X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FJPredClient.java;h=ac36baa86ec8dbcfa4087e1ea2356ac7ce9a4424;hb=93642d621a7f86318a7777b0a70f6113dcd299dc;hp=4302df203a6e0e231ae142db3c9a5eb28f7147cf;hpb=74e4d71835fd0031dd7c309e37ec6bf934e4de4a;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 4302df2..ac36baa 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -1,524 +1,390 @@
-/*
- * 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 java.util.*;
-
-import javax.swing.*;
-
-import ext.vamsas.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-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) {
-    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\".";
-    WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
-
-    WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
-                                               WebServiceReference);
-
-    return wsInfo;
-  }
-
-  private boolean locateWebService()
-  {
-    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // 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;
-  }
-
-  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()));
-    }
-
-    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))
-      {
-        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.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)
-          {
-          }
-        }
-      }
-      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)
-        {
-          jobId = server.predictOnMsa(msa);
-        }
-        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);
-      }
-
-      al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
-                                               annotations, min, max, winLength));
-    }
-
-    void parseResult()
-    {
-      // 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+"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");
-        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))
-        {
-          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");
-
-          if (jalview.io.FormatAdapter.formats.contains(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()));
-          }
-        }
-        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();
-
-        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;
-
-        while (i < preds.length)
-        {
-          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"))
-            {
-              for (int j = 0; j < width; j++)
-              {
-                annotations[gapmap[j]] = new Annotation("", "",
-                    preds[i].getCharAt(j), 0);
-              }
-            }
-            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);
-              }
-            }
-            else
-            {
-              for (int j = 0; j < width; j++)
-              {
-                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);
-            }
-            else
-            {
-              annot = new AlignmentAnnotation(preds[i].getName(),
-                                              "JNet Output", annotations);
-            }
-
-            al.addAnnotation(annot);
-
-            if (noMsa)
-            {
-              al.deleteSequence(preds[i]);
-            }
-          }
-
-          i++;
-        }
-
-        Hashtable scores = prediction.getScores();
-
-        /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
-                              "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
-
-          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
-         "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);
-
-          addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
-                              "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
-         */
-
-        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);
-      }
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.ws;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.*;
+
+import javax.swing.*;
+
+import ext.vamsas.*;
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+public class JPredClient extends WSClient
+{
+  /**
+   * crate a new GUI JPred Job
+   * 
+   * @param sh
+   *          ServiceHandle
+   * @param title
+   *          String
+   * @param msa
+   *          boolean - true - submit alignment as a sequence profile
+   * @param alview
+   *          AlignmentView
+   * @param viewonly
+   *          TODO
+   */
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+          boolean msa, AlignmentView alview, AlignFrame parentFrame,
+          boolean viewonly)
+  {
+    super();
+    wsInfo = setWebService(sh);
+    startJPredClient(title, msa, alview, parentFrame, viewonly);
+
+  }
+
+  /**
+   * startJPredClient TODO: refine submission to cope with local prediction of
+   * visible regions or multiple single sequence jobs TODO: sequence
+   * representative support - could submit alignment of representatives as msa.
+   * TODO: msa hidden region prediction - submit each chunk for prediction.
+   * concatenate results of each. TODO: single seq prediction - submit each
+   * contig of each sequence for prediction (but must cope with flanking regions
+   * and short seqs)
+   * 
+   * @param title
+   *          String
+   * @param msa
+   *          boolean
+   * @param alview
+   *          AlignmentView
+   * @param viewonly
+   *          if true then the prediction will be made just on the concatenated
+   *          visible regions
+   */
+  private void startJPredClient(String title, boolean msa,
+          jalview.datamodel.AlignmentView alview, AlignFrame parentFrame,
+          boolean viewonly)
+  {
+    AlignmentView input = alview;
+    if (wsInfo == null)
+    {
+      wsInfo = setWebService();
+    }
+    Jpred server = locateWebService();
+    if (server == null)
+    {
+      Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
+      return;
+    }
+    SeqCigar[] msf = null;
+    SequenceI seq = null;
+    int[] delMap = null;
+    // original JNetClient behaviour - submit full length of sequence or profile
+    // and mask result.
+    msf = input.getSequences();
+    seq = msf[0].getSeq('-');
+
+    if (viewonly)
+    {
+      int[] viscontigs = alview.getVisibleContigs();
+      int spos = 0;
+      int i = 0;
+      if (viscontigs != null)
+      {
+        // Construct the delMap - mapping from the positions within the input to
+        // Jnet to the contigs in the original sequence
+
+        delMap = new int[seq.getEnd() - seq.getStart() + 1];
+        int gapMap[] = seq.gapMap();
+        for (int contig = 0; contig < viscontigs.length; contig += 2)
+        {
+
+          while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
+          {
+            spos++;
+          }
+          while (spos < gapMap.length
+                  && gapMap[spos] <= viscontigs[contig + 1])
+          {
+            delMap[i++] = spos++;
+          }
+        }
+        int tmap[] = new int[i];
+        System.arraycopy(delMap, 0, tmap, 0, i);
+        delMap = tmap;
+      }
+    }
+    if (msa && msf.length > 1)
+    {
+
+      String altitle = getPredictionName(WebServiceName) + " on "
+              + (viewonly ? "visible " : "") + seq.getName()
+              + " using alignment from " + title;
+
+      SequenceI aln[] = new SequenceI[msf.length];
+      for (int i = 0, j = msf.length; i < j; i++)
+      {
+        aln[i] = msf[i].getSeq('-');
+      }
+
+      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+              true);
+      if (viewonly)
+      {
+        // Remove hidden regions from sequence objects.
+        String seqs[] = alview.getSequenceStrings('-');
+        for (int i = 0, j = msf.length; i < j; i++)
+        {
+          aln[i].setSequence(seqs[i]);
+        }
+        seq.setSequence(seqs[0]);
+      }
+      wsInfo.setProgressText("Job details for "
+              + (viewonly ? "visible " : "") + "MSA based prediction ("
+              + title + ") on sequence :\n>" + seq.getName() + "\n"
+              + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+              + "\n");
+      JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+              SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
+      wsInfo.setthisService(jthread);
+      jthread.start();
+    }
+    else
+    {
+      if (!msa && msf.length > 1)
+      {
+        throw new Error(
+                "Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
+      }
+
+      String altitle = getPredictionName(WebServiceName) + " for "
+              + (viewonly ? "visible " : "") + "sequence " + seq.getName()
+              + " from " + title;
+      String seqname = seq.getName();
+      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+              .SeqCharacterHash(seq);
+      if (viewonly)
+      {
+        // Remove hidden regions from input sequence
+        String seqs[] = alview.getSequenceStrings('-');
+        seq.setSequence(seqs[0]);
+      }
+      wsInfo.setProgressText("Job details for prediction on "
+              + (viewonly ? "visible " : "") + "sequence :\n>" + seqname
+              + "\n"
+              + AlignSeq.extractGaps("-. ", seq.getSequenceAsString())
+              + "\n");
+      JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
+              SequenceInfo, seq, delMap, alview, parentFrame);
+      wsInfo.setthisService(jthread);
+      jthread.start();
+    }
+  }
+
+  private String getPredictionName(String webServiceName)
+  {
+    if (webServiceName.toLowerCase().indexOf(
+            "secondary structure prediction") > -1)
+    {
+      return webServiceName;
+    }
+    else
+    {
+      return webServiceName + "secondary structure prediction";
+    }
+  }
+
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+          SequenceI seq, AlignFrame parentFrame)
+  {
+    super();
+    wsInfo = setWebService(sh);
+    startJPredClient(title, seq, parentFrame);
+  }
+
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title,
+          SequenceI[] msa, AlignFrame parentFrame)
+  {
+    wsInfo = setWebService(sh);
+    startJPredClient(title, msa, parentFrame);
+  }
+
+  public JPredClient(String title, SequenceI[] msf)
+  {
+    startJPredClient(title, msf, null);
+  }
+
+  public JPredClient(String title, SequenceI seq)
+  {
+    startJPredClient(title, seq, null);
+  }
+
+  public JPredClient()
+  {
+
+    super();
+    // add a class reference to the list
+  }
+
+  private void startJPredClient(String title, SequenceI[] msf,
+          AlignFrame parentFrame)
+  {
+    if (wsInfo == null)
+    {
+      wsInfo = setWebService();
+    }
+
+    SequenceI seq = msf[0];
+
+    String 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.getSequenceAsString())
+                    + "\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]);
+    }
+
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln,
+            true);
+
+    Jpred server = locateWebService();
+    if (server == null)
+    {
+      return;
+    }
+
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server,
+            SequenceInfo, aln, null, null, parentFrame, WsURL);
+    wsInfo.setthisService(jthread);
+    jthread.start();
+  }
+
+  public void startJPredClient(String title, SequenceI seq,
+          AlignFrame parentFrame)
+  {
+    if (wsInfo == null)
+    {
+      wsInfo = setWebService();
+    }
+    wsInfo
+            .setProgressText("Job details for prediction on sequence :\n>"
+                    + seq.getName()
+                    + "\n"
+                    + AlignSeq
+                            .extractGaps("-. ", seq.getSequenceAsString())
+                    + "\n");
+    String altitle = "JNet prediction for sequence " + seq.getName()
+            + " from " + title;
+
+    Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
+            .SeqCharacterHash(seq);
+
+    Jpred server = locateWebService();
+    if (server == null)
+    {
+      return;
+    }
+
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
+            SequenceInfo, seq, null, null, parentFrame);
+    wsInfo.setthisService(jthread);
+    jthread.start();
+  }
+
+  private WebserviceInfo setWebService()
+  {
+    WebServiceName = "JNetWS";
+    WebServiceJobTitle = "JNet secondary structure prediction";
+    WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
+            + "multiple sequence alignment profiles to improve protein secondary structure prediction, "
+            + "Proteins 40:502-511\".";
+    WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
+
+    WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
+            WebServiceReference);
+
+    return wsInfo;
+  }
+
+  private ext.vamsas.Jpred locateWebService()
+  {
+    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
+    ext.vamsas.Jpred server = null;
+    try
+    {
+      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)
+    {
+      JOptionPane.showMessageDialog(Desktop.desktop,
+              "The Secondary Structure Prediction Service named "
+                      + WebServiceName + " at " + WsURL
+                      + " couldn't be located.", "Internal Jalview Error",
+              JOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText("Serious! " + WebServiceName
+              + " Service location failed\nfor URL :" + WsURL + "\n"
+              + ex.getMessage());
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+
+    }
+
+    return server;
+  }
+
+  public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
+          final AlignFrame af)
+  {
+    final JMenuItem method = new JMenuItem(sh.getName());
+    method.setToolTipText(sh.getEndpointURL());
+    method.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
+        if (msa.getSequences().length == 1)
+        {
+          // Single Sequence prediction
+          new jalview.ws.JPredClient(sh, af.getTitle(), false, msa, af,
+                  true);
+        }
+        else
+        {
+          if (msa.getSequences().length > 1)
+          {
+            // Sequence profile based prediction
+            new jalview.ws.JPredClient(sh, af.getTitle(), true, msa, af,
+                    true);
+          }
+        }
+      }
+    });
+    wsmenu.add(method);
+  }
+}