1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.ws.jws1

File MsaWSThread.java

 

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Classes

Class
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Actions
MsaWSThread 44 145 57
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MsaWSThread.MsaWSJob 54 83 41
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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.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.SequenceI;
31    import jalview.gui.AlignFrame;
32    import jalview.gui.Desktop;
33    import jalview.gui.WebserviceInfo;
34    import jalview.util.MessageManager;
35    import jalview.ws.AWsJob;
36    import jalview.ws.JobStateSummary;
37    import jalview.ws.WSClientI;
38   
39    import java.util.Hashtable;
40    import java.util.Vector;
41   
42    import vamsas.objects.simple.MsaResult;
43   
 
44    class MsaWSThread extends JWS1Thread implements WSClientI
45    {
46    boolean submitGaps = false; // pass sequences including gaps to alignment
47   
48    // service
49   
50    boolean preserveOrder = true; // and always store and recover sequence
51   
52    // order
53   
 
54    class MsaWSJob extends WSJob
55    {
56    // hold special input for this
57    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
58   
59    /**
60    * MsaWSJob
61    *
62    * @param jobNum
63    * int
64    * @param jobId
65    * String
66    */
 
67  0 toggle public MsaWSJob(int jobNum, SequenceI[] inSeqs)
68    {
69  0 this.jobnum = jobNum;
70  0 if (!prepareInput(inSeqs, 2))
71    {
72  0 submitted = true;
73  0 subjobComplete = true;
74  0 result = new MsaResult();
75  0 result.setFinished(true);
76  0 result.setStatus(MessageManager.getString("label.job_never_ran"));
77    }
78   
79    }
80   
81    Hashtable SeqNames = new Hashtable();
82   
83    Vector emptySeqs = new Vector();
84   
85    /**
86    * prepare input sequences for MsaWS service
87    *
88    * @param seqs
89    * jalview sequences to be prepared
90    * @param minlen
91    * minimum number of residues required for this MsaWS service
92    * @return true if seqs contains sequences to be submitted to service.
93    */
 
94  0 toggle private boolean prepareInput(SequenceI[] seqs, int minlen)
95    {
96  0 int nseqs = 0;
97  0 if (minlen < 0)
98    {
99  0 throw new Error(MessageManager.getString(
100    "error.implementation_error_minlen_must_be_greater_zero"));
101    }
102  0 for (int i = 0; i < seqs.length; i++)
103    {
104  0 if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
105    {
106  0 nseqs++;
107    }
108    }
109  0 boolean valid = nseqs > 1; // need at least two seqs
110  0 vamsas.objects.simple.Sequence[] seqarray = (valid)
111    ? new vamsas.objects.simple.Sequence[nseqs]
112    : null;
113  0 for (int i = 0, n = 0; i < seqs.length; i++)
114    {
115   
116  0 String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
117    // for
118    // any
119    // subjob
120  0 SeqNames.put(newname,
121    jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
122  0 if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
123    {
124  0 seqarray[n] = new vamsas.objects.simple.Sequence();
125  0 seqarray[n].setId(newname);
126  0 seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequenceAsString()
127    : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
128    seqs[i].getSequenceAsString()));
129    }
130    else
131    {
132  0 String empty = null;
133  0 if (seqs[i].getEnd() >= seqs[i].getStart())
134    {
135  0 empty = (submitGaps) ? seqs[i].getSequenceAsString()
136    : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
137    seqs[i].getSequenceAsString());
138    }
139  0 emptySeqs.add(new String[] { newname, empty });
140    }
141    }
142  0 this.seqs = new vamsas.objects.simple.SequenceSet();
143  0 this.seqs.setSeqs(seqarray);
144  0 return valid;
145    }
146   
147    /**
148    *
149    * @return true if getAlignment will return a valid alignment result.
150    */
 
151  0 toggle @Override
152    public boolean hasResults()
153    {
154  0 if (subjobComplete && result != null && result.isFinished()
155    && ((MsaResult) result).getMsa() != null
156    && ((MsaResult) result).getMsa().getSeqs() != null)
157    {
158  0 return true;
159    }
160  0 return false;
161    }
162   
 
