Merge remote-tracking branch 'origin/merge/Jalview-JS/develop_feature/JAL-3690_callba...

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 0d6a03f..25db31a 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,20 +20,6 @@
  */
 package jalview.jbgui;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.GeneticCodeI;
-import jalview.analysis.GeneticCodes;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.hmmer.HmmerCommand;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormats;
-import jalview.schemes.ResidueColourScheme;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.GridLayout;
@@ -41,6 +27,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
 import java.awt.event.FocusEvent;
+import java.awt.event.InputEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
@@ -64,6 +51,21 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.hmmer.HmmerCommand;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+
 @SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
@@ -231,7 +233,8 @@ public class GAlignFrame extends JInternalFrame
     {
 
       // for Web-page embedding using id=align-frame-div
-      setName("jalview-alignment");
+      setName(Platform.getAppID("alignment"));
+
 
       jbInit();
       setJMenuBar(alignFrameMenuBar);
@@ -286,15 +289,12 @@ public class GAlignFrame extends JInternalFrame
     };
   
     // FIXME getDefaultToolkit throws an exception in Headless mode
-    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
   
     closeMenuItem.setText(MessageManager.getString("action.close"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -320,7 +320,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -347,7 +347,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -383,7 +383,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -397,7 +397,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -411,7 +411,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -425,8 +425,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -553,7 +553,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -755,7 +755,7 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -769,7 +769,7 @@ public class GAlignFrame extends JInternalFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -793,7 +793,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -819,7 +819,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -981,7 +981,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1006,7 +1006,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1020,8 +1020,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1035,7 +1035,7 @@ public class GAlignFrame extends JInternalFrame
   
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
 
     al = new ActionListener()
     {
@@ -1049,7 +1049,7 @@ public class GAlignFrame extends JInternalFrame
   
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1075,8 +1075,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1098,7 +1098,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1247,6 +1247,24 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
+        enableSortMenuOptions();
+      }
+
+      @Override
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      @Override
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
+    sortByTreeMenu.addMenuListener(new MenuListener()
+    {
+      @Override
+      public void menuSelected(MenuEvent e)
+      {
         buildTreeSortMenu();
       }
   
@@ -1628,8 +1646,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
-                    | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
+            Platform.SHORTCUT_KEY_MASK
+                    | InputEvent.ALT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1692,7 +1710,7 @@ public class GAlignFrame extends JInternalFrame
   
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1717,7 +1735,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+            Platform.SHORTCUT_KEY_MASK, false);
     al = new ActionListener()
     {
       @Override
@@ -1794,8 +1812,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem selectHighlighted = new JMenuItem(
             MessageManager.getString("action.select_highlighted_columns"));
-    selectHighlighted.setToolTipText(
-            MessageManager.getString("tooltip.select_highlighted_columns"));
+    selectHighlighted.setToolTipText(JvSwingUtils.wrapTooltip(true, 
+            MessageManager.getString("tooltip.select_highlighted_columns")));
     al = new ActionListener()
     {
       @Override
@@ -2181,6 +2199,10 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void enableSortMenuOptions()
+  {
+  }
+  
   protected void loadVcf_actionPerformed()
   {
   }
@@ -3019,4 +3041,6 @@ public class GAlignFrame extends JInternalFrame
   protected void showComplement_actionPerformed(boolean complement)
   {
   }
+  
+
 }