X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=8a4368c0284133e28ddb59e44b0d293f0beb08d3;hb=65df62f4b048a1615d32ea2c3576082ad2b63af8;hp=8d3ae3598374e1412e21bdf0474183df9d0819a9;hpb=6601dbb702c89e6ed22b7493cf23f94e4406cdd6;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 8d3ae35..8a4368c 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,200 +1,272 @@
+/*
+ * 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 jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.FormatAdapter;
 
 public class JPredClient
     extends WSClient
 {
-  ext.vamsas.JPredWS server;
+  ext.vamsas.Jpred server;
   String altitle = "";
   java.util.Hashtable SequenceInfo = null;
+  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(String title, SequenceI seq) {
+    startJPredClient(title, seq);
+  }
+
+  private void startJPredClient(String title, SequenceI[] msf)
+  {
+    if (wsInfo==null)
+      wsInfo = setWebService();
+
+    SequenceI seq = msf[0];
+
+    altitle = "JNet prediction on " + seq.getName() +
+        " using alignment from " + title;
+
+    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]);
+    }
+
+    SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+
+    if (!locateWebService())
+    {
+      return;
+    }
+
+    JPredThread jthread = new JPredThread(aln);
+    jthread.start();
+  }
+
+  public void startJPredClient(String title, SequenceI seq)
+  {
+    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 " +
+        title;
+
+    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+
+    if (!locateWebService())
+    {
+      return;
+    }
+
+    JPredThread jthread = new JPredThread(seq);
+    jthread.start();
+  }
+
   private WebserviceInfo setWebService()
   {
     WebServiceName = "JNetWS";
     WebServiceJobTitle = "JNet secondary structure prediction";
     WebServiceReference =
-        "\"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\".";
+        "\"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;
   }
 
-    private boolean locateWebService()
-    {
-
-      JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
-      try
-      {
-        this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
-        ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub
-      }
-      catch (Exception ex)
-      {
-        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(wsInfo.STATE_STOPPED_SERVERERROR);
-        return false;
-      }
-      return true;
-    }
+  private boolean locateWebService()
+  {
+    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
 
-    public JPredClient(String title, SequenceI[] msf)
+    try
     {
-      wsInfo = setWebService();
-      SequenceI seq = msf[0];
-      altitle = "JNet prediction on " + seq.getName() +
-          " using alignment from " + title;
-
-      wsInfo.setProgressText("Job details for MSA based prediction (" + title +
-                             ") on sequence :\n>"
-                             + seq.getName() + "\n"
-                             + AlignSeq.extractGaps("-. ", seq.getSequence()) +
-                             "\n");
-
-      SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
-      if (!locateWebService())
-        return;
-
-      JPredThread jthread = new JPredThread(msf);
-      jthread.start();
+      this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties
+      ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub
     }
-
-    public JPredClient(String title, SequenceI seq)
+    catch (Exception ex)
     {
-      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 " +
-          title;
-
-      SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+      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 false;
+    }
 
-      if (!locateWebService())
-              return;
+    return true;
+  }
 
-      JPredThread jthread = new JPredThread(seq);
-      jthread.start();
+  class JPredThread
+      extends Thread
+  {
+    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)
+    {
+      OutputHeader = wsInfo.getProgressText();
+      this.sequence = new vamsas.objects.simple.Sequence();
+      this.sequence.setId(seq.getName());
+      this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
     }
 
-    class JPredThread
-        extends Thread
+    JPredThread(SequenceI[] msf)
     {
-      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)
-      {
-        OutputHeader = wsInfo.getProgressText();
-        this.sequence = new ext.vamsas.Sequence();
-        this.sequence.setId(seq.getName());
-        this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
-      }
+      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));
+    }
 
-      JPredThread(SequenceI[] msf)
-      {
-        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.PileUpfile mwrite = new jalview.io.PileUpfile();
-        this.msa = new ext.vamsas.Msfalignment();
-        msa.setMsf(mwrite.print(msf));
-      }
+    public void run()
+    {
+      StartJob();
 
-      public void run()
+      while (!jobComplete && (allowedServerExceptions > 0))
       {
-
-        StartJob();
-
-        while (!jobComplete && (allowedServerExceptions > 0))
+        try
         {
-          try
+          if ( (result = server.getresult(jobId)) == null)
           {
-            if ( (result = server.getresult(jobId)) == null)
-            {
-              throw (new Exception(
-                  "Timed out when communicating with server\nTry again later.\n"));
-            }
+            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);
+          }
 