163  0 toggle public Object[] getAlignment()
164    {
165   
166  0 if (result != null && result.isFinished())
167    {
168  0 SequenceI[] alseqs = null;
169  0 char alseq_gapchar = '-';
170  0 int alseq_l = 0;
171  0 if (((MsaResult) result).getMsa() != null)
172    {
173  0 alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
174  0 alseq_gapchar = ((MsaResult) result).getMsa().getGapchar()
175    .charAt(0);
176  0 alseq_l = alseqs.length;
177    }
178  0 if (emptySeqs.size() > 0)
179    {
180  0 SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
181    // get width
182  0 int i, w = 0;
183  0 if (alseq_l > 0)
184    {
185  0 for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
186    {
187  0 if (w < alseqs[i].getLength())
188    {
189  0 w = alseqs[i].getLength();
190    }
191  0 t_alseqs[i] = alseqs[i];
192  0 alseqs[i] = null;
193    }
194    }
195    // check that aligned width is at least as wide as emptySeqs width.
196  0 int ow = w, nw = w;
197  0 for (i = 0, w = emptySeqs.size(); i < w; i++)
198    {
199  0 String[] es = (String[]) emptySeqs.get(i);
200  0 if (es != null && es[1] != null)
201    {
202  0 int sw = es[1].length();
203  0 if (nw < sw)
204    {
205  0 nw = sw;
206    }
207    }
208    }
209    // make a gapped string.
210  0 StringBuffer insbuff = new StringBuffer(w);
211  0 for (i = 0; i < nw; i++)
212    {
213  0 insbuff.append(alseq_gapchar);
214    }
215  0 if (ow < nw)
216    {
217  0 for (i = 0; i < alseq_l; i++)
218    {
219  0 int sw = t_alseqs[i].getLength();
220  0 if (nw > sw)
221    {
222    // pad at end
223  0 alseqs[i].setSequence(t_alseqs[i].getSequenceAsString()
224    + insbuff.substring(0, sw - nw));
225    }
226    }
227    }
228  0 for (i = 0, w = emptySeqs.size(); i < w; i++)
229    {
230  0 String[] es = (String[]) emptySeqs.get(i);
231  0 if (es[1] == null)
232    {
233  0 t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
234    insbuff.toString(), 1, 0);
235    }
236    else
237    {
238  0 if (es[1].length() < nw)
239    {
240  0 t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
241    es[0],
242    es[1] + insbuff.substring(0, nw - es[1].length()),
243    1, 1 + es[1].length());
244    }
245    else
246    {
247  0 t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(
248    es[0], es[1]);
249    }
250    }
251    }
252  0 alseqs = t_alseqs;
253    }
254  0 AlignmentOrder msaorder = new AlignmentOrder(alseqs);
255    // always recover the order - makes parseResult()'s life easier.
256  0 jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
257    // account for any missing sequences
258  0 jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
259  0 return new Object[] { alseqs, msaorder };
260    }
261  0 return null;
262    }
263   
264    /**
265    * mark subjob as cancelled and set result object appropriatly
266    */
 
267  0 toggle void cancel()
268    {
269  0 cancelled = true;
270  0 subjobComplete = true;
271  0 result = null;
272    }
273   
274    /**
275    *
276    * @return boolean true if job can be submitted.
277    */
 
278  0 toggle @Override
279    public boolean hasValidInput()
280    {
281  0 if (seqs.getSeqs() != null)
282    {
283  0 return true;
284    }
285  0 return false;
286    }
287    }
288   
289    String alTitle; // name which will be used to form new alignment window.
290   
291    AlignmentI dataset; // dataset to which the new alignment will be
292   
293    // associated.
294   
295    ext.vamsas.MuscleWS server = null;
296   
297    /**
298    * set basic options for this (group) of Msa jobs
299    *
300    * @param subgaps
301    * boolean
302    * @param presorder
303    * boolean
304    */
 
305  0 toggle MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
306    WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
307    AlignmentView alview, String wsname, boolean subgaps,
308    boolean presorder)
309    {
310  0 super(alFrame, wsinfo, alview, wsname, wsUrl);
311  0 this.server = server;
312  0 this.submitGaps = subgaps;
313  0 this.preserveOrder = presorder;
314    }
315   
316    /**
317    * create one or more Msa jobs to align visible seuqences in _msa
318    *
319    * @param title
320    * String
321    * @param _msa
322    * AlignmentView
323    * @param subgaps
324    * boolean
325    * @param presorder
326    * boolean
327    * @param seqset
328    * Alignment
329    */
 
