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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49 * Creates a new MsaWSClient object that uses a service
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50 * given by an externally retrieved ServiceHandle
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52 * @param sh service handle of type AbstractName(MsaWS)
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53 * @param altitle DOCUMENT ME!
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54 * @param msa DOCUMENT ME!
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55 * @param submitGaps DOCUMENT ME!
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56 * @param preserveOrder DOCUMENT ME!
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59 public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,
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60 boolean submitGaps, boolean preserveOrder)
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63 if (!sh.getAbstractName().equals("MsaWS"))
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65 JOptionPane.showMessageDialog(Desktop.desktop,
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66 "The Service called \n" + sh.getName() +
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67 "\nis not a \nMultiple Sequence Alignment Service !",
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68 "Internal Jalview Error",
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69 JOptionPane.WARNING_MESSAGE);
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74 if ((wsInfo = this.setWebService(sh))==null)
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76 JOptionPane.showMessageDialog(Desktop.desktop,
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77 "The Multiple Sequence Alignment Service named " +
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79 " is unknown", "Internal Jalview Error",
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80 JOptionPane.WARNING_MESSAGE);
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84 startMsaWSClient(altitle, msa, submitGaps, preserveOrder);
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89 private void startMsaWSClient(String altitle, SequenceI[] msa,
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90 boolean submitGaps, boolean preserveOrder)
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92 if (!locateWebService())
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97 wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
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98 " of " + altitle + "\nJob details\n");
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100 MsaWSThread musclethread = new MsaWSThread(WebServiceName +
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101 " alignment of " + altitle, msa,
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102 submitGaps, preserveOrder);
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103 wsInfo.setthisService(musclethread);
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104 musclethread.start();
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108 * Initializes the server field with a valid service implementation.
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110 * @return true if service was located.
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112 private boolean locateWebService()
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114 // TODO: MuscleWS transmuted to generic MsaWS client
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115 MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
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119 this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
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120 ( (MuscleWSSoapBindingStub)this.server).setTimeout(60000); // One minute timeout
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122 catch (Exception ex)
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124 wsInfo.setProgressText("Serious! " + WebServiceName +
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125 " Service location failed\nfor URL :" + WsURL +
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128 wsInfo.setStatus(wsInfo.ERROR);
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129 ex.printStackTrace();
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134 loc.getEngine().setOption("axis", "1");
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139 protected class MsaWSThread
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140 extends Thread implements WSClientI
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142 String ServiceName = WebServiceName;
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143 String OutputHeader;
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144 vamsas.objects.simple.MsaResult result = null;
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145 vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
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147 Hashtable SeqNames = null;
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148 boolean submitGaps = false; // and always store and recover sequence order
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149 boolean preserveOrder = true; // and always store and recover sequence order
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151 String alTitle; // name which will be used to form new alignment window.
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152 int allowedServerExceptions = 3; // thread dies if too many exceptions.
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153 boolean jobComplete = false;
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155 MsaWSThread(String title, SequenceI[] msa, boolean subgaps,
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159 submitGaps = subgaps;
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160 preserveOrder = presorder;
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162 OutputHeader = wsInfo.getProgressText();
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163 SeqNames = new Hashtable();
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165 vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
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166 Sequence[msa.length];
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168 for (int i = 0; i < msa.length; i++)
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170 String newname = jalview.analysis.SeqsetUtils.unique_name(i);
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172 // uniquify as we go
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173 // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
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174 SeqNames.put(newname,
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175 jalview.analysis.SeqsetUtils.SeqCharacterHash(msa[i]));
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176 seqarray[i] = new vamsas.objects.simple.Sequence();
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177 seqarray[i].setId(newname);
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178 seqarray[i].setSeq( (submitGaps) ? msa[i].getSequence()
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179 : AlignSeq.extractGaps(
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180 jalview.util.Comparison.GapChars,
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181 msa[i].getSequence()));
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184 this.seqs = new vamsas.objects.simple.SequenceSet();
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185 this.seqs.setSeqs(seqarray);
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188 public boolean isCancellable()
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193 public void cancelJob()
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195 if ( (jobId != null) && !jobId.equals("") && !jobComplete)
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197 String cancelledMessage = "";
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201 vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
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203 if (cancelledJob.getStatus() == 2)
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206 cancelledMessage = "Job cancelled.";
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207 wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
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208 jobComplete = true;
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212 else if (cancelledJob.getStatus() == 3)
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214 // VALID UNSTOPPABLE JOB
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215 cancelledMessage +=
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216 "Server cannot cancel this job. just close the window.\n";
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219 if (cancelledJob.getJobId() != null)
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221 cancelledMessage += ("[" + cancelledJob.getJobId() +
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225 cancelledMessage += "\n";
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227 catch (Exception exc)
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229 cancelledMessage +=
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230 ("\nProblems cancelling the job : Exception received...\n" +
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232 exc.printStackTrace();
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235 wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
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241 wsInfo.setProgressText(OutputHeader +
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242 "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
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251 while (!jobComplete && (allowedServerExceptions > 0))
