From 4272f31e9cc505f9a1496e2cd002dc9250c77928 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 13 May 2014 15:12:30 +0100
Subject: [PATCH] JAL-1239 make doubly sure sub job status is set to
 complete/cancelled

---
 src/jalview/ws/jws2/MsaWSThread.java |    5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index a54d0b5..08accba 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -545,6 +545,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI
           }
           wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
                   + cancelledMessage + "\n");
+        } else {
+          // if we hadn't submitted then just mark the job as cancelled.
+          jobs[job].setSubjobComplete(true);
+          wsInfo.setStatus(jobs[job].getJobnum(), WebserviceInfo.STATE_CANCELLED_OK);
+          
         }
       }
       if (cancelled)
-- 
1.7.10.2