From: jprocter <Jim Procter>
Date: Wed, 6 Apr 2005 16:20:55 +0000 (+0000)
Subject: next version of Jpred functionality using new client code.
X-Git-Tag: Release_2_0~488
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7535505ef73485ad43881cb72a6c52cfb0033c63;p=jalview.git

next version of Jpred functionality using new client code.
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 8c7c9be..5ee6c62 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1131,11 +1131,51 @@ if ( viewport.getConservationSelected() )
   protected void jpred_actionPerformed(ActionEvent e)
 {
 
+    JInternalFrame frame = new JInternalFrame();
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.getSequenceAt(0));
+      }
+      else
+      {
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
 
-      JInternalFrame frame = new JInternalFrame();
-      JPredClient ct = new JPredClient((SequenceI)
-                                       viewport.getAlignment().getSequences().elementAt(0));
     }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.elementAt(0));
+      }
+      else
+      {
+        SequenceI[] msa = new SequenceI[seqs.size()];
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+  }
 
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index c94a5a8..5c6bcf4 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -308,7 +308,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, MouseMotio
     }
 
     int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    if(row>-1 && aa[row].annotations[res]!=null)
+    if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)
       this.setToolTipText(aa[row].annotations[res].description);
 
   }
diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
index 7c2675d..00ff545 100755
--- a/src/jalview/io/JPredClient.java
+++ b/src/jalview/io/JPredClient.java
@@ -11,6 +11,7 @@ import java.awt.*;
 import jalview.analysis.AlignSeq;
 import ext.vamsas.*;
 
+
 public class JPredClient
 {
 
@@ -19,13 +20,41 @@ public class JPredClient
   int jobsRunning = 0;
   ext.vamsas.JpredSoapBindingStub server;
 
+  public JPredClient(SequenceI[] msf)
+  {
+    SequenceI seq = msf[0];
+    output.formatForOutput();
+    outputFrame.setContentPane(output);
+
+    output.setText("Job details for MSA based prediction on sequence :\nName : "
+                   + seq.getName() + "\nSequence : "
+                   + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
+    Desktop.addInternalFrame(outputFrame,
+                             "JNet secondary structure prediction job", 800,
+                             300);
+
+    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
+    try {
+      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
+    }
+    catch (Exception ex) {
+      output.setText("Serious! JPred Service location failed\nfor URL :"
+                     +loc.getjpredAddress()+"\n"+ex.getMessage());
+    }
+
+    JPredThread jthread = new JPredThread(msf);
+    jthread.start();
+    ImageTwirler thread = new ImageTwirler();
+    thread.start();
+  }
+
   public JPredClient(SequenceI seq)
   {
     output.formatForOutput();
     outputFrame.setContentPane(output);
 
     output.setText("Job details for prediction on sequence :\nName : "
-                   + seq.getName() + "\nSequence : " + seq.getSequence() + "\n");
+                   + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");
     Desktop.addInternalFrame(outputFrame,
                              "JNet secondary structure prediction job", 800,
                              300);
@@ -87,8 +116,9 @@ public class JPredClient
       extends Thread
   {
     String OutputHeader;
-    ext.vamsas.Secstructpred result;
+    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.
@@ -100,6 +130,18 @@ public class JPredClient
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));
     }
 
+    JPredThread(SequenceI[] msf)
+    {
+      OutputHeader = output.getText();
+      this.sequence = new ext.vamsas.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();
+      msa.setMsf(mwrite.print(msf));
+    }
+
+
     public void run()
     {
 
@@ -110,9 +152,9 @@ public class JPredClient
       {
         try
         {
-          result = server.getpredict(jobId);
+          result = server.getresult(jobId);
 
-          if (result.getOutput().indexOf("Job") != 0)
+          if (result.isFinished())
           {
             parseResult();
             jobComplete = true;
@@ -120,11 +162,13 @@ public class JPredClient
           }
           else
           {
-            output.setText(OutputHeader + "\n" + result.getOutput());
+            output.setText(OutputHeader + "\n" + result.getStatus());
+            if (! (result.isJobFailed() || result.isServerError()))
+            {
+              Thread.sleep(5000);
+              //      System.out.println("I'm alive "+seqid+" "+jobid);
+            }
           }
-          Thread.sleep(5000);
-          //      System.out.println("I'm alive "+seqid+" "+jobid);
-
         }
         catch (Exception ex)
         {
@@ -139,7 +183,11 @@ public class JPredClient
     {
       try
       {
-        jobId = server.predict(sequence);
+        if (msa!=null)  {
+          jobId = server.predictOnMsa(msa);
+        } else {
+          jobId = server.predict(sequence);
+        }
         System.out.println(jobId);
       }
       catch (Exception e)
@@ -150,23 +198,78 @@ public class JPredClient
       }
     }
 
+    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()
     {
-      output.setText(OutputHeader + result.getOutput());
+      // OutputHeader = output.getText();
+      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();
+      }
+      output.setText(OutputHeader);
       try {
         // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
-        JPredFile prediction=new JPredFile(result.getOutput(), "Paste");
+        jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste");
         SequenceI[] preds = prediction.getSeqsAsArray();
-        Alignment al = new Alignment(preds);
+        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) {
+          // 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.FormatProperties.contains(format))
+          {
+            al = new Alignment(jalview.io.FormatAdapter.read(result.getAligfile(),"Paste",format));
+            noMsa = false;
+            FirstSeq = 0;
+          }
+          else
+          {
+            throw (new Exception("Unknown format 'format' for file : \n" +
+                             result.getAligfile()));
+          }
+
+        } else {
+          al = new Alignment(preds);
+          FirstSeq = prediction.QuerySeqPosition;
+        }
 
