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Coverage Report

  1. Project Clover database Tue Oct 29 2024 21:36:55 GMT
  2. Package jalview.ws.jws1

File JPredThread.java

 

Coverage histogram

../../../img/srcFileCovDistChart0.png
58% of files have more coverage

Code metrics

96
203
20
2
683
544
80
0.39
10.15
10
4

Classes

Class Line # Actions
JPredThread 53 98 37
0.00%
JPredThread.JPredJob 57 105 43
0.00%
 

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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.jws1;
22   
23    import jalview.analysis.AlignSeq;
24    import jalview.analysis.SeqsetUtils;
25    import jalview.bin.Console;
26    import jalview.datamodel.Alignment;
27    import jalview.datamodel.AlignmentAnnotation;
28    import jalview.datamodel.AlignmentI;
29    import jalview.datamodel.AlignmentView;
30    import jalview.datamodel.HiddenColumns;
31    import jalview.datamodel.SequenceI;
32    import jalview.gui.AlignFrame;
33    import jalview.gui.Desktop;
34    import jalview.gui.WebserviceInfo;
35    import jalview.io.DataSourceType;
36    import jalview.io.FileFormatI;
37    import jalview.io.FormatAdapter;
38    import jalview.io.IdentifyFile;
39    import jalview.io.JPredFile;
40    import jalview.io.JnetAnnotationMaker;
41    import jalview.io.PileUpfile;
42    import jalview.util.Comparison;
43    import jalview.util.MessageManager;
44    import jalview.ws.AWsJob;
45    import jalview.ws.JobStateSummary;
46    import jalview.ws.WSClientI;
47   
48    import java.util.Hashtable;
49    import java.util.List;
50   
51    import vamsas.objects.simple.JpredResult;
52   
 
53    class JPredThread extends JWS1Thread implements WSClientI
54    {
55    // TODO: put mapping between JPredJob input and input data here -
56    // JNetAnnotation adding is done after result parsing.
 
57    class JPredJob extends WSJob
58    {
59    // TODO: make JPredJob deal only with what was sent to and received from a
60    // JNet service
61    int[] predMap = null; // mapping from sequence(i) to the original
62   
63    // sequence(predMap[i]) being predicted on
64   
65    vamsas.objects.simple.Sequence sequence;
66   
67    vamsas.objects.simple.Msfalignment msa;
68   
69    java.util.Hashtable SequenceInfo = null;
70   
71    int msaIndex = 0; // the position of the original sequence in the array of
72   
73    // Sequences in the input object that this job holds a
74    // prediction for
75   
76    /**
77    *
78    * @return true if getResultSet will return a valid alignment and prediction
79    * result.
80    */
 
81  0 toggle @Override
82    public boolean hasResults()
83    {
84  0 if (subjobComplete && result != null && result.isFinished()
85    && ((JpredResult) result).getPredfile() != null
86    && ((JpredResult) result).getAligfile() != null)
87    {
88  0 return true;
89    }
90  0 return false;
91    }
92   
 
93  0 toggle @Override
94    public boolean hasValidInput()
95    {
96  0 if (sequence != null)
97    {
98  0 return true;
99    }
100  0 return false;
101    }
102   
103    /**
104    *
105    * @return null or Object[] { annotated alignment for this prediction,
106    * ColumnSelection for this prediction} or null if no results
107    * available.
108    * @throws Exception
109    */
 
