2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import ext.vamsas.*;
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23 import jalview.analysis.AlignSeq;
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25 import jalview.datamodel.*;
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27 import jalview.gui.*;
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31 import javax.swing.*;
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37 * @version $Revision$
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39 public class MsaWSClient
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43 * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
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45 ext.vamsas.MuscleWS server;
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46 AlignFrame alignFrame;
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50 * Creates a new MsaWSClient object that uses a service
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51 * given by an externally retrieved ServiceHandle
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53 * @param sh service handle of type AbstractName(MsaWS)
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54 * @param altitle DOCUMENT ME!
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55 * @param msa DOCUMENT ME!
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56 * @param submitGaps DOCUMENT ME!
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57 * @param preserveOrder DOCUMENT ME!
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60 public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle,
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61 jalview.datamodel.AlignmentView msa,
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62 boolean submitGaps, boolean preserveOrder,
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63 Alignment seqdataset,
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64 AlignFrame _alignFrame)
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67 alignFrame = _alignFrame;
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68 if (!sh.getAbstractName().equals("MsaWS"))
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70 JOptionPane.showMessageDialog(Desktop.desktop,
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71 "The Service called \n" + sh.getName() +
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72 "\nis not a \nMultiple Sequence Alignment Service !",
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73 "Internal Jalview Error",
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74 JOptionPane.WARNING_MESSAGE);
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79 if ((wsInfo = this.setWebService(sh))==null)
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81 JOptionPane.showMessageDialog(Desktop.desktop,
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82 "The Multiple Sequence Alignment Service named " +
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84 " is unknown", "Internal Jalview Error",
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85 JOptionPane.WARNING_MESSAGE);
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89 startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);
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94 private void startMsaWSClient(String altitle, AlignmentView msa,
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95 boolean submitGaps, boolean preserveOrder, Alignment seqdataset)
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97 if (!locateWebService())
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102 wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
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103 " of " + altitle + "\nJob details\n");
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105 MsaWSThread musclethread = new MsaWSThread(WebServiceName +
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106 " alignment of " + altitle, msa,
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107 submitGaps, preserveOrder, seqdataset);
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108 wsInfo.setthisService(musclethread);
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109 musclethread.start();
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113 * Initializes the server field with a valid service implementation.
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115 * @return true if service was located.
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117 private boolean locateWebService()
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119 // TODO: MuscleWS transmuted to generic MsaWS client
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120 MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
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124 this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
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125 ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
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127 catch (Exception ex)
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129 wsInfo.setProgressText("Serious! " + WebServiceName +
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130 " Service location failed\nfor URL :" + WsURL +
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133 wsInfo.setStatus(WebserviceInfo.ERROR);
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134 ex.printStackTrace();
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139 loc.getEngine().setOption("axis", "1");
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144 protected String getServiceActionKey()
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149 protected String getServiceActionDescription()
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151 return "Multiple Sequence Alignment";
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154 protected class MsaWSThread
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155 extends Thread implements WSClientI
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157 String ServiceName = WebServiceName;
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158 String OutputHeader;
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159 vamsas.objects.simple.MsaResult result = null;
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160 vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
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162 Hashtable SeqNames = null;
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163 boolean submitGaps = false; // pass sequences including gaps to alignment service
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164 boolean preserveOrder = true; // and always store and recover sequence order
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166 String alTitle; // name which will be used to form new alignment window.
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167 int allowedServerExceptions = 3; // thread dies if too many exceptions.
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168 boolean jobComplete = false;
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170 Alignment dataset; // dataset to which the new alignment will be associated.
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172 MsaWSThread(String title, AlignmentView _msa, boolean subgaps,
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173 boolean presorder, Alignment seqset)
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175 // jbpnote - transformation should be above here - this is per sequence set contig, not for many contigs.
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177 submitGaps = subgaps;
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178 preserveOrder = presorder;
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180 OutputHeader = wsInfo.getProgressText();
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181 SeqNames = new Hashtable();
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182 SeqCigar[] msa = _msa.getSequences();
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183 vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
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184 Sequence[msa.length];
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186 for (int i = 0,n=0; i < msa.length; i++)
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188 String newname = jalview.analysis.SeqsetUtils.unique_name(i);
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189 SequenceI mseq = msa[i].getSeq('-');
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190 // uniquify as we go
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191 // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
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192 SeqNames.put(newname,
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193 jalview.analysis.SeqsetUtils.SeqCharacterHash(mseq));
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194 seqarray[i] = new vamsas.objects.simple.Sequence();
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195 seqarray[i].setId(newname);
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196 seqarray[i].setSeq( (submitGaps) ? mseq.getSequence()
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197 : AlignSeq.extractGaps(
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198 jalview.util.Comparison.GapChars,
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199 mseq.getSequence()));
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202 this.seqs = new vamsas.objects.simple.SequenceSet();
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203 this.seqs.setSeqs(seqarray);
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206 public boolean isCancellable()
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211 public void cancelJob()
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213 if ( (jobId != null) && !jobId.equals("") && !jobComplete)
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215 String cancelledMessage = "";
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219 vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
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221 if (cancelledJob.getStatus() == 2)
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224 cancelledMessage = "Job cancelled.";
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225 wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
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226 jobComplete = true;
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230 else if (cancelledJob.getStatus() == 3)
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232 // VALID UNSTOPPABLE JOB
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233 cancelledMessage +=
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234 "Server cannot cancel this job. just close the window.\n";
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237 if (cancelledJob.getJobId() != null)
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239 cancelledMessage += ("[" + cancelledJob.getJobId() +
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243 cancelledMessage += "\n";
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245 catch (Exception exc)
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247 cancelledMessage +=
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248 ("\nProblems cancelling the job : Exception received...\n" +
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250 exc.printStackTrace();
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253 wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
