X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=2ec8e1e8999728b726291fc586ccadbd3a7d0f37;hb=f0821f93f0d678fafdd2d6156b0c2bd50a061055;hp=45d4bd1d8dcf04b06a25768bb0bb18a1bc786a24;hpb=98eb909d0a4fe04ff6ad93f71086f1127fe4a530;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 45d4bd1..2ec8e1e 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -24,39 +24,50 @@ import javax.swing.*;
 
 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
 {
-  ext.vamsas.Jpred server;
-  String altitle = "";
-  java.util.Hashtable SequenceInfo = null;
-  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) {
+  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) {
+
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa)
+  {
     wsInfo = setWebService(sh);
     startJPredClient(title, msa);
   }
 
-  public JPredClient(String title, SequenceI[] msf) {
+  public JPredClient(String title, SequenceI[] msf)
+  {
     startJPredClient(title, msf);
   }
 
-  public JPredClient(String title, SequenceI seq) {
+  public JPredClient(String title, SequenceI seq)
+  {
     startJPredClient(title, seq);
   }
 
   private void startJPredClient(String title, SequenceI[] msf)
   {
-    if (wsInfo==null)
+    if (wsInfo == null)
+    {
       wsInfo = setWebService();
+    }
 
     SequenceI seq = msf[0];
-    altitle = "JNet prediction on " + seq.getName() +
+
+    String altitle = "JNet prediction on " + seq.getName() +
         " using alignment from " + title;
 
     wsInfo.setProgressText("Job details for MSA based prediction (" +
@@ -64,38 +75,47 @@ public class JPredClient
                            AlignSeq.extractGaps("-. ", seq.getSequence()) +
                            "\n");
     SequenceI aln[] = new SequenceI[msf.length];
-    for (int i=0,j=msf.length; i<j;i++)
+    for (int i = 0, j = msf.length; i < j; i++)
+    {
       aln[i] = new jalview.datamodel.Sequence(msf[i]);
-    SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+    }
+
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
-    if (!locateWebService())
+    Jpred server = locateWebService();
+    if (server==null)
     {
       return;
     }
 
-    JPredThread jthread = new JPredThread(aln);
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln);
+    wsInfo.setthisService(jthread);
     jthread.start();
   }
 
   public void startJPredClient(String title, SequenceI seq)
   {
-    if (wsInfo==null)
+    if (wsInfo == null)
+    {
       wsInfo = setWebService();
+    }
     wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
                            seq.getName() + "\n" +
                            AlignSeq.extractGaps("-. ", seq.getSequence()) +
                            "\n");
-    altitle = "JNet prediction for sequence " + seq.getName() + " from " +
+    String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
         title;
 
-    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
 
-    if (!locateWebService())
+    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();
   }
 
@@ -104,7 +124,7 @@ public class JPredClient
     WebServiceName = "JNetWS";
     WebServiceJobTitle = "JNet secondary structure prediction";
     WebServiceReference =
-        "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +
+        "\"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";
@@ -115,14 +135,16 @@ public class JPredClient
     return wsInfo;
   }
 
-  private boolean locateWebService()
+  private ext.vamsas.Jpred locateWebService()
   {
     ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
-
+    ext.vamsas.Jpred server=null;
     try
     {
-      this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
-      ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub
+      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);
+
     }
     catch (Exception ex)
     {
@@ -136,279 +158,100 @@ public class JPredClient
                              " Service location failed\nfor URL :" + WsURL +
                              "\n" +
                              ex.getMessage());
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
-      return false;
     }
 
-    return true;
+    return server;
   }
 
   class JPredThread
-      extends Thread
+      extends WSThread
+      implements WSClientI
   {
-    String OutputHeader;
-    vamsas.objects.simple.JpredResult result;
-    vamsas.objects.simple.Sequence sequence;
-    vamsas.objects.simple.Msfalignment msa;
-    String jobId;
-    boolean jobComplete = false;
-    int allowedServerExceptions = 3; // thread dies if too many exceptions.
-
-    JPredThread(SequenceI seq)
+    class JPredJob
+        extends WSThread.WSJob
     {
-      OutputHeader = wsInfo.getProgressText();
-      this.sequence = new vamsas.objects.simple.Sequence();
-      this.sequence.setId(seq.getName());
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
-    }
 
-    JPredThread(SequenceI[] msf)
-    {
-      OutputHeader = wsInfo.getProgressText();
-      this.sequence = new vamsas.objects.simple.Sequence();
-      this.sequence.setId(msf[0].getName());
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ",
-                                                msf[0].getSequence()));
-
-      jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();
-      this.msa = new vamsas.objects.simple.Msfalignment();
-      msa.setMsf(mwrite.print(msf));
-    }
-
-    public void run()
-    {
-      StartJob();
-
-      while (!jobComplete && (allowedServerExceptions > 0))
+      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()
       {
-        try
+        if (subjobComplete && result != null && result.isFinished()
+            && ( (JpredResult) result).getPredfile() != null &&
+            ( (JpredResult) result).getAligfile() != null)
         {
-          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.Jalview.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();
+          return true;
         }
+        return false;
       }
-      if (result!=null)
-        if (! (result.isJobFailed() || result.isServerError()))
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        }
-        else
-        {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-        }
-    }
 
