JAL-1148 reinstate sequence references for annotation regardless of whether they...

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 7a99a20..acdae46 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -529,7 +529,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
       Vector regions = new Vector();
       if (sg != null)
       {
-        // TODO test change case behaves identically in JvLite
         int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
                 sg.getEndRes() + 1);
 
@@ -800,8 +799,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
   {
     SequenceGroup sg = getGroup();
     sg.cs = new ClustalxColourScheme(
-            sg.getSequences(ap.av.getHiddenRepSequences()),
-            ap.av.getAlignment().getWidth());
+            sg,ap.av.getHiddenRepSequences());
     refresh();
   }