         AlignmentAnnotation annot;
         Annotation [] annotations = null;
         int i = 0;
-        // Rename the query sequence
+        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"));
+        }
+        // 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"))
+          if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED"))
           {
             annotations = new Annotation[al.getWidth()];
 
@@ -174,80 +277,55 @@ public class JPredClient
                || id.equals("JNETPSSM")
                || id.equals("JNETFREQ")
                || id.equals("JNETHMM")
-               || id.equals("JNETALIGN"))
+               || id.equals("JNETALIGN")
+               || id.equals("JPRED"))
             {
-              for (int j = 0; j < al.getWidth(); j++)
-                annotations[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);
             }
             else if(id.equals("JNETCONF"))
             {
-              for (int j = 0; j < al.getWidth(); j++)
+              for (int j = 0; j < width; j++)
               {
                 float value = Float.parseFloat(preds[i].getCharAt(j)+"");
-                annotations[j] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);
+                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);
               }
             }
             else
             {
-              for (int j = 0; j < al.getWidth(); j++)
-                annotations[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"))
               annot = new AlignmentAnnotation(preds[i].getName(),
-                                           "Jpred Output",
+                                           "JNet Output",
                                            annotations,0f,10f,1);
 
             else   annot = new AlignmentAnnotation(preds[i].getName(),
-                                            "Jpred Output",
+                                            "JNet Output",
                                             annotations);
             al.addAnnotation(annot);
-            al.deleteSequence(preds[i]);
+            if (noMsa)
+              al.deleteSequence(preds[i]);
           }
           i++;
         }
 
         Hashtable scores = prediction.Scores;
+        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
+                            "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
 
-        Vector values = (Vector)scores.get("JNETPROPH");
-        annotations = new Annotation[al.getWidth()];
-        for (int j = 0; j < al.getWidth(); j++)
-        {
-          float value = Float.parseFloat(values.get(j).toString());
-          annotations[j] = new Annotation("", value+"",' ',value);
-        }
-        annot = new AlignmentAnnotation("Jnetproph", "Jpred Output", annotations, 0f,1f,1);
-        al.addAnnotation(annot);
-
-        values = (Vector)scores.get("JNETPROPB");
-             annotations = new Annotation[al.getWidth()];
-             for (int j = 0; j < al.getWidth(); j++)
-             {
-               float value = Float.parseFloat(values.get(j).toString());
-               annotations[j] = new Annotation("", value+"",' ',value);
-             }
-             annot = new AlignmentAnnotation("JnetpropB", "Jpred Output", annotations, 0f,1f,1);
-             al.addAnnotation(annot);
-
-             values = (Vector)scores.get("JNETPROPC");
-                  annotations = new Annotation[al.getWidth()];
-                  for (int j = 0; j < al.getWidth(); j++)
-                  {
-                    float value = Float.parseFloat(values.get(j).toString());
-                    annotations[j] = new Annotation("", value+"",' ',value);
-                  }
-                  annot = new AlignmentAnnotation("JnetpropC", "Jpred Output", annotations, 0f,1f,1);
-                  al.addAnnotation(annot);
-
+        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),
+                            "JnetpropB", "Jnet Beta Sheed Propensity", 0f,1f,1);
 
+        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
+                            "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
 
         AlignFrame af = new AlignFrame(al);
 
 
-        /*  JBPNote - need to set correct style of display for the secstrpred alignment object.
-            af.clustalColour.setSelected(true);
-            af.clustalColour_actionPerformed(null);
-         */
         Desktop.addInternalFrame(af,
                                  "JNet Prediction for sequence ",
                                  700, 500);
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 92d9819..636a8d6 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -28,6 +28,9 @@ public class JPredFile
 
     super.initData();
     Scores = new Hashtable();
+    ids = null;
+    conf = null;
+    QuerySeqPosition = -1;
   }
 
   public JPredFile(String inFile, String type)
@@ -40,13 +43,13 @@ public class JPredFile
   /**
    * parse a JPred concise file into a sequence-alignment like object.
    */
-
+  int QuerySeqPosition;
   public void parse()
       throws IOException
   {
 System.out.println("all read in ");
     String line;
-
+    QuerySeqPosition = -1;
     noSeqs = 0;
     Vector seq_entries = new Vector();
     Vector ids = new Vector();
@@ -144,6 +147,7 @@ System.out.println("all read in ");
               name = id.substring(id.indexOf(";")+1)+"_"+1;
             }
             ids.addElement(name);
+
             noSeqs++;
           }
           else
@@ -187,6 +191,10 @@ System.out.println("all read in ");
                               ids.elementAt(i).toString()
                               + ") has an unexpected number of columns");
       }
+      if (newSeq.getName().startsWith("QUERY") && QuerySeqPosition==-1) {
+        QuerySeqPosition = seqs.size();
+      }
+
       seqs.addElement(newSeq);
 
     }