X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=de19fd8bfdf9f428e8ca5ae5d41befea3dd2ff23;hb=9cc5cb837b899016311e8f80e0e4e689e4a54ff6;hp=df5b1a60cc5c85bfb18aeaeb232ce692f493e62a;hpb=d5912abc02b0fd206d9705cf13a0383f09d3d951;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index df5b1a6..de19fd8 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -825,10 +825,11 @@ public void itemStateChanged(ItemEvent evt)
     //For sequence removal and addition, we need to fire
    //the property change event FROM the viewport where the
    //original alignment was altered
+   AlignmentI al = null;
     if (command instanceof EditCommand)
     {
       EditCommand editCommand = (EditCommand) command;
-      AlignmentI al = editCommand.getAlignment();
+      al = editCommand.getAlignment();
       Vector comps = (Vector) PaintRefresher.components
           .get(viewport.getSequenceSetId());
       for (int i = 0; i < comps.size(); i++)
@@ -842,17 +843,19 @@ public void itemStateChanged(ItemEvent evt)
           }
         }
       }
-      if (originalSource == null)
-      {
-        //The original view is closed, we must validate
-        //the current view against the closed view first
-        if (al != null)
-          PaintRefresher.validateSequences(al, viewport.alignment);
-        originalSource = viewport;
-      }
+    }
 
+    if (originalSource == null)
+    {
+      //The original view is closed, we must validate
+      //the current view against the closed view first
+      if (al != null)
+        PaintRefresher.validateSequences(al, viewport.alignment);
+
+      originalSource = viewport;
     }
 
+
     return originalSource;
   }