X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FJPredClient.java;h=65f03253c61d59314c0f655640090c586714303f;hb=0149a3aec3e61c36ee788adfbd53bf560407e1e0;hp=e6f3899892a6058fff4b0021eb61e9528582b67f;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index e6f3899..65f0325 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -30,13 +30,30 @@ import jalview.gui.*;
 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[] msf)
+  public JPredClient(String title, SequenceI seq) {
+    startJPredClient(title, seq);
+  }
+
+  private void startJPredClient(String title, SequenceI[] msf)
   {
-    wsInfo = setWebService();
+    if (wsInfo==null)
+      wsInfo = setWebService();
 
     SequenceI seq = msf[0];
     altitle = "JNet prediction on " + seq.getName() +
@@ -46,21 +63,24 @@ public class JPredClient
                            title + ") on sequence :\n>" + seq.getName() + "\n" +
                            AlignSeq.extractGaps("-. ", seq.getSequence()) +
                            "\n");
-
-    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);
+    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(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 +117,7 @@ public class JPredClient
 
   private boolean locateWebService()
   {
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
+    ext.vamsas.JpredServiceLocator loc = new JpredServiceLocator(); // Default
 
     try
     {
@@ -128,9 +148,9 @@ 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 +158,7 @@ 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()));
     }
@@ -146,13 +166,13 @@ 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();
+      this.msa = new vamsas.objects.simple.Msfalignment();
       msa.setMsf(mwrite.print(msf));
     }
 
@@ -169,27 +189,28 @@ public class JPredClient
             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);
           }
-          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 +226,8 @@ public class JPredClient
             else
             {
               wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+              jobsRunning--;
+              jobComplete = true;
             }
           }
         }
@@ -280,10 +303,12 @@ public class JPredClient
             "JPredWS Client: Failed to submit the prediction (Probably a server error - see below)\n" +
             e.toString() + "\n");
 
-        // e.printStackTrace(); TODO: JBPNote DEBUG
+        jalview.bin.Jalview.log.debug("Failed Submission",e);
       }
     }
 
+
+
     private void addFloatAnnotations(Alignment al, int[] gapmap,
                                      Vector values, String Symname,
                                      String Visname, float min,
@@ -327,21 +352,24 @@ public class JPredClient
         OutputHeader += ("\n" + result.getAligfile());
       }
 
-      wsInfo.setProgressText(OutputHeader);
+      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");
@@ -350,6 +378,16 @@ public class JPredClient
           {
             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;
           }
@@ -364,14 +402,14 @@ 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!"));
-        }
 
         AlignmentAnnotation annot;
         Annotation[] annotations = null;
@@ -466,6 +504,9 @@ public class JPredClient
           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,
@@ -474,7 +515,8 @@ public class JPredClient
       }
       catch (Exception ex)
       {
-        ex.printStackTrace();
+        jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
+        jalview.bin.Jalview.log.debug("Exception: ",ex);
       }
     }
   }