X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=6fd0a4a702b638ab129dbf6400040c77dc3b8c90;hb=01cc9bf86a687fa7c8a741128264b23eb7feba9b;hp=e6f3899892a6058fff4b0021eb61e9528582b67f;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index e6f3899..6fd0a4a 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -26,19 +26,38 @@ import ext.vamsas.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
+import jalview.io.FormatAdapter;
 
 public class JPredClient
     extends WSClient
 {
-  ext.vamsas.JPredWS server;
+  ext.vamsas.Jpred server;
   String altitle = "";
   java.util.Hashtable SequenceInfo = null;
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI seq) {
+    wsInfo = setWebService(sh);
+    startJPredClient(title, seq);
+  }
+  public JPredClient(ext.vamsas.ServiceHandle sh, String title, SequenceI[] msa) {
+    wsInfo = setWebService(sh);
+    startJPredClient(title, msa);
+  }
+
+  public JPredClient(String title, SequenceI[] msf) {
+    startJPredClient(title, msf);
+  }
+
+  public JPredClient(String title, SequenceI seq) {
+    startJPredClient(title, seq);
+  }
 
-  public JPredClient(String title, SequenceI[] msf)
+  private void startJPredClient(String title, SequenceI[] msf)
   {
-    wsInfo = setWebService();
+    if (wsInfo==null)
+      wsInfo = setWebService();
 
     SequenceI seq = msf[0];
+
     altitle = "JNet prediction on " + seq.getName() +
         " using alignment from " + title;
 
@@ -46,21 +65,26 @@ public class JPredClient
                            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.SeqCharacterHash(seq);
+    SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
     if (!locateWebService())
     {
       return;
     }
 
-    JPredThread jthread = new JPredThread(msf);
+    JPredThread jthread = new JPredThread(aln);
     jthread.start();
   }
 
-  public JPredClient(String title, SequenceI seq)
+  public void startJPredClient(String title, SequenceI seq)
   {
-    wsInfo = setWebService();
+    if (wsInfo==null)
+      wsInfo = setWebService();
     wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
                            seq.getName() + "\n" +
                            AlignSeq.extractGaps("-. ", seq.getSequence()) +
@@ -97,7 +121,7 @@ public class JPredClient
 
   private boolean locateWebService()
   {
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
+    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
 
     try
     {
@@ -116,7 +140,7 @@ public class JPredClient
                              " Service location failed\nfor URL :" + WsURL +
                              "\n" +
                              ex.getMessage());
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
       return false;
     }
@@ -128,9 +152,9 @@ public class JPredClient
       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.
@@ -138,7 +162,7 @@ public class JPredClient
     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()));
     }
@@ -146,14 +170,14 @@ public class JPredClient
     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.PileUpfile mwrite = new jalview.io.PileUpfile();
-      this.msa = new ext.vamsas.Msfalignment();
-      msa.setMsf(mwrite.print(msf));
+      this.msa = new vamsas.objects.simple.Msfalignment();
+      jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
+      msa.setMsf(pileup.print(msf));
     }
 
     public void run()
@@ -169,27 +193,28 @@ public class JPredClient
             throw (new Exception(
                 "Timed out when communicating with server\nTry again later.\n"));
           }
-
+          if (result.getState()==0)
+            jalview.bin.Cache.log.debug("Finished "+jobId);
           if (result.isRunning())
           {
             wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
           }
-          else if (result.isQueued())
+          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()))
             {
               try
@@ -205,6 +230,8 @@ public class JPredClient
             else
             {
               wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+              jobsRunning--;
+              jobComplete = true;
             }
           }
         }
@@ -225,16 +252,29 @@ public class JPredClient
           {
           }
         }
+        catch (OutOfMemoryError er)
+        {
+          jobComplete = true;
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                "Out of memory handling result!!"
+                                                +
+              "\nSee help files for increasing Java Virtual Machine memory."
+                                                , "Out of memory",
+                                                JOptionPane.WARNING_MESSAGE);
+          System.out.println("JPredClient: "+er);
+          System.gc();
+        }
       }
-
-      if (! (result.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()
@@ -268,23 +308,36 @@ public class JPredClient
       }
       catch (Exception e)
       {
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        allowedServerExceptions = 0;
-        jobComplete = false;
-
-        wsInfo.appendProgressText("Failed to submit the prediction.\n"
-                                  +
-                                  "It is most likely that there is a problem with the server.\n"
-                                  + "Just close the window\n");
-        System.err.println(
-            "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +
-            e.toString() + "\n");
-
-        // e.printStackTrace(); TODO: JBPNote DEBUG
+        if (e.getMessage().indexOf("Exception")>-1) {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+          wsInfo.setProgressText(
+              "Failed to submit the prediction. (Just close the window)\n"
+              +
+              "It is most likely that there is a problem with the server.\n");
+          System.err.println(
+              "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +
+              e.getMessage() + "\n");
+
+          jalview.bin.Cache.log.warn("Server Exception",e);
+        } else {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+          // JBPNote - this could be a popup informing the user of the problem.
+          wsInfo.setProgressText("Failed to submit the prediction:\n"
+                                 +e.getMessage()+
+                                 wsInfo.getProgressText());
+
+          jalview.bin.Cache.log.debug("Failed Submission",e);
+
+        }
+        allowedServerExceptions = -1;
+        jobComplete = true;
+
       }
     }
 
