
768    WebserviceInfo.STATE_STOPPED_SERVERERROR);
769    } finally
770    {
771  0 if (!j.isSubmitted())
772    {
773    // Boilerplate code here
774    // TODO: JBPNote catch timeout or other fault types explicitly
775   
776  0 j.setAllowedServerExceptions(0);
777  0 wsInfo.appendProgressText(j.getJobnum(), MessageManager.getString(
778    "info.failed_to_submit_sequences_for_alignment"));
779    }
780    }
781    }
782   
 
783  0 toggle @Override
784    public void parseResult()
785    {
786  0 long progbar = System.currentTimeMillis();
787  0 wsInfo.setProgressBar(
788    MessageManager.getString("status.collecting_job_results"),
789    progbar);
790  0 int results = 0; // number of result sets received
791  0 JobStateSummary finalState = new JobStateSummary();
792  0 try
793    {
794  0 for (int j = 0; j < jobs.length; j++)
795    {
796  0 MsaWSJob msjob = ((MsaWSJob) jobs[j]);
797  0 if (jobs[j].isFinished() && msjob.alignment == null)
798    {
799  0 int nunchanged = 3, nexcept = 3;
800  0 boolean jpchanged = false, jpex = false;
801  0 do
802    {
803  0 try
804    {
805  0 jpchanged = updateJobProgress(msjob);
806  0 jpex = false;
807  0 if (jpchanged)
808    {
809  0 nexcept = 3;
810    }
811    } catch (Exception e)
812    {
813   
814  0 Console.warn(
815    "Exception when retrieving remaining Job progress data for job "
816    + msjob.getJobId() + " on server " + WsUrl);
817  0 e.printStackTrace();
818  0 nexcept--;
819  0 nunchanged = 3;
820    // set flag remember that we've had an exception.
821  0 jpex = true;
822  0 jpchanged = false;
823    }
824  0 if (!jpchanged)
825    {
826  0 try
827    {
828  0 Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we
829    // experienced an exception.
830    } catch (Exception ex)
831    {
832    }
833  0 ;
834  0 nunchanged--;
835    }
836  0 } while (nunchanged > 0 && nexcept > 0);
837   
838  0 if (Console.isDebugEnabled())
839    {
840  0 jalview.bin.Console.outPrintln("Job Execution file for job: "
841    + msjob.getJobId() + " on server " + WsUrl);
842  0 jalview.bin.Console.outPrintln(msjob.getStatus());
843  0 jalview.bin.Console.outPrintln("*** End of status");
844   
845    }
846  0 try
847    {
848  0 msjob.alignment = server.getResult(msjob.getJobId());
849    } catch (compbio.metadata.ResultNotAvailableException e)
850    {
851    // job has failed for some reason - probably due to invalid
852    // parameters
853  0 Console.debug(
854    "Results not available for finished job - marking as broken job.",
855    e);
856  0 msjob.jobProgress.append(
857    "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
858    + e.getLocalizedMessage());
859  0 msjob.setjobStatus(JobStatus.FAILED);
860    } catch (Exception e)
861    {
862  0 Console.error("Couldn't get Alignment for job.", e);
863    // TODO: Increment count and retry ?
864  0 msjob.setjobStatus(JobStatus.UNDEFINED);
865    }
866    }
867  0 finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
868  0 if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete()
869    && jobs[j].hasResults())
870    {
871  0 results++;
872  0 compbio.data.sequence.Alignment alignment = ((MsaWSJob) jobs[j]).alignment;
873  0 if (alignment != null)
874    {
875    // server.close(jobs[j].getJobnum());
876    // wsInfo.appendProgressText(jobs[j].getJobnum(),
877    // "\nAlignment Object Method Notes\n");
878    // wsInfo.appendProgressText(jobs[j].getJobnum(),
879    // "Calculated with
880    // "+alignment.getMetadata().getProgram().toString());
881    // JBPNote The returned files from a webservice could be
882    // hidden behind icons in the monitor window that,
883    // when clicked, pop up their corresponding data
884    }
885    }
886    }
887    } catch (Exception ex)
888    {
889   
890  0 Console.error(
891    "Unexpected exception when processing results for " + alTitle,
892    ex);
893  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
894    }
895  0 if (results > 0)
896    {
897  0 wsInfo.showResultsNewFrame
898    .addActionListener(new java.awt.event.ActionListener()
899    {
 
900  0 toggle @Override
901    public void actionPerformed(java.awt.event.ActionEvent evt)
902    {
903  0 displayResults(true);
904    }
905    });
906  0 wsInfo.mergeResults
907    .addActionListener(new java.awt.event.ActionListener()
908    {
 
909  0 toggle @Override
910    public void actionPerformed(java.awt.event.ActionEvent evt)
911    {
912  0 displayResults(false);
913    }
914    });
915  0 wsInfo.setResultsReady();
916    }
917    else
918    {
919  0 wsInfo.setFinishedNoResults();
920    }
921  0 updateGlobalStatus(finalState);
922  0 wsInfo.setProgressBar(null, progbar);
923    }
924   
925    /**
926    * Display alignment results in a new frame (or - not currently supported -
927    * added to an existing alignment).
928    *
929    * @param newFrame
930    */
 
931  0 toggle void displayResults(boolean newFrame)
932    {
933    // view input or result data for each block
934  0 List<AlignmentOrder> alorders = new ArrayList<AlignmentOrder>();
935  0 SequenceI[][] results = new SequenceI[jobs.length][];
936  0 AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
937  0 String lastProgram = null;
938  0 MsaWSJob msjob;
939  0 for (int j = 0; j < jobs.length; j++)
940    {
941  0 if (jobs[j].hasResults())
942    {
943  0 msjob = (MsaWSJob) jobs[j];
944  0 Object[] res = msjob.getAlignment();
945  0 lastProgram = msjob.getAlignmentProgram();
946  0 alorders.add((AlignmentOrder) res[1]);
947  0 results[j] = (SequenceI[]) res[0];
948  0 orders[j] = (AlignmentOrder) res[1];
949   
950    // SequenceI[] alignment = input.getUpdated
951    }
952    else
953    {
954  0 results[j] = null;
955    }
956    }
957  0 Object[] newview = input.getUpdatedView(results, orders, getGapChar());
958    // trash references to original result data
959  0 for (int j = 0; j < jobs.length; j++)
960    {
961  0 results[j] = null;
962  0 orders[j] = null;
963    }
964  0 SequenceI[] alignment = (SequenceI[]) newview[0];
965  0 HiddenColumns hidden = (HiddenColumns) newview[1];
966  0 Alignment al = new Alignment(alignment);
967    // TODO: add 'provenance' property to alignment from the method notes
968  0 if (lastProgram != null)
969    {
970  0 al.setProperty("Alignment Program", lastProgram);
971    }
972    // accompanying each subjob
973  0 if (dataset != null)
974    {
975  0 al.setDataset(dataset);
976    }
977   
978  0 propagateDatasetMappings(al);
979    // JBNote- TODO: warn user if a block is input rather than aligned data ?
980   
981  0 if (newFrame)
982    {
983  0 displayInNewFrame(al, alorders, hidden);
984   
985    }
986    else
987    {
988    // TODO 2.9.x feature
989  0 jalview.bin.Console.outPrintln("MERGE WITH OLD FRAME");
990    // TODO: modify alignment in original frame, replacing old for new
991    // alignment using the commands.EditCommand model to ensure the update can
992    // be undone
993    }
994    }
995   
996    /**
997    * Display the alignment result in a new frame.
998    *
999    * @param al
1000    * @param alorders
1001    * @param columnselection
1002    */
 
