X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=6fd0a4a702b638ab129dbf6400040c77dc3b8c90;hb=01cc9bf86a687fa7c8a741128264b23eb7feba9b;hp=4302df203a6e0e231ae142db3c9a5eb28f7147cf;hpb=74e4d71835fd0031dd7c309e37ec6bf934e4de4a;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 4302df2..6fd0a4a 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -26,6 +26,7 @@ import ext.vamsas.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
+import jalview.io.FormatAdapter;
 
 public class JPredClient
     extends WSClient
@@ -56,6 +57,7 @@ public class JPredClient
       wsInfo = setWebService();
 
     SequenceI seq = msf[0];
+
     altitle = "JNet prediction on " + seq.getName() +
         " using alignment from " + title;
 
@@ -64,8 +66,10 @@ public class JPredClient
                            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]);
+    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())
@@ -136,7 +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;
     }
@@ -171,9 +175,9 @@ public class JPredClient
       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));
+      jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
+      msa.setMsf(pileup.print(msf));
     }
 
     public void run()
@@ -190,7 +194,7 @@ public class JPredClient
                 "Timed out when communicating with server\nTry again later.\n"));
           }
           if (result.getState()==0)
-            jalview.bin.Jalview.log.debug("Finished "+jobId);
+            jalview.bin.Cache.log.debug("Finished "+jobId);
           if (result.isRunning())
           {
             wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
@@ -248,6 +252,19 @@ 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!=null)
         if (! (result.isJobFailed() || result.isServerError()))
@@ -291,26 +308,36 @@ public class JPredClient
       }
       catch (Exception e)
       {
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        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;
 
-        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,
+  /*  private void addFloatAnnotations(Alignment al, int[] gapmap,
                                      Vector values, String Symname,
                                      String Visname, float min,
                                      float max, int winLength)
@@ -326,7 +353,7 @@ public class JPredClient
 
       al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
                                                annotations, min, max, winLength));
-    }
+    }*/
 
     void parseResult()
     {
@@ -357,38 +384,39 @@ public class JPredClient
 
       try
       {
-        jalview.bin.Jalview.log.debug("Parsing output from JNet job.");
+        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.Jalview.log.debug("Got prediction profile.");
+        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.Jalview.log.debug("Getting associated alignment.");
+          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++) {
-              SequenceI sq = al.getSequenceAt(i);
-              if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-                  sq, (Hashtable) SequenceInfo.get(sq.getName())))
+              sqs[i] = al.getSequenceAt(i);
+            }
+            if (!jalview.analysis.SeqsetUtils.deuniquify(
+                  (Hashtable) SequenceInfo,sqs))
               {
                 throw (new Exception(
-                    "Couldn't recover sequence properties for JNet "
-                    +((i==0) ? "Query sequence" : "alignment sequence ("+i+")")));
+                    "Couldn't recover sequence properties for alignment."));
               }
-            }
+
             noMsa = false;
             FirstSeq = 0;
           }
@@ -411,6 +439,7 @@ public class JPredClient
           }
         }
 
+        al.setDataset(null);
 
         AlignmentAnnotation annot;
         Annotation[] annotations = null;
@@ -432,6 +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();
@@ -475,7 +506,8 @@ public class JPredClient
             {
               annot = new AlignmentAnnotation(preds[i].getName(),
                                               "JNet Output", annotations, 0f,
-                                              10f, 1);
+                                              10f,
+                                              AlignmentAnnotation.BAR_GRAPH);
             }
             else
             {
@@ -483,7 +515,7 @@ public class JPredClient
                                               "JNet Output", annotations);
             }
 
-            al.addAnnotation(annot);
+            al.addAnnotation(annot, seqRef);
 
             if (noMsa)
             {
@@ -494,7 +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);
@@ -507,7 +539,7 @@ public class JPredClient
          */
 
         wsInfo.setProgressText(OutputHeader);
-        jalview.bin.Jalview.log.debug("Finished parsing output.");
+        jalview.bin.Cache.log.debug("Finished parsing output.");
         AlignFrame af = new AlignFrame(al);
 
         Desktop.addInternalFrame(af, altitle,
@@ -516,8 +548,7 @@ public class JPredClient
       }
       catch (Exception ex)
       {
-        jalview.bin.Jalview.log.warn("Exception whilst parsing JNet style secondary structure prediction.");
-        jalview.bin.Jalview.log.debug("Exception: ",ex);
+        jalview.bin.Cache.log.warn("Exception whilst parsing JNet style secondary structure prediction.",ex);
       }
     }
   }