110  0 toggle public Object[] getResultSet() throws Exception
111    {
112  0 if (result == null || !result.isFinished())
113    {
114  0 return null;
115    }
116  0 AlignmentI al = null;
117  0 HiddenColumns alhidden = null;
118  0 int FirstSeq = -1; // the position of the query sequence in Alignment al
119   
120  0 JpredResult result = (JpredResult) this.result;
121   
122  0 Console.debug("Parsing output from JNet job.");
123    // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt",
124    // "File");
125  0 JPredFile prediction = new JPredFile(result.getPredfile(),
126    DataSourceType.PASTE);
127  0 SequenceI[] preds = prediction.getSeqsAsArray();
128  0 Console.debug("Got prediction profile.");
129   
130  0 if ((this.msa != null) && (result.getAligfile() != null))
131    {
132  0 Console.debug("Getting associated alignment.");
133    // we ignore the returned alignment if we only predicted on a single
134    // sequence
135  0 FileFormatI format = new IdentifyFile()
136    .identify(result.getAligfile(), DataSourceType.PASTE);
137   
138  0 if (format != null)
139    {
140  0 SequenceI sqs[];
141  0 if (predMap != null)
142    {
143  0 Object[] alandcolsel = input
144    .getAlignmentAndHiddenColumns(getGapChar());
145  0 sqs = (SequenceI[]) alandcolsel[0];
146  0 al = new Alignment(sqs);
147  0 alhidden = (HiddenColumns) alandcolsel[1];
148    }
149    else
150    {
151  0 al = new FormatAdapter().readFile(result.getAligfile(),
152    DataSourceType.PASTE, format);
153  0 sqs = new SequenceI[al.getHeight()];
154   
155  0 for (int i = 0, j = al.getHeight(); i < j; i++)
156    {
157  0 sqs[i] = al.getSequenceAt(i);
158    }
159  0 if (!SeqsetUtils.deuniquify(SequenceInfo, sqs))
160    {
161  0 throw (new Exception(MessageManager.getString(
162    "exception.couldnt_recover_sequence_properties_for_alignment")));
163    }
164    }
165  0 FirstSeq = 0;
166  0 if (currentView.getDataset() != null)
167    {
168  0 al.setDataset(currentView.getDataset());
169   
170    }
171    else
172    {
173  0 al.setDataset(null);
174    }
175  0 JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
176    false, predMap);
177   
178    }
179    else
180    {
181  0 throw (new Exception(MessageManager.formatMessage(
182    "exception.unknown_format_for_file", new String[]
183    { "", result.getAligfile() })));
184    }
185    }
186    else
187    {
188  0 al = new Alignment(preds);
189  0 FirstSeq = prediction.getQuerySeqPosition();
190  0 if (predMap != null)
191    {
192  0 char gc = getGapChar();
193  0 SequenceI[] sqs = (SequenceI[]) input
194    .getAlignmentAndHiddenColumns(gc)[0];
195  0 if (this.msaIndex >= sqs.length)
196    {
197  0 throw new Error(MessageManager.getString(
198    "error.implementation_error_invalid_msa_index_for_job"));
199    }
200   
201    // ///
202    // Uses RemoveGapsCommand
203    // ///
204  0 new jalview.commands.RemoveGapsCommand(
205    MessageManager.getString("label.remove_gaps"),
206    new SequenceI[]
207    { sqs[msaIndex] }, currentView);
208   
209  0 SequenceI profileseq = al.getSequenceAt(FirstSeq);
210  0 profileseq.setSequence(sqs[msaIndex].getSequenceAsString());
211    }
212   
213  0 if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
214    al.getSequenceAt(FirstSeq), SequenceInfo))
215    {
216  0 throw (new Exception(MessageManager.getString(
217    "exception.couldnt_recover_sequence_props_for_jnet_query")));
218    }
219    else
220    {
221  0 if (currentView.getDataset() != null)
222    {
223  0 al.setDataset(currentView.getDataset());
224   
225    }
226    else
227    {
228  0 al.setDataset(null);
229    }
230  0 jalview.io.JnetAnnotationMaker.add_annotation(prediction, al,
231    FirstSeq, true, predMap);
232  0 SequenceI profileseq = al.getSequenceAt(0); // this includes any gaps.
233  0 alignToProfileSeq(al, profileseq);
234  0 if (predMap != null)
235    {
236    // Adjust input view for gaps
237    // propagate insertions into profile
238  0 alhidden = al.propagateInsertions(profileseq, input);
239    }
240    }
241    }
242    // transfer to dataset
243  0 for (AlignmentAnnotation alant : al.getAlignmentAnnotation())
244    {
245  0 if (alant.sequenceRef != null)
246    {
247  0 replaceAnnotationOnAlignmentWith(alant, alant.label,
248  0 "jalview.jws1.Jpred" + (this.msa == null ? "" : "MSA"),
249    alant.sequenceRef);
250    }
251    }
252  0 return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
253    }
254   
255    /**
256    * copied from JabawsCalcWorker
257    *
258    * @param newAnnot
259    * @param typeName
260    * @param calcId
261    * @param aSeq
262    */
 
