Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1cf482d..075b490 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,18 +21,20 @@
 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.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;
-import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusAdapter;
@@ -75,7 +77,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sortByAnnotScore = new JMenu();
 
-  public JLabel statusBar = new JLabel();
+  protected JLabel statusBar = new JLabel();
 
   protected JMenu outputTextboxMenu = new JMenu();
 
@@ -123,7 +125,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
@@ -137,7 +139,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 
-  protected JMenuItem showTranslation = new JMenuItem();
+  protected JMenu showTranslation = new JMenu();
 
   protected JMenuItem showReverse = new JMenuItem();
 
@@ -201,7 +203,7 @@ public class GAlignFrame extends JInternalFrame
 
   private boolean showAutoCalculatedAbove = false;
 
-  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 
   private SplitContainerI splitFrame;
 
@@ -263,14 +265,14 @@ 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
@@ -293,7 +295,7 @@ 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
@@ -320,7 +322,7 @@ 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
@@ -356,7 +358,7 @@ 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
@@ -370,7 +372,7 @@ 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
@@ -384,7 +386,7 @@ 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
@@ -398,8 +400,8 @@ 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()
     {
@@ -506,7 +508,7 @@ 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
@@ -681,7 +683,7 @@ 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
@@ -695,7 +697,7 @@ 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
@@ -719,7 +721,7 @@ 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
@@ -745,7 +747,7 @@ 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()
@@ -906,7 +908,7 @@ 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
@@ -931,7 +933,7 @@ 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
@@ -945,8 +947,8 @@ 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()
     {
@@ -960,7 +962,7 @@ 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()
     {
@@ -974,7 +976,7 @@ 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
@@ -1000,8 +1002,8 @@ 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()
     {
@@ -1016,7 +1018,7 @@ 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
@@ -1221,16 +1223,33 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation
-            .setText(MessageManager.getString("label.translate_cDNA"));
-    showTranslation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
+
+    /*
+     * Translate as cDNA with sub-menu of translation tables
+     */
+    showTranslation.setText(MessageManager
+            .getString("label.translate_cDNA"));
+    boolean first = true;
+    for (final GeneticCodeI table : GeneticCodes.getInstance()
+            .getCodeTables())
+    {
+      JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+      showTranslation.add(item);
+      item.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          showTranslation_actionPerformed(table);
+        }
+      });
+      if (first)
       {
-        showTranslation_actionPerformed(e);
+        showTranslation.addSeparator();
       }
-    });
+      first = false;
+    }
+
     showReverse.setText(MessageManager.getString("label.reverse"));
     showReverse.addActionListener(new ActionListener()
     {
@@ -1511,8 +1530,8 @@ 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()
     {
@@ -1575,7 +1594,7 @@ 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
@@ -1600,7 +1619,7 @@ 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
@@ -1943,8 +1962,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    annotationColour = new JMenuItem(
+    annotationColour = new JRadioButtonMenuItem(
             MessageManager.getString("action.by_annotation"));
+    annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
     annotationColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2440,7 +2460,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }