X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FSeqSearchWSThread.java;h=761b758ecf825efa84012b37cb9ce20d8831ed2a;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=259a0b9786adc8726fd2da1e6a6f7a415eb52a34;hpb=add30afdc46a14e61ccf55881fa91b9ca9abfe80;p=jalview.git diff --git a/src/jalview/ws/jws1/SeqSearchWSThread.java b/src/jalview/ws/jws1/SeqSearchWSThread.java index 259a0b9..761b758 100644 --- a/src/jalview/ws/jws1/SeqSearchWSThread.java +++ b/src/jalview/ws/jws1/SeqSearchWSThread.java @@ -1,55 +1,49 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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; -/** - *

- * 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 +72,7 @@ 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")); } } @@ -101,8 +95,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI int nseqs = 0; if (minlen < 0) { - throw new Error( - "Implementation error: minlen must be zero or more."); + throw new Error(MessageManager.getString( + "error.implementation_error_minlen_must_be_greater_zero")); } for (int i = 0; i < seqs.length; i++) { @@ -113,7 +107,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI } boolean valid = nseqs >= 1; // need at least one sequence for valid input // TODO: generalise - 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; boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted // with gaps @@ -124,8 +119,8 @@ 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(); @@ -139,12 +134,11 @@ class SeqSearchWSThread 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, seqs[i] - .getSequenceAsString()); + 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 }); } } if (submitGaps) @@ -160,13 +154,13 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI * * @return true if getAlignment will return a valid alignment result. */ + @Override public boolean hasResults() { - if (subjobComplete - && result != null - && result.isFinished() + if (subjobComplete && result != null && result.isFinished() && ((SeqSearchResult) result).getAlignment() != null - && ((SeqSearchResult) result).getAlignment().getSeqs() != null) + && ((SeqSearchResult) result).getAlignment() + .getSeqs() != null) { return true; } @@ -178,7 +172,8 @@ 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()) @@ -188,8 +183,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI // int alseq_l = 0; if (((SeqSearchResult) result).getAlignment() != null) { - alseqs = getVamsasAlignment(((SeqSearchResult) result) - .getAlignment()); + alseqs = getVamsasAlignment( + ((SeqSearchResult) result).getAlignment()); // alseq_gapchar = ( (SeqSearchResult) // result).getAlignment().getGapchar().charAt(0); // alseq_l = alseqs.length; @@ -213,12 +208,12 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI if (inFile != null && inFile.length() > 0) { new jalview.io.AnnotationFile().readAnnotationFile(al, inFile, - jalview.io.AppletFormatAdapter.PASTE); + jalview.io.DataSourceType.PASTE); } } catch (Exception e) { - System.err - .println("Failed to parse the annotation file associated with the alignment."); + System.err.println( + "Failed to parse the annotation file associated with the alignment."); System.err.println(">>>EOF" + inFile + "\n<< 0) { - jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile( - inFile, jalview.io.AppletFormatAdapter.PASTE); + jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(inFile, + jalview.io.DataSourceType.PASTE); ff.parse(al, featureColours, false); } } catch (Exception e) { - System.err - .println("Failed to parse the Features file associated with the alignment."); + System.err.println( + "Failed to parse the Features file associated with the alignment."); System.err.println(">>>EOF" + inFile + "\n<< 0) { nf = new jalview.io.NewickFile(inFile, - jalview.io.AppletFormatAdapter.PASTE); + jalview.io.DataSourceType.PASTE); if (!nf.isValid()) { nf.close(); @@ -255,8 +250,8 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI } } catch (Exception e) { - System.err - .println("Failed to parse the treeFile associated with the alignment."); + System.err.println( + "Failed to parse the treeFile associated with the alignment."); System.err.println(">>>EOF" + inFile + "\n<< 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); } } } + @Override public boolean isCancellable() { return true; } + @Override public void cancelJob() { if (!jobComplete && jobs != null) @@ -430,10 +426,11 @@ 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"); + wsInfo.setProgressText(jobs[job].getJobnum(), + OutputHeader + cancelledMessage + "\n"); } } if (cancelled) @@ -447,33 +444,35 @@ 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"); } } } + @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("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()) { 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; } @@ -483,13 +482,14 @@ 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 +502,10 @@ 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()); @@ -514,20 +514,16 @@ class SeqSearchWSThread 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(), - "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 } @@ -541,13 +537,14 @@ 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; } + @Override public void parseResult() { int results = 0; // number of result sets received @@ -561,16 +558,17 @@ 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, @@ -581,8 +579,9 @@ class SeqSearchWSThread 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) @@ -590,6 +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); @@ -598,6 +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); @@ -623,7 +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()) @@ -661,11 +662,13 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI * propagateDatasetMappings(al); } */ - AlignFrame af = new AlignFrame(al,// columnselection, + AlignFrame af = new AlignFrame(al, // columnselection, 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); @@ -674,6 +677,7 @@ class SeqSearchWSThread extends JWS1Thread implements WSClientI } } + @Override public boolean canMergeResults() { return false;