added SeqSearch service interface. Documented and refactored web service client ...
[jalview.git] / src / jalview / ws / JPredClient.java
index 3711db0..e14816c 100755 (executable)
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-package jalview.ws;\r
-\r
-import ext.vamsas.*;\r
-\r
-import jalview.analysis.AlignSeq;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import org.apache.axis.client.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-import javax.xml.namespace.QName;\r
-\r
-\r
-public class JPredClient extends WSClient {\r
-    ext.vamsas.JPredWS server;\r
-    String altitle = "";\r
-    java.util.Hashtable SequenceInfo = null;\r
-\r
-    public JPredClient(String title, SequenceI[] msf) {\r
-        wsInfo = setWebService();\r
-\r
-        SequenceI seq = msf[0];\r
-        altitle = "JNet prediction on " + seq.getName() +\r
-            " using alignment from " + title;\r
-\r
-        wsInfo.setProgressText("Job details for MSA based prediction (" +\r
-            title + ") on sequence :\n>" + seq.getName() + "\n" +\r
-            AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
-\r
-        SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
-\r
-        if (!locateWebService()) {\r
-            return;\r
-        }\r
-\r
-        JPredThread jthread = new JPredThread(msf);\r
-        jthread.start();\r
-    }\r
-\r
-    public JPredClient(String title, SequenceI seq) {\r
-        wsInfo = setWebService();\r
-        wsInfo.setProgressText("Job details for prediction on sequence :\n>" +\r
-            seq.getName() + "\n" +\r
-            AlignSeq.extractGaps("-. ", seq.getSequence()) + "\n");\r
-        altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
-            title;\r
-\r
-        SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
-\r
-        if (!locateWebService()) {\r
-            return;\r
-        }\r
-\r
-        JPredThread jthread = new JPredThread(seq);\r
-        jthread.start();\r
-    }\r
-\r
-    private WebserviceInfo setWebService() {\r
-        WebServiceName = "JNetWS";\r
-        WebServiceJobTitle = "JNet secondary structure prediction";\r
-        WebServiceReference = "\"Cuff J. A and Barton G.J (1999) Application of enhanced " +\r
-            "multiple sequence alignment profiles to improve protein secondary structure prediction, " +\r
-            "Proteins 40:502-511\".";\r
-        WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
-\r
-        WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
-                WebServiceReference);\r
-\r
-        return wsInfo;\r
-    }\r
-\r
-    private boolean locateWebService() {\r
-        JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
-\r
-        try {\r
-            this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
-            ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub\r
-        } catch (Exception ex) {\r
-            JOptionPane.showMessageDialog(Desktop.desktop,\r
-                "The Secondary Structure Prediction Service named " +\r
-                WebServiceName + " at " + WsURL + " couldn't be located.",\r
-                "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
-            wsInfo.setProgressText("Serious! " + WebServiceName +\r
-                " Service location failed\nfor URL :" + WsURL + "\n" +\r
-                ex.getMessage());\r
-            wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
-\r
-            return false;\r
-        }\r
-\r
-        return true;\r
-    }\r
-\r
-    class JPredThread extends Thread {\r
-        String OutputHeader;\r
-        ext.vamsas.JpredResult result;\r
-        ext.vamsas.Sequence sequence;\r
-        ext.vamsas.Msfalignment msa;\r
-        String jobId;\r
-        boolean jobComplete = false;\r
-        int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
-\r
-        JPredThread(SequenceI seq) {\r
-            OutputHeader = wsInfo.getProgressText();\r
-            this.sequence = new ext.vamsas.Sequence();\r
-            this.sequence.setId(seq.getName());\r
-            this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
-        }\r
-\r
-        JPredThread(SequenceI[] msf) {\r
-            OutputHeader = wsInfo.getProgressText();\r
-            this.sequence = new ext.vamsas.Sequence();\r
-            this.sequence.setId(msf[0].getName());\r
-            this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
-                    msf[0].getSequence()));\r
-\r
-            jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
-            this.msa = new ext.vamsas.Msfalignment();\r
-            msa.setMsf(mwrite.print(msf));\r
-        }\r
-\r
-        public void run() {\r
-            StartJob();\r
-\r
-            while (!jobComplete && (allowedServerExceptions > 0)) {\r
-                try {\r
-                    if ((result = server.getresult(jobId)) == null) {\r
-                        throw (new Exception(\r
-                            "Timed out when communicating with server\nTry again later.\n"));\r
-                    }\r
-\r
-                    if (result.isRunning()) {\r
-                        wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
-                    } else if (result.isQueued()) {\r