-    void StartJob()
-    {
-      try
+      boolean hasValidInput()
       {
-        if (msa != null)
+        if (sequence != null)
         {
-          jobId = server.predictOnMsa(msa);
+          return true;
         }
-        else
-        {
-          jobId = server.predict(sequence);
-        }
-
-        if (jobId != null)
-        {
-          if (jobId.startsWith("Broken"))
-          {
-            throw new Exception("Submission " + jobId);
-          }
-          else
-          {
-            System.out.println(WsURL + " Job Id '" + jobId + "'");
-          }
-        }
-        else
-        {
-          throw new Exception("Server timed out - try again later\n");
-        }
-      }
-      catch (Exception e)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        allowedServerExceptions = -1;
-        jobComplete = true;
-
-        wsInfo.setProgressText("Failed to submit the prediction. (Just close the window)\n"
-                                  + ((e.getMessage().indexOf("Exception")>-1) ? (
-                                  "It is most likely that there is a problem with the server.\n")
-                              : e.getMessage())
-                                  +wsInfo.getProgressText());
-        System.err.println(
-            "JPredWS Client: Failed to submit the prediction (Possibly a server error - see below)\n" +
-            e.getMessage() + "\n");
-
-        jalview.bin.Jalview.log.debug("Failed Submission",e);
-      }
-    }
-
-
-
-    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()];
-
-      for (int j = 0; j < values.size(); j++)
-      {
-        float value = Float.parseFloat(values.get(j).toString());
-        annotations[gapmap[j]] = new Annotation("", value + "", ' ',
-                                                value);
+        return false;
       }
 
-      al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
-                                               annotations, min, max, winLength));
-    }
-
-    void parseResult()
-    {
-      // OutputHeader = output.getText();
-      if (result.isFailed())
+      public Alignment getResultSet()
+          throws Exception
       {
-        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
-      }
-
-      if (result.getAligfile() != null)
-      {
-        OutputHeader += ("\n" + result.getAligfile());
-      }
+        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
 
-      wsInfo.setProgressText(OutputHeader+"Parsing...");
+        JpredResult result = (JpredResult)this.result;
 
-      try
-      {
-        jalview.bin.Jalview.log.debug("Parsing output from JNet job.");
+        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.Jalview.log.debug("Got prediction profile.");
-        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
+        jalview.bin.Cache.log.debug("Got prediction profile.");
 
         if ( (this.msa != null) && (result.getAligfile() != null))
         {
-          jalview.bin.Jalview.log.debug("Getting associated alignment.");
+          jalview.bin.Cache.log.debug("Getting associated alignment.");
           // we ignore the returned alignment if we only predicted on a single sequence
-          String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),
+          String format = new jalview.io.IdentifyFile().Identify(result.
+              getAligfile(),
               "Paste");
 
-          if (jalview.io.FormatAdapter.formats.contains(format))
+          if (jalview.io.FormatAdapter.isValidFormat(format))
           {
-            al = new Alignment(jalview.io.FormatAdapter.readFile(
-                result.getAligfile(), "Paste", format));
-            for (int i=0, j=al.getHeight(); i<j; i++) {
-              SequenceI sq = al.getSequenceAt(i);
-              if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-                  sq, (Hashtable) SequenceInfo.get(sq.getName())))
-              {
-                throw (new Exception(
-                    "Couldn't recover sequence properties for JNet "
-                    +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));
-              }
+            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
           {
             throw (new Exception(
-                "Unknown format 'format' for file : \n" +
+                "Unknown format "+format+" for file : \n" +
                 result.getAligfile()));
           }
         }
@@ -424,114 +267,388 @@ public class JPredClient
           }
         }
 
+        al.setDataset(null);
 
-        AlignmentAnnotation annot;
-        Annotation[] annotations = null;
-        int i = 0;
-        int width = preds[0].getSequence().length();
-
-        int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
+        jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
+            noMsa);
+        return al; // , FirstSeq, noMsa};
+      }
+      public JPredJob(Hashtable SequenceInfo, SequenceI seq)
+      {
+        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);
+        }
+      }
 
-        if (gapmap.length != width)
+      public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)
+      {
+        this(SequenceInfo, msf[0]);
+        if (sequence != null)
         {
-          throw (new Exception(
-              "Jnet 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"));
+          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;
+    }
 