1003  0 toggle protected void displayInNewFrame(AlignmentI al,
1004    List<AlignmentOrder> alorders, HiddenColumns hidden)
1005    {
1006  0 AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
1007    AlignFrame.DEFAULT_HEIGHT);
1008   
1009    // initialise with same renderer settings as in parent alignframe.
1010  0 af.getFeatureRenderer().transferSettings(this.featureSettings);
1011   
1012  0 if (alorders.size() > 0)
1013    {
1014  0 addSortByMenuItems(af, alorders);
1015    }
1016   
1017    // TODO: refactor retrieve and show as new splitFrame as Desktop method
1018   
1019    /*
1020    * If alignment was requested from one half of a SplitFrame, show in a
1021    * SplitFrame with the other pane similarly aligned.
1022    */
1023  0 AlignFrame requestedBy = getRequestingAlignFrame();
1024  0 if (requestedBy != null && requestedBy.getSplitViewContainer() != null
1025    && requestedBy.getSplitViewContainer()
1026    .getComplement(requestedBy) != null)
1027    {
1028  0 AlignmentI complement = requestedBy.getSplitViewContainer()
1029    .getComplement(requestedBy);
1030  0 String complementTitle = requestedBy.getSplitViewContainer()
1031    .getComplementTitle(requestedBy);
1032    // becomes null if the alignment window was closed before the alignment
1033    // job finished.
1034  0 AlignmentI copyComplement = new Alignment(complement);
1035    // todo should this be done by copy constructor?
1036  0 copyComplement.setGapCharacter(complement.getGapCharacter());
1037    // share the same dataset (and the mappings it holds)
1038  0 copyComplement.setDataset(complement.getDataset());
1039  0 copyComplement.alignAs(al);
1040  0 if (copyComplement.getHeight() > 0)
1041    {
1042  0 af.setTitle(alTitle);
1043  0 AlignFrame af2 = new AlignFrame(copyComplement,
1044    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
1045  0 af2.setTitle(complementTitle);
1046  0 String linkedTitle = MessageManager
1047    .getString("label.linked_view_title");
1048  0 JInternalFrame splitFrame = new SplitFrame(
1049  0 al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
1050  0 Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
1051  0 return;
1052    }
1053    }
1054   
1055    /*
1056    * Not from SplitFrame, or failed to created a complementary alignment
1057    */
1058  0 Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
1059    AlignFrame.DEFAULT_HEIGHT);
1060    }
1061   
1062    /**
1063    * Add sort order options to the AlignFrame menus.
1064    *
1065    * @param af
1066    * @param alorders
1067    */
 
1068  0 toggle protected void addSortByMenuItems(AlignFrame af,
1069    List<AlignmentOrder> alorders)
1070    {
1071    // update orders
1072  0 if (alorders.size() == 1)
1073    {
1074  0 af.addSortByOrderMenuItem(WebServiceName + " Ordering",
1075    alorders.get(0));
1076    }
1077    else
1078    {
1079    // construct a non-redundant ordering set
1080  0 List<String> names = new ArrayList<String>();
1081  0 for (int i = 0, l = alorders.size(); i < l; i++)
1082    {
1083  0 String orderName = " Region " + i;
1084  0 int j = i + 1;
1085   
1086  0 while (j < l)
1087    {
1088  0 if (alorders.get(i).equals(alorders.get(j)))
1089    {
1090  0 alorders.remove(j);
1091  0 l--;
1092  0 orderName += "," + j;
1093    }
1094    else
1095    {
1096  0 j++;
1097    }
1098    }
1099   
1100  0 if (i == 0 && j == 1)
1101    {
1102  0 names.add("");
1103    }
1104    else
1105    {
1106  0 names.add(orderName);
1107    }
1108    }
1109  0 for (int i = 0, l = alorders.size(); i < l; i++)
1110    {
1111  0 af.addSortByOrderMenuItem(
1112    WebServiceName + (names.get(i)) + " Ordering",
1113    alorders.get(i));
1114    }
1115    }
1116    }
1117   
 
1118  0 toggle @Override
1119    public boolean canMergeResults()
1120    {
1121  0 return false;
1122    }
1123    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 09:10:40 GMT using coverage data from Wed Nov 12 2025 09:10:27 GMT.
  • OpenClover is free and open-source software.