-                        wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
-                    }\r
-\r
-                    if (result.isFinished()) {\r
-                        parseResult();\r
-                        jobComplete = true;\r
-                        jobsRunning--;\r
-                    } else {\r
-                        wsInfo.setProgressText(OutputHeader + "\n" +\r
-                            result.getStatus());\r
-\r
-                        if (!(result.isJobFailed() || result.isServerError())) {\r
-                            try {\r
-                                Thread.sleep(5000);\r
-                            } catch (InterruptedException ex1) {\r
-                            }\r
-\r
-                            //  System.out.println("I'm alive "+seqid+" "+jobid);\r
-                        } else {\r
-                            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
-                        }\r
-                    }\r
-                } catch (Exception ex) {\r
-                    allowedServerExceptions--;\r
-                    wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
-                        ex.getMessage());\r
-\r
-                    try {\r
-                        if (allowedServerExceptions > 0) {\r
-                            Thread.sleep(5000);\r
-                        }\r
-                    } catch (InterruptedException ex1) {\r
-                    }\r
-                }\r
-            }\r
-\r
-            if (!(result.isJobFailed() || result.isServerError())) {\r
-                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
-            } else {\r
-                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
-            }\r
-        }\r
-\r
-        void StartJob() {\r
-            try {\r
-                if (msa != null) {\r
-                    jobId = server.predictOnMsa(msa);\r
-                } else {\r
-                    jobId = server.predict(sequence);\r
-                }\r
-\r
-                if (jobId != null) {\r
-                    if (jobId.startsWith("Broken")) {\r
-                        throw new Exception("Submission " + jobId);\r
-                    } else {\r
-                        System.out.println(WsURL + " Job Id '" + jobId + "'");\r
-                    }\r
-                } else {\r
-                    throw new Exception("Server timed out - try again later\n");\r
-                }\r
-            } catch (Exception e) {\r
-                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
-                allowedServerExceptions = 0;\r
-                jobComplete = false;\r
-                wsInfo.appendProgressText("Failed to submit the prediction: " +\r
-                    e.toString() + "\nJust close the window\n");\r
-                System.err.println(\r
-                    "JPredWS Client: Failed to submit the prediction\n" +\r
-                    e.toString() + "\n");\r
-\r
-                // e.printStackTrace(); TODO: JBPNote DEBUG\r
-            }\r
-        }\r
-\r
-        private void addFloatAnnotations(Alignment al, int[] gapmap,\r
-            Vector values, String Symname, String Visname, float min,\r
-            float max, int winLength) {\r
-            Annotation[] annotations = new Annotation[al.getWidth()];\r
-\r
-            for (int j = 0; j < values.size(); j++) {\r
-                float value = Float.parseFloat(values.get(j).toString());\r
-                annotations[gapmap[j]] = new Annotation("", value + "", ' ',\r
-                        value);\r
-            }\r
-\r
-            al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
-                    annotations, min, max, winLength));\r
-        }\r
-\r
-        void parseResult() {\r
-            // OutputHeader = output.getText();\r
-            if (result.isFailed()) {\r
-                OutputHeader += "Job failed.\n";\r
-            }\r
-\r
-            if (result.getStatus() != null) {\r
-                OutputHeader += ("\n" + result.getStatus());\r
-            }\r
-\r
-            if (result.getPredfile() != null) {\r
-                OutputHeader += ("\n" + result.getPredfile());\r
-\r
-                // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
-            }\r
-\r
-            if (result.getAligfile() != null) {\r
-                OutputHeader += ("\n" + result.getAligfile());\r
-            }\r
-\r
-            wsInfo.setProgressText(OutputHeader);\r
-\r
-            try {\r
-                // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
-                jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(),\r
-                        "Paste");\r
-                SequenceI[] preds = prediction.getSeqsAsArray();\r
-                Alignment al;\r
-                int FirstSeq; // the position of the query sequence in Alignment al\r
-                boolean noMsa = true; // set if no MSA has been returned by JPred\r
-\r
-                if ((this.msa != null) && (result.getAligfile() != null)) {\r
-                    // we ignore the returned alignment if we only predicted on a single sequence\r
-                    String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
-                            "Paste");\r
-\r
-                    if (jalview.io.FormatAdapter.formats.contains(format)) {\r
