added proper state check for failedJob flag.

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 4e358a0..23c4ed4 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -174,11 +174,14 @@ public class MsaWSClient
           }
           else
           {
-            wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
+            if (result.getStatus()!=null)
+              wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());
             if (! (result.isJobFailed() || result.isServerError()))
             {
               Thread.sleep(5000);
               //  System.out.println("I'm alive "+seqid+" "+jobid);
+            } else {
+              break;
             }
           }
         }
@@ -189,12 +192,16 @@ public class MsaWSClient
           ex.printStackTrace();
         }
       }
-
-      if (! (result!=null && (result.isJobFailed() || result.isServerError())))
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-      else
+      if (allowedServerExceptions==0) {
         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-    }
+      } else {
+        if (! (result!=null && (result.isJobFailed() || result.isServerError())))
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        else {
+          if (result.isJobFailed()
+
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        }
 
     void StartJob()
     {