- * Title: - *
- * - *- * Description: - *
- * - *- * Copyright: Copyright (c) 2004 - *
- * - *- * Company: Dundee University - *
- * - * @author not attributable - * @version 1.0 - */ class MsaWSThread extends JWS1Thread implements WSClientI { boolean submitGaps = false; // pass sequences including gaps to alignment @@ -80,7 +73,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI subjobComplete = true; result = new MsaResult(); result.setFinished(true); - result.setStatus("Job never ran - input returned to user."); + result.setStatus(MessageManager.getString("label.job_never_ran")); } } @@ -103,8 +96,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI int nseqs = 0; if (minlen < 0) { - throw new Error( - "Implementation error: minlen must be zero or more."); + throw new Error(MessageManager.getString( + "error.implementation_error_minlen_must_be_greater_zero")); } for (int i = 0; i < seqs.length; i++) { @@ -114,7 +107,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI } } boolean valid = nseqs > 1; // need at least two seqs - vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs] + vamsas.objects.simple.Sequence[] seqarray = (valid) + ? new vamsas.objects.simple.Sequence[nseqs] : null; for (int i = 0, n = 0; i < seqs.length; i++) { @@ -123,8 +117,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI // for // any // subjob - SeqNames.put(newname, jalview.analysis.SeqsetUtils - .SeqCharacterHash(seqs[i])); + SeqNames.put(newname, + jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i])); if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1) { seqarray[n] = new vamsas.objects.simple.Sequence(); @@ -138,12 +132,11 @@ class MsaWSThread extends JWS1Thread implements WSClientI String empty = null; if (seqs[i].getEnd() >= seqs[i].getStart()) { - empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq - .extractGaps(jalview.util.Comparison.GapChars, seqs[i] - .getSequenceAsString()); + empty = (submitGaps) ? seqs[i].getSequenceAsString() + : AlignSeq.extractGaps(jalview.util.Comparison.GapChars, + seqs[i].getSequenceAsString()); } - emptySeqs.add(new String[] - { newname, empty }); + emptySeqs.add(new String[] { newname, empty }); } } this.seqs = new vamsas.objects.simple.SequenceSet(); @@ -155,6 +148,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI * * @return true if getAlignment will return a valid alignment result. */ + @Override public boolean hasResults() { if (subjobComplete && result != null && result.isFinished() @@ -262,8 +256,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI jalview.analysis.AlignmentSorter.recoverOrder(alseqs); // account for any missing sequences jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs); - return new Object[] - { alseqs, msaorder }; + return new Object[] { alseqs, msaorder }; } return null; } @@ -282,6 +275,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI * * @return boolean true if job can be submitted. */ + @Override public boolean hasValidInput() { if (seqs.getSeqs() != null) @@ -294,7 +288,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI String alTitle; // name which will be used to form new alignment window. - Alignment dataset; // dataset to which the new alignment will be + AlignmentI dataset; // dataset to which the new alignment will be // associated. @@ -336,7 +330,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl, WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, String wsname, String title, AlignmentView _msa, boolean subgaps, - boolean presorder, Alignment seqset) + boolean presorder, AlignmentI seqset) { this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder); OutputHeader = wsInfo.getProgressText(); @@ -360,20 +354,21 @@ class MsaWSThread extends JWS1Thread implements WSClientI } if (njobs > 0) { - wsinfo - .setProgressName("region " + jobs[j].getJobnum(), - jobs[j].getJobnum()); + wsinfo.setProgressName("region " + jobs[j].getJobnum(), + jobs[j].getJobnum()); } wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader); } } } + @Override public boolean isCancellable() { return true; } + @Override public void cancelJob() { if (!jobComplete && jobs != null) @@ -415,11 +410,12 @@ class MsaWSThread extends JWS1Thread implements WSClientI { cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" + exc + "\n"); - Cache.log.warn( - "Exception whilst cancelling " + jobs[job].getJobId(), exc); + Console.warn( + "Exception whilst cancelling " + jobs[job].getJobId(), + exc); } - wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader - + cancelledMessage + "\n"); + wsInfo.setProgressText(jobs[job].getJobnum(), + OutputHeader + cancelledMessage + "\n"); } } if (cancelled) @@ -433,32 +429,34 @@ class MsaWSThread extends JWS1Thread implements WSClientI { if (!jobComplete) { - wsInfo - .setProgressText(OutputHeader - + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n"); + wsInfo.setProgressText(OutputHeader + + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n"); } } } + @Override public void pollJob(AWsJob job) throws Exception { ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).getJobId()); } + @Override public void StartJob(AWsJob job) { if (!