src/jalview/ws/JPredClient.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 package jalview.ws;\r
  20 \r
  21 import ext.vamsas.*;\r
  22 \r
  23 import jalview.analysis.AlignSeq;\r
  24 \r
  25 import jalview.datamodel.*;\r
  26 \r
  27 import jalview.gui.*;\r
  28 \r
  29 import org.apache.axis.client.*;\r
  30 \r
  31 import java.awt.*;\r
  32 \r
  33 import java.util.*;\r
  34 \r
  35 import javax.swing.*;\r
  36 \r
  37 import javax.xml.namespace.QName;\r
  38 \r
  39 \r
  40 public class JPredClient extends WSClient {\r
  41     ext.vamsas.JPredWS server;\r
  42     String altitle = "";\r
  43     java.util.Hashtable SequenceInfo = null;\r
  44 \r
  45     public JPredClient(String title, SequenceI[] msf) {\r
  46         wsInfo = setWebService();\r
  47 \r
  48         SequenceI seq = msf[0];\r
  49         altitle = "JNet prediction on " + seq.getName() +\r
  50             " using alignment from " + title;\r
  51 \r
  52         wsInfo.setProgressText("Job details for MSA based prediction (" +\r
  53             title + ") on sequence :\n>" + seq.getName() + "\n" +\r
  54             AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
  55 \r
  56         SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
  57 \r
  58         if (!locateWebService()) {\r
  59             return;\r
  60         }\r
  61 \r
  62         JPredThread jthread = new JPredThread(msf);\r
  63         jthread.start();\r
  64     }\r
  65 \r
  66     public JPredClient(String title, SequenceI seq) {\r
  67         wsInfo = setWebService();\r
  68         wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
  69             seq.getName() + "\n" +\r
  70             AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
  71         altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
  72             title;\r
  73 \r
  74         SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
  75 \r
  76         if (!locateWebService()) {\r
  77             return;\r
  78         }\r
  79 \r
  80         JPredThread jthread = new JPredThread(seq);\r
  81         jthread.start();\r
  82     }\r
  83 \r
  84     private WebserviceInfo setWebService() {\r
  85         WebServiceName = "JNetWS";\r
  86         WebServiceJobTitle = "JNet secondary structure prediction";\r
  87         WebServiceReference = "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +\r
  88             "multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
  89             "Proteins 40:502-511\".";\r
  90         WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
  91 \r
  92         WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
  93                 WebServiceReference);\r
  94 \r
  95         return wsInfo;\r
  96     }\r
  97 \r
  98     private boolean locateWebService() {\r
  99         JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
 100 \r
 101         try {\r
 102             this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
 103             ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub\r
 104         } catch (Exception ex) {\r
 105             JOptionPane.showMessageDialog(Desktop.desktop,\r
 106                 "The Secondary Structure Prediction Service named " +\r
 107                 WebServiceName + " at " + WsURL + " couldn't be located.",\r
 108                 "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
 109             wsInfo.setProgressText("Serious! " + WebServiceName +\r
 110                 " Service location failed\nfor URL :" + WsURL + "\n" +\r
 111                 ex.getMessage());\r
 112             wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
 113 \r
 114             return false;\r
 115         }\r
 116 \r
 117         return true;\r
 118     }\r
 119 \r
 120     class JPredThread extends Thread {\r
 121         String OutputHeader;\r
 122         ext.vamsas.JpredResult result;\r
 123         ext.vamsas.Sequence sequence;\r
 124         ext.vamsas.Msfalignment msa;\r
 125         String jobId;\r
 126         boolean jobComplete = false;\r
 127         int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
 128 \r
 129         JPredThread(SequenceI seq) {\r
 130             OutputHeader = wsInfo.getProgressText();\r
 131             this.sequence = new ext.vamsas.Sequence();\r
 132             this.sequence.setId(seq.getName());\r
 133             this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
 134         }\r
 135 \r
 136         JPredThread(SequenceI[] msf) {\r
 137             OutputHeader = wsInfo.getProgressText();\r
 138             this.sequence = new ext.vamsas.Sequence();\r
 139             this.sequence.setId(msf[0].getName());\r
 140             this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
 141                     msf[0].getSequence()));\r
 142 \r
 143             jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
 144             this.msa = new ext.vamsas.Msfalignment();\r
 145             msa.setMsf(mwrite.print(msf));\r
 146         }\r
 147 \r
 148         public void run() {\r
 149             StartJob();\r
 150 \r
 151             while (!jobComplete && (allowedServerExceptions > 0)) {\r
 152                 try {\r
 153                     if ((result = server.getresult(jobId)) == null) {\r
 154                         throw (new Exception(\r
 155                             "Timed out when communicating with server\nTry again later.\n"));\r
 156                     }\r
 157 \r
 158                     if (result.isRunning()) {\r
 159                         wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
 160                     } else if (result.isQueued()) {\r