-            if (result.isRunning())
-            {
-              wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-            }
-            else if (result.isQueued())
-            {
-              wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-            }
+          wsInfo.setProgressText(OutputHeader + "\n" +
+                                 result.getStatus());
 
-            if (result.isFinished())
-            {
-              parseResult();
-              jobComplete = true;
-              jobsRunning--;
-            }
-            else
+          if (result.isFinished())
+          {
+
+            parseResult();
+            jobComplete = true;
+            jobsRunning--;
+          } else {
+            // catch exceptions
+            if (! (result.isJobFailed() || result.isServerError()))
             {
-              wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
-              if (! (result.isJobFailed() || result.isServerError()))
+              try
               {
-                try
-                {
-                  Thread.sleep(5000);
-                }
-                catch (InterruptedException ex1)
-                {
-                }
-                //  System.out.println("I'm alive "+seqid+" "+jobid);
+                Thread.sleep(5000);
               }
-              else
+              catch (InterruptedException ex1)
               {
-                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
               }
+
+              //  System.out.println("I'm alive "+seqid+" "+jobid);
             }
-          }
-          catch (Exception ex)
-          {
-            allowedServerExceptions--;
-            wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
-                                      ex.getMessage());
-            try
+            else
             {
-              if (allowedServerExceptions > 0)
-              {
-                Thread.sleep(5000);
-              }
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+              jobsRunning--;
+              jobComplete = true;
             }
-            catch (InterruptedException ex1)
+          }
+        }
+        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);
@@ -203,232 +275,281 @@ public class JPredClient
         {
           wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
         }
-      }
+    }
 
-      void StartJob()
+    void StartJob()
+    {
+      try
       {
-        try
+        if (msa != null)
         {
-          if (msa != null)
-          {
-            jobId = server.predictOnMsa(msa);
-          }
-          else
-          {
-            jobId = server.predict(sequence);
-          }
-          if (jobId != null)
+          jobId = server.predictOnMsa(msa);
+        }
+        else
+        {
+          jobId = server.predict(sequence);
+        }
+
+        if (jobId != null)
+        {
+          if (jobId.startsWith("Broken"))
           {
-            if (jobId.startsWith("Broken"))
-            {
-              throw new Exception("Submission " + jobId);
-            }
-            else
-            {
-              System.out.println(WsURL + " Job Id '" + jobId + "'");
-            }
+            throw new Exception("Submission " + jobId);
           }
           else
           {
-            throw new Exception("Server timed out - try again later\n");
-
+            System.out.println(WsURL + " Job Id '" + jobId + "'");
           }
         }
-        catch (Exception e)
+        else
         {
+          throw new Exception("Server timed out - try again later\n");
+        }
+      }
+      catch (Exception e)
+      {
+        if (e.getMessage().indexOf("Exception")>-1) {
           wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-          allowedServerExceptions = 0;
-          jobComplete = false;
-          wsInfo.appendProgressText("Failed to submit the prediction: " +
-                                    e.toString() + "\nJust close the window\n");
+          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");
           System.err.println(
-              "JPredWS Client: Failed to submit the prediction\n" +
-              e.toString() + "\n");
-          // e.printStackTrace(); TODO: JBPNote DEBUG
+              "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);
+          // JBPNote - this could be a popup informing the user of the problem.
+          wsInfo.setProgressText("Failed to submit the prediction:\n"
+                                 +e.getMessage()+
+                                 wsInfo.getProgressText());
+
+          jalview.bin.Cache.log.debug("Failed Submission",e);
+
         }
+        allowedServerExceptions = -1;
+        jobComplete = true;
+
       }
+    }
 
-      private void addFloatAnnotations(Alignment al, int[] gapmap,
-                                       Vector values, String Symname,
-                                       String Visname, float min, float max,
-                                       int winLength)
+
+
+  /*  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);
+      }
 
-        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())
+      {
+        OutputHeader += "Job failed.\n";
       }
 
-      void parseResult()
+      if (result.getStatus() != null)
       {
-        // 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
-        }
-        if (result.getAligfile() != null)
-        {
-          OutputHeader += "\n" + result.getAligfile();
-        }
-        wsInfo.setProgressText(OutputHeader);
-        try
+        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());
+      }
+
+      wsInfo.setProgressText(OutputHeader+"Parsing...");
+
+      try
+      {
+        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))
         {
-          // 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
-
-          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.formats.contains(format))
           {
-            // 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))
-            {
-              al = new Alignment(jalview.io.FormatAdapter.readFile(result.
-                  getAligfile(), "Paste", format));
-              noMsa = false;
-              FirstSeq = 0;
-            }
-            else
-            {
-              throw (new Exception("Unknown format 'format' for file : \n" +
-                                   result.getAligfile()));
+            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
           {
-            al = new Alignment(preds);
-            FirstSeq = prediction.getQuerySeqPosition();
+            throw (new Exception(
+                "Unknown format 'format' for file : \n" +
+                result.getAligfile()));
           }
-
-          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al.getSequenceAt(
-              FirstSeq), SequenceInfo))
+        }
+        else
+        {
+          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!"));
           }
+        }
 
