From d438fa16745a7998c9c1d92ff9ae4d47000f8784 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 17 Jan 2011 13:51:25 +0000
Subject: [PATCH] JAL-750 and JAL-451

---
 src/jalview/appletgui/AlignFrame.java    |   18 ++++++++++++++++++
 src/jalview/appletgui/AlignViewport.java |    8 ++++++--
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2fde9ad..1496595 100755
--- 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
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index ed61bc5..cd7857e 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -130,7 +130,7 @@ public class AlignViewport implements SelectionSource
 
   boolean ignoreGapsInConsensusCalculation = false;
 
-  jalview.bin.JalviewLite applet;
+  public jalview.bin.JalviewLite applet;
 
   Hashtable sequenceColours;
 
@@ -257,7 +257,11 @@ public class AlignViewport implements SelectionSource
       {
         sortByTree = Boolean.valueOf(param).booleanValue();
       }
-
+      param = applet.getParameter("automaticScrolling");
+      if (param!=null) {
+        followHighlight = Boolean.valueOf(param).booleanValue();
+        followSelection = followHighlight;
+      }
     }
 
     if (applet != null)
-- 
1.7.10.2