 161                         wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
 162                     }\r
 163 \r
 164                     if (result.isFinished()) {\r
 165                         parseResult();\r
 166                         jobComplete = true;\r
 167                         jobsRunning--;\r
 168                     } else {\r
 169                         wsInfo.setProgressText(OutputHeader + "\n" +\r
 170                             result.getStatus());\r
 171 \r
 172                         if (!(result.isJobFailed() || result.isServerError())) {\r
 173                             try {\r
 174                                 Thread.sleep(5000);\r
 175                             } catch (InterruptedException ex1) {\r
 176                             }\r
 177 \r
 178                             //  System.out.println("I'm alive "+seqid+" "+jobid);\r
 179                         } else {\r
 180                             wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
 181                         }\r
 182                     }\r
 183                 } catch (Exception ex) {\r
 184                     allowedServerExceptions--;\r
 185                     wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
 186                         ex.getMessage());\r
 187 \r
 188                     try {\r
 189                         if (allowedServerExceptions > 0) {\r
 190                             Thread.sleep(5000);\r
 191                         }\r
 192                     } catch (InterruptedException ex1) {\r
 193                     }\r
 194                 }\r
 195             }\r
 196 \r
 197             if (!(result.isJobFailed() || result.isServerError())) {\r
 198                 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
 199             } else {\r
 200                 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
 201             }\r
 202         }\r
 203 \r
 204         void StartJob() {\r
 205             try {\r
 206                 if (msa != null) {\r
 207                     jobId = server.predictOnMsa(msa);\r
 208                 } else {\r
 209                     jobId = server.predict(sequence);\r
 210                 }\r
 211 \r
 212                 if (jobId != null) {\r
 213                     if (jobId.startsWith("Broken")) {\r
 214                         throw new Exception("Submission " + jobId);\r
 215                     } else {\r
 216                         System.out.println(WsURL + " Job Id '" + jobId + "'");\r
 217                     }\r
 218                 } else {\r
 219                     throw new Exception("Server timed out - try again later\n");\r
 220                 }\r
 221             } catch (Exception e) {\r
 222                 wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
 223                 allowedServerExceptions = 0;\r
 224                 jobComplete = false;\r
 225                 wsInfo.appendProgressText("Failed to submit the prediction: " +\r
 226                     e.toString() + "\nJust close the window\n");\r
 227                 System.err.println(\r
 228                     "JPredWS Client: Failed to submit the prediction\n" +\r
 229                     e.toString() + "\n");\r
 230 \r
 231                 // e.printStackTrace(); TODO: JBPNote DEBUG\r
 232             }\r
 233         }\r
 234 \r
 235         private void addFloatAnnotations(Alignment al, int[] gapmap,\r
 236             Vector values, String Symname, String Visname, float min,\r
 237             float max, int winLength) {\r
 238             Annotation[] annotations = new Annotation[al.getWidth()];\r
 239 \r
 240             for (int j = 0; j < values.size(); j++) {\r
 241                 float value = Float.parseFloat(values.get(j).toString());\r
 242                 annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
 243                         value);\r
 244             }\r
 245 \r
 246             al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
 247                     annotations, min, max, winLength));\r
 248         }\r
 249 \r
 250         void parseResult() {\r
 251             // OutputHeader = output.getText();\r
 252             if (result.isFailed()) {\r
 253                 OutputHeader += "Job failed.\n";\r
 254             }\r
 255 \r
 256             if (result.getStatus() != null) {\r
 257                 OutputHeader += ("\n" + result.getStatus());\r
 258             }\r
 259 \r
 260             if (result.getPredfile() != null) {\r
 261                 OutputHeader += ("\n" + result.getPredfile());\r
 262 \r
 263                 // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
 264             }\r
 265 \r
 266             if (result.getAligfile() != null) {\r
 267                 OutputHeader += ("\n" + result.getAligfile());\r
 268             }\r
 269 \r
 270             wsInfo.setProgressText(OutputHeader);\r
 271 \r
 272             try {\r
 273                 // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
 274                 jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(),\r
 275                         "Paste");\r
 276                 SequenceI[] preds = prediction.getSeqsAsArray();\r
 277                 Alignment al;\r
 278                 int FirstSeq; // the position of the query sequence in Alignment al\r
 279                 boolean noMsa = true; // set if no MSA has been returned by JPred\r
 280 \r
 281                 if ((this.msa != null) && (result.getAligfile() != null)) {\r
 282                     // we ignore the returned alignment if we only predicted on a single sequence\r
 283                     String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
