X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=8f94e97a6d6946f4a1e9c08d9aade46da18f7d66;hb=83b24eab35785ea8473763ea5ed175a1fa63a4d1;hp=65f03253c61d59314c0f655640090c586714303f;hpb=503023b56eda1ae799c73b4189921bb2d60cc5d7;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 65f0325..8f94e97 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
@@ -190,7 +191,7 @@ 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);
@@ -248,16 +249,29 @@ 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()
@@ -291,19 +305,30 @@ 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");
-
-        jalview.bin.Jalview.log.debug("Failed Submission",e);
+        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;
+
       }
     }
 
@@ -356,27 +381,27 @@ 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));
             for (int i=0, j=al.getHeight(); i<j; i++) {
               SequenceI sq = al.getSequenceAt(i);
@@ -506,7 +531,7 @@ 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,
@@ -515,8 +540,8 @@ 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.");
+        jalview.bin.Cache.log.debug("Exception: ",ex);
       }
     }
   }