263  0 toggle protected void replaceAnnotationOnAlignmentWith(
264    AlignmentAnnotation newAnnot, String typeName, String calcId,
265    SequenceI aSeq)
266    {
267  0 SequenceI dsseq = aSeq.getDatasetSequence();
268  0 while (dsseq.getDatasetSequence() != null)
269    {
270  0 dsseq = dsseq.getDatasetSequence();
271    }
272    // look for same annotation on dataset and lift this one over
273  0 List<AlignmentAnnotation> dsan = dsseq.getAlignmentAnnotations(calcId,
274    typeName);
275  0 if (dsan != null && dsan.size() > 0)
276    {
277  0 for (AlignmentAnnotation dssan : dsan)
278    {
279  0 dsseq.removeAlignmentAnnotation(dssan);
280    }
281    }
282  0 AlignmentAnnotation dssan = new AlignmentAnnotation(newAnnot);
283  0 dsseq.addAlignmentAnnotation(dssan);
284  0 dssan.adjustForAlignment();
285    }
286   
287    /**
288    * Given an alignment where all other sequences except profileseq are
289    * aligned to the ungapped profileseq, insert gaps in the other sequences to
290    * realign them with the residues in profileseq
291    *
292    * @param al
293    * @param profileseq
294    */
 
295  0 toggle private void alignToProfileSeq(AlignmentI al, SequenceI profileseq)
296    {
297  0 char gc = al.getGapCharacter();
298  0 int[] gapMap = profileseq.gapMap();
299    // insert gaps into profile
300  0 for (int lp = 0, r = 0; r < gapMap.length; r++)
301    {
302  0 if (gapMap[r] - lp > 1)
303    {
304  0 StringBuffer sb = new StringBuffer();
305  0 for (int s = 0, ns = gapMap[r] - lp; s < ns; s++)
306    {
307  0 sb.append(gc);
308    }
309  0 for (int s = 1, ns = al.getHeight(); s < ns; s++)
310    {
311  0 String sq = al.getSequenceAt(s).getSequenceAsString();
312  0 int diff = gapMap[r] - sq.length();
313  0 if (diff > 0)
314    {
315    // pad gaps
316  0 sq = sq + sb;
317  0 while ((diff = gapMap[r] - sq.length()) > 0)
318    {
319  0 sq = sq + ((diff >= sb.length()) ? sb.toString()
320    : sb.substring(0, diff));
321    }
322  0 al.getSequenceAt(s).setSequence(sq);
323    }
324    else
325    {
326  0 al.getSequenceAt(s).setSequence(sq.substring(0, gapMap[r])
327    + sb.toString() + sq.substring(gapMap[r]));
328    }
329    }
330    }
331  0 lp = gapMap[r];
332    }
333    }
334   
 
335  0 toggle public JPredJob(Hashtable SequenceInfo, SequenceI seq, int[] delMap)
336    {
337  0 super();
338  0 this.predMap = delMap;
339  0 String sq = AlignSeq.extractGaps(Comparison.GapChars,
340    seq.getSequenceAsString());
341  0 if (sq.length() >= 20)
342    {
343  0 this.SequenceInfo = SequenceInfo;
344  0 sequence = new vamsas.objects.simple.Sequence();
345  0 sequence.setId(seq.getName());
346  0 sequence.setSeq(sq);
347    }
348    else
349    {
350  0 errorMessage = "Sequence is too short to predict with JPred - need at least 20 amino acids.";
351    }
352    }
353   
 
354  0 toggle public JPredJob(Hashtable SequenceInfo, SequenceI[] msf, int[] delMap)
355    {
356  0 this(SequenceInfo, msf[0], delMap);
357  0 if (sequence != null)
358    {
359  0 if (msf.length > 1)
360    {
361  0 msa = new vamsas.objects.simple.Msfalignment();
362  0 PileUpfile pileup = new PileUpfile();
363  0 msa.setMsf(pileup.print(msf, true));
364    }
365    }
366    }
367   
368    String errorMessage = "";
369   
 
370  0 toggle public String getValidationMessages()
371    {
372  0 return errorMessage + "\n";
373    }
374    }
375   
376    ext.vamsas.Jpred server;
377   
378    String altitle = "";
379   
 
380  0 toggle JPredThread(WebserviceInfo wsinfo, String altitle,
381    ext.vamsas.Jpred server, String wsurl, AlignmentView alview,
382    AlignFrame alframe)
383    {
384  0 super(alframe, wsinfo, alview, wsurl);
385  0 this.altitle = altitle;
386  0 this.server = server;
387    }
388   
 
389  0 toggle JPredThread(WebserviceInfo wsinfo, String altitle,
390    ext.vamsas.Jpred server, String wsurl, Hashtable SequenceInfo,
391    SequenceI seq, int[] delMap, AlignmentView alview,
392    AlignFrame alframe)
393    {
394  0 this(wsinfo, altitle, server, wsurl, alview, alframe);
395  0 JPredJob job = new JPredJob(SequenceInfo, seq, delMap);
396  0 if (job.hasValidInput())
397    {
398  0 OutputHeader = wsInfo.getProgressText();
399  0 jobs = new WSJob[] { job };
400  0 job.setJobnum(0);
401    }
402    else
403    {
404  0 wsInfo.appendProgressText(job.getValidationMessages());
405    }
406    }
407   
 