(job instanceof MsaWSJob)) { - throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " - + job.getClass()); + throw new Error(MessageManager.formatMessage( + "error.implementation_error_msawbjob_called", new String[] + { job.getClass().toString() })); } MsaWSJob j = (MsaWSJob) job; if (j.isSubmitted()) { - if (Cache.log.isDebugEnabled()) + if (Console.isDebugEnabled()) { - Cache.log.debug("Tried to submit an already submitted job " - + j.getJobId()); + Console.debug( + "Tried to submit an already submitted job " + j.getJobId()); } return; } @@ -468,7 +466,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI j.setSubmitted(true); j.result = new MsaResult(); j.result.setFinished(true); - j.result.setStatus("Empty Alignment Job"); + j.result.setStatus( + MessageManager.getString("label.empty_alignment_job")); ((MsaResult) j.result).setMsa(null); } try @@ -486,10 +485,10 @@ class MsaWSThread extends JWS1Thread implements WSClientI { if (jobsubmit == null) { - throw new Exception( - "Server at " - + WsUrl - + " returned null object, it probably cannot be contacted. Try again later ?"); + throw new Exception(MessageManager.formatMessage( + "exception.web_service_returned_null_try_later", + new String[] + { WsUrl })); } throw new Exception(jobsubmit.getJobId()); @@ -498,20 +497,16 @@ class MsaWSThread extends JWS1Thread implements WSClientI { // TODO: JBPNote catch timeout or other fault types explicitly // For unexpected errors - System.err - .println(WebServiceName - + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" - + "When contacting Server:" + WsUrl + "\n" - + e.toString() + "\n"); + System.err.println(WebServiceName + + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" + + "When contacting Server:" + WsUrl + "\n" + e.toString() + + "\n"); j.setAllowedServerExceptions(0); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR); - wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR); - wsInfo - .appendProgressText( - j.getJobnum(), - "Failed to submit sequences for alignment.\n" - + "It is most likely that there is a problem with the server.\n" - + "Just close the window\n"); + wsInfo.setStatus(j.getJobnum(), + WebserviceInfo.STATE_STOPPED_SERVERERROR); + wsInfo.appendProgressText(j.getJobnum(), MessageManager + .getString("info.failed_to_submit_sequences_for_alignment")); // e.printStackTrace(); // TODO: JBPNote DEBUG } @@ -526,13 +521,14 @@ class MsaWSThread extends JWS1Thread implements WSClientI for (int i = 0, j = seqs.length; i < j; i++) { - msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), seqs[i] - .getSeq()); + msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(), + seqs[i].getSeq()); } return msa; } + @Override public void parseResult() { int results = 0; // number of result sets received @@ -546,28 +542,38 @@ class MsaWSThread extends JWS1Thread implements WSClientI && jobs[j].hasResults()) { results++; - vamsas.objects.simple.Alignment valign = ((MsaResult)((MsaWSJob) jobs[j]).result) + // if (Cache.isDebugEnabled()) + // { + // System.out.println("Job lob for job + // "+jobs[j].getJobId()+":"+jobs[j].getJobnum()); + // System.out.println(jobs[j].getStatus()); + // } + + vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result) .getMsa(); if (valign != null) { - wsInfo.appendProgressText(jobs[j].getJobnum(), - "\nAlignment Object Method Notes\n"); + wsInfo.appendProgressText(jobs[j].getJobnum(), MessageManager + .getString("info.alignment_object_method_notes")); String[] lines = valign.getMethod(); for (int line = 0; line < lines.length; line++) { - wsInfo.appendProgressText(jobs[j].getJobnum(), lines[line] + "\n"); + wsInfo.appendProgressText(jobs[j].getJobnum(), + lines[line] + "\n"); } // JBPNote The returned files from a webservice could be // hidden behind icons in the monitor window that, // when clicked, pop up their corresponding data + } } } } catch (Exception ex) { - Cache.log.error("Unexpected exception when processing results for " - + alTitle, ex); + Console.error( + "Unexpected exception when processing results for " + alTitle, + ex); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } if (results > 0) @@ -575,6 +581,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI wsInfo.showResultsNewFrame .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(true); @@ -583,6 +590,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI wsInfo.mergeResults .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(false); @@ -626,7 +634,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI orders[j] = null; } SequenceI[] alignment = (SequenceI[]) newview[0]; - ColumnSelection columnselection = (ColumnSelection) newview[1]; + HiddenColumns hidden = (HiddenColumns) newview[1]; Alignment al = new Alignment(alignment); // TODO: add 'provenance' property to alignment from the method notes // accompanying each subjob @@ -640,8 +648,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI if (newFrame) { - AlignFrame af = new AlignFrame(al, columnselection, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + AlignFrame af = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); // initialise with same renderer settings as in parent alignframe. af.getFeatureRenderer().transferSettings(this.featureSettings); @@ -665,7 +673,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI while (j < l) { if (((AlignmentOrder) alorders.get(i)) - .equals(((AlignmentOrder) alorders.get(j)))) + .equals((alorders.get(j)))) { alorders.remove(j); l--; @@ -688,8 +696,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI } for (int i = 0, l = alorders.size(); i < l; i++) { - af.addSortByOrderMenuItem(WebServiceName - + ((String) names.get(i)) + " Ordering", + af.addSortByOrderMenuItem( + WebServiceName + ((String) names.get(i)) + " Ordering", (AlignmentOrder) alorders.get(i)); } } @@ -708,6 +716,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI } } + @Override public boolean canMergeResults() { return false;