-                        al = new Alignment(jalview.io.FormatAdapter.readFile(\r
-                                    result.getAligfile(), "Paste", format));\r
-                        noMsa = false;\r
-                        FirstSeq = 0;\r
-                    } else {\r
-                        throw (new Exception(\r
-                            "Unknown format 'format' for file : \n" +\r
-                            result.getAligfile()));\r
-                    }\r
-                } else {\r
-                    al = new Alignment(preds);\r
-                    FirstSeq = prediction.getQuerySeqPosition();\r
-                }\r
-\r
-                if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(\r
-                            al.getSequenceAt(FirstSeq), SequenceInfo)) {\r
-                    throw (new Exception(\r
-                        "Couldn't recover sequence properties for JNet Query sequence!"));\r
-                }\r
-\r
-                AlignmentAnnotation annot;\r
-                Annotation[] annotations = null;\r
-                int i = 0;\r
-                int width = preds[0].getSequence().length();\r
-\r
-                int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
-\r
-                if (gapmap.length != width) {\r
-                    throw (new Exception(\r
-                        "Jnet Client Error\nNumber of residues in supposed query sequence :\n" +\r
-                        al.getSequenceAt(FirstSeq).getName() + "\n" +\r
-                        al.getSequenceAt(FirstSeq).getSequence() +\r
-                        "\nDiffer from number of prediction sites in \n" +\r
-                        result.getPredfile() + "\n"));\r
-                }\r
-\r
-                // JBPNote Should also rename the query sequence sometime...\r
-                i = 0;\r
-\r
-                while (i < preds.length) {\r
-                    String id = preds[i].getName().toUpperCase();\r
-\r
-                    if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
-                            id.startsWith("JPRED")) {\r
-                        annotations = new Annotation[al.getWidth()];\r
-\r
-                        if (id.equals("JNETPRED") || id.equals("JNETPSSM") ||\r
-                                id.equals("JNETFREQ") || id.equals("JNETHMM") ||\r
-                                id.equals("JNETALIGN") || id.equals("JPRED")) {\r
-                            for (int j = 0; j < width; j++) {\r
-                                annotations[gapmap[j]] = new Annotation("", "",\r
-                                        preds[i].getCharAt(j), 0);\r
-                            }\r
-                        } else if (id.equals("JNETCONF")) {\r
-                            for (int j = 0; j < width; j++) {\r
-                                float value = Float.parseFloat(preds[i].getCharAt(\r
-                                            j) + "");\r
-                                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
-                                            j) + "", "", preds[i].getCharAt(j),\r
-                                        value);\r
-                            }\r
-                        } else {\r
-                            for (int j = 0; j < width; j++) {\r
-                                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(\r
-                                            j) + "", "", ' ', 0);\r
-                            }\r
-                        }\r
-\r
-                        if (id.equals("JNETCONF")) {\r
-                            annot = new AlignmentAnnotation(preds[i].getName(),\r
-                                    "JNet Output", annotations, 0f, 10f, 1);\r
-                        }\r
-                        else {\r
-                            annot = new AlignmentAnnotation(preds[i].getName(),\r
-                                    "JNet Output", annotations);\r
-                        }\r
-\r
-                        al.addAnnotation(annot);\r
-\r
-                        if (noMsa) {\r
-                            al.deleteSequence(preds[i]);\r
-                        }\r
-                    }\r
-\r
-                    i++;\r
-                }\r
-\r
-                Hashtable scores = prediction.getScores();\r
-\r
-                /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),\r
-                                      "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
-\r
-                  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),\r
-                 "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
-\r
-                  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),\r
-                                      "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
-                 */\r
-                AlignFrame af = new AlignFrame(al);\r
-\r
-                Desktop.addInternalFrame(af, altitle,\r
-                    AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
-            } catch (Exception ex) {\r
-                ex.printStackTrace();\r
-            }\r
-        }\r
-    }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.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);
+  }
+}