src/jalview/ws/JPredClient.java

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