X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=eb5ef20372ec2396af208c5bdd0421b179f6e58c;hb=990fd5f012601024aaeeb09e2901791d242636c4;hp=cbb19fb99f2a23ecbd585b9613130f6cc878892a;hpb=fd618c7346eab858aa0039376872820aca37783a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index cbb19fb..eb5ef20 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -29,6 +29,7 @@ import jalview.bin.*;
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
 
 /**
  * DOCUMENT ME!
@@ -916,7 +917,15 @@ public class AlignViewport
      */
     public void setAlignment(AlignmentI align)
     {
+      if (alignment!=null && alignment.getCodonFrames()!=null)
+      {
+        StructureSelectionManager.getStructureSelectionManager().removeMappings(alignment.getCodonFrames());
+      }
         this.alignment = align;
+        if (alignment.getCodonFrames()!=null)
+        {
+          StructureSelectionManager.getStructureSelectionManager().addMappings(alignment.getCodonFrames());
+        }
     }
 
     /**