X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=2ec8e1e8999728b726291fc586ccadbd3a7d0f37;hb=f0821f93f0d678fafdd2d6156b0c2bd50a061055;hp=2eecf46963f042df7f59b97c9504799cdd451398;hpb=61b0b38d322aef9105cc564d3f5340fd529039ba;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 2eecf46..2ec8e1e 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,302 +1,652 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
-import org.apache.axis.client.*;
-import javax.xml.namespace.QName;
 import java.util.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+
 import javax.swing.*;
-import java.util.*;
-import java.awt.*;
-import jalview.analysis.AlignSeq;
-import ext.vamsas.*;
 
+import ext.vamsas.*;
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.gui.*;
+import jalview.io.*;
+import jalview.ws.WSThread.*;
+import vamsas.objects.simple.*;
+import jalview.util.Comparison;
 
 public class JPredClient
+    extends WSClient
 {
-  int jobsRunning = 0;
-  ext.vamsas.JpredSoapBindingStub server;
-  WebserviceInfo wsInfo;
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq)
+  {
+    wsInfo = setWebService(sh);
+    startJPredClient(title, seq);
+  }
+
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa)
+  {
+    wsInfo = setWebService(sh);
+    startJPredClient(title, msa);
+  }
+
+  public JPredClient(String title, SequenceI[] msf)
+  {
+    startJPredClient(title, msf);
+  }
 
-  public JPredClient(SequenceI[] msf)
+  public JPredClient(String title, SequenceI seq)
   {
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",
-          "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");
+    startJPredClient(title, seq);
+  }
+
+  private void startJPredClient(String title, SequenceI[] msf)
+  {
+    if (wsInfo == null)
+    {
+      wsInfo = setWebService();
+    }
 
     SequenceI seq = msf[0];
-    wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : "
-                   + seq.getName() + "\nSequence : "
-                   + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
 
+    String altitle = "JNet prediction on " + seq.getName() +
+        " using alignment from " + title;
 
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
-    try {
-      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
+    wsInfo.setProgressText("Job details for MSA based prediction (" +
+                           title + ") on sequence :\n>" + seq.getName() + "\n" +
+                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           "\n");
+    SequenceI aln[] = new SequenceI[msf.length];
+    for (int i = 0, j = msf.length; i < j; i++)
+    {
+      aln[i] = new jalview.datamodel.Sequence(msf[i]);
     }
-    catch (Exception ex) {
-      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"
-                     +loc.getjpredAddress()+"\n"+ex.getMessage());
+
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+
+    Jpred server = locateWebService();
+    if (server==null)
+    {
+      return;
     }
 
-    JPredThread jthread = new JPredThread(msf);
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln);
+    wsInfo.setthisService(jthread);
     jthread.start();
   }
 
-  public JPredClient(SequenceI seq)
+  public void startJPredClient(String title, SequenceI seq)
   {
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",
-                                "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");
-
+    if (wsInfo == null)
+    {
+      wsInfo = setWebService();
+    }
+    wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
+                           seq.getName() + "\n" +
+                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           "\n");
+    String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
+        title;
 
-    wsInfo.setProgressText("Job details for prediction on sequence :\nName : "
-                   + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
 
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
-    try {
-      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
-    }
-    catch (Exception ex) {
-      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"
-                     +loc.getjpredAddress()+"\n"+ex.getMessage());
+    Jpred server = locateWebService();
+    if (server==null)
+    {
+      return;
     }
 
-    JPredThread jthread = new JPredThread(seq);
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq);
+    wsInfo.setthisService(jthread);
     jthread.start();
   }
 
+  private WebserviceInfo setWebService()
+  {
+    WebServiceName = "JNetWS";
+    WebServiceJobTitle = "JNet secondary structure prediction";
+    WebServiceReference =
+        "\"Cuff J. A and Barton G.J (2000) Application of " +
+        "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
+        "Proteins 40:502-511\".";
+    WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+
+    WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
+                                               WebServiceReference);
+
+    return wsInfo;
+  }
 
-  class JPredThread
-      extends Thread
+  private ext.vamsas.Jpred locateWebService()
   {
-    String OutputHeader;
-    ext.vamsas.JpredResult result;
-    ext.vamsas.Sequence sequence;
-    ext.vamsas.Msfalignment msa;
-    String jobId;
-    boolean jobComplete = false;
-    int allowedServerExceptions = 3; // thread dies if too many exceptions.
-    JPredThread(SequenceI seq)
+    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
+    ext.vamsas.Jpred server=null;
+    try
     {
-      OutputHeader = wsInfo.getProgressText();
-      this.sequence = new ext.vamsas.Sequence();
-      this.sequence.setId(seq.getName());
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));
-    }
+      server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
+      ( (JpredSoapBindingStub)server).setTimeout(60000); // one minute stub
+      //((JpredSoapBindingStub)this.server)._setProperty(org.apache.axis.encoding.C, Boolean.TRUE);
 
