JAL-976 better logging/error reporting for disorder/conservation jobs

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index b2751c3..45117e4 100644 (file)
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -118,7 +118,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     long progressId = -1;
 
     String rslt = "JOB NOT DEFINED";
-
+    StringBuffer msg=new StringBuffer();
     try
     {
       if (checkDone())
@@ -216,6 +216,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
           if (stats != null)
           {
             System.out.print(stats.getChunk());
+            msg.append(stats);
             rpos = stats.getNextPosition();
           }
         } while (stats != null && rpos > cpos);
@@ -230,7 +231,6 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
           }
           ;
         }
-
       } while (!finished);
       try
       {
@@ -247,7 +247,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     } catch (JobSubmissionException x)
     {
 
-      System.err.println("submission error:");
+      System.err.println("submission error with "+getServiceActionText()+" :");
       x.printStackTrace();
       calcMan.workerCannotRun(this);
     } catch (ResultNotAvailableException x)
@@ -285,6 +285,14 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         }
         ap.paintAlignment(true);
       }
+      if (msg.length()>0)
+      {
+        // TODO: stash message somewhere in annotation or alignment view.
+        // code below shows result in a text box popup
+        /* jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+        cap.setText(msg.toString());
+        jalview.gui.Desktop.addInternalFrame(cap, "Job Status for "+getServiceActionText(), 600, 400); */
+      }
     }
 
   }