330  0 toggle MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
331    WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
332    String wsname, String title, AlignmentView _msa, boolean subgaps,
333    boolean presorder, AlignmentI seqset)
334    {
335  0 this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
336  0 OutputHeader = wsInfo.getProgressText();
337  0 alTitle = title;
338  0 dataset = seqset;
339   
340  0 SequenceI[][] conmsa = _msa.getVisibleContigs('-');
341  0 if (conmsa != null)
342    {
343  0 int njobs = conmsa.length;
344  0 jobs = new MsaWSJob[njobs];
345  0 for (int j = 0; j < njobs; j++)
346    {
347  0 if (j != 0)
348    {
349  0 jobs[j] = new MsaWSJob(wsinfo.addJobPane(), conmsa[j]);
350    }
351    else
352    {
353  0 jobs[j] = new MsaWSJob(0, conmsa[j]);
354    }
355  0 if (njobs > 0)
356    {
357  0 wsinfo.setProgressName("region " + jobs[j].getJobnum(),
358    jobs[j].getJobnum());
359    }
360  0 wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
361    }
362    }
363    }
364   
 
365  0 toggle @Override
366    public boolean isCancellable()
367    {
368  0 return true;
369    }
370   
 
371  0 toggle @Override
372    public void cancelJob()
373    {
374  0 if (!jobComplete && jobs != null)
375    {
376  0 boolean cancelled = true;
377  0 for (int job = 0; job < jobs.length; job++)
378    {
379  0 if (jobs[job].isSubmitted() && !jobs[job].isSubjobComplete())
380    {
381  0 String cancelledMessage = "";
382  0 try
383    {
384  0 vamsas.objects.simple.WsJobId cancelledJob = server
385    .cancel(jobs[job].getJobId());
386  0 if (cancelledJob.getStatus() == 2)
387    {
388    // CANCELLED_JOB
389  0 cancelledMessage = "Job cancelled.";
390  0 ((MsaWSJob) jobs[job]).cancel();
391  0 wsInfo.setStatus(jobs[job].getJobnum(),
392    WebserviceInfo.STATE_CANCELLED_OK);
393    }
394  0 else if (cancelledJob.getStatus() == 3)
395    {
396    // VALID UNSTOPPABLE JOB
397  0 cancelledMessage += "Server cannot cancel this job. just close the window.\n";
398  0 cancelled = false;
399    // wsInfo.setStatus(jobs[job].jobnum,
400    // WebserviceInfo.STATE_RUNNING);
401    }
402   
403  0 if (cancelledJob.getJobId() != null)
404    {
405  0 cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
406    }
407   
408  0 cancelledMessage += "\n";
409    } catch (Exception exc)
410    {
411  0 cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
412    + exc + "\n");
413  0 Console.warn(
414    "Exception whilst cancelling " + jobs[job].getJobId(),
415    exc);
416    }
417  0 wsInfo.setProgressText(jobs[job].getJobnum(),
418    OutputHeader + cancelledMessage + "\n");
419    }
420    }
421  0 if (cancelled)
422    {
423  0 wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
424  0 jobComplete = true;
425    }
426  0 this.interrupt(); // kick thread to update job states.
427    }
428    else
429    {
430  0 if (!jobComplete)
431    {
432  0 wsInfo.setProgressText(OutputHeader
433    + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
434    }
435    }
436    }
437   
 
438  0 toggle @Override
439    public void pollJob(AWsJob job) throws Exception
440    {
441  0 ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).getJobId());
442    }
443   
 
