X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FConservationThread.java;fp=src%2Fjalview%2Fgui%2FConservationThread.java;h=92f66da5be02becef9632e8c8ccb2566f0f52f8f;hb=399514cca430f9f64b14c446e275fee599ba5881;hp=fa70bccda47913053f2f7f422a068e3cc9d4d63f;hpb=d803f2708fc809fb8be7547727e6ab62c0451989;p=jalview.git

diff --git a/src/jalview/gui/ConservationThread.java b/src/jalview/gui/ConservationThread.java
index fa70bcc..92f66da 100644
--- a/src/jalview/gui/ConservationThread.java
+++ b/src/jalview/gui/ConservationThread.java
@@ -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;
       }