X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;fp=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=6d6a3e6635b2bbaf7dd3126469645b8e8034eacc;hb=a7168a947828a74899fff98c5f4f59515f60432a;hp=804b590867c5741efe414fcb34b8c6ac84faa49a;hpb=3e5a7e8e9e336b68a97f083e4c2d70001068c537;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 804b590..6d6a3e6 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -371,9 +371,11 @@ public class AlignViewport
 
         UPDATING_CONSERVATION = true;
 
-        int alWidth = alignment.getWidth();
+        int alWidth = (alignment==null) ? -1 : alignment.getWidth();
         if (alWidth < 0)
         {
+          updatingConservation = false;
+          UPDATING_CONSERVATION = false;
           return;
         }
 
@@ -548,9 +550,11 @@ public class AlignViewport
 
       try
       {
-        int aWidth = alignment.getWidth();
+        int aWidth = alignment==null ? -1 : alignment.getWidth();
         if (aWidth < 0)
         {
+          UPDATING_CONSENSUS = false;
+          updatingConsensus = false;
           return;
         }