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259 wsInfo.setProgressText(OutputHeader +
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260 "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
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269 while (!jobComplete && (allowedServerExceptions > 0))
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273 if ( (result = server.getResult(jobId)) == null)
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275 throw (new Exception(
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276 "Timed out when communicating with server\nTry again later.\n"));
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278 jalview.bin.Cache.log.debug("Result state " + result.getState() +
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279 "(ServerError=" + result.isServerError() +
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281 if (result.isRunning())
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283 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
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285 else if (result.isQueued())
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287 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
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290 if (result.isFinished())
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292 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
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293 wsInfo.showResultsNewFrame.addActionListener(new java.awt.event.ActionListener()
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295 public void actionPerformed(java.awt.event.ActionEvent evt)
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297 displayResults(true);
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300 wsInfo.mergeResults.addActionListener(new java.awt.event.ActionListener()
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302 public void actionPerformed(java.awt.event.ActionEvent evt)
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304 displayResults(false);
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307 wsInfo.setResultsReady();
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309 jobComplete = true;
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314 if (result.getStatus() != null)
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316 wsInfo.setProgressText(OutputHeader + "\n"+ result.getStatus());
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318 if (result.isServerError())
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320 jobComplete = true;
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325 if (! (result.isJobFailed() || result.isServerError() ||
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326 result.isBroken() || result.isFailed()))
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328 Thread.sleep(5000);
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330 // System.out.println("I'm alive "+seqid+" "+jobid);
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334 jobComplete = true;
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340 catch (Exception ex)
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342 allowedServerExceptions--;
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343 wsInfo.appendProgressText("\n" + ServiceName +
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344 " Server exception!\n" + ex.getMessage());
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345 System.err.println(ServiceName + " Server exception: " +
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348 // ex.printStackTrace(); JBPNote Debug
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351 if (allowedServerExceptions > 0)
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353 Thread.sleep(5000);
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356 catch (InterruptedException ex1)
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360 catch(OutOfMemoryError er)
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362 jobComplete = true;
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363 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
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364 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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365 "Out of memory handling result!!"
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366 +"\nSee help files for increasing Java Virtual Machine memory."
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367 ,"Out of memory", JOptionPane.WARNING_MESSAGE );
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368 System.out.println("MsaWSClient: "+er);
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373 if (allowedServerExceptions == 0)
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375 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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379 if (result != null)
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381 if ( !(result.isJobFailed() || result.isServerError()))
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383 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
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386 if (result.isBroken() || result.isFailed())
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388 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
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391 if (result.isServerError())
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393 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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403 vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
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405 if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
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407 jobId = jobsubmit.getJobId();
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408 System.out.println(WsURL + " Job Id '" + jobId + "'");
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412 if (jobsubmit == null)
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414 throw new Exception("Server at " + WsURL +
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415 " returned null object, it probably cannot be contacted. Try again later ?");
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418 throw new Exception(jobsubmit.getJobId());
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421 catch (Exception e)
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423 // TODO: JBPNote catch timeout or other fault types explicitly
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424 // For unexpected errors
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425 System.err.println(WebServiceName +
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426 "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +
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427 "When contacting Server:" + WsURL + "\n" +
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430 this.allowedServerExceptions = 0;
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431 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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432 wsInfo.appendProgressText(
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433 "Failed to submit sequences for alignment.\n" +
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434 "It is most likely that there is a problem with the server.\n" +
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435 "Just close the window\n");
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437 // e.printStackTrace(); // TODO: JBPNote DEBUG
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441 private jalview.datamodel.Sequence[] getVamsasAlignment(
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442 vamsas.objects.simple.Alignment valign)
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444 vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
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445 jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
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448 for (int i = 0, j = seqs.length; i < j; i++)
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450 msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
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462 // OutputHeader = output.getText();
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463 if (result.isFailed())
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465 OutputHeader += "Job failed.\n";
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468 if (result.getStatus() != null)
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470 OutputHeader += ("\n" + result.getStatus());
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473 if (result.getMsa() != null)
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475 OutputHeader += "\nAlignment Object Method Notes\n";
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477 String[] lines = result.getMsa().getMethod();
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479 for (int line = 0; line < lines.length; line++)
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481 OutputHeader += (lines[line] + "\n");
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484 // JBPNote The returned files from a webservice could be
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485 // hidden behind icons in the monitor window that,
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486 // when clicked, pop up their corresponding data
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489 wsInfo.setProgressText(OutputHeader);
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491 catch (Exception ex)
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493 ex.printStackTrace();
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497 void displayResults(boolean newFrame)
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499 SequenceI [] seqs = getVamsasAlignment(result.getMsa());
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503 AlignmentOrder msaorder = new AlignmentOrder(seqs);
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507 jalview.analysis.AlignmentSorter.recoverOrder(seqs);
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510 jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
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512 Alignment al = new Alignment(seqs);
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515 al.setDataset(dataset);
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520 // TODO: JBPNote Should also rename the query sequence sometime...
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521 AlignFrame af = new AlignFrame(al);
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523 //>>>This is a fix for the moment, until a better solution is found!!<<<
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524 af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
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526 af.addSortByOrderMenuItem(ServiceName + " Ordering",
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529 Desktop.addInternalFrame(af, alTitle,
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530 AlignFrame.NEW_WINDOW_WIDTH,
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531 AlignFrame.NEW_WINDOW_HEIGHT);
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536 System.out.println("MERGE WITH OLD FRAME");
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