- * Title: - *
- * - *- * Description: - *
- * - *- * Copyright: Copyright (c) 2004 - *
- * - *- * Company: Dundee University - *
- * - * @author not attributable - * @version 1.0 - */ class SeqSearchWSThread extends JWS1Thread implements WSClientI { String dbs = null; @@ -78,7 +68,7 @@ class SeqSearchWSThread 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")); } } @@ -102,7 +92,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI if (minlen < 0) { throw new Error( - "Implementation error: minlen must be zero or more."); + MessageManager + .getString("error.implementation_error_minlen_must_be_greater_zero")); } for (int i = 0; i < seqs.length; i++) { @@ -124,8 +115,8 @@ class SeqSearchWSThread 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(); @@ -140,11 +131,10 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI if (seqs[i].getEnd() >= seqs[i].getStart()) { empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq - .extractGaps(jalview.util.Comparison.GapChars, seqs[i] - .getSequenceAsString()); + .extractGaps(jalview.util.Comparison.GapChars, + seqs[i].getSequenceAsString()); } - emptySeqs.add(new String[] - { newname, empty }); + emptySeqs.add(new String[] { newname, empty }); } } if (submitGaps) @@ -276,8 +266,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI * trigger a 'fetchDBids' to annotate sequences with database ids... */ - return new Object[] - { al, nf }; + return new Object[] { al, nf }; } return null; } @@ -374,9 +363,8 @@ class SeqSearchWSThread 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); } @@ -430,7 +418,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI cancelledMessage += ("\nProblems cancelling the job : Exception received...\n" + exc + "\n"); Cache.log.warn( - "Exception whilst cancelling " + jobs[job].getJobId(), exc); + "Exception whilst cancelling " + jobs[job].getJobId(), + exc); } wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader + cancelledMessage + "\n"); @@ -447,25 +436,25 @@ class SeqSearchWSThread 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"); } } } public void pollJob(AWsJob job) throws Exception { - ((SeqSearchWSJob) job).result = server - .getResult(((SeqSearchWSJob) job).getJobId()); + ((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job) + .getJobId()); } public void StartJob(AWsJob job) { if (!(job instanceof SeqSearchWSJob)) { - 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() })); } SeqSearchWSJob j = (SeqSearchWSJob) job; if (j.isSubmitted()) @@ -483,13 +472,14 @@ class SeqSearchWSThread 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 { - vamsas.objects.simple.WsJobId jobsubmit = server.search(j.seqs - .getSeqs()[0], dbArg); + vamsas.objects.simple.WsJobId jobsubmit = server.search( + j.seqs.getSeqs()[0], dbArg); if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) { @@ -502,10 +492,9 @@ class SeqSearchWSThread 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()); @@ -521,13 +510,10 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI + 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 } @@ -541,8 +527,8 @@ class SeqSearchWSThread 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; @@ -561,16 +547,17 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI && jobs[j].hasResults()) { results++; - vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob)jobs[j]).result) + vamsas.objects.simple.Alignment valign = ((SeqSearchResult) ((SeqSearchWSJob) jobs[j]).result) .getAlignment(); 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, @@ -665,7 +652,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); if (nf != null) { - af.ShowNewickTree(nf, "Tree from " + this.alTitle); + af.ShowNewickTree(nf, MessageManager.formatMessage( + "label.tree_from", new String[] { this.alTitle })); } // initialise with same renderer settings as in parent alignframe. af.getFeatureRenderer().transferSettings(this.featureSettings);