X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=afb0dc1237db61f04c21e4535fd84536878dc4e7;hb=2e7da637a195ff484f92a333675284f071657cd6;hp=36378d4afa25885661e77854bd98f88565ed4366;hpb=40ecea964afaaf404465d75873ec915b901117a3;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 36378d4..afb0dc1 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,155 +1,367 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.jbgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.schemes.*;
-
-public class GAlignFrame
-    extends JInternalFrame
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
+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;
+import java.awt.event.FocusEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTabbedPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
+
+public class GAlignFrame extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
+
   protected JMenu fileMenu = new JMenu();
+
   protected JMenuItem closeMenuItem = new JMenuItem();
+
   protected JMenu editMenu = new JMenu();
+
   protected JMenu viewMenu = new JMenu();
+
   protected JMenu colourMenu = new JMenu();
+
   protected JMenu calculateMenu = new JMenu();
+
   protected JMenu webService = new JMenu();
+
   protected JMenuItem webServiceNoServices;
+
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
+
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
+
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
+
   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+
   protected JMenuItem remove2RightMenuItem = new JMenuItem();
+
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+
   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
+
   protected JMenuItem sortIDMenuItem = new JMenuItem();
+
+  protected JMenuItem sortLengthMenuItem = new JMenuItem();
+
   protected JMenuItem sortGroupMenuItem = new JMenuItem();
+
   protected JMenu sortByAnnotScore = new JMenu();
+
   protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
+
   protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
+
   protected JMenuItem PCAMenuItem = new JMenuItem();
+
   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
+
   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   public JLabel statusBar = new JLabel();
+
   protected JMenuItem saveAs = new JMenuItem();
+
   protected JMenu outputTextboxMenu = new JMenu();
+
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new
-      JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
+  // protected JRadioButtonMenuItem covariationColour = new
+  // JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
+
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem htmlMenuItem = new JMenuItem();
+
   JMenuItem overviewMenuItem = new JMenuItem();
+
   protected JMenuItem undoMenuItem = new JMenuItem();
+
   protected JMenuItem redoMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
   public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem printMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem findMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
-  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+  public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
+
   JMenuItem deleteGroups = new JMenuItem();
+
+  JMenuItem createGroup = new JMenuItem();
+
+  JMenuItem unGroup = new JMenuItem();
+
   JMenuItem delete = new JMenuItem();
+
   JMenuItem copy = new JMenuItem();
+
   JMenuItem cut = new JMenuItem();
+
   JMenu pasteMenu = new JMenu();
+
   JMenuItem pasteNew = new JMenuItem();
+
   JMenuItem pasteThis = new JMenuItem();
+
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+
   JMenuItem createPNG = new JMenuItem();
+
   protected JMenuItem font = new JMenuItem();
+
   public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
   JMenuItem epsFile = new JMenuItem();
+
   JMenuItem LoadtreeMenuItem = new JMenuItem();
+
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+
   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+
   protected JMenuItem modifyPID = new JMenuItem();
+
   protected JMenuItem modifyConservation = new JMenuItem();
+
   protected JMenu sortByTreeMenu = new JMenu();
+
   protected JMenu sort = new JMenu();
-  JMenu calculate = new JMenu();
+
+  protected JMenu calculateTree = new JMenu();
+
   JMenu jMenu2 = new JMenu();
+
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
+
   protected ButtonGroup colours = new ButtonGroup();
+
   JMenuItem vamsasStore = new JMenuItem();
+
   protected JMenuItem showTranslation = new JMenuItem();
+
   protected JMenuItem extractScores = new JMenuItem();
+
+  protected JMenuItem expandAlignment = new JMenuItem();
+
   protected JMenu showProducts = new JMenu();
-  public JMenuItem featureSettings = new JMenuItem();
+
