X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FMsaWSThread.java;h=e4247f7eca92ce1568123f96752dde6e6d6bef7f;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=44359cf9989eba46eef93aceaeae6540d9d80eef;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/ws/jws1/MsaWSThread.java b/src/jalview/ws/jws1/MsaWSThread.java index 44359cf..e4247f7 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 2.8.2b1) - * 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.ColumnSelection; +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 +96,9 @@ 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++) { @@ -125,8 +136,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI .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) @@ -422,16 +435,20 @@ 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()) @@ -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 +485,9 @@ 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()); @@ -485,9 +505,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI 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 @@ -532,8 +552,8 @@ 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++) { @@ -559,6 +579,7 @@ 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 +588,7 @@ 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); @@ -648,8 +670,8 @@ class MsaWSThread extends JWS1Thread implements WSClientI while (j < l) { - if (((AlignmentOrder) alorders.get(i)) - .equals(((AlignmentOrder) alorders.get(j)))) + if (((AlignmentOrder) alorders.get(i)).equals((alorders + .get(j)))) { alorders.remove(j); l--; @@ -692,6 +714,7 @@ class MsaWSThread extends JWS1Thread implements WSClientI } } + @Override public boolean canMergeResults() { return false;