From: jprocter <Jim Procter>
Date: Tue, 15 Aug 2006 10:59:31 +0000 (+0000)
Subject: first stage of adapting JNet client to hidden regions and new WSClient
X-Git-Tag: Release_2_1~55
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d32e3804460b3e145f96a1ad68cbed279ac545f4;p=jalview.git

first stage of adapting JNet client to hidden regions and new WSClient
structure.
---

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index ec3f737..2ec8e1e 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -24,42 +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.FormatAdapter;
 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 (" +
@@ -67,40 +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++) {
-        aln[i] = new jalview.datamodel.Sequence(msf[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();
   }
 
@@ -120,14 +135,14 @@ 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);
 
     }
@@ -145,164 +160,317 @@ public class JPredClient
                              ex.getMessage());
       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()));
-
-      this.msa = new vamsas.objects.simple.Msfalignment();
-      jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
-      msa.setMsf(pileup.print(msf));
-    }
+      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;
+      }
 
-    public void run()
-    {
-      StartJob();
+      boolean hasValidInput()
+      {
+        if (sequence != null)
+        {
+          return true;
+        }
+        return false;
+      }
 
-      while (!jobComplete && (allowedServerExceptions > 0))
+      public Alignment getResultSet()
+          throws Exception
       {
-        try
+        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 ( (this.msa != null) && (result.getAligfile() != null))
         {
-          if ( (result = server.getresult(jobId)) == 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))
+          {
+            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(
-                "Timed out when communicating with server\nTry again later.\n"));
+                "Unknown format "+format+" for file : \n" +
+                result.getAligfile()));
           }
-          if (result.getState()==0)
-            jalview.bin.Cache.log.debug("Finished "+jobId);
-          if (result.isRunning())
+        }
+        else
+        {
+          al = new Alignment(preds);
+          FirstSeq = prediction.getQuerySeqPosition();
+          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
+              al.getSequenceAt(FirstSeq), SequenceInfo))
           {
-            wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
+            throw (new Exception(
+                "Couldn't recover sequence properties for JNet Query sequence!"));
           }
-          if (result.isQueued())
+        }
+
+        al.setDataset(null);
+
+        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);
+        }
+      }
+
+      public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)
+      {
+        this(SequenceInfo, msf[0]);
+        if (sequence != null)
+        {
+          if (msf.length > 1)
           {
-            wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
+            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;
+    }
 
-          wsInfo.setProgressText(OutputHeader + "\n" +
-                                 result.getStatus());
+//    String OutputHeader;
+//    vamsas.objects.simple.JpredResult result;
 
-          if (result.isFinished())
+    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()
+        {
+          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);
+              }
 
-            parseResult();
-            jobComplete = true;
-            jobsRunning--;
-          } else {
-            // catch exceptions
-            if (! (result.isJobFailed() || result.isServerError()))
+              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
               {
-                Thread.sleep(5000);
+                if (allowedServerExceptions > 0)
+                {
+                  Thread.sleep(5000);
+                }
               }
               catch (InterruptedException ex1)
               {
               }
-
-              //  System.out.println("I'm alive "+seqid+" "+jobid);
             }
-            else
+            catch (OutOfMemoryError er)
             {
-              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-              jobsRunning--;
               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();
             }
           }
-        }
-        catch (Exception ex)
-        {
-          allowedServerExceptions--;
-
-          wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
-                                    ex.getMessage());
-
-          try
-          {
-            if (allowedServerExceptions > 0)
+          if (result!=null)
+            if (! (result.isJobFailed() || result.isServerError()))
             {
-              Thread.sleep(5000);
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+            }
+            else
+            {
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
             }
-          }
-          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()
+     */
+    void StartJob(WSJob j)
     {
+      if (! (j instanceof JPredJob))
+      {
+        throw new Error("Implementation error - StartJob(JpredJob) called on " +
+                        j.getClass());
+      }
       try
       {
-        if (msa != null)
+        JPredJob job = (JPredJob) j;
+        if (job.msa != null)
         {
-          jobId = server.predictOnMsa(msa);
+          job.jobId = server.predictOnMsa(job.msa);
         }
         else
-        {
-          jobId = server.predict(sequence);
-        }
+          if (job.sequence!=null)
+          {
+            job.jobId = server.predict(job.sequence);
+          }
 
