JAL-750 and JAL-451

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2fde9ad..1496595 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -70,6 +70,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     annotationPanelMenuItem.setState(viewport.showAnnotation);
     displayNonconservedMenuItem.setState(viewport.getShowunconserved());
+    followMouseOverFlag.setState(viewport.getFollowHighlight());
 
     seqLimits.setState(viewport.showJVSuffix);
 
@@ -3142,6 +3143,23 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               viewport.applet.getSize().height - embeddedMenu.HEIGHT
                       - statusBar.HEIGHT);
       viewport.applet.add(alignPanel, BorderLayout.CENTER);
+      final AlignFrame me = this;
+      viewport.applet.addFocusListener(new FocusListener()
+      {
+        
+        @Override
+        public void focusLost(FocusEvent e)
+        {
+          if (me.viewport.applet.currentAlignFrame==me) {
+                  me.viewport.applet.currentAlignFrame = null;
+        }}
+        
+        @Override
+        public void focusGained(FocusEvent e)
+        {
+          me.viewport.applet.currentAlignFrame = me;
+        }
+      });
       viewport.applet.validate();
     }
     else