408  0 toggle JPredThread(WebserviceInfo wsinfo, String altitle,
409    ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf,
410    int[] delMap, AlignmentView alview, AlignFrame alframe,
411    String wsurl)
412    {
413  0 this(wsinfo, altitle, server, wsurl, alview, alframe);
414  0 JPredJob job = new JPredJob(SequenceInfo, msf, delMap);
415  0 if (job.hasValidInput())
416    {
417  0 jobs = new WSJob[] { job };
418  0 OutputHeader = wsInfo.getProgressText();
419  0 job.setJobnum(0);
420    }
421    else
422    {
423  0 wsInfo.appendProgressText(job.getValidationMessages());
424    }
425    }
426   
 
427  0 toggle @Override
428    public void StartJob(AWsJob j)
429    {
430  0 if (!(j instanceof JPredJob))
431    {
432  0 throw new Error(MessageManager.formatMessage(
433    "error.implementation_error_startjob_called", new String[]
434    { j.getClass().toString() }));
435    }
436  0 try
437    {
438  0 JPredJob job = (JPredJob) j;
439  0 if (job.msa != null)
440    {
441  0 job.setJobId(server.predictOnMsa(job.msa));
442    }
443  0 else if (job.sequence != null)
444    {
445  0 job.setJobId(server.predict(job.sequence)); // debug like : job.jobId =
446    // "/jobs/www-jpred/jp_Yatat29";//
447    }
448   
449  0 if (job.getJobId() != null)
450    {
451  0 if (job.getJobId().startsWith("Broken"))
452    {
453  0 job.result = new JpredResult();
454  0 job.result.setInvalid(true);
455  0 job.result.setStatus(MessageManager
456    .formatMessage("label.submission_params", new String[]
457    { job.getJobId().toString() }));
458  0 throw new Exception(job.getJobId());
459    }
460    else
461    {
462  0 job.setSubmitted(true);
463  0 job.setSubjobComplete(false);
464  0 Console.info(WsUrl + " Job Id '" + job.getJobId() + "'");
465    }
466    }
467    else
468    {
469  0 throw new Exception(MessageManager
470    .getString("exception.server_timeout_try_later"));
471    }
472    } catch (Exception e)
473    {
474    // kill the whole job.
475  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
476  0 if (e.getMessage().indexOf("Exception") > -1)
477    {
478  0 wsInfo.setStatus(j.getJobnum(),
479    WebserviceInfo.STATE_STOPPED_SERVERERROR);
480  0 wsInfo.setProgressText(j.getJobnum(),
481    "Failed to submit the prediction. (Just close the window)\n"
482    + "It is most likely that there is a problem with the server.\n");
483  0 jalview.bin.Console.errPrintln(
484    "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n"
485    + e.getMessage() + "\n");
486   
487  0 Console.warn("Server Exception", e);
488    }
489    else
490    {
491  0 wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
492    // JBPNote - this could be a popup informing the user of the problem.
493  0 wsInfo.appendProgressText(j.getJobnum(),
494    MessageManager.formatMessage(
495    "info.failed_to_submit_prediction", new String[]
496    { e.getMessage(), wsInfo.getProgressText() }));
497   
498  0 Console.debug("Failed Submission of job " + j.getJobnum(), e);
499   
500    }
501  0 j.setAllowedServerExceptions(-1);
502  0 j.setSubjobComplete(true);
503    }
504    }
505   
 
506  0 toggle @Override
507    public void parseResult()
508    {
509  0 int results = 0; // number of result sets received
510  0 JobStateSummary finalState = new JobStateSummary();
511  0 try
512    {
513  0 for (int j = 0; j < jobs.length; j++)
514    {
515  0 finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
516  0 if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete()
517    && jobs[j].hasResults())
518    {
519  0 results++;
520    }
521    }
522    } catch (Exception ex)
523    {
524   
525  0 Console.error(
526    "Unexpected exception when processing results for " + altitle,
527    ex);
528  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
529    }
530  0 if (results > 0)
531    {
532  0 wsInfo.showResultsNewFrame
533    .addActionListener(new java.awt.event.ActionListener()
534    {
 
535  0 toggle @Override
536    public void actionPerformed(java.awt.event.ActionEvent evt)
537    {
538  0 displayResults(true);
539    }
540    });
541  0 wsInfo.mergeResults
542    .addActionListener(new java.awt.event.ActionListener()
543    {
 
