X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FJPredClient.java;h=80a66c382150c0cdf8f1ba6b290a278fba084cd3;hb=e5c2e37b24f09c90f2f7c748f6be10ce025da261;hp=2eecf46963f042df7f59b97c9504799cdd451398;hpb=61b0b38d322aef9105cc564d3f5340fd529039ba;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 2eecf46..80a66c3 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,304 +1,536 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws;
 
-import org.apache.axis.client.*;
-import javax.xml.namespace.QName;
 import java.util.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
+
 import javax.swing.*;
-import java.util.*;
-import java.awt.*;
-import jalview.analysis.AlignSeq;
-import ext.vamsas.*;
 
+import ext.vamsas.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
 
 public class JPredClient
+    extends WSClient
 {
-  int jobsRunning = 0;
-  ext.vamsas.JpredSoapBindingStub server;
-  WebserviceInfo wsInfo;
+  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);
+  }
 
-  public JPredClient(SequenceI[] msf)
+  private void startJPredClient(String title, SequenceI[] msf)
   {
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",
-          "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");
+    if (wsInfo==null)
+      wsInfo = setWebService();
 
     SequenceI seq = msf[0];
-    wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : "
-                   + seq.getName() + "\nSequence : "
-                   + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
+    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();
+  }
 
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
-    try {
-      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
-    }
-    catch (Exception ex) {
-      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"
-                     +loc.getjpredAddress()+"\n"+ex.getMessage());
+  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(msf);
+    JPredThread jthread = new JPredThread(seq);
     jthread.start();
   }
 
-  public JPredClient(SequenceI seq)
+  private WebserviceInfo setWebService()
   {
-    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",
-                                "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");
-
+    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\".";
+    WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+
+    WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
+                                               WebServiceReference);
+
+    return wsInfo;
+  }
 
-    wsInfo.setProgressText("Job details for prediction on sequence :\nName : "
-                   + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
+  private boolean locateWebService()
+  {
+    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
 
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
-    try {
-      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
+    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) {
-      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"
-                     +loc.getjpredAddress()+"\n"+ex.getMessage());
+    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;
     }
 
-    JPredThread jthread = new JPredThread(seq);
-    jthread.start();
+    return true;
   }
 
-
   class JPredThread
       extends Thread
   {
     String OutputHeader;
-    ext.vamsas.JpredResult result;
-    ext.vamsas.Sequence sequence;
-    ext.vamsas.Msfalignment msa;
+    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 ext.vamsas.Sequence();
+      this.sequence = new vamsas.objects.simple.Sequence();
       this.sequence.setId(seq.getName());
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));
+      this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));
     }
 
     JPredThread(SequenceI[] msf)
     {
       OutputHeader = wsInfo.getProgressText();
-      this.sequence = new ext.vamsas.Sequence();
+      this.sequence = new vamsas.objects.simple.Sequence();
       this.sequence.setId(msf[0].getName());
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence()));
-      jalview.io.MSFfile mwrite = new jalview.io.MSFfile();
-      this.msa = new ext.vamsas.Msfalignment();
+      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))
       {
         try
         {
-          result = server.getresult(jobId);
+          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);
+          }
 
-         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
-          {
-            wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
+          } else {
+            // catch exceptions
             if (! (result.isJobFailed() || result.isServerError()))
             {
-              Thread.sleep(5000);
+              try
+              {
+                Thread.sleep(5000);
+              }
+              catch (InterruptedException ex1)
+              {
+              }
+
               //  System.out.println("I'm alive "+seqid+" "+jobid);
-            } else {
+            }
+            else
+            {
               wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+              jobsRunning--;
+              jobComplete = true;
             }
           }
         }
         catch (Exception ex)
         {
           allowedServerExceptions--;
-          wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());
+          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);
         }
       }
-
-      if (! (result.isJobFailed() || result.isServerError()))
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-      else
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+      if (result!=null)
+        if (! (result.isJobFailed() || result.isServerError()))
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        }
     }
 
     void StartJob()
     {
       try
       {
-        if (msa!=null)  {
+        if (msa != null)
+        {
           jobId = server.predictOnMsa(msa);
-        } else {
+        }
+        else
+        {
           jobId = server.predict(sequence);
         }
-        System.out.println(jobId);
+
+        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)
       {
-        System.out.println("JPredWS Client: Failed to submit the prediction\n" +
-                           e.toString() + "\n");
-        e.printStackTrace();
+        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) {
 
