X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FConservationThread.java;h=5ed536c4ee4179a696686cb3ce80292e90a612bc;hb=34e81d4c2a02e30ccbea5295e550137b57810f25;hp=fa70bccda47913053f2f7f422a068e3cc9d4d63f;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/ConservationThread.java b/src/jalview/gui/ConservationThread.java
index fa70bcc..5ed536c 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;
       }
 
@@ -85,7 +88,6 @@ class ConservationThread extends Thread
 
       this.alignViewport.conservation = null;
       this.alignViewport.quality = null;
-
     }
 
     AlignViewport.UPDATING_CONSERVATION = false;