-    JPredThread(SequenceI[] msf)
+    }
+    catch (Exception ex)
     {
-      OutputHeader = wsInfo.getProgressText();
-      this.sequence = new ext.vamsas.Sequence();
-      this.sequence.setId(msf[0].getName());
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence()));
-      jalview.io.MSFfile mwrite = new jalview.io.MSFfile();
-      this.msa = new ext.vamsas.Msfalignment();
-      msa.setMsf(mwrite.print(msf));
+      JOptionPane.showMessageDialog(Desktop.desktop,
+                                    "The Secondary Structure Prediction Service named " +
+                                    WebServiceName + " at " + WsURL +
+                                    " couldn't be located.",
+                                    "Internal Jalview Error",
+                                    JOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText("Serious! " + WebServiceName +
+                             " Service location failed\nfor URL :" + WsURL +
+                             "\n" +
+                             ex.getMessage());
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+
     }
 
+    return server;
+  }
 
-    public void run()
+  class JPredThread
+      extends WSThread
+      implements WSClientI
+  {
+    class JPredJob
+        extends WSThread.WSJob
     {
 
-      StartJob();
+      vamsas.objects.simple.Sequence sequence;
+      vamsas.objects.simple.Msfalignment msa;
+      java.util.Hashtable SequenceInfo = null;
+      /**
+       *
+       * @return true if getResultSet will return a valid alignment and prediction result.
+       */
+      public boolean hasResults()
+      {
+        if (subjobComplete && result != null && result.isFinished()
+            && ( (JpredResult) result).getPredfile() != null &&
+            ( (JpredResult) result).getAligfile() != null)
+        {
+          return true;
+        }
+        return false;
+      }
 
-      while (!jobComplete && (allowedServerExceptions > 0))
+      boolean hasValidInput()
       {
-        try
+        if (sequence != null)
         {
-          result = server.getresult(jobId);
+          return true;
+        }
+        return false;
+      }
 
-         if( result.isRunning() )
-           wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-         else if( result.isQueued() )
-           wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+      public Alignment getResultSet()
+          throws Exception
+      {
+        if (result == null || !result.isFinished())
+        {
+          return null;
+        }
+        Alignment al = null;
+        int FirstSeq = -1; // the position of the query sequence in Alignment al
+        boolean noMsa = true; // set if no MSA has been returned by JPred
+
+        JpredResult result = (JpredResult)this.result;
+
+        jalview.bin.Cache.log.debug("Parsing output from JNet job.");
+        // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
+        jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
+            getPredfile(),
+            "Paste");
+        SequenceI[] preds = prediction.getSeqsAsArray();
+        jalview.bin.Cache.log.debug("Got prediction profile.");
 
-          if (result.isFinished())
+        if ( (this.msa != null) && (result.getAligfile() != null))
+        {
+          jalview.bin.Cache.log.debug("Getting associated alignment.");
+          // we ignore the returned alignment if we only predicted on a single sequence
+          String format = new jalview.io.IdentifyFile().Identify(result.
+              getAligfile(),
+              "Paste");
+
+          if (jalview.io.FormatAdapter.isValidFormat(format))
           {
-            parseResult();
-            jobComplete = true;
-            jobsRunning--;
+            al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),
+                "Paste", format));
+            SequenceI sqs[] = new SequenceI[al.getHeight()];
+            for (int i = 0, j = al.getHeight(); i < j; i++)
+            {
+              sqs[i] = al.getSequenceAt(i);
+            }
+            if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
+                SequenceInfo, sqs))
+            {
+              throw (new Exception(
+                  "Couldn't recover sequence properties for alignment."));
+            }
+
+            noMsa = false;
+            FirstSeq = 0;
           }
           else
           {
-            wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
-            if (! (result.isJobFailed() || result.isServerError()))
-            {
-              Thread.sleep(5000);
-              //  System.out.println("I'm alive "+seqid+" "+jobid);
-            } else {
-              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-            }
+            throw (new Exception(
+                "Unknown format "+format+" for file : \n" +
+                result.getAligfile()));
           }
         }
-        catch (Exception ex)
+        else
         {
-          allowedServerExceptions--;
-          wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());
+          al = new Alignment(preds);
+          FirstSeq = prediction.getQuerySeqPosition();
+          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+              al.getSequenceAt(FirstSeq), SequenceInfo))
+          {
+            throw (new Exception(
+                "Couldn't recover sequence properties for JNet Query sequence!"));
+          }
         }
-      }
 
