Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 58034d9..18731ad 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,11 +21,14 @@
 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;
 
@@ -75,7 +78,7 @@ 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 +126,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
@@ -137,7 +140,7 @@ 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();
 
@@ -147,6 +150,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
+  protected JMenuItem loadVcf;
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -167,7 +172,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 
-  protected JTabbedPane tabbedPane = new JTabbedPane();
+  protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
 
   protected JMenuItem reload = new JMenuItem();
 
@@ -194,12 +199,14 @@ 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;
 
@@ -220,7 +227,7 @@ public class GAlignFrame extends JInternalFrame
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            outputText_actionPerformed(e);
+            outputText_actionPerformed(e.getActionCommand());
           }
         });
 
@@ -231,7 +238,7 @@ public class GAlignFrame extends JInternalFrame
       System.err.println(e.toString());
     }
 
-    if (!Platform.isAMac())
+    if (Platform.allowMnemonics()) // was "not mac and not JS"
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -255,19 +262,20 @@ 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, false);
+    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 
     closeMenuItem.setText(MessageManager.getString("action.close"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -289,8 +297,8 @@ public class GAlignFrame extends JInternalFrame
     webService.setText(MessageManager.getString("action.web_service"));
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -316,8 +324,8 @@ 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);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -340,8 +348,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem expandAlignment = new JMenuItem(
             MessageManager.getString("action.view_flanking_regions"));
-    expandAlignment.setToolTipText(MessageManager
-            .getString("label.view_flanking_regions"));
+    expandAlignment.setToolTipText(
+            MessageManager.getString("label.view_flanking_regions"));
     expandAlignment.addActionListener(new ActionListener()
     {
       @Override
@@ -352,8 +360,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -366,8 +374,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -380,8 +388,8 @@ 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);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -394,9 +402,10 @@ 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, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -447,8 +456,8 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    showNonconservedMenuItem.setText(MessageManager
-            .getString("label.show_non_conserved"));
+    showNonconservedMenuItem
+            .setText(MessageManager.getString("label.show_non_conserved"));
     showNonconservedMenuItem.setState(false);
     showNonconservedMenuItem.addActionListener(new ActionListener()
     {
@@ -501,8 +510,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -530,14 +539,14 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
-    outputTextboxMenu.setText(MessageManager
-            .getString("label.out_to_textbox"));
+    outputTextboxMenu
+            .setText(MessageManager.getString("label.out_to_textbox"));
 
     annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText(MessageManager
-            .getString("label.show_annotations"));
-    annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
-            true));
+    annotationPanelMenuItem
+            .setText(MessageManager.getString("label.show_annotations"));
+    annotationPanelMenuItem
+            .setState(Cache.getDefault("SHOW_ANNOTATIONS", true));
     annotationPanelMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -546,8 +555,8 @@ public class GAlignFrame extends JInternalFrame
         annotationPanelMenuItem_actionPerformed(e);
       }
     });
-    showAllAlAnnotations.setText(MessageManager
-            .getString("label.show_all_al_annotations"));
+    showAllAlAnnotations.setText(
+            MessageManager.getString("label.show_all_al_annotations"));
     final boolean isAnnotationPanelShown = annotationPanelMenuItem
             .getState();
     showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
@@ -559,8 +568,8 @@ public class GAlignFrame extends JInternalFrame
         showAllAnnotations_actionPerformed(false, true);
       }
     });
-    hideAllAlAnnotations.setText(MessageManager
-            .getString("label.hide_all_al_annotations"));
+    hideAllAlAnnotations.setText(
+            MessageManager.getString("label.hide_all_al_annotations"));
     hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
     hideAllAlAnnotations.addActionListener(new ActionListener()
     {
@@ -570,8 +579,8 @@ public class GAlignFrame extends JInternalFrame
         hideAllAnnotations_actionPerformed(false, true);
       }
     });
-    showAllSeqAnnotations.setText(MessageManager
-            .getString("label.show_all_seq_annotations"));
+    showAllSeqAnnotations.setText(
+            MessageManager.getString("label.show_all_seq_annotations"));
     showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
     showAllSeqAnnotations.addActionListener(new ActionListener()
     {
@@ -581,8 +590,8 @@ public class GAlignFrame extends JInternalFrame
         showAllAnnotations_actionPerformed(true, false);
       }
     });
-    hideAllSeqAnnotations.setText(MessageManager
-            .getString("label.hide_all_seq_annotations"));
+    hideAllSeqAnnotations.setText(
+            MessageManager.getString("label.hide_all_seq_annotations"));
     hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
     hideAllSeqAnnotations.addActionListener(new ActionListener()
     {
@@ -600,8 +609,8 @@ public class GAlignFrame extends JInternalFrame
     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
             MessageManager.getString("label.sort_annotations_by_label"));
 
-    sortAnnBySequence
-            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+    sortAnnBySequence.setSelected(
+            sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     sortAnnBySequence.addActionListener(new ActionListener()
     {
       @Override
@@ -609,13 +618,14 @@ public class GAlignFrame extends JInternalFrame
       {
         boolean newState = sortAnnBySequence.getState();
         sortAnnByLabel.setSelected(false);
-        setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
-                : SequenceAnnotationOrder.NONE);
+        setAnnotationSortOrder(
+                newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+                        : SequenceAnnotationOrder.NONE);
         sortAnnotations_actionPerformed();
       }
     });
-    sortAnnByLabel
-            .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+    sortAnnByLabel.setSelected(
+            sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
     sortAnnByLabel.addActionListener(new ActionListener()
     {
       @Override
@@ -623,14 +633,14 @@ public class GAlignFrame extends JInternalFrame
       {
         boolean newState = sortAnnByLabel.getState();
         sortAnnBySequence.setSelected(false);
-        setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
-                : SequenceAnnotationOrder.NONE);
+        setAnnotationSortOrder(
+                newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+                        : SequenceAnnotationOrder.NONE);
         sortAnnotations_actionPerformed();
       }
     });
     colourTextMenuItem = new JCheckBoxMenuItem(
-            MessageManager
-            .getString("label.colour_text"));
+            MessageManager.getString("label.colour_text"));
     colourTextMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -675,8 +685,8 @@ public class GAlignFrame extends JInternalFrame
 
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -689,8 +699,8 @@ public class GAlignFrame extends JInternalFrame
 
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -713,8 +723,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -739,8 +749,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -753,8 +763,8 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 
-    showSeqFeatures.setText(MessageManager
-            .getString("label.show_sequence_features"));
+    showSeqFeatures.setText(
+            MessageManager.getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -769,8 +779,8 @@ public class GAlignFrame extends JInternalFrame
      * void actionPerformed(ActionEvent actionEvent) {
      * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
      */
-    showDbRefsMenuitem.setText(MessageManager
-            .getString("label.show_database_refs"));
+    showDbRefsMenuitem
+            .setText(MessageManager.getString("label.show_database_refs"));
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
 
@@ -781,8 +791,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showNpFeatsMenuitem.setText(MessageManager
-            .getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.setText(
+            MessageManager.getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
 
@@ -793,8 +803,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showGroupConservation.setText(MessageManager
-            .getString("label.group_conservation"));
+    showGroupConservation
+            .setText(MessageManager.getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
 
@@ -806,8 +816,8 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    showGroupConsensus.setText(MessageManager
-            .getString("label.group_consensus"));
+    showGroupConsensus
+            .setText(MessageManager.getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
 
@@ -818,8 +828,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showConsensusHistogram.setText(MessageManager
-            .getString("label.show_consensus_histogram"));
+    showConsensusHistogram.setText(
+            MessageManager.getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
 
@@ -830,8 +840,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showSequenceLogo.setText(MessageManager
-            .getString("label.show_consensus_logo"));
+    showSequenceLogo
+            .setText(MessageManager.getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
 
@@ -842,8 +852,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    normaliseSequenceLogo.setText(MessageManager
-            .getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo
+            .setText(MessageManager.getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
 
@@ -854,8 +864,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    applyAutoAnnotationSettings.setText(MessageManager
-            .getString("label.apply_all_groups"));
+    applyAutoAnnotationSettings
+            .setText(MessageManager.getString("label.apply_all_groups"));
     applyAutoAnnotationSettings.setState(false);
     applyAutoAnnotationSettings.setVisible(true);
     applyAutoAnnotationSettings.addActionListener(new ActionListener()
@@ -874,8 +884,8 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.show_last"));
     buttonGroup.add(showAutoFirst);
     buttonGroup.add(showAutoLast);
-    final boolean autoFirst = 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()
@@ -900,8 +910,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -925,8 +935,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -939,9 +949,10 @@ 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, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -953,28 +964,28 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, unGroup, al);
 
     copy.setText(MessageManager.getString("action.copy"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), 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);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        cut_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
@@ -986,16 +997,17 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        delete_actionPerformed(e);
+        delete_actionPerformed();
       }
     });
 
     pasteMenu.setText(MessageManager.getString("action.paste"));
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask()
-            | KeyEvent.SHIFT_MASK, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.SHIFT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1008,8 +1020,8 @@ 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);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1029,8 +1041,8 @@ public class GAlignFrame extends JInternalFrame
         createPNG(null);
       }
     });
-    createPNG.setActionCommand(MessageManager
-            .getString("label.save_png_image"));
+    createPNG.setActionCommand(
+            MessageManager.getString("label.save_png_image"));
 
     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
     font.addActionListener(new ActionListener()
@@ -1041,8 +1053,8 @@ public class GAlignFrame extends JInternalFrame
         font_actionPerformed(e);
       }
     });
-    seqLimits.setText(MessageManager
-            .getString("label.show_sequence_limits"));
+    seqLimits.setText(
+            MessageManager.getString("label.show_sequence_limits"));
     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new ActionListener()
     {
@@ -1074,8 +1086,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem loadTreeMenuItem = new JMenuItem(
             MessageManager.getString("label.load_associated_tree"));
-    loadTreeMenuItem.setActionCommand(MessageManager
-            .getString("label.load_tree_for_sequence_set"));
+    loadTreeMenuItem.setActionCommand(
+            MessageManager.getString("label.load_tree_for_sequence_set"));
     loadTreeMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1119,8 +1131,8 @@ public class GAlignFrame extends JInternalFrame
     });
     centreColumnLabelsMenuItem.setVisible(true);
     centreColumnLabelsMenuItem.setState(false);
-    centreColumnLabelsMenuItem.setText(MessageManager
-            .getString("label.centre_column_labels"));
+    centreColumnLabelsMenuItem.setText(
+            MessageManager.getString("label.centre_column_labels"));
     centreColumnLabelsMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1131,8 +1143,8 @@ public class GAlignFrame extends JInternalFrame
     });
     followHighlightMenuItem.setVisible(true);
     followHighlightMenuItem.setState(true);
-    followHighlightMenuItem.setText(MessageManager
-            .getString("label.automatic_scrolling"));
+    followHighlightMenuItem
+            .setText(MessageManager.getString("label.automatic_scrolling"));
     followHighlightMenuItem.addActionListener(new ActionListener()
     {
 
@@ -1165,8 +1177,8 @@ public class GAlignFrame extends JInternalFrame
       {
       }
     });
-    sortByAnnotScore.setText(MessageManager
-            .getString("label.sort_by_score"));
+    sortByAnnotScore
+            .setText(MessageManager.getString("label.sort_by_score"));
     sort.add(sortByAnnotScore);
     sort.addMenuListener(new javax.swing.event.MenuListener()
     {
@@ -1189,12 +1201,12 @@ public class GAlignFrame extends JInternalFrame
     });
     sortByAnnotScore.setVisible(false);
 
-    calculateTree.setText(MessageManager
-            .getString("action.calculate_tree_pca"));
+    calculateTree
+            .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(jalview.bin.Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       @Override
@@ -1214,16 +1226,33 @@ 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()
+      {
+        @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()
     {
@@ -1233,8 +1262,8 @@ public class GAlignFrame extends JInternalFrame
         showReverse_actionPerformed(false);
       }
     });
-    showReverseComplement.setText(MessageManager
-            .getString("label.reverse_complement"));
+    showReverseComplement
+            .setText(MessageManager.getString("label.reverse_complement"));
     showReverseComplement.addActionListener(new ActionListener()
     {
       @Override
@@ -1261,8 +1290,8 @@ public class GAlignFrame extends JInternalFrame
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
 
     runGroovy.setText(MessageManager.getString("label.run_groovy"));
-    runGroovy.setToolTipText(MessageManager
-            .getString("label.run_groovy_tip"));
+    runGroovy.setToolTipText(
+            MessageManager.getString("label.run_groovy_tip"));
     runGroovy.addActionListener(new ActionListener()
     {
       @Override
@@ -1272,7 +1301,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem openFeatureSettings = new JMenuItem(
+    openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
@@ -1282,6 +1311,10 @@ 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()
@@ -1289,7 +1322,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        fetchSequence_actionPerformed(e);
+        fetchSequence_actionPerformed();
       }
     });
 
@@ -1303,10 +1336,20 @@ public class GAlignFrame extends JInternalFrame
         associatedData_actionPerformed(e);
       }
     });
-    autoCalculate.setText(MessageManager
-            .getString("label.autocalculate_consensus"));
-    autoCalculate.setState(jalview.bin.Cache.getDefault(
-            "AUTO_CALC_CONSENSUS", true));
+    loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+    loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+    loadVcf.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadVcf_actionPerformed();
+      }
+    });
+    autoCalculate.setText(
+            MessageManager.getString("label.autocalculate_consensus"));
+    autoCalculate.setState(
+            jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1315,12 +1358,10 @@ public class GAlignFrame extends JInternalFrame
         autoCalculate_actionPerformed(e);
       }
     });
-    sortByTree.setText(MessageManager
-            .getString("label.sort_alignment_new_tree"));
-    sortByTree
-            .setToolTipText("<html>"
-                    + MessageManager
-                            .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+    sortByTree.setText(
+            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.addActionListener(new ActionListener()
@@ -1332,12 +1373,11 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    listenToViewSelections.setText(MessageManager
-            .getString("label.listen_for_selections"));
+    listenToViewSelections.setText(
+            MessageManager.getString("label.listen_for_selections"));
     listenToViewSelections
-            .setToolTipText("<html>"
-                    + MessageManager
-                            .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+            .setToolTipText("<html>" + MessageManager.getString(
+                    "label.selections_mirror_selections_made_same_sequences_other_views"));
     listenToViewSelections.setState(false);
     listenToViewSelections.addActionListener(new ActionListener()
     {
@@ -1403,8 +1443,8 @@ public class GAlignFrame extends JInternalFrame
     statusPanel.setLayout(new GridLayout());
     JMenuItem showAllSeqs = new JMenuItem(
             MessageManager.getString("label.all_sequences"));
-    showAllSeqs.setToolTipText(MessageManager
-            .getString("label.toggle_sequence_visibility"));
+    showAllSeqs.setToolTipText(
+            MessageManager.getString("label.toggle_sequence_visibility"));
     showAllSeqs.addActionListener(new ActionListener()
     {
       @Override
@@ -1415,8 +1455,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem showAllColumns = new JMenuItem(
             MessageManager.getString("label.all_columns"));
-    showAllColumns.setToolTipText(MessageManager
-            .getString("label.toggle_columns_visibility"));
+    showAllColumns.setToolTipText(
+            MessageManager.getString("label.toggle_columns_visibility"));
     showAllColumns.addActionListener(new ActionListener()
     {
       @Override
@@ -1428,8 +1468,8 @@ public class GAlignFrame extends JInternalFrame
     JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
     JMenuItem hideSelSequences = new JMenuItem(
             MessageManager.getString("label.selected_sequences"));
-    hideSelSequences.setToolTipText(MessageManager
-            .getString("label.toggle_sequence_visibility"));
+    hideSelSequences.setToolTipText(
+            MessageManager.getString("label.toggle_sequence_visibility"));
     hideSelSequences.addActionListener(new ActionListener()
     {
       @Override
@@ -1440,8 +1480,8 @@ public class GAlignFrame extends JInternalFrame
     });
     JMenuItem hideSelColumns = new JMenuItem(
             MessageManager.getString("label.selected_columns"));
-    hideSelColumns.setToolTipText(MessageManager
-            .getString("label.toggle_columns_visibility"));
+    hideSelColumns.setToolTipText(
+            MessageManager.getString("label.toggle_columns_visibility"));
     hideSelColumns.addActionListener(new ActionListener()
     {
       @Override
@@ -1483,8 +1523,8 @@ public class GAlignFrame extends JInternalFrame
         showAllhidden_actionPerformed(e);
       }
     });
-    hiddenMarkers.setText(MessageManager
-            .getString("action.show_hidden_markers"));
+    hiddenMarkers.setText(
+            MessageManager.getString("action.show_hidden_markers"));
     hiddenMarkers.addActionListener(new ActionListener()
     {
       @Override
@@ -1496,9 +1536,10 @@ 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, false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
+                    | KeyEvent.ALT_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1559,8 +1600,8 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1584,8 +1625,8 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
-    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
-            .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
     {
       @Override
@@ -1603,8 +1644,8 @@ public class GAlignFrame extends JInternalFrame
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
 
-    idRightAlign.setText(MessageManager
-            .getString("label.right_align_sequence_id"));
+    idRightAlign.setText(
+            MessageManager.getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
     {
       @Override
@@ -1662,8 +1703,8 @@ 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(
+            MessageManager.getString("tooltip.select_highlighted_columns"));
     al = new ActionListener()
     {
       @Override
@@ -1689,7 +1730,10 @@ 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);
@@ -1707,6 +1751,10 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
+    if (!Platform.isJS())
+    {
+      fileMenu.add(loadVcf);
+    }
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
 
@@ -1782,7 +1830,6 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
 
-
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1802,17 +1849,26 @@ 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);
@@ -1853,10 +1909,8 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
-  protected void configureSelectMenu()
+  protected void loadVcf_actionPerformed()
   {
-    // TODO Auto-generated method stub
-
   }
 
   /**
@@ -1894,8 +1948,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed(conservationMenuItem
-                .isSelected());
+        conservationMenuItem_actionPerformed(
+                conservationMenuItem.isSelected());
       }
     });
 
@@ -1919,8 +1973,7 @@ public class GAlignFrame extends JInternalFrame
         modifyPID_actionPerformed();
       }
     });
-    modifyConservation = new JMenuItem(
-            MessageManager
+    modifyConservation = new JMenuItem(MessageManager
             .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
     {
@@ -1931,8 +1984,9 @@ 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
@@ -2152,7 +2206,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  protected void outputText_actionPerformed(String formatName)
   {
   }
 
@@ -2318,15 +2372,15 @@ 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()
   {
   }
 
@@ -2410,7 +2464,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed()
   {
   }
 
@@ -2428,7 +2482,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }
@@ -2438,7 +2492,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed()
   {
 
   }