X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FSeqSearchWSThread.java;h=70056a6644376e4d49c596915148b442b70d5033;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=d920e37ea2bcad3acb246bd1f178a8b24560bb27;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java index d920e37..70056a6 100644 --- a/src/jalview/ws/jws1/SeqSearchWSThread.java +++ b/src/jalview/ws/jws1/SeqSearchWSThread.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. * @@ -20,17 +20,27 @@ */ 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.api.FeatureColourI; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.WebserviceInfo; import jalview.io.NewickFile; import jalview.util.MessageManager; import jalview.ws.AWsJob; import jalview.ws.JobStateSummary; import jalview.ws.WSClientI; + +import java.util.HashMap; +import java.util.Hashtable; +import java.util.Map; +import java.util.Vector; + import vamsas.objects.simple.MsaResult; import vamsas.objects.simple.SeqSearchResult; @@ -85,7 +95,9 @@ class SeqSearchWSThread 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++) { @@ -126,8 +138,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI .extractGaps(jalview.util.Comparison.GapChars, seqs[i].getSequenceAsString()); } - emptySeqs.add(new String[] - { newname, empty }); + emptySeqs.add(new String[] { newname, empty }); } } if (submitGaps) @@ -143,6 +154,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI * * @return true if getAlignment will return a valid alignment result. */ + @Override public boolean hasResults() { if (subjobComplete @@ -161,7 +173,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI * * @return null or { Alignment(+features and annotation), NewickFile)} */ - public Object[] getAlignment(Alignment dataset, Hashtable featureColours) + public Object[] getAlignment(AlignmentI dataset, + Map featureColours) { if (result != null && result.isFinished()) @@ -259,8 +272,7 @@ 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; } @@ -279,6 +291,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI * * @return boolean true if job can be submitted. */ + @Override public boolean hasValidInput() { if (seqs.getSeqs() != null) @@ -291,7 +304,7 @@ class SeqSearchWSThread 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. @@ -333,7 +346,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl, WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, String wsname, String title, AlignmentView _msa, String db, - Alignment seqset) + AlignmentI seqset) { this(server, wsUrl, wsinfo, alFrame, _msa, wsname, db); OutputHeader = wsInfo.getProgressText(); @@ -365,11 +378,13 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI } } + @Override public boolean isCancellable() { return true; } + @Override public void cancelJob() { if (!jobComplete && jobs != null) @@ -436,17 +451,21 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI } } + @Override public void pollJob(AWsJob job) throws Exception { ((SeqSearchWSJob) job).result = server.getResult(((SeqSearchWSJob) job) .getJobId()); } + @Override public void StartJob(AWsJob job) { if (!(job instanceof SeqSearchWSJob)) { - 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() })); } SeqSearchWSJob j = (SeqSearchWSJob) job; if (j.isSubmitted()) @@ -464,7 +483,8 @@ class SeqSearchWSThread 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 @@ -483,7 +503,9 @@ class SeqSearchWSThread 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()); @@ -501,9 +523,8 @@ class SeqSearchWSThread 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 } @@ -524,6 +545,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI return msa; } + @Override public void parseResult() { int results = 0; // number of result sets received @@ -541,8 +563,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI .getAlignment(); 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++) { @@ -567,6 +589,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI wsInfo.showResultsNewFrame .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(true); @@ -575,6 +598,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI wsInfo.mergeResults .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(false); @@ -600,7 +624,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI // NewickFile nf[] = new NewickFile[jobs.length]; for (int j = 0; j < jobs.length; j++) { - Hashtable featureColours = new Hashtable(); + Map featureColours = new HashMap(); Alignment al = null; NewickFile nf = null; if (jobs[j].hasResults()) @@ -642,7 +666,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); if (nf != null) { - af.ShowNewickTree(nf, MessageManager.formatMessage("label.tree_from", new String[]{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); @@ -651,6 +676,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI } } + @Override public boolean canMergeResults() { return false;