-      if (! (result.isJobFailed() || result.isServerError()))
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-      else
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
+        al.setDataset(null);
 
-    void StartJob()
-    {
-      try
+        jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+            noMsa);
+        return al; // , FirstSeq, noMsa};
+      }
+      public JPredJob(Hashtable SequenceInfo, SequenceI seq)
       {
-        if (msa!=null)  {
-          jobId = server.predictOnMsa(msa);
-        } else {
-          jobId = server.predict(sequence);
+        super();
+        String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());
+        if (sq.length() >= 20)
+        {
+          this.SequenceInfo = SequenceInfo;
+          sequence = new vamsas.objects.simple.Sequence();
+          sequence.setId(seq.getName());
+          sequence.setSeq(sq);
         }
-        System.out.println(jobId);
       }
-      catch (Exception e)
+
+      public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)
       {
-        System.out.println("JPredWS Client: Failed to submit the prediction\n" +
-                           e.toString() + "\n");
-        e.printStackTrace();
+        this(SequenceInfo, msf[0]);
+        if (sequence != null)
+        {
+          if (msf.length > 1)
+          {
+            msa = new vamsas.objects.simple.Msfalignment();
+            jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
+            msa.setMsf(pileup.print(msf));
+          }
+        }
       }
     }
+    ext.vamsas.Jpred server;
+    String altitle = "";
+    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server) {
+      this.altitle = altitle;
+      this.server = server;
+      this.wsInfo = wsinfo;
+    }
 
-    private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {
+//    String OutputHeader;
+//    vamsas.objects.simple.JpredResult result;
 
-      Annotation[] annotations = new Annotation[al.getWidth()];
-      for (int j = 0; j < values.size(); j++)
+    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq)
+    {
+      this(wsinfo, altitle, server);
+      JPredJob job = new JPredJob(SequenceInfo, seq);
+      if (job.hasValidInput())
       {
-        float value = Float.parseFloat(values.get(j).toString());
-        annotations[gapmap[j]] = new Annotation("", value+"",' ',value);
+        OutputHeader = wsInfo.getProgressText();
+        jobs = new WSJob[]
+            {
+            job};
+        job.jobnum = 0;
       }
-      al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));
     }
 
-    void parseResult()
+    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf)
     {
-      // OutputHeader = output.getText();
-      if (result.isFailed()) {
-        OutputHeader +="Job failed.\n";
-      }
-      if (result.getStatus()!=null) {
-        OutputHeader += "\n"+result.getStatus();
-      }
-      if (result.getPredfile()!=null) {
-        OutputHeader += "\n"+result.getPredfile();
-      // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data
+      this(wsinfo, altitle, server);
+      JPredJob job = new JPredJob(SequenceInfo, msf);
+      if (job.hasValidInput())
+      {
+        jobs = new WSJob[]
+            {
+            job};
+        OutputHeader = wsInfo.getProgressText();
+        job.jobnum = 0;
       }
-      if (result.getAligfile()!=null) {
-        OutputHeader += "\n"+result.getAligfile();
+    }
+
+    /*
+        public void run()
+        {
+          StartJob();
+
+          while (!jobComplete && (allowedServerExceptions > 0))
+          {
+            try
+            {
+              if ( (result = server.getresult(jobId)) == null)
+              {
+                throw (new Exception(
+     "Timed out when communicating with server\nTry again later.\n"));
+              }
+              if (result.getState()==0)
+                jalview.bin.Cache.log.debug("Finished "+jobId);
+              if (result.isRunning())
+              {
+                wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+              }
+              if (result.isQueued())
+              {
+                wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+              }
+
+              wsInfo.setProgressText(OutputHeader + "\n" +
+                                     result.getStatus());
+
+              if (result.isFinished())
+              {
+
+                parseResult();
+                jobComplete = true;
+                jobsRunning--;
+              } else {
+                // catch exceptions
+                if (! (result.isJobFailed() || result.isServerError()))
+                {
+                  try
+                  {
+                    Thread.sleep(5000);
+                  }
+                  catch (InterruptedException ex1)
+                  {
+                  }
+
+                  //  System.out.println("I'm alive "+seqid+" "+jobid);
+                }
+                else
+                {
+                  wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+                  jobsRunning--;
+                  jobComplete = true;
+                }
+              }
+            }
+            catch (Exception ex)
+            {
+              allowedServerExceptions--;
+
+              wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
+                                        ex.getMessage());
+
+              try
+              {
+                if (allowedServerExceptions > 0)
+                {
+                  Thread.sleep(5000);
+                }
+              }
+              catch (InterruptedException ex1)
+              {
+              }
+            }
+            catch (OutOfMemoryError er)
+            {
+              jobComplete = true;
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,
+     "Out of memory handling result!!"
+                                                    +
+     "\nSee help files for increasing Java Virtual Machine memory."
+                                                    , "Out of memory",
+     JOptionPane.WARNING_MESSAGE);
+              System.out.println("JPredClient: "+er);
+              System.gc();
+            }
+          }
+          if (result!=null)
+            if (! (result.isJobFailed() || result.isServerError()))
+            {
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+            }
+            else
+            {
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+            }
+        }
+     */
+    void StartJob(WSJob j)
+    {
+      if (! (j instanceof JPredJob))
+      {
+        throw new Error("Implementation error - StartJob(JpredJob) called on " +
+                        j.getClass());
       }
-      wsInfo.setProgressText(OutputHeader);
-      try {
-        // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
-        jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste");
-        SequenceI[] preds = prediction.getSeqsAsArray();
-        Alignment al;
-        int FirstSeq; // the position of the query sequence in Alignment al
-        boolean noMsa = true; // set if no MSA has been returned by JPred
+      try
+      {
+        JPredJob job = (JPredJob) j;
+        if (job.msa != null)
+        {
+          job.jobId = server.predictOnMsa(job.msa);
+        }
+        else
+          if (job.sequence!=null)
+          {
+            job.jobId = server.predict(job.sequence);
+          }
 
