X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=870aa898093ac3fd298f8f117f34c25251650790;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=b759d64026a27efcd0fc99be86fd0d019665475e;hpb=d4a9ea73ba6f86fdcb69e08529f38600db3a99fc;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b759d64..870aa89 100755
--- 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;
@@ -59,15 +61,18 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+@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();
 
@@ -123,13 +130,13 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem modifyPID;
 
-  protected JMenuItem annotationColour;
+  protected JRadioButtonMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
   protected JMenu sort = new JMenu();
 
-  protected JMenu calculateTree = new JMenu();
+  protected JMenuItem calculateTree = new JMenuItem();
 
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 
@@ -137,7 +144,7 @@ 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 +154,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
+  protected JMenuItem loadVcf;
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -195,11 +204,13 @@ public class GAlignFrame extends JInternalFrame
 
   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;
 
@@ -207,6 +218,10 @@ public class GAlignFrame extends JInternalFrame
   {
     try
     {
+
+      // for Web-page embedding using id=align-frame-div
+      setName("jalview-alignment");
+
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
@@ -220,7 +235,7 @@ public class GAlignFrame extends JInternalFrame
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            outputText_actionPerformed(e);
+            outputText_actionPerformed(e.getActionCommand());
           }
         });
 
@@ -231,7 +246,7 @@ 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 +270,22 @@ 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, false);
+    KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+            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);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -289,8 +307,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -316,8 +336,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -340,8 +362,8 @@ 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 +374,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -366,8 +390,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -380,8 +406,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -394,9 +422,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -447,8 +476,8 @@ 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 +530,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -523,36 +554,6 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    JMenuItem PCAMenuItem = new JMenuItem(
-            MessageManager.getString("label.principal_component_analysis"));
-    PCAMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        PCAMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_identity"));
-    averageDistanceTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem neighbourTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_joining_identity"));
-    neighbourTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
 
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -560,35 +561,14 @@ 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"));
 
-    JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_blosum62"));
-    avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        avTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem njTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_blosum62"));
-    njTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
     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
@@ -597,8 +577,8 @@ 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);
@@ -610,8 +590,8 @@ 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()
     {
@@ -621,8 +601,8 @@ 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()
     {
@@ -632,8 +612,8 @@ 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()
     {
@@ -651,8 +631,8 @@ 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
@@ -660,13 +640,14 @@ 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
@@ -674,14 +655,14 @@ 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
@@ -726,8 +707,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -740,8 +723,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -764,8 +749,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -790,8 +777,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -804,8 +793,8 @@ 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
@@ -820,8 +809,8 @@ 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()
     {
 
@@ -832,8 +821,8 @@ 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()
     {
 
@@ -844,8 +833,8 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
-    showGroupConservation.setText(MessageManager
-            .getString("label.group_conservation"));
+    showGroupConservation
+            .setText(MessageManager.getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
 
@@ -857,8 +846,8 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    showGroupConsensus.setText(MessageManager
-            .getString("label.group_consensus"));
+    showGroupConsensus
+            .setText(MessageManager.getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
 
@@ -869,8 +858,8 @@ 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()
     {
 
@@ -881,8 +870,8 @@ 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()
     {
 
@@ -893,8 +882,8 @@ 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()
     {
 
@@ -905,8 +894,8 @@ 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()
@@ -925,8 +914,8 @@ 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()
@@ -951,8 +940,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -976,8 +967,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -990,9 +983,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1004,28 +998,32 @@ 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,
+            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);
+    keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        cut_actionPerformed();
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
@@ -1037,16 +1035,17 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1059,8 +1058,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1080,8 +1081,8 @@ 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()
@@ -1092,9 +1093,9 @@ public class GAlignFrame extends JInternalFrame
         font_actionPerformed(e);
       }
     });
-    seqLimits.setText(MessageManager
-            .getString("label.show_sequence_limits"));
-    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.setText(
+            MessageManager.getString("label.show_sequence_limits"));
+    seqLimits.setState(Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new ActionListener()
     {
       @Override
@@ -1123,11 +1124,10 @@ 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.addActionListener(new ActionListener()
+    JMenuItem loadTreeFile = new JMenuItem(
+            MessageManager.getString("label.from_file"));
+
+    loadTreeFile.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1136,6 +1136,89 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
+    JMenuItem loadTreeUrl = new JMenuItem(
+            MessageManager.getString("label.from_url"));
+    loadTreeUrl.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadTreeUrlItem_actionPerformed(e);
+      }
+    });
+
+
+
+    JMenuItem loadTreeBaseStudy = new JMenuItem(
+            MessageManager.getString("label.treebase_study"));
+    loadTreeBaseStudy.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadTreeBaseStudy_actionPerformed(e);
+
+      }    });
+
+
+
+    JMenuItem loadTreeBase = new JMenuItem(
+            MessageManager.getString("label.treebase"));
+    loadTreeBase.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadTreeBase_actionPerformed(e);
+
+      }
+
+
+    });
+    JMenuItem loadTreePfam = new JMenuItem(
+            MessageManager.getString("label.pfam"));
+    loadTreePfam.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadTreePfam_actionPerformed(e);
+
+      }
+
+    });
+    JMenuItem loadTreeFam = new JMenuItem(
+            MessageManager.getString("label.treefam"));
+    loadTreeFam.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadTreeFam_actionPerformed(e);
+
+      }
+
+    });
+
+    JMenuItem loadTreeOfLife = new JMenuItem(
+            MessageManager.getString("label.tree_of_life"));
+    loadTreeOfLife.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadTreeOfLife_actionPerformed(e);
+
+      }
+
+
+    });
+
     scaleAbove.setVisible(false);
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
     scaleAbove.addActionListener(new ActionListener()
@@ -1170,8 +1253,8 @@ 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
@@ -1182,8 +1265,8 @@ 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()
     {
 
@@ -1203,7 +1286,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeMenu();
+        buildTreeSortMenu();
       }
 
       @Override
@@ -1216,8 +1299,8 @@ 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()
     {
@@ -1241,11 +1324,10 @@ public class GAlignFrame extends JInternalFrame
     sortByAnnotScore.setVisible(false);
 
     calculateTree
-            .setText(MessageManager.getString("action.calculate_tree"));
+            .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
@@ -1265,16 +1347,33 @@ 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()
     {
@@ -1284,8 +1383,8 @@ 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
@@ -1312,8 +1411,8 @@ 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
@@ -1323,7 +1422,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem openFeatureSettings = new JMenuItem(
+    openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
     {
@@ -1333,6 +1432,10 @@ 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()
@@ -1340,7 +1443,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        fetchSequence_actionPerformed(e);
+        fetchSequence_actionPerformed();
       }
     });
 
@@ -1354,10 +1457,20 @@ 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(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       @Override
@@ -1366,14 +1479,11 @@ 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
-            .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+    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(Cache.getDefault("SORT_BY_TREE", false));
     sortByTree.addActionListener(new ActionListener()
     {
       @Override
@@ -1383,12 +1493,11 @@ 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()
     {
@@ -1454,8 +1563,8 @@ 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
@@ -1466,8 +1575,8 @@ 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
@@ -1479,8 +1588,8 @@ 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
@@ -1491,8 +1600,8 @@ 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
@@ -1534,8 +1643,8 @@ 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
@@ -1547,9 +1656,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+                    | jalview.util.ShortcutKeyMaskExWrapper.ALT_DOWN_MASK,
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1610,8 +1720,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1635,8 +1747,10 @@ 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,
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx(),
+            false);
     al = new ActionListener()
     {
       @Override
@@ -1654,8 +1768,8 @@ 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
@@ -1713,8 +1827,8 @@ 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
@@ -1731,7 +1845,27 @@ public class GAlignFrame extends JInternalFrame
 
     JMenu exportImageMenu = new JMenu(
             MessageManager.getString("label.export_image"));
+
+    JMenu loadTreeDb = new JMenu(
+            MessageManager.getString("label.from_database"));
+
+    JMenu loadTreeMenu = new JMenu(
+            MessageManager.getString("label.load_associated_tree"));
+    // loadTreeMenu.setToolTipText(
+    // MessageManager.getString("label.load_tree_for_sequence_set"));
+    
     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
+
+    loadTreeDb.add(loadTreeBaseStudy);
+    loadTreeDb.add(loadTreeBase);
+    loadTreeDb.add(loadTreePfam);
+    loadTreeDb.add(loadTreeFam);
+    loadTreeDb.add(loadTreeOfLife);
+
+    loadTreeMenu.add(loadTreeFile);
+    loadTreeMenu.add(loadTreeUrl);
+    loadTreeMenu.add(loadTreeDb);
+
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
@@ -1740,7 +1874,10 @@ 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);
@@ -1756,8 +1893,12 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportImageMenu);
     fileMenu.add(exportFeatures);
     fileMenu.add(exportAnnotations);
-    fileMenu.add(loadTreeMenuItem);
+    fileMenu.add(loadTreeMenu);
     fileMenu.add(associatedData);
+    if (!Platform.isJS())
+    {
+      fileMenu.add(loadVcf);
+    }
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
 
@@ -1833,7 +1974,6 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
 
-
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1843,7 +1983,6 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(showReverse);
@@ -1854,17 +1993,26 @@ 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);
@@ -1903,14 +2051,44 @@ public class GAlignFrame extends JInternalFrame
     // JAL-574
     // selectMenu.addSeparator();
     // selectMenu.add(listenToViewSelections);
+
+
+  }
+
+  protected void loadTreeOfLife_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void loadTreeFam_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void loadTreePfam_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void loadTreeBase_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
   }
 
-  protected void configureSelectMenu()
+  protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
 
   }
 
+  protected void loadVcf_actionPerformed()
+  {
+  }
+
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
@@ -1946,8 +2124,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed(conservationMenuItem
-                .isSelected());
+        conservationMenuItem_actionPerformed(
+                conservationMenuItem.isSelected());
       }
     });
 
@@ -1971,8 +2149,7 @@ public class GAlignFrame extends JInternalFrame
         modifyPID_actionPerformed();
       }
     });
-    modifyConservation = new JMenuItem(
-            MessageManager
+    modifyConservation = new JMenuItem(MessageManager
             .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(new ActionListener()
     {
@@ -1983,8 +2160,9 @@ 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
@@ -2204,7 +2382,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  protected void outputText_actionPerformed(String formatName)
   {
   }
 
@@ -2330,26 +2508,10 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
@@ -2386,15 +2548,15 @@ 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()
   {
   }
 
@@ -2441,6 +2603,13 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void loadTreeUrlItem_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+
+
   /**
    * Template method to handle the 'load T-Coffee scores' menu event.
    * <p>
@@ -2478,7 +2647,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed()
   {
   }
 
@@ -2496,7 +2665,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void showTranslation_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
 
   }
@@ -2506,7 +2675,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed()
   {
 
   }
@@ -2634,7 +2803,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
 
   }