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