444  0 toggle @Override
445    public void StartJob(AWsJob job)
446    {
447  0 if (!(job instanceof MsaWSJob))
448    {
449  0 throw new Error(MessageManager.formatMessage(
450    "error.implementation_error_msawbjob_called", new String[]
451    { job.getClass().toString() }));
452    }
453  0 MsaWSJob j = (MsaWSJob) job;
454  0 if (j.isSubmitted())
455    {
456  0 if (Console.isDebugEnabled())
457    {
458  0 Console.debug(
459    "Tried to submit an already submitted job " + j.getJobId());
460    }
461  0 return;
462    }
463  0 if (j.seqs.getSeqs() == null)
464    {
465    // special case - selection consisted entirely of empty sequences...
466  0 j.setSubmitted(true);
467  0 j.result = new MsaResult();
468  0 j.result.setFinished(true);
469  0 j.result.setStatus(
470    MessageManager.getString("label.empty_alignment_job"));
471  0 ((MsaResult) j.result).setMsa(null);
472    }
473  0 try
474    {
475  0 vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
476   
477  0 if ((jobsubmit != null) && (jobsubmit.getStatus() == 1))
478    {
479  0 j.setJobId(jobsubmit.getJobId());
480  0 j.setSubmitted(true);
481  0 j.setSubjobComplete(false);
482    // jalview.bin.Console.outPrintln(WsURL + " Job Id '" + jobId + "'");
483    }
484    else
485    {
486  0 if (jobsubmit == null)
487    {
488  0 throw new Exception(MessageManager.formatMessage(
489    "exception.web_service_returned_null_try_later",
490    new String[]
491    { WsUrl }));
492    }
493   
494  0 throw new Exception(jobsubmit.getJobId());
495    }
496    } catch (Exception e)
497    {
498    // TODO: JBPNote catch timeout or other fault types explicitly
499    // For unexpected errors
500  0 jalview.bin.Console.errPrintln(WebServiceName
501    + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
502    + "When contacting Server:" + WsUrl + "\n" + e.toString()
503    + "\n");
504  0 j.setAllowedServerExceptions(0);
505  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
506  0 wsInfo.setStatus(j.getJobnum(),
507    WebserviceInfo.STATE_STOPPED_SERVERERROR);
508  0 wsInfo.appendProgressText(j.getJobnum(), MessageManager
509    .getString("info.failed_to_submit_sequences_for_alignment"));
510   
511    // e.printStackTrace(); // TODO: JBPNote DEBUG
512    }
513    }
514   
 
515  0 toggle private jalview.datamodel.Sequence[] getVamsasAlignment(
516    vamsas.objects.simple.Alignment valign)
517    {
518    // TODO: refactor to helper class for vamsas.objects.simple objects
519  0 vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
520  0 jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.length];
521   
522  0 for (int i = 0, j = seqs.length; i < j; i++)
523    {
524  0 msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
525    seqs[i].getSeq());
526    }
527   
528  0 return msa;
529    }
530   
 
531  0 toggle @Override
532    public void parseResult()
533    {
534  0 int results = 0; // number of result sets received
535  0 JobStateSummary finalState = new JobStateSummary();
536  0 try
537    {
538  0 for (int j = 0; j < jobs.length; j++)
539    {
540  0 finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
541  0 if (jobs[j].isSubmitted() && jobs[j].isSubjobComplete()
542    && jobs[j].hasResults())
543    {
544  0 results++;
545    // if (Cache.isDebugEnabled())
546    // {
547    // jalview.bin.Console.outPrintln("Job lob for job
548    // "+jobs[j].getJobId()+":"+jobs[j].getJobnum());
549    // jalview.bin.Console.outPrintln(jobs[j].getStatus());
550    // }
551   
552  0 vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result)
553    .getMsa();
554  0 if (valign != null)
555    {
556  0 wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager
557    .getString("info.alignment_object_method_notes"));
558  0 String[] lines = valign.getMethod();
559  0 for (int line = 0; line < lines.length; line++)
560    {
561  0 wsInfo.appendProgressText(jobs[j].getJobnum(),
562    lines[line] + "\n");
563    }
564    // JBPNote The returned files from a webservice could be
565    // hidden behind icons in the monitor window that,
566    // when clicked, pop up their corresponding data
567   
568    }
569    }
570    }
571    } catch (Exception ex)
572    {
573   
574  0 Console.error(
575    "Unexpected exception when processing results for " + alTitle,
576    ex);
577  0 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
578    }
579  0 if (results > 0)
580    {
581  0 wsInfo.showResultsNewFrame
582    .addActionListener(new java.awt.event.ActionListener()
583    {
 
