JAL-819 menu options to reinstate missing auto-calculated annotation

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 9f41c92..63bc050 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -35,7 +35,6 @@ import jalview.util.Platform;
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
-import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
@@ -208,6 +207,12 @@ public class GAlignFrame extends JInternalFrame
 
   private SplitContainerI splitFrame;
 
+  protected JMenu autoAnnMenu;
+
+  protected JRadioButtonMenuItem showAutoFirst;
+
+  protected JRadioButtonMenuItem showAutoLast;
+
   public GAlignFrame()
   {
     try
@@ -266,14 +271,14 @@ public class GAlignFrame extends JInternalFrame
 
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -296,7 +301,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -323,7 +328,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -359,7 +364,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -373,7 +378,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -387,7 +392,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -401,8 +406,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -509,7 +514,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -684,7 +689,7 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -698,7 +703,7 @@ public class GAlignFrame extends JInternalFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -722,7 +727,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -748,7 +753,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -876,9 +881,9 @@ public class GAlignFrame extends JInternalFrame
     });
 
     ButtonGroup buttonGroup = new ButtonGroup();
-    final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
+    showAutoFirst = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_first"));
-    final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
+    showAutoLast = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_last"));
     buttonGroup.add(showAutoFirst);
     buttonGroup.add(showAutoLast);
@@ -909,7 +914,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -934,7 +939,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -948,8 +953,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -963,7 +968,7 @@ public class GAlignFrame extends JInternalFrame
 
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
 
     al = new ActionListener()
     {
@@ -977,7 +982,7 @@ public class GAlignFrame extends JInternalFrame
 
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1003,8 +1008,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1019,7 +1024,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1531,8 +1536,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.ALT_MASK,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1595,7 +1600,7 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1620,7 +1625,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1710,7 +1715,7 @@ public class GAlignFrame extends JInternalFrame
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
-    JMenu autoAnnMenu = new JMenu(
+    autoAnnMenu = new JMenu(
             MessageManager.getString("label.autocalculated_annotation"));
 
     JMenu exportImageMenu = new JMenu(
@@ -1806,17 +1811,7 @@ public class GAlignFrame extends JInternalFrame
     annotationsMenu.add(sortAnnBySequence);
     annotationsMenu.add(sortAnnByLabel);
     annotationsMenu.addSeparator();
-    autoAnnMenu.add(showAutoFirst);
-    autoAnnMenu.add(showAutoLast);
-    autoAnnMenu.addSeparator();
-    autoAnnMenu.add(applyAutoAnnotationSettings);
-    autoAnnMenu.add(showConsensusHistogram);
-    autoAnnMenu.add(showSequenceLogo);
-    autoAnnMenu.add(normaliseSequenceLogo);
-    autoAnnMenu.addSeparator();
-    autoAnnMenu.add(showGroupConservation);
-    autoAnnMenu.add(showGroupConsensus);
-    annotationsMenu.add(autoAnnMenu);
+    annotationsMenu.add(autoAnnMenu); // autoAnnMenu is populated later
 
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);