Merge branch 'develop' into features/JAL-1705_ensembl

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index befa3b1..73d34c2 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,6 +20,14 @@
  */
 package jalview.jbgui;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
@@ -52,14 +60,6 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-
 public class GAlignFrame extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
@@ -262,7 +262,7 @@ public class GAlignFrame extends JInternalFrame
       System.err.println(e.toString());
     }
 
-    if (!new jalview.util.Platform().isAMac())
+    if (!jalview.util.Platform.isAMac())
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -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;
   }