X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=2e361c7d89d7d51e43ff5d842a68f392ea921e5c;hb=57dd16688caa6dacaeaf465bab3ee8b6126e1a51;hp=3504ea493c1902d50e658ad84379874a84d829e2;hpb=c86442e455c858f4a092fbb2e9394faa3e161a89;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 3504ea4..2e361c7 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -491,8 +491,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
-            MessageManager
-            .getString("action.select_all"));
+            MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -703,8 +702,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem removeRedundancyMenuItem = new JMenuItem(MessageManager
-.getString("action.remove_redundancy"));
+    JMenuItem removeRedundancyMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1296,8 +1295,10 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.show_last"));
     buttonGroup.add(showAutoFirst);
     buttonGroup.add(showAutoLast);
-    showAutoFirst.setSelected(Cache.getDefault(
-            Preferences.SHOW_AUTOCALC_ABOVE, false));
+    final boolean autoFirst = Cache.getDefault(
+            Preferences.SHOW_AUTOCALC_ABOVE, false);
+    showAutoFirst.setSelected(autoFirst);
+    setShowAutoCalculatedAbove(autoFirst);
     showAutoFirst.addActionListener(new ActionListener()
     {
       @Override
@@ -1959,8 +1960,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+            .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.ALT_MASK, false);
     al = new ActionListener()
     {
@@ -2803,6 +2804,7 @@ public class GAlignFrame extends JInternalFrame
   {
 
   }
+
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -3057,7 +3059,8 @@ public class GAlignFrame extends JInternalFrame
     return annotationSortOrder;
   }
 
-  protected void setAnnotationSortOrder(SequenceAnnotationOrder annotationSortOrder)
+  protected void setAnnotationSortOrder(
+          SequenceAnnotationOrder annotationSortOrder)
   {
     this.annotationSortOrder = annotationSortOrder;
   }