-          AlignmentAnnotation annot;
-          Annotation[] annotations = null;
-          int i = 0;
-          int width = preds[0].getSequence().length();
+        al.setDataset(null);
 
-          int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
+        AlignmentAnnotation annot;
+        Annotation[] annotations = null;
+        int i = 0;
+        int width = preds[0].getSequence().length();
 
-          if (gapmap.length != width)
-          {
-            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"));
-          }
-          // JBPNote Should also rename the query sequence sometime...
-          i = 0;
-          while (i < preds.length)
+        int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
+
+        if (gapmap.length != width)
+        {
+          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"));
+        }
+
+        // JBPNote Should also rename the query sequence sometime...
+        i = 0;
+
+        SequenceI seqRef = al.getSequenceAt(FirstSeq);
+
+        while (i < preds.length)
+        {
+          String id = preds[i].getName().toUpperCase();
+
+          if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
+              id.startsWith("JPRED"))
           {
-            String id = preds[i].getName().toUpperCase();
-            if (id.startsWith("LUPAS") || id.startsWith("JNET") ||
-                id.startsWith("JPRED"))
+            annotations = new Annotation[al.getWidth()];
+
+            if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
+                id.equals("JNETFREQ") || id.equals("JNETHMM") ||
+                id.equals("JNETALIGN") || id.equals("JPRED"))
             {
-              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++)
               {
-                for (int j = 0; j < width; j++)
-                {
-                  annotations[gapmap[j]] = new Annotation("", "",
-                      preds[i].getCharAt(j), 0);
-                }
+                annotations[gapmap[j]] = new Annotation("", "",
+                    preds[i].getCharAt(j), 0);
               }
-              else if (id.equals("JNETCONF"))
+            }
+            else if (id.equals("JNETCONF"))
+            {
+              for (int j = 0; j < width; j++)
               {
-                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);
-                }
+                float value = Float.parseFloat(preds[i].getCharAt(
+                    j) + "");
+                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                    j) + "", "", preds[i].getCharAt(j),
+                    value);
               }
-              else
+            }
+            else
+            {
+              for (int j = 0; j < width; j++)
               {
-                for (int j = 0; j < width; j++)
-                {
-                  annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +
-                      "", "", ' ', 0);
-                }
+                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                    j) + "", "", ' ', 0);
               }
+            }
 
-              if (id.equals("JNETCONF"))
-              {
-                annot = new AlignmentAnnotation(preds[i].getName(),
-                                                "JNet Output",
-                                                annotations, 0f, 10f, 1);
-              }
+            if (id.equals("JNETCONF"))
+            {
+              annot = new AlignmentAnnotation(preds[i].getName(),
+                                              "JNet Output", annotations, 0f,
+                                              10f,
+                                              AlignmentAnnotation.BAR_GRAPH);
+            }
+            else
+            {
+              annot = new AlignmentAnnotation(preds[i].getName(),
+                                              "JNet Output", annotations);
+            }
 
-              else
-              {
-                annot = new AlignmentAnnotation(preds[i].getName(),
-                                                "JNet Output",
-                                                annotations);
-              }
-              al.addAnnotation(annot);
-              if (noMsa)
-              {
-                al.deleteSequence(preds[i]);
-              }
+            al.addAnnotation(annot, seqRef);
+
+            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);
+          i++;
+        }
 
-            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-           "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
+        //Hashtable scores = prediction.getScores();
 
-            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                                "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-           */
-          AlignFrame af = new AlignFrame(al);
+        /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
+                              "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
 
-          Desktop.addInternalFrame(af,
-                                   altitle,
-                                   AlignFrame.NEW_WINDOW_WIDTH,
-                                   AlignFrame.NEW_WINDOW_HEIGHT);
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
+          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);
+         */
+
+        wsInfo.setProgressText(OutputHeader);
+        jalview.bin.Cache.log.debug("Finished parsing output.");
+        AlignFrame af = new AlignFrame(al);
 
+        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);
+      }
     }
   }
+}