544  0 toggle @Override
545    public void actionPerformed(java.awt.event.ActionEvent evt)
546    {
547  0 displayResults(false);
548    }
549    });
550  0 wsInfo.setResultsReady();
551    }
552    else
553    {
554  0 wsInfo.setStatus(wsInfo.STATE_STOPPED_ERROR);
555  0 wsInfo.appendInfoText("No jobs ran.");
556  0 wsInfo.setFinishedNoResults();
557    }
558    }
559   
 
560  0 toggle void displayResults(boolean newWindow)
561    {
562    // TODO: cope with multiple subjobs.
563  0 if (jobs != null)
564    {
565  0 Object[] res = null;
566  0 boolean msa = false;
567  0 for (int jn = 0; jn < jobs.length; jn++)
568    {
569  0 Object[] jobres = null;
570  0 JPredJob j = (JPredJob) jobs[jn];
571   
572  0 if (j.hasResults())
573    {
574    // hack - we only deal with all single seuqence predictions or all
575    // profile predictions
576  0 msa = (j.msa != null) ? true : msa;
577  0 try
578    {
579  0 Console.debug("Parsing output of job " + jn);
580  0 jobres = j.getResultSet();
581  0 Console.debug("Finished parsing output.");
582  0 if (jobs.length == 1)
583    {
584  0 res = jobres;
585    }
586    else
587    {
588    // do merge with other job results
589  0 throw new Error(MessageManager.getString(
590    "error.multiple_jnet_subjob_merge_not_implemented"));
591    }
592    } catch (Exception e)
593    {
594  0 Console.error("JNet Client: JPred Annotation Parse Error", e);
595  0 wsInfo.setStatus(j.getJobnum(),
596    WebserviceInfo.STATE_STOPPED_ERROR);
597  0 wsInfo.appendProgressText(j.getJobnum(),
598    MessageManager.formatMessage(
599    "info.invalid_jnet_job_result_data",
600    new String[]
601    { OutputHeader.toString(), j.result.getStatus(),
602    e.getMessage() }));
603  0 j.result.setBroken(true);
604    }
605    }
606    }
607   
608  0 if (res != null)
609    {
610  0 if (newWindow)
611    {
612  0 AlignFrame af;
613  0 ((AlignmentI) res[0])
614    .setSeqrep(((AlignmentI) res[0]).getSequenceAt(0));
615  0 if (input == null)
616    {
617  0 if (res[1] != null)
618    {
619  0 af = new AlignFrame((Alignment) res[0],
620    (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH,
621    AlignFrame.DEFAULT_HEIGHT);
622    }
623    else
624    {
625  0 af = new AlignFrame((Alignment) res[0],
626    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
627    }
628    }
629    else
630    {
631    /*
632    * java.lang.Object[] alandcolsel =
633    * input.getAlignmentAndColumnSelection
634    * (alignFrame.getViewport().getGapCharacter()); if
635    * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
636    * if (msa) { throw new Error("Implementation Error! ColumnSelection
637    * from input alignment will not map to result alignment!"); } } if
638    * (!msa) { // update hidden regions to account for loss of gaps in
639    * profile. - if any // gapMap returns insert list, interpreted as
640    * delete list by pruneDeletions //((ColumnSelection)
641    * alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[])
642    * alandcolsel[0])[0].gapMap())); }
643    */
644   
645  0 af = new AlignFrame((Alignment) res[0], (HiddenColumns) res[1],
646    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
647    }
648  0 Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,
649    AlignFrame.DEFAULT_HEIGHT);
650    }
651    else
652    {
653  0 Console.info("Append results onto existing alignment.");
654    }
655    }
656    }
657    }
658   
 
659  0 toggle @Override
660    public void pollJob(AWsJob job) throws Exception
661    {
662  0 ((JPredJob) job).result = server.getresult(job.getJobId());
663    }
664   
 
665  0 toggle @Override
666    public boolean isCancellable()
667    {
668  0 return false;
669    }
670   
 
671  0 toggle @Override
672    public void cancelJob()
673    {
674  0 throw new Error(MessageManager.getString("error.implementation_error"));
675    }
676   
 
677  0 toggle @Override
678    public boolean canMergeResults()
679    {
680  0 return false;
681    }
682   
683    }
  • Report generated by OpenClover v 4.4.1 on Tue Oct 29 2024 21:44:08 GMT using coverage data from Tue Oct 29 2024 21:43:45 GMT.
  • OpenClover is free and open-source software.