X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=f40c250de3ad07b700040f60ae33bab621ae7957;hb=d197025c26793dc26ef790633ee6ab394c8eff85;hp=4df8108ac2baf90d822dfefaf0addd78b24c3b33;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 4df8108..f40c250 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,27 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jws2;
 
 import java.util.*;
 
 import compbio.data.msa.MsaWS;
-import compbio.data.sequence.AlignmentMetadata;
-import compbio.data.sequence.Program;
 import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
@@ -547,6 +548,14 @@ 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)
       {