-        if (this.msa!=null && result.getAligfile()!=null) {
-          // we ignore the returned alignment if we only predicted on a single sequence
-          String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");
-          if (jalview.io.FormatAdapter.formats.contains(format))
+        if (job.jobId != null)
+        {
+          if (job.jobId.startsWith("Broken"))
           {
-            al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));
-            noMsa = false;
-            FirstSeq = 0;
+            job.result = (vamsas.objects.simple.Result)new JpredResult();
+            job.result.setInvalid(true);
+            job.result.setStatus("Submission " + job.jobId);
           }
           else
           {
-            throw (new Exception("Unknown format 'format' for file : \n" +
-                             result.getAligfile()));
+            job.submitted = true;
+            job.subjobComplete = false;
+            Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");
           }
+        }
+        else
+        {
+          throw new Exception("Server timed out - try again later\n");
+        }
+      }
+      catch (Exception e)
+      {
+        if (e.getMessage().indexOf("Exception") > -1)
+        {
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+          wsInfo.setProgressText(j.jobnum,
+                                 "Failed to submit the prediction. (Just close the window)\n"
+                                 +
+                                 "It is most likely that there is a problem with the server.\n");
+          System.err.println(
+              "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +
+              e.getMessage() + "\n");
+
+          jalview.bin.Cache.log.warn("Server Exception", e);
+        }
+        else
+        {
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+          // JBPNote - this could be a popup informing the user of the problem.
+          wsInfo.appendProgressText(j.jobnum,
+                                    "Failed to submit the prediction:\n"
+                                    + e.getMessage() +
+                                    wsInfo.getProgressText());
+
+          jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);
 
-        } else {
-          al = new Alignment(preds);
-          FirstSeq = prediction.getQuerySeqPosition();
         }
+        j.allowedServerExceptions = -1;
+        j.subjobComplete = true;
+      }
+    }
+
+    /*  private void addFloatAnnotations(Alignment al, int[] gapmap,
+                                       Vector values, String Symname,
+                                       String Visname, float min,
+                                       float max, int winLength)
+      {
+        Annotation[] annotations = new Annotation[al.getWidth()];
 
-        AlignmentAnnotation annot;
-        Annotation [] annotations = null;
-        int i = 0;
-        int width = preds[0].getSequence().length();
+        for (int j = 0; j < values.size(); j++)
+        {
+          float value = Float.parseFloat(values.get(j).toString());
+          annotations[gapmap[j]] = new Annotation("", value + "", ' ',
+                                                  value);
+        }
 
+        al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
+     annotations, min, max, winLength));
+      }*/
 