584  0 toggle @Override
585    public void actionPerformed(java.awt.event.ActionEvent evt)
586    {
587  0 displayResults(true);
588    }
589    });
590  0 wsInfo.mergeResults
591    .addActionListener(new java.awt.event.ActionListener()
592    {
 
593  0 toggle @Override
594    public void actionPerformed(java.awt.event.ActionEvent evt)
595    {
596  0 displayResults(false);
597    }
598    });
599  0 wsInfo.setResultsReady();
600    }
601    else
602    {
603  0 wsInfo.setFinishedNoResults();
604    }
605    }
606   
 
607  0 toggle void displayResults(boolean newFrame)
608    {
609    // view input or result data for each block
610  0 Vector alorders = new Vector();
611  0 SequenceI[][] results = new SequenceI[jobs.length][];
612  0 AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
613  0 for (int j = 0; j < jobs.length; j++)
614    {
615  0 if (jobs[j].hasResults())
616    {
617  0 Object[] res = ((MsaWSJob) jobs[j]).getAlignment();
618  0 alorders.add(res[1]);
619  0 results[j] = (SequenceI[]) res[0];
620  0 orders[j] = (AlignmentOrder) res[1];
621   
622    // SequenceI[] alignment = input.getUpdated
623    }
624    else
625    {
626  0 results[j] = null;
627    }
628    }
629  0 Object[] newview = input.getUpdatedView(results, orders, getGapChar());
630    // trash references to original result data
631  0 for (int j = 0; j < jobs.length; j++)
632    {
633  0 results[j] = null;
634  0 orders[j] = null;
635    }
636  0 SequenceI[] alignment = (SequenceI[]) newview[0];
637  0 HiddenColumns hidden = (HiddenColumns) newview[1];
638  0 Alignment al = new Alignment(alignment);
639    // TODO: add 'provenance' property to alignment from the method notes
640    // accompanying each subjob
641  0 if (dataset != null)
642    {
643  0 al.setDataset(dataset);
644    }
645   
646  0 propagateDatasetMappings(al);
647    // JBNote- TODO: warn user if a block is input rather than aligned data ?
648   
649  0 if (newFrame)
650    {
651  0 AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
652    AlignFrame.DEFAULT_HEIGHT);
653   
654    // initialise with same renderer settings as in parent alignframe.
655  0 af.getFeatureRenderer().transferSettings(this.featureSettings);
656    // update orders
657  0 if (alorders.size() > 0)
658    {
659  0 if (alorders.size() == 1)
660    {
661  0 af.addSortByOrderMenuItem(WebServiceName + " Ordering",
662    (AlignmentOrder) alorders.get(0));
663    }
664    else
665    {
666    // construct a non-redundant ordering set
667  0 Vector names = new Vector();
668  0 for (int i = 0, l = alorders.size(); i < l; i++)
669    {
670  0 String orderName = new String(" Region " + i);
671  0 int j = i + 1;
672   
673  0 while (j < l)
674    {
675  0 if (((AlignmentOrder) alorders.get(i))
676    .equals((alorders.get(j))))
677    {
678  0 alorders.remove(j);
679  0 l--;
680  0 orderName += "," + j;
681    }
682    else
683    {
684  0 j++;
685    }
686    }
687   
688  0 if (i == 0 && j == 1)
689    {
690  0 names.add(new String(""));
691    }
692    else
693    {
694  0 names.add(orderName);
695    }
696    }
697  0 for (int i = 0, l = alorders.size(); i < l; i++)
698    {
699  0 af.addSortByOrderMenuItem(
700    WebServiceName + ((String) names.get(i)) + " Ordering",
701    (AlignmentOrder) alorders.get(i));
702    }
703    }
704    }
705   
706  0 Desktop.addInternalFrame(af, alTitle, AlignFrame.DEFAULT_WIDTH,
707    AlignFrame.DEFAULT_HEIGHT);
708   
709    }
710    else
711    {
712  0 jalview.bin.Console.outPrintln("MERGE WITH OLD FRAME");
713    // TODO: modify alignment in original frame, replacing old for new
714    // alignment using the commands.EditCommand model to ensure the update can
715    // be undone
716    }
717    }
718   
 
719  0 toggle @Override
720    public boolean canMergeResults()
721    {
722  0 return false;
723    }
724    }