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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23 import javax.swing.*;
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25 import ext.vamsas.*;
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26 import jalview.analysis.*;
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27 import jalview.datamodel.*;
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28 import jalview.gui.*;
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30 public class JPredClient
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33 ext.vamsas.Jpred server;
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34 String altitle = "";
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35 java.util.Hashtable SequenceInfo = null;
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36 public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) {
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37 wsInfo = setWebService(sh);
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38 startJPredClient(title, seq);
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40 public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) {
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41 wsInfo = setWebService(sh);
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42 startJPredClient(title, msa);
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45 public JPredClient(String title, SequenceI[] msf) {
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46 startJPredClient(title, msf);
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49 public JPredClient(String title, SequenceI seq) {
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50 startJPredClient(title, seq);
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53 private void startJPredClient(String title, SequenceI[] msf)
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56 wsInfo = setWebService();
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58 SequenceI seq = msf[0];
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59 altitle = "JNet prediction on " + seq.getName() +
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60 " using alignment from " + title;
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62 wsInfo.setProgressText("Job details for MSA based prediction (" +
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63 title + ") on sequence :\n>" + seq.getName() + "\n" +
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64 AlignSeq.extractGaps("-. ", seq.getSequence()) +
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66 SequenceI aln[] = new SequenceI[msf.length];
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67 for (int i=0,j=msf.length; i<j;i++)
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68 aln[i] = new jalview.datamodel.Sequence(msf[i]);
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69 SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
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71 if (!locateWebService())
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76 JPredThread jthread = new JPredThread(aln);
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80 public void startJPredClient(String title, SequenceI seq)
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83 wsInfo = setWebService();
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84 wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
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85 seq.getName() + "\n" +
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86 AlignSeq.extractGaps("-. ", seq.getSequence()) +
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88 altitle = "JNet prediction for sequence " + seq.getName() + " from " +
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91 SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
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93 if (!locateWebService())
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98 JPredThread jthread = new JPredThread(seq);
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102 private WebserviceInfo setWebService()
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104 WebServiceName = "JNetWS";
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105 WebServiceJobTitle = "JNet secondary structure prediction";
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106 WebServiceReference =
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107 "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +
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108 "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
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109 "Proteins 40:502-511\".";
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110 WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
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112 WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
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113 WebServiceReference);
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118 private boolean locateWebService()
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120 ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
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124 this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
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125 ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub
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127 catch (Exception ex)
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129 JOptionPane.showMessageDialog(Desktop.desktop,
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130 "The Secondary Structure Prediction Service named " +
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131 WebServiceName + " at " + WsURL +
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132 " couldn't be located.",
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133 "Internal Jalview Error",
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134 JOptionPane.WARNING_MESSAGE);
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135 wsInfo.setProgressText("Serious! " + WebServiceName +
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136 " Service location failed\nfor URL :" + WsURL +
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139 wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
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150 String OutputHeader;
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151 vamsas.objects.simple.JpredResult result;
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152 vamsas.objects.simple.Sequence sequence;
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153 vamsas.objects.simple.Msfalignment msa;
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155 boolean jobComplete = false;
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156 int allowedServerExceptions = 3; // thread dies if too many exceptions.
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158 JPredThread(SequenceI seq)
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160 OutputHeader = wsInfo.getProgressText();
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161 this.sequence = new vamsas.objects.simple.Sequence();
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162 this.sequence.setId(seq.getName());
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163 this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
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166 JPredThread(SequenceI[] msf)
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168 OutputHeader = wsInfo.getProgressText();
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169 this.sequence = new vamsas.objects.simple.Sequence();
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170 this.sequence.setId(msf[0].getName());
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171 this.sequence.setSeq(AlignSeq.extractGaps("-. ",
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172 msf[0].getSequence()));
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174 jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();
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175 this.msa = new vamsas.objects.simple.Msfalignment();
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176 msa.setMsf(mwrite.print(msf));
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183 while (!jobComplete && (allowedServerExceptions > 0))
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187 if ( (result = server.getresult(jobId)) == null)
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189 throw (new Exception(
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190 "Timed out when communicating with server\nTry again later.\n"));
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192 if (result.getState()==0)
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193 jalview.bin.Jalview.log.debug("Finished "+jobId);
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194 if (result.isRunning())
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196 wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
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198 if (result.isQueued())
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200 wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
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203 wsInfo.setProgressText(OutputHeader + "\n" +
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204 result.getStatus());
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206 if (result.isFinished())
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210 jobComplete = true;
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213 // catch exceptions
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214 if (! (result.isJobFailed() || result.isServerError()))
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218 Thread.sleep(5000);
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220 catch (InterruptedException ex1)
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224 // System.out.println("I'm alive "+seqid+" "+jobid);
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228 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
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230 jobComplete = true;
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234 catch (Exception ex)
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236 allowedServerExceptions--;
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237 wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
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242 if (allowedServerExceptions > 0)
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244 Thread.sleep(5000);
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247 catch (InterruptedException ex1)
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253 if (! (result.isJobFailed() || result.isServerError()))
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255 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
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259 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
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269 jobId = server.predictOnMsa(msa);
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273 jobId = server.predict(sequence);
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278 if (jobId.startsWith("Broken"))
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280 throw new Exception("Submission " + jobId);
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284 System.out.println(WsURL + " Job Id '" + jobId + "'");
