X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FMsaWSThread.java;h=006f014e918dabeed6f28f3d0de13917fe83907d;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=a6ba7517e66dcc91090d17f47427fe897699aaa1;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java index a6ba751..006f014 100644 --- a/src/jalview/ws/jws1/MsaWSThread.java +++ b/src/jalview/ws/jws1/MsaWSThread.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,16 +20,25 @@ */ package jalview.ws.jws1; -import java.util.*; - -import jalview.analysis.*; -import jalview.bin.*; -import jalview.datamodel.*; -import jalview.gui.*; +import jalview.analysis.AlignSeq; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.WebserviceInfo; import jalview.util.MessageManager; import jalview.ws.AWsJob; import jalview.ws.JobStateSummary; import jalview.ws.WSClientI; + +import java.util.Hashtable; +import java.util.Vector; + import vamsas.objects.simple.MsaResult; class MsaWSThread extends JWS1Thread implements WSClientI @@ -87,7 +96,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI int nseqs = 0; if (minlen < 0) { - throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero")); + throw new Error(MessageManager.getString( + "error.implementation_error_minlen_must_be_greater_zero")); } for (int i = 0; i < seqs.length; i++) { @@ -97,7 +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++) { @@ -121,12 +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, + 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(); @@ -138,6 +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() @@ -245,8 +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; } @@ -265,6 +275,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI * * @return boolean true if job can be submitted. */ + @Override public boolean hasValidInput() { if (seqs.getSeqs() != null) @@ -277,7 +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. @@ -319,7 +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(); @@ -351,11 +362,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI } } + @Override public boolean isCancellable() { return true; } + @Override public void cancelJob() { if (!jobComplete && jobs != null) @@ -401,8 +414,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI "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) @@ -422,24 +435,28 @@ class MsaWSThread extends JWS1Thread implements WSClientI } } + @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(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()})); + 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()) { - Cache.log.debug("Tried to submit an already submitted job " - + j.getJobId()); + Cache.log.debug( + "Tried to submit an already submitted job " + j.getJobId()); } return; } @@ -449,7 +466,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI j.setSubmitted(true); j.result = new MsaResult(); j.result.setFinished(true); - j.result.setStatus(MessageManager.getString("label.empty_alignment_job")); + j.result.setStatus( + MessageManager.getString("label.empty_alignment_job")); ((MsaResult) j.result).setMsa(null); } try @@ -467,7 +485,10 @@ class MsaWSThread extends JWS1Thread implements WSClientI { if (jobsubmit == null) { - throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl})); + throw new Exception(MessageManager.formatMessage( + "exception.web_service_returned_null_try_later", + new String[] + { WsUrl })); } throw new Exception(jobsubmit.getJobId()); @@ -476,18 +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(), - MessageManager.getString("info.failed_to_submit_sequences_for_alignment")); + wsInfo.appendProgressText(j.getJobnum(), MessageManager + .getString("info.failed_to_submit_sequences_for_alignment")); // e.printStackTrace(); // TODO: JBPNote DEBUG } @@ -509,6 +528,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI return msa; } + @Override public void parseResult() { int results = 0; // number of result sets received @@ -524,7 +544,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI results++; // if (Cache.log.isDebugEnabled()) // { - // System.out.println("Job lob for job "+jobs[j].getJobId()+":"+jobs[j].getJobnum()); + // System.out.println("Job lob for job + // "+jobs[j].getJobId()+":"+jobs[j].getJobnum()); // System.out.println(jobs[j].getStatus()); // } @@ -532,13 +553,13 @@ class MsaWSThread extends JWS1Thread implements WSClientI .getMsa(); if (valign != null) { - wsInfo.appendProgressText(jobs[j].getJobnum(), - MessageManager.getString("info.alignment_object_method_notes")); + 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, @@ -550,8 +571,9 @@ class MsaWSThread extends JWS1Thread implements WSClientI } catch (Exception ex) { - Cache.log.error("Unexpected exception when processing results for " - + alTitle, ex); + Cache.log.error( + "Unexpected exception when processing results for " + alTitle, + ex); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } if (results > 0) @@ -559,6 +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); @@ -567,6 +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); @@ -610,7 +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 @@ -624,8 +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); @@ -649,7 +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--; @@ -692,6 +716,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI } } + @Override public boolean canMergeResults() { return false;