-        if (jobId != null)
+        if (job.jobId != null)
         {
-          if (jobId.startsWith("Broken"))
+          if (job.jobId.startsWith("Broken"))
           {
-            throw new Exception("Submission " + jobId);
+            job.result = (vamsas.objects.simple.Result)new JpredResult();
+            job.result.setInvalid(true);
+            job.result.setStatus("Submission " + job.jobId);
           }
           else
           {
-            System.out.println(WsURL + " Job Id '" + jobId + "'");
+            job.submitted = true;
+            job.subjobComplete = false;
+            Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");
           }
         }
         else
@@ -312,158 +480,175 @@ public class JPredClient
       }
       catch (Exception e)
       {
-        if (e.getMessage().indexOf("Exception")>-1) {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-          wsInfo.setProgressText(
-              "Failed to submit the prediction. (Just close the window)\n"
-              +
-              "It is most likely that there is a problem with the server.\n");
+        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(WebserviceInfo.STATE_STOPPED_ERROR);
+          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.setProgressText("Failed to submit the prediction:\n"
-                                 +e.getMessage()+
-                                 wsInfo.getProgressText());
+          wsInfo.appendProgressText(j.jobnum,
+                                    "Failed to submit the prediction:\n"
+                                    + e.getMessage() +
+                                    wsInfo.getProgressText());
 
-          jalview.bin.Cache.log.debug("Failed Submission",e);
+          jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);
 
         }
-        allowedServerExceptions = -1;
-        jobComplete = true;
-
+        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()];
-
-      for (int j = 0; j < values.size(); j++)
+    /*  private void addFloatAnnotations(Alignment al, int[] gapmap,
+                                       Vector values, String Symname,
+                                       String Visname, float min,
+                                       float max, int winLength)
       {
-        float value = Float.parseFloat(values.get(j).toString());
-        annotations[gapmap[j]] = new Annotation("", value + "", ' ',
-                                                value);
-      }
+        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);
+        }
 
-      al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
-                                               annotations, min, max, winLength));
-    }*/
+        al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
+     annotations, min, max, winLength));
+      }*/
 
     void parseResult()
     {
-      // OutputHeader = output.getText();
-      if (result.isFailed())
+      int results = 0; // number of result sets received
+      JobStateSummary finalState = new JobStateSummary();
+      try
       {
-        OutputHeader += "Job failed.\n";
+        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++;
+          }
+        }
       }
-
-      if (result.getStatus() != null)
+      catch (Exception ex)
       {
-        OutputHeader += ("\n" + result.getStatus());
-      }
 
-      if (result.getPredfile() != null)
+        Cache.log.error("Unexpected exception when processing results for " +
+                        altitle, ex);
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+      }
+      if (results > 0)
       {
-        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
+        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();
       }
-
-      if (result.getAligfile() != null)
+      else
       {
-        OutputHeader += ("\n" + result.getAligfile());
+        wsInfo.setFinishedNoResults();
       }
+    }
 
-      wsInfo.setProgressText(OutputHeader+"Parsing...");
-
-      try
+    void displayResults(boolean newWindow)
+    {
+      if (jobs != null)
       {
-        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.");
-        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
-
-        if ( (this.msa != null) && (result.getAligfile() != null))
+        Alignment res = null;
+        for (int jn = 0; jn < jobs.length; jn++)
         {
-          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");
+          Alignment jobres = null;
+          JPredJob j = (JPredJob) jobs[jn];
 
-          if (jalview.io.FormatAdapter.isValidFormat(format))
+          if (j.hasResults())
           {
-            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."));
+            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
               }
-
-            noMsa = false;
-            FirstSeq = 0;
-          }
-          else
-          {
-            throw (new Exception(
-                "Unknown format 'format' for file : \n" +
-                result.getAligfile()));
+            }
+            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);
+            }
           }
         }
-        else
+
+        if (res != null)
         {
-          al = new Alignment(preds);
-          FirstSeq = prediction.getQuerySeqPosition();
-          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-              al.getSequenceAt(FirstSeq), SequenceInfo))
+          if (newWindow)
           {
-            throw (new Exception(
-                "Couldn't recover sequence properties for JNet Query sequence!"));
+            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.");
           }
         }
+      }
+    }
 
-        al.setDataset(null);
-
-        try {
-          jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
-              noMsa);
-        }
-        catch (Exception e) {
-          jalview.bin.Cache.log.error("JNet Client: JPred Annotation Parse Error", e);
-        }
-        wsInfo.setProgressText(OutputHeader);
-        jalview.bin.Cache.log.debug("Finished parsing output.");
-        AlignFrame af = new AlignFrame(al);
+    void pollJob(WSJob job)
+        throws Exception
+    {
+      job.result = server.getresult(job.jobId);
+    }
+    public boolean isCancellable()
+    {
+      return false;
+    }
 
-        Desktop.addInternalFrame(af, altitle,
-                                 AlignFrame.NEW_WINDOW_WIDTH,
-                                 AlignFrame.NEW_WINDOW_HEIGHT);
-      }
-      catch (Exception ex)
-      {
-        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);
-      }
+    public void cancelJob()
+    {
+      throw new Error("Implementation error!");
     }
+
   }
 }
+