-        int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
-        if (gapmap.length!=width) {
-          throw (new Exception("Jpred Client Error\nNumber of residues in supposed query sequence :\n"
-                               +al.getSequenceAt(FirstSeq).getName()+"\n"
-                               +al.getSequenceAt(FirstSeq).getSequence()
-                               +"\nDiffer from number of prediction sites in \n"+result.getPredfile()+"\n"));
+    void parseResult()
+    {
+      int results = 0; // number of result sets received
+      JobStateSummary finalState = new JobStateSummary();
+      try
+      {
+        for (int j = 0; j < jobs.length; j++)
+        {
+          finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
+          if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+          {
+            results++;
+          }
         }
-        // JBPNote Should also rename the query sequence sometime...
-        i=0;
-        while (i < preds.length)
+      }
+      catch (Exception ex)
+      {
+
+        Cache.log.error("Unexpected exception when processing results for " +
+                        altitle, ex);
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+      }
+      if (results > 0)
+      {
+        wsInfo.showResultsNewFrame
+            .addActionListener(new java.awt.event.ActionListener()
         {
-          String id = preds[i].getName().toUpperCase();
-          if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED"))
+          public void actionPerformed(
+              java.awt.event.ActionEvent evt)
           {
-            annotations = new Annotation[al.getWidth()];
-
-            if(id.equals("JNETPRED")
-               || id.equals("JNETPSSM")
-               || id.equals("JNETFREQ")
-               || id.equals("JNETHMM")
-               || id.equals("JNETALIGN")
-               || id.equals("JPRED"))
-            {
-              for (int j = 0; j < width; j++)
-                annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0);
-            }
-            else if(id.equals("JNETCONF"))
+            displayResults(true);
+          }
+        });
+        wsInfo.mergeResults
+            .addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(
+              java.awt.event.ActionEvent evt)
+          {
+            displayResults(false);
+          }
+        });
+        wsInfo.setResultsReady();
+      }
+      else
+      {
+        wsInfo.setFinishedNoResults();
+      }
+    }
+
+    void displayResults(boolean newWindow)
+    {
+      if (jobs != null)
+      {
+        Alignment res = null;
+        for (int jn = 0; jn < jobs.length; jn++)
+        {
+          Alignment jobres = null;
+          JPredJob j = (JPredJob) jobs[jn];
+
+          if (j.hasResults())
+          {
+            try
             {
-              for (int j = 0; j < width; j++)
-              {
-                float value = Float.parseFloat(preds[i].getCharAt(j)+"");
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);
+              jalview.bin.Cache.log.debug("Parsing output of job " + jn);
+              jobres = j.getResultSet();
+              jalview.bin.Cache.log.debug("Finished parsing output.");
+              if (jobs.length==1)
+                res = jobres;
+              else {
+                  // do merge with other job results
               }
             }
-            else
+            catch (Exception e)
             {
-              for (int j = 0; j < width; j++) {
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0);
-              }
+              jalview.bin.Cache.log.error(
+                  "JNet Client: JPred Annotation Parse Error",
+                  e);
+              wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+              wsInfo.appendProgressText(j.jobnum,
+                                        OutputHeader + "\n" +
+                                        j.result.getStatus() +
+                                        "\nInvalid JNet job result data!\n" +
+                                        e.getMessage());
+              j.result.setBroken(true);
             }
-
-            if(id.equals("JNETCONF"))
-              annot = new AlignmentAnnotation(preds[i].getName(),
-                                           "JNet Output",
-                                           annotations,0f,10f,1);
-
-            else   annot = new AlignmentAnnotation(preds[i].getName(),
-                                            "JNet Output",
-                                            annotations);
-            al.addAnnotation(annot);
-            if (noMsa)
-              al.deleteSequence(preds[i]);
           }
-          i++;
         }
 
-        Hashtable scores = prediction.getScores();
-      /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
-                            "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
-
-        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-                            "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
-
-        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                            "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-       */
-        AlignFrame af = new AlignFrame(al);
-
+        if (res != null)
+        {
+          if (newWindow)
+          {
+            AlignFrame af = new AlignFrame(res);
+            Desktop.addInternalFrame(af, altitle,
+                                     AlignFrame.NEW_WINDOW_WIDTH,
+                                     AlignFrame.NEW_WINDOW_HEIGHT);
+          }
+          else
+          {
+            Cache.log.info("Append results onto existing alignment.");
+          }
+        }
+      }
+    }
 
-        Desktop.addInternalFrame(af,
-                                 "JNet Prediction for sequence ",
-                                 AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
-      }catch(Exception ex){ex.printStackTrace();}
+    void pollJob(WSJob job)
+        throws Exception
+    {
+      job.result = server.getresult(job.jobId);
+    }
+    public boolean isCancellable()
+    {
+      return false;
+    }
 
+    public void cancelJob()
+    {
+      throw new Error("Implementation error!");
     }
 
   }