From 0417dab63ac557755d765b04ff083995763080be Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 17 Dec 2010 16:48:26 +0000
Subject: [PATCH] refined modification test

---
 src/jalview/ws/rest/RestClient.java |    7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 04c9561..64333c6 100644
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -175,14 +175,17 @@ public class RestClient extends WSClient implements WSClientI,
    */
   protected boolean isAlignmentModified()
   {
-    if (undoredo == null)
+    if (undoredo == null || av==null || av.getAlignment()==null)
     {
+      // always return modified if we don't have access to live GUI elements anymore.
       return true;
     }
     if (av.isUndoRedoHashModified(undoredo))
     {
-
+      // alignment has been modified in some way. 
+      return true;
     }
+    // TODO: look deeper into modification of selection state, etc that may affect RestJobThread.realiseResults(boolean merge); 
     return false;
 
   }
-- 
1.7.10.2