JAL-2430 colour columns hidden in alignment gray on structure

[jalview.git] / src / jalview / javascript / MouseOverStructureListener.java

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index b08aeca..6d366d0 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -222,7 +222,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       ArrayList<String> pdbfn = new ArrayList<String>();
       StructureMappingcommandSet[] colcommands = JmolCommands
               .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
-                      ((AlignmentViewPanel) source).getAlignment());
+                      ((AlignmentViewPanel) source).getAlignViewport());
       if (colcommands == null)
       {
         return;
@@ -298,7 +298,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalise()
+  @Override
+  public void finalize() throws Throwable
   {
     jvlite = null;
     super.finalize();