-        // JBPNote Should also rename the query sequence sometime...
-        i = 0;
+//    String OutputHeader;
+//    vamsas.objects.simple.JpredResult result;
 
-        while (i < preds.length)
+    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())
+      {
+        OutputHeader = wsInfo.getProgressText();
+        jobs = new WSJob[]
+            {
+            job};
+        job.jobnum = 0;
+      }
+    }
+
+    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf)
+    {
+      this(wsinfo, altitle, server);
+      JPredJob job = new JPredJob(SequenceInfo, msf);
+      if (job.hasValidInput())
+      {
+        jobs = new WSJob[]
+            {
+            job};
+        OutputHeader = wsInfo.getProgressText();
+        job.jobnum = 0;
+      }
+    }
+
+    /*
+        public void run()
         {
-          String id = preds[i].getName().toUpperCase();
+          StartJob();
 
-          if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
-              id.startsWith("JPRED"))
+          while (!jobComplete && (allowedServerExceptions > 0))
           {
-            annotations = new Annotation[al.getWidth()];
-
-            if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
-                id.equals("JNETFREQ") || id.equals("JNETHMM") ||
-                id.equals("JNETALIGN") || id.equals("JPRED"))
+            try
             {
-              for (int j = 0; j < width; j++)
+              if ( (result = server.getresult(jobId)) == null)
               {
-                annotations[gapmap[j]] = new Annotation("", "",
-                    preds[i].getCharAt(j), 0);
+                throw (new Exception(
+     "Timed out when communicating with server\nTry again later.\n"));
               }
-            }
-            else if (id.equals("JNETCONF"))
-            {
-              for (int j = 0; j < width; j++)
+              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())
               {
-                float value = Float.parseFloat(preds[i].getCharAt(
-                    j) + "");
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                    j) + "", "", preds[i].getCharAt(j),
-                    value);
+
+                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;
+                }
               }
             }
-            else
+            catch (Exception ex)
             {
-              for (int j = 0; j < width; j++)
+              allowedServerExceptions--;
+
+              wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
+                                        ex.getMessage());
+
+              try
+              {
+                if (allowedServerExceptions > 0)
+                {
+                  Thread.sleep(5000);
+                }
+              }
+              catch (InterruptedException ex1)
               {
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
-                    j) + "", "", ' ', 0);
               }
             }
-
-            if (id.equals("JNETCONF"))
+            catch (OutOfMemoryError er)
             {
-              annot = new AlignmentAnnotation(preds[i].getName(),
-                                              "JNet Output", annotations, 0f,
-                                              10f, 1);
+              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();
             }
-            else
+          }
+          if (result!=null)
+            if (! (result.isJobFailed() || result.isServerError()))
             {
-              annot = new AlignmentAnnotation(preds[i].getName(),
-                                              "JNet Output", annotations);
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
             }
-
-            al.addAnnotation(annot);
-
-            if (noMsa)
+            else
             {
-              al.deleteSequence(preds[i]);
+              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());
+      }
+      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);
           }
 
-          i++;
+        if (job.jobId != null)
+        {
+          if (job.jobId.startsWith("Broken"))
+          {
+            job.result = (vamsas.objects.simple.Result)new JpredResult();
+            job.result.setInvalid(true);
+            job.result.setStatus("Submission " + job.jobId);
+          }
+          else
+          {
+            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());
 
-        Hashtable scores = prediction.getScores();
+          jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);
 
-        /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
-                              "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
+        }
+        j.allowedServerExceptions = -1;
+        j.subjobComplete = true;
+      }
+    }
 
-          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-         "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
+    /*  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()];
 
-          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                              "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-         */
+        for (int j = 0; j < values.size(); j++)
+        {
+          float value = Float.parseFloat(values.get(j).toString());
+          annotations[gapmap[j]] = new Annotation("", value + "", ' ',
+                                                  value);
+        }
 
-        wsInfo.setProgressText(OutputHeader);
-        jalview.bin.Jalview.log.debug("Finished parsing output.");
-        AlignFrame af = new AlignFrame(al);
+        al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
+     annotations, min, max, winLength));
+      }*/
 
-        Desktop.addInternalFrame(af, altitle,
-                                 AlignFrame.NEW_WINDOW_WIDTH,
-                                 AlignFrame.NEW_WINDOW_HEIGHT);
+    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++;
+          }
+        }
       }
       catch (Exception ex)
       {
-        jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
-        jalview.bin.Jalview.log.debug("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()
+        {
+          public void actionPerformed(
+              java.awt.event.ActionEvent evt)
+          {
+            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
+            {
+              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
+              }
+            }
+            catch (Exception e)
+            {
+              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 (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.");
+          }
+        }
+      }
+    }
+
+    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!");
+    }
+
   }
 }
+