X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FConservationThread.java;h=92f66da5be02becef9632e8c8ccb2566f0f52f8f;hb=6403068c0c328cfb63af451f7fa1bd568fa0fdd3;hp=3e0c923f320394a3ee0dc6c71226f1f9683f0465;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/ConservationThread.java b/src/jalview/gui/ConservationThread.java
index 3e0c923..92f66da 100644
--- a/src/jalview/gui/ConservationThread.java
+++ b/src/jalview/gui/ConservationThread.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -60,9 +60,12 @@ class ConservationThread extends Thread
 
       AlignViewport.UPDATING_CONSERVATION = true;
 
-      int alWidth = this.alignViewport.alignment.getWidth();
-      if (alWidth < 0)
+      int alWidth;
+      
+      if (alignViewport==null || alignViewport.alignment==null || (alWidth=alignViewport.alignment.getWidth())< 0)
       {
+        this.alignViewport.updatingConservation = false;
+        AlignViewport.UPDATING_CONSERVATION = false;
         return;
       }