- * 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 @@ -123,8 +106,8 @@ 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(); @@ -139,8 +122,8 @@ class MsaWSThread 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 }); @@ -360,9 +343,8 @@ 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); } @@ -416,7 +398,8 @@ 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); + "Exception whilst cancelling " + jobs[job].getJobId(), + exc); } wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader + cancelledMessage + "\n"); @@ -433,9 +416,8 @@ 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"); } } } @@ -505,13 +487,13 @@ class MsaWSThread 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(), + "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"); // e.printStackTrace(); // TODO: JBPNote DEBUG } @@ -526,8 +508,8 @@ 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; @@ -546,13 +528,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI && jobs[j].hasResults()) { results++; - //if (Cache.log.isDebugEnabled()) - // { - // System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum()); - // System.out.println(jobs[j].getStatus()); - // } + // if (Cache.log.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) + vamsas.objects.simple.Alignment valign = ((MsaResult) ((MsaWSJob) jobs[j]).result) .getMsa(); if (valign != null) { @@ -561,12 +543,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI 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 - + } } } @@ -695,8 +678,8 @@ 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)); } }