+
+    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);
+        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";
+      if (result.isFailed())
+      {
+        OutputHeader += "Job failed.\n";
       }
-      if (result.getStatus()!=null) {
-        OutputHeader += "\n"+result.getStatus();
+
+      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.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.getAligfile() != null)
+      {
+        OutputHeader += ("\n" + result.getAligfile());
       }
-      wsInfo.setProgressText(OutputHeader);
-      try {
+
+      wsInfo.setProgressText(OutputHeader+"Parsing...");
+
+      try
+      {
+        jalview.bin.Jalview.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");
+        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
 
-        if (this.msa!=null && result.getAligfile()!=null) {
+        if ( (this.msa != null) && (result.getAligfile() != null))
+        {
+          jalview.bin.Jalview.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(), "Paste");
+          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));
+            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+")")));
+              }
+            }
             noMsa = false;
             FirstSeq = 0;
           }
           else
           {
-            throw (new Exception("Unknown format 'format' for file : \n" +
-                             result.getAligfile()));
+            throw (new Exception(
+                "Unknown format 'format' for file : \n" +
+                result.getAligfile()));
           }
-
-        } else {
+        }
+        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;
+        Annotation[] annotations = null;
         int i = 0;
         int width = preds[0].getSequence().length();
 
-
         int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();
-        if (gapmap.length!=width) {
-          throw (new Exception("Jpred Client Error\nNumber of residues in supposed query sequence :\n"
-                               +al.getSequenceAt(FirstSeq).getName()+"\n"
-                               +al.getSequenceAt(FirstSeq).getSequence()
-                               +"\nDiffer from number of prediction sites in \n"+result.getPredfile()+"\n"));
+
+        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;
+        i = 0;
+
         while (i < preds.length)
         {
           String id = preds[i].getName().toUpperCase();
-          if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED"))
+
+          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"))
+            if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||
+                id.equals("JNETFREQ") || id.equals("JNETHMM") ||
+                id.equals("JNETALIGN") || id.equals("JPRED"))
             {
               for (int j = 0; j < width; j++)
-                annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0);
+              {
+                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++)
               {
-                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
             {
-              for (int j = 0; j < width; j++) {
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0);
+              for (int j = 0; j < width; j++)
+              {
+                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(
+                    j) + "", "", ' ', 0);
               }
             }
 
-            if(id.equals("JNETCONF"))
+            if (id.equals("JNETCONF"))
+            {
               annot = new AlignmentAnnotation(preds[i].getName(),
-                                           "JNet Output",
-                                           annotations,0f,10f,1);
+                                              "JNet Output", annotations, 0f,
+                                              10f, 1);
+            }
+            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]);
+            }
           }
+
           i++;
         }
 
         Hashtable scores = prediction.getScores();
-      /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
-                            "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
 
-        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-                            "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
+        /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
+                              "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
 
-        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("JNETPROPB"),
+         "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
 
+          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
+                              "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
+         */
 
-        Desktop.addInternalFrame(af,
-                                 "JNet Prediction for sequence ",
-                                 AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
-      }catch(Exception ex){ex.printStackTrace();}
+        wsInfo.setProgressText(OutputHeader);
+        jalview.bin.Jalview.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.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
+        jalview.bin.Jalview.log.debug("Exception: ",ex);
+      }
     }
-
   }
 }
-