+  public JMenuItem openFeatureSettings = new JMenuItem();
+
   JMenuItem fetchSequence = new JMenuItem();
+
   JMenuItem annotationColour = new JMenuItem();
+
+  protected JMenuItem rnahelicesColour = new JMenuItem();
+
   JMenuItem associatedData = new JMenuItem();
+
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
+
   JMenu addSequenceMenu = new JMenu();
+
   JMenuItem addFromFile = new JMenuItem();
+
   JMenuItem addFromText = new JMenuItem();
+
   JMenuItem addFromURL = new JMenuItem();
+
   JMenuItem exportAnnotations = new JMenuItem();
+
   JMenuItem exportFeatures = new JMenuItem();
+
   protected JPanel statusPanel = new JPanel();
+
   GridLayout gridLayout1 = new GridLayout();
+
   JMenu jMenu3 = new JMenu();
+
   JMenuItem showAllSeqs = new JMenuItem();
+
   JMenuItem showAllColumns = new JMenuItem();
+
   JMenu hideMenu = new JMenu();
+
   JMenuItem hideSelSequences = new JMenuItem();
+
   JMenuItem hideSelColumns = new JMenuItem();
+
+  JMenuItem hideAllButSelection = new JMenuItem();
+
+  JMenuItem hideAllSelection = new JMenuItem();
+
+  JMenuItem showAllhidden = new JMenuItem();
+
+  protected JMenuItem showAllAnnotations = new JMenuItem();
+
+  protected JMenuItem hideAllAnnotations = new JMenuItem();
+
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+
   JMenuItem invertColSel = new JMenuItem();
+
   protected JTabbedPane tabbedPane = new JTabbedPane();
+
   JMenuItem save = new JMenuItem();
+
   protected JMenuItem reload = new JMenuItem();
+
   JMenuItem newView = new JMenuItem();
+
   JMenuItem textColour = new JMenuItem();
+
   JMenu formatMenu = new JMenu();
+
   JMenu selectMenu = new JMenu();
+
   protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
+
   protected JMenuItem gatherViews = new JMenuItem();
+
   protected JMenuItem expandViews = new JMenuItem();
+
   JMenuItem pageSetup = new JMenuItem();
+
   JMenuItem alignmentProperties = new JMenuItem();
+
+  JMenu tooltipSettingsMenu = new JMenu();
+
+  private JMenuItem justifyLeftMenuItem = new JMenuItem();
+
+  private JMenuItem justifyRightMenuItem = new JMenuItem();
+
+  JMenu autoAnnMenu = new JMenu();
+
+  protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+
+  private JMenuItem grpsFromSelection = new JMenuItem();
+
   public GAlignFrame()
   {
     try
@@ -160,11 +372,12 @@ public class GAlignFrame
       // dynamically fill save as menu with available formats
       for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
-        JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
-                                       WRITEABLE_FORMATS[i]);
+        JMenuItem item = new JMenuItem(
+                jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 
         item.addActionListener(new java.awt.event.ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             outputText_actionPerformed(e);
@@ -173,12 +386,12 @@ public class GAlignFrame
 
         outputTextboxMenu.add(item);
       }
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
+      System.err.println(e.toString());
     }
 
-    if (!System.getProperty("os.name").startsWith("Mac"))
+    if (!new jalview.util.Platform().isAMac())
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -192,38 +405,42 @@ public class GAlignFrame
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-            userColours.
-            nextElement().toString());
+                userColours.nextElement().toString());
         radioItem.setName("USER_DEFINED");
         radioItem.addMouseListener(new MouseAdapter()
         {
+          @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+            if (evt.isControlDown()
+                    || SwingUtilities.isRightMouseButton(evt))
             {
               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
-                  Desktop.desktop,
-                  "Remove from default list?",
-                  "Remove user defined colour",
-                  JOptionPane.YES_NO_OPTION);
+              int option = JOptionPane.showInternalConfirmDialog(
+                      jalview.gui.Desktop.desktop,
+                      MessageManager
+                              .getString("label.remove_from_default_list"),
+                      MessageManager
+                              .getString("label.remove_user_defined_colour"),
+                      JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
-                jalview.gui.UserDefinedColours.removeColourFromDefaults(
-                    radioItem.getText());
+                jalview.gui.UserDefinedColours
+                        .removeColourFromDefaults(radioItem.getText());
                 colourMenu.remove(radioItem);
               }
               else
               {
                 radioItem.addActionