X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=7daeb37454a764857c0a2be4ba519b7ac5c4bd68;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=a5c2a367b31ead357815a929a25565e6fe9cd55d;hpb=65a4ec4dee935394e57a2af5a9daa2f6ecc4aef3;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a5c2a36..7daeb37 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,19 +20,9 @@
  */
 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.io.FileFormats;
-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;
@@ -59,15 +49,30 @@ 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.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+@SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu webService = new JMenu();
+  public JMenu webService = new JMenu();// BH 2019 was protected, but not
+                                        // sufficient for AlignFrame thread run
 
-  protected JMenuItem webServiceNoServices;
+  public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
+                                        // sufficient for AlignFrame thread run
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
 
@@ -75,7 +80,9 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu sortByAnnotScore = new JMenu();
 
-  public JLabel statusBar = new JLabel();
+  public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+                                          // sufficient for
+                                          // AlignFrame.printWriter
 
   protected JMenu outputTextboxMenu = new JMenu();
 
@@ -97,6 +104,8 @@ public class GAlignFrame extends JInternalFrame
 
   JMenuItem copy = new JMenuItem();
 
+  JMenuItem copyHighlighted = new JMenuItem();
+
   JMenuItem cut = new JMenuItem();
 
   JMenu pasteMenu = new JMenu();
@@ -123,7 +132,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
@@ -137,7 +146,7 @@ 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();
 
@@ -169,7 +178,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 
-  protected JTabbedPane tabbedPane = jalview.jbgui.swing.JTabbedPane.createTabbedPane();
+  protected JTabbedPane tabbedPane = new JTabbedPane();
 
   protected JMenuItem reload = new JMenuItem();
 
@@ -196,14 +205,14 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
-  
+
   protected JMenuItem openFeatureSettings;
 
   private SequenceAnnotationOrder annotationSortOrder;
 
   private boolean showAutoCalculatedAbove = false;
 
-  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 
   private SplitContainerI splitFrame;
 
@@ -211,6 +220,11 @@ public class GAlignFrame extends JInternalFrame
   {
     try
     {
+      setFrameIcon(null);
+
+      // for Web-page embedding using id=align-frame-div
+      setName("jalview-alignment");
+
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
@@ -224,7 +238,7 @@ public class GAlignFrame extends JInternalFrame
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            outputText_actionPerformed(e);
+            outputText_actionPerformed(e.getActionCommand());
           }
         });
 
@@ -232,10 +246,10 @@ public class GAlignFrame extends JInternalFrame
       }
     } catch (Exception e)
     {
-      System.err.println(e.toString());
+      jalview.bin.Console.errPrintln(e.toString());
     }
 
-    if (!Platform.isAMac())
+    if (Platform.allowMnemonics()) // was "not mac and not JS"
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -250,6 +264,7 @@ public class GAlignFrame extends JInternalFrame
 
   private void jbInit() throws Exception
   {
+    setFrameIcon(null);
     initColourMenu();
 
     JMenuItem saveAs = new JMenuItem(
@@ -259,20 +274,22 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        saveAs_actionPerformed(e);
+        saveAs_actionPerformed();
       }
     };
 
     // 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
@@ -284,16 +301,7 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
 
     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
-    JMenu viewMenu = new JMenu(MessageManager.getString("action.view")) {
-      
-      public void setPopupMenuVisible(boolean b) {
-        if (b) {
-          openFeatureSettings.setEnabled(haveAlignmentFeatures());
-        }
-        super.setPopupMenuVisible(b);
-      }
-
-    };
+    JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
     JMenu annotationsMenu = new JMenu(
             MessageManager.getString("action.annotations"));
     JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
@@ -304,7 +312,9 @@ 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
@@ -331,7 +341,9 @@ 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
@@ -367,7 +379,9 @@ 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
@@ -381,7 +395,9 @@ 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
@@ -395,7 +411,9 @@ 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
@@ -409,8 +427,8 @@ 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()
     {
@@ -517,7 +535,9 @@ 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
@@ -692,7 +712,9 @@ 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
@@ -706,7 +728,9 @@ 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
@@ -730,7 +754,9 @@ 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
@@ -756,7 +782,9 @@ 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()
@@ -917,7 +945,9 @@ 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
@@ -942,7 +972,9 @@ 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
@@ -956,8 +988,8 @@ 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()
     {
@@ -971,27 +1003,31 @@ 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()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        copy_actionPerformed(e);
+        copy_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, copy, al);
 
     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
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        cut_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
@@ -1003,7 +1039,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        delete_actionPerformed(e);
+        delete_actionPerformed();
       }
     });
 
@@ -1011,8 +1047,8 @@ 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()
     {
@@ -1027,7 +1063,9 @@ 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
@@ -1044,7 +1082,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        createPNG(null);
+        createPNG_actionPerformed(e);
       }
     });
     createPNG.setActionCommand(
@@ -1061,7 +1099,7 @@ public class GAlignFrame extends JInternalFrame
     });
     seqLimits.setText(
             MessageManager.getString("label.show_sequence_limits"));
-    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new ActionListener()
     {
       @Override
@@ -1076,7 +1114,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        createEPS(null);
+        createEPS_actionPerformed(e);
       }
     });
 
@@ -1086,7 +1124,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        createSVG(null);
+        createSVG_actionPerformed(e);
       }
     });
 
@@ -1211,8 +1249,7 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
-    padGapsMenuitem
-            .setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       @Override
@@ -1232,16 +1269,33 @@ public class GAlignFrame extends JInternalFrame
         vamsasStore_actionPerformed(e);
       }
     });
+
+    /*
+     * Translate as cDNA with sub-menu of translation tables
+     */
     showTranslation
             .setText(MessageManager.getString("label.translate_cDNA"));
-    showTranslation.addActionListener(new ActionListener()
+    boolean first = true;
+    for (final GeneticCodeI table : GeneticCodes.getInstance()
+            .getCodeTables())
     {
-      @Override
-      public void actionPerformed(ActionEvent e)
+      JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+      showTranslation.add(item);
+      item.addActionListener(new ActionListener()
       {
-        showTranslation_actionPerformed(e);
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          showTranslation_actionPerformed(table);
+        }
+      });
+      if (first)
+      {
+        showTranslation.addSeparator();
       }
-    });
+      first = false;
+    }
+
     showReverse.setText(MessageManager.getString("label.reverse"));
     showReverse.addActionListener(new ActionListener()
     {
@@ -1292,7 +1346,6 @@ public class GAlignFrame extends JInternalFrame
 
     openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
-    openFeatureSettings.setEnabled(false);
     openFeatureSettings.addActionListener(new ActionListener()
     {
       @Override
@@ -1301,6 +1354,10 @@ public class GAlignFrame extends JInternalFrame
         featureSettings_actionPerformed(e);
       }
     });
+
+    /*
+     * add sub-menu of database we can fetch from
+     */
     JMenuItem fetchSequence = new JMenuItem(
             MessageManager.getString("label.fetch_sequences"));
     fetchSequence.addActionListener(new ActionListener()
@@ -1308,7 +1365,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        fetchSequence_actionPerformed(e);
+        fetchSequence_actionPerformed();
       }
     });
 
@@ -1322,7 +1379,8 @@ public class GAlignFrame extends JInternalFrame
         associatedData_actionPerformed(e);
       }
     });
-    loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+    loadVcf = new JMenuItem(
+            MessageManager.getString("label.load_vcf_file"));
     loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
     loadVcf.addActionListener(new ActionListener()
     {
@@ -1334,8 +1392,7 @@ public class GAlignFrame extends JInternalFrame
     });
     autoCalculate.setText(
             MessageManager.getString("label.autocalculate_consensus"));
-    autoCalculate.setState(
-            jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1348,8 +1405,7 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.sort_alignment_new_tree"));
     sortByTree.setToolTipText("<html>" + MessageManager.getString(
             "label.enable_automatically_sort_alignment_when_open_new_tree"));
-    sortByTree
-            .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+    sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
     {
       @Override
@@ -1523,8 +1579,8 @@ 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()
     {
@@ -1587,7 +1643,9 @@ 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
@@ -1612,7 +1670,9 @@ 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
@@ -1700,6 +1760,26 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     selectHighlighted.addActionListener(al);
+
+    copyHighlighted = new JMenuItem(
+            MessageManager.getString("action.copy_highlighted_regions"));
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            false);
+    copyHighlighted.setToolTipText(
+            MessageManager.getString("tooltip.copy_highlighted_regions"));
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        copyHighlightedColumns_actionPerformed(actionEvent);
+      }
+    };
+    addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
+    copyHighlighted.addActionListener(al);
+
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
     JMenu autoAnnMenu = new JMenu(
@@ -1716,7 +1796,10 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(webService);
+    if (!Platform.isJS())
+    {
+      alignFrameMenuBar.add(webService);
+    }
 
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
@@ -1734,10 +1817,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
-    /*
-     * No VCF import in Jalview-JS
-     * @j2sNative
-     */
+    if (!Platform.isJS())
     {
       fileMenu.add(loadVcf);
     }
@@ -1750,6 +1830,7 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(redoMenuItem);
     editMenu.add(cut);
     editMenu.add(copy);
+    editMenu.add(copyHighlighted);
     editMenu.add(pasteMenu);
     editMenu.add(delete);
     editMenu.addSeparator();
@@ -1835,17 +1916,26 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();
     calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
-    calculateMenu.addSeparator();
-    calculateMenu.add(runGroovy);
+    if (!Platform.isJS())
+    {
+      calculateMenu.addSeparator();
+      calculateMenu.add(runGroovy);
+    }
 
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    exportImageMenu.add(htmlMenuItem);
+    if (!Platform.isJS())
+    {
+      exportImageMenu.add(htmlMenuItem);
+    }
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
-    exportImageMenu.add(createBioJS);
-    exportImageMenu.add(createSVG);
+    if (!Platform.isJS())
+    {
+      exportImageMenu.add(createBioJS);
+      exportImageMenu.add(createSVG);
+    }
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);
@@ -1886,10 +1976,28 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
-  protected boolean haveAlignmentFeatures()
+  protected void createPNG_actionPerformed(ActionEvent object)
   {
-    // because gAlignFrame is not an abstract class  -- see AlignFrame
-    return false;
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void createEPS_actionPerformed(ActionEvent object)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void createSVG_actionPerformed(ActionEvent object)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void copyHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+
   }
 
   protected void loadVcf_actionPerformed()
@@ -1967,8 +2075,9 @@ 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
@@ -2068,7 +2177,7 @@ public class GAlignFrame extends JInternalFrame
    * @param forAlignment
    *          update non-sequence-related annotations
    */
-  protected void setAnnotationsVisibility(boolean visible,
+  public void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
 
@@ -2188,7 +2297,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  protected void outputText_actionPerformed(String formatName)
   {
   }
 
@@ -2354,15 +2463,15 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void copy_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed()
   {
   }
 
-  protected void cut_actionPerformed(ActionEvent e)
+  protected void cut_actionPerformed()
   {
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed()
   {
   }
 
@@ -2378,10 +2487,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  public void createPNG(java.io.File f)
-  {
-  }
-
   protected void font_actionPerformed(ActionEvent e)
   {
   }
@@ -2395,15 +2500,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void createEPS(java.io.File f)
-  {
-  }
-
-  public void createSVG(java.io.File f)
-  {
-
-  }
-
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -2446,7 +2542,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed()
   {
   }
 
@@ -2464,7 +2560,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }
@@ -2474,7 +2570,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed()
   {
 
   }