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255 if ( (result = server.getResult(jobId)) == null)
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257 throw (new Exception(
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258 "Timed out when communicating with server\nTry again later.\n"));
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260 jalview.bin.Cache.log.debug("Result state " + result.getState() +
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261 "(ServerError=" + result.isServerError() +
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263 if (result.isRunning())
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265 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
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267 else if (result.isQueued())
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269 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
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272 if (result.isFinished())
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274 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
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276 jobComplete = true;
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281 if (result.getStatus() != null)
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283 wsInfo.setProgressText(OutputHeader + "\n"+ result.getStatus());
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285 if (result.isServerError())
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287 jobComplete = true;
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292 if (! (result.isJobFailed() || result.isServerError() ||
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293 result.isBroken() || result.isFailed()))
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295 Thread.sleep(5000);
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297 // System.out.println("I'm alive "+seqid+" "+jobid);
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301 jobComplete = true;
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307 catch (Exception ex)
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309 allowedServerExceptions--;
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310 wsInfo.appendProgressText("\n" + ServiceName +
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311 " Server exception!\n" + ex.getMessage());
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312 System.err.println(ServiceName + " Server exception: " +
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315 // ex.printStackTrace(); JBPNote Debug
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318 if (allowedServerExceptions > 0)
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320 Thread.sleep(5000);
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323 catch (InterruptedException ex1)
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327 catch(OutOfMemoryError er)
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329 jobComplete = true;
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330 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
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331 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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332 "Out of memory handling result!!"
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333 +"\nSee help files for increasing Java Virtual Machine memory."
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334 ,"Out of memory", JOptionPane.WARNING_MESSAGE );
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335 System.out.println("MsaWSClient: "+er);
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340 if (allowedServerExceptions == 0)
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342 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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346 if (result != null)
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348 if ( !(result.isJobFailed() || result.isServerError()))
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350 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
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353 if (result.isBroken() || result.isFailed())
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355 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
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358 if (result.isServerError())
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360 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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370 vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
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372 if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
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374 jobId = jobsubmit.getJobId();
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375 System.out.println(WsURL + " Job Id '" + jobId + "'");
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379 if (jobsubmit == null)
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381 throw new Exception("Server at " + WsURL +
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382 " returned null object, it probably cannot be contacted. Try again later ?");
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385 throw new Exception(jobsubmit.getJobId());
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388 catch (Exception e)
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390 // TODO: JBPNote catch timeout or other fault types explicitly
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391 // For unexpected errors
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392 System.err.println(WebServiceName +
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393 "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +
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394 "When contacting Server:" + WsURL + "\n" +
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397 this.allowedServerExceptions = 0;
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398 wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
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399 wsInfo.appendProgressText(
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400 "Failed to submit sequences for alignment.\n" +
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401 "It is most likely that there is a problem with the server.\n" +
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402 "Just close the window\n");
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404 // e.printStackTrace(); // TODO: JBPNote DEBUG
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408 private jalview.datamodel.Sequence[] getVamsasAlignment(
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409 vamsas.objects.simple.Alignment valign)
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411 vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
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412 jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
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415 for (int i = 0, j = seqs.length; i < j; i++)
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417 msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
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426 SequenceI[] seqs = null;
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430 // OutputHeader = output.getText();
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431 if (result.isFailed())
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433 OutputHeader += "Job failed.\n";
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436 if (result.getStatus() != null)
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438 OutputHeader += ("\n" + result.getStatus());
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441 if (result.getMsa() != null)
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443 OutputHeader += "\nAlignment Object Method Notes\n";
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445 String[] lines = result.getMsa().getMethod();
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447 for (int line = 0; line < lines.length; line++)
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449 OutputHeader += (lines[line] + "\n");
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452 // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
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453 seqs = getVamsasAlignment(result.getMsa());
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456 wsInfo.setProgressText(OutputHeader);
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460 AlignmentOrder msaorder = new AlignmentOrder(seqs);
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464 jalview.analysis.AlignmentSorter.recoverOrder(seqs);
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467 jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
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469 Alignment al = new Alignment(seqs);
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471 // TODO: JBPNote Should also rename the query sequence sometime...
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472 AlignFrame af = new AlignFrame(al);
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473 af.addSortByOrderMenuItem(ServiceName + " Ordering",
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476 Desktop.addInternalFrame(af, alTitle,
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477 AlignFrame.NEW_WINDOW_WIDTH,
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478 AlignFrame.NEW_WINDOW_HEIGHT);
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481 catch (Exception ex)
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483 ex.printStackTrace();
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