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289 throw new Exception("Server timed out - try again later\n");
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292 catch (Exception e)
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294 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
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295 allowedServerExceptions = 0;
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296 jobComplete = false;
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298 wsInfo.appendProgressText("Failed to submit the prediction.\n"
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300 "It is most likely that there is a problem with the server.\n"
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301 + "Just close the window\n");
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302 System.err.println(
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303 "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +
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304 e.toString() + "\n");
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306 jalview.bin.Jalview.log.debug("Failed Submission",e);
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312 private void addFloatAnnotations(Alignment al, int[] gapmap,
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313 Vector values, String Symname,
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314 String Visname, float min,
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315 float max, int winLength)
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317 Annotation[] annotations = new Annotation[al.getWidth()];
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319 for (int j = 0; j < values.size(); j++)
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321 float value = Float.parseFloat(values.get(j).toString());
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322 annotations[gapmap[j]] = new Annotation("", value + "", ' ',
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326 al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
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327 annotations, min, max, winLength));
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332 // OutputHeader = output.getText();
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333 if (result.isFailed())
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335 OutputHeader += "Job failed.\n";
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338 if (result.getStatus() != null)
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340 OutputHeader += ("\n" + result.getStatus());
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343 if (result.getPredfile() != null)
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345 OutputHeader += ("\n" + result.getPredfile());
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347 // 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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350 if (result.getAligfile() != null)
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352 OutputHeader += ("\n" + result.getAligfile());
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355 wsInfo.setProgressText(OutputHeader+"Parsing...");
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359 jalview.bin.Jalview.log.debug("Parsing output from JNet job.");
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360 // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
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361 jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
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364 SequenceI[] preds = prediction.getSeqsAsArray();
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365 jalview.bin.Jalview.log.debug("Got prediction profile.");
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367 int FirstSeq; // the position of the query sequence in Alignment al
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368 boolean noMsa = true; // set if no MSA has been returned by JPred
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370 if ( (this.msa != null) && (result.getAligfile() != null))
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372 jalview.bin.Jalview.log.debug("Getting associated alignment.");
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373 // we ignore the returned alignment if we only predicted on a single sequence
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374 String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),
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377 if (jalview.io.FormatAdapter.formats.contains(format))
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379 al = new Alignment(jalview.io.FormatAdapter.readFile(
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380 result.getAligfile(), "Paste", format));
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381 for (int i=0, j=al.getHeight(); i<j; i++) {
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382 SequenceI sq = al.getSequenceAt(i);
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383 if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
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384 sq, (Hashtable) SequenceInfo.get(sq.getName())))
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386 throw (new Exception(
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387 "Couldn't recover sequence properties for JNet "
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388 +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));
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396 throw (new Exception(
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397 "Unknown format 'format' for file : \n" +
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398 result.getAligfile()));
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403 al = new Alignment(preds);
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404 FirstSeq = prediction.getQuerySeqPosition();
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405 if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
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406 al.getSequenceAt(FirstSeq), SequenceInfo))
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408 throw (new Exception(
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409 "Couldn't recover sequence properties for JNet Query sequence!"));
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414 AlignmentAnnotation annot;
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415 Annotation[] annotations = null;
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417 int width = preds[0].getSequence().length();
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419 int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
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421 if (gapmap.length != width)
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423 throw (new Exception(
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424 "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +
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425 al.getSequenceAt(FirstSeq).getName() + "\n" +
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426 al.getSequenceAt(FirstSeq).getSequence() +
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427 "\nDiffer from number of prediction sites in \n" +
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428 result.getPredfile() + "\n"));
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431 // JBPNote Should also rename the query sequence sometime...
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434 while (i < preds.length)
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436 String id = preds[i].getName().toUpperCase();
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438 if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
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439 id.startsWith("JPRED"))
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441 annotations = new Annotation[al.getWidth()];
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443 if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
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444 id.equals("JNETFREQ") || id.equals("JNETHMM") ||
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445 id.equals("JNETALIGN") || id.equals("JPRED"))
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447 for (int j = 0; j < width; j++)
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449 annotations[gapmap[j]] = new Annotation("", "",
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450 preds[i].getCharAt(j), 0);
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453 else if (id.equals("JNETCONF"))
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455 for (int j = 0; j < width; j++)
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457 float value = Float.parseFloat(preds[i].getCharAt(
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459 annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
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460 j) + "", "", preds[i].getCharAt(j),
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466 for (int j = 0; j < width; j++)
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468 annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
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469 j) + "", "", ' ', 0);
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473 if (id.equals("JNETCONF"))
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475 annot = new AlignmentAnnotation(preds[i].getName(),
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476 "JNet Output", annotations, 0f,
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481 annot = new AlignmentAnnotation(preds[i].getName(),
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482 "JNet Output", annotations);
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485 al.addAnnotation(annot);
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489 al.deleteSequence(preds[i]);
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496 Hashtable scores = prediction.getScores();
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498 /* addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPH"),
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499 "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
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501 addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPB"),
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502 "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
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504 addFloatAnnotations(al, gapmap, (Vector)scores.get("JNETPROPC"),
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505 "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
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508 wsInfo.setProgressText(OutputHeader);
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509 jalview.bin.Jalview.log.debug("Finished parsing output.");
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510 AlignFrame af = new AlignFrame(al);
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512 Desktop.addInternalFrame(af, altitle,
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513 AlignFrame.NEW_WINDOW_WIDTH,
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514 AlignFrame.NEW_WINDOW_HEIGHT);
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516 catch (Exception ex)
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518 jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
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519 jalview.bin.Jalview.log.debug("Exception: ",ex);
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