 284                             "Paste");\r
 285 \r
 286                     if (jalview.io.FormatAdapter.formats.contains(format)) {\r
 287                         al = new Alignment(jalview.io.FormatAdapter.readFile(\r
 288                                     result.getAligfile(), "Paste", format));\r
 289                         noMsa = false;\r
 290                         FirstSeq = 0;\r
 291                     } else {\r
 292                         throw (new Exception(\r
 293                             "Unknown format 'format' for file : \n" +\r
 294                             result.getAligfile()));\r
 295                     }\r
 296                 } else {\r
 297                     al = new Alignment(preds);\r
 298                     FirstSeq = prediction.getQuerySeqPosition();\r
 299                 }\r
 300 \r
 301                 if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
 302                             al.getSequenceAt(FirstSeq), SequenceInfo)) {\r
 303                     throw (new Exception(\r
 304                         "Couldn't recover sequence properties for JNet Query sequence!"));\r
 305                 }\r
 306 \r
 307                 AlignmentAnnotation annot;\r
 308                 Annotation[] annotations = null;\r
 309                 int i = 0;\r
 310                 int width = preds[0].getSequence().length();\r
 311 \r
 312                 int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
 313 \r
 314                 if (gapmap.length != width) {\r
 315                     throw (new Exception(\r
 316                         "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +\r
 317                         al.getSequenceAt(FirstSeq).getName() + "\n" +\r
 318                         al.getSequenceAt(FirstSeq).getSequence() +\r
 319                         "\nDiffer from number of prediction sites in \n" +\r
 320                         result.getPredfile() + "\n"));\r
 321                 }\r
 322 \r
 323                 // JBPNote Should also rename the query sequence sometime...\r
 324                 i = 0;\r
 325 \r
 326                 while (i < preds.length) {\r
 327                     String id = preds[i].getName().toUpperCase();\r
 328 \r
 329                     if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
 330                             id.startsWith("JPRED")) {\r
 331                         annotations = new Annotation[al.getWidth()];\r
 332 \r
 333                         if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
 334                                 id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
 335                                 id.equals("JNETALIGN") || id.equals("JPRED")) {\r
 336                             for (int j = 0; j < width; j++) {\r
 337                                 annotations[gapmap[j]] = new Annotation("", "",\r
 338                                         preds[i].getCharAt(j), 0);\r
 339                             }\r
 340                         } else if (id.equals("JNETCONF")) {\r
 341                             for (int j = 0; j < width; j++) {\r
 342                                 float value = Float.parseFloat(preds[i].getCharAt(\r
 343                                             j) + "");\r
 344                                 annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
 345                                             j) + "", "", preds[i].getCharAt(j),\r
 346                                         value);\r
 347                             }\r
 348                         } else {\r
 349                             for (int j = 0; j < width; j++) {\r
 350                                 annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
 351                                             j) + "", "", ' ', 0);\r
 352                             }\r
 353                         }\r
 354 \r
 355                         if (id.equals("JNETCONF")) {\r
 356                             annot = new AlignmentAnnotation(preds[i].getName(),\r
 357                                     "JNet Output", annotations, 0f, 10f, 1);\r
 358                         }\r
 359                         else {\r
 360                             annot = new AlignmentAnnotation(preds[i].getName(),\r
 361                                     "JNet Output", annotations);\r
 362                         }\r
 363 \r
 364                         al.addAnnotation(annot);\r
 365 \r
 366                         if (noMsa) {\r
 367                             al.deleteSequence(preds[i]);\r
 368                         }\r
 369                     }\r
 370 \r
 371                     i++;\r
 372                 }\r
 373 \r
 374                 Hashtable scores = prediction.getScores();\r
 375 \r
 376                 /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),\r
 377                                       "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
 378 \r
 379                   addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),\r
 380                  "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
 381 \r
 382                   addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),\r
 383                                       "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
 384                  */\r
 385                 AlignFrame af = new AlignFrame(al);\r
 386 \r
 387                 Desktop.addInternalFrame(af, altitle,\r
 388                     AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
 389             } catch (Exception ex) {\r
 390                 ex.printStackTrace();\r
 391             }\r
 392         }\r
 393     }\r
 394 }\r