JAL-1925 update source version in license

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c6a042b..c99d894 100755 (executable)
--- 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -454,7 +454,7 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     JMenuItem saveAs = new JMenuItem(
-            MessageManager.getString("action.save_as") + "...");
+            MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
     {
       @Override
@@ -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").concat("..."));
+    JMenuItem removeRedundancyMenuItem = new JMenuItem(
+            MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1124,7 +1123,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem printMenuItem = new JMenuItem(
-            MessageManager.getString("action.print") + "...");
+            MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, 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
@@ -1687,7 +1688,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem extractScores = new JMenuItem(
-            MessageManager.getString("label.extract_scores") + "...");
+            MessageManager.getString("label.extract_scores"));
     extractScores.addActionListener(new ActionListener()
     {
       @Override
@@ -1703,7 +1704,7 @@ public class GAlignFrame extends JInternalFrame
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
     JMenuItem openFeatureSettings = new JMenuItem(
-            MessageManager.getString("label.feature_settings"));
+            MessageManager.getString("action.feature_settings"));
     openFeatureSettings.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()
     {
@@ -2051,7 +2052,7 @@ public class GAlignFrame extends JInternalFrame
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
     JMenuItem textColour = new JMenuItem(
-            MessageManager.getString("label.colour_text") + "...");
+            MessageManager.getString("action.set_text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2100,7 +2101,7 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
 
     JMenuItem pageSetup = new JMenuItem(
-            MessageManager.getString("action.page_setup") + "...");
+            MessageManager.getString("action.page_setup"));
     pageSetup.addActionListener(new ActionListener()
     {
       @Override
@@ -2110,7 +2111,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     JMenuItem alignmentProperties = new JMenuItem(
-            MessageManager.getString("label.alignment_props") + "...");
+            MessageManager.getString("label.alignment_props"));
     alignmentProperties.addActionListener(new ActionListener()
     {
       @Override
@@ -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;
   }