-    private void addFloatAnnotations(Alignment al, int[] gapmap,
+
+
+  /*  private void addFloatAnnotations(Alignment al, int[] gapmap,
                                      Vector values, String Symname,
                                      String Visname, float min,
                                      float max, int winLength)
@@ -300,7 +353,7 @@ public class JPredClient
 
       al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
                                                annotations, min, max, winLength));
-    }
+    }*/
 
     void parseResult()
     {
@@ -327,29 +380,43 @@ public class JPredClient
         OutputHeader += ("\n" + result.getAligfile());
       }
 
-      wsInfo.setProgressText(OutputHeader);
+      wsInfo.setProgressText(OutputHeader+"Parsing...");
 
       try
       {
+        jalview.bin.Cache.log.debug("Parsing output from JNet job.");
         // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
         jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
             getPredfile(),
             "Paste");
         SequenceI[] preds = prediction.getSeqsAsArray();
+        jalview.bin.Cache.log.debug("Got prediction profile.");
         Alignment al;
         int FirstSeq; // the position of the query sequence in Alignment al
         boolean noMsa = true; // set if no MSA has been returned by JPred
 
         if ( (this.msa != null) && (result.getAligfile() != null))
         {
+          jalview.bin.Cache.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(
+            al = new Alignment(new FormatAdapter().readFile(
                 result.getAligfile(), "Paste", format));
+            SequenceI sqs[] = new SequenceI[al.getHeight()];
+            for (int i=0, j=al.getHeight(); i<j; i++) {
+              sqs[i] = al.getSequenceAt(i);
+            }
+            if (!jalview.analysis.SeqsetUtils.deuniquify(
+                  (Hashtable) SequenceInfo,sqs))
+              {
+                throw (new Exception(
+                    "Couldn't recover sequence properties for alignment."));
+              }
+
             noMsa = false;
             FirstSeq = 0;
           }
@@ -364,14 +431,15 @@ public class JPredClient
         {
           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!"));
+          }
         }
 
-        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-            al.getSequenceAt(FirstSeq), SequenceInfo))
-        {
-          throw (new Exception(
-              "Couldn't recover sequence properties for JNet Query sequence!"));
-        }
+        al.setDataset(null);
 
         AlignmentAnnotation annot;
         Annotation[] annotations = null;
@@ -393,6 +461,8 @@ public class JPredClient
         // JBPNote Should also rename the query sequence sometime...
         i = 0;
 
+        SequenceI seqRef = al.getSequenceAt(FirstSeq);
+
         while (i < preds.length)
         {
           String id = preds[i].getName().toUpperCase();
@@ -436,7 +506,8 @@ public class JPredClient
             {
               annot = new AlignmentAnnotation(preds[i].getName(),
                                               "JNet Output", annotations, 0f,
-                                              10f, 1);
+                                              10f,
+                                              AlignmentAnnotation.BAR_GRAPH);
             }
             else
             {
@@ -444,7 +515,7 @@ public class JPredClient
                                               "JNet Output", annotations);
             }
 
-            al.addAnnotation(annot);
+            al.addAnnotation(annot, seqRef);
 
             if (noMsa)
             {
@@ -455,7 +526,7 @@ public class JPredClient
           i++;
         }
 
-        Hashtable scores = prediction.getScores();
+        //Hashtable scores = prediction.getScores();
 
         /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),
                               "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);
@@ -466,6 +537,9 @@ public class JPredClient
           addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),
                               "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);
          */
+
+        wsInfo.setProgressText(OutputHeader);
+        jalview.bin.Cache.log.debug("Finished parsing output.");
         AlignFrame af = new AlignFrame(al);
 
         Desktop.addInternalFrame(af, altitle,
@@ -474,7 +548,7 @@ public class JPredClient
       }
       catch (Exception ex)
       {
-        ex.printStackTrace();
+        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);
       }
     }
   }