must do any modification to menus before they are embedded onto a panel.

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 22537f6..5b6a8a5 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2808,10 +2808,10 @@ public class AlignFrame
       //////
       // Explicly build the embedded menu panel for the on-page applet
       //
-      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", Font.PLAIN, 10, false); // use our own fonts.
       // view cannot be closed if its actually on the page
       fileMenu.remove(closeMenuItem);
       fileMenu.remove(3); // Remove Seperator
+      embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial", Font.PLAIN, 10, false); // use our own fonts.
       // and actually add the components to the applet area
       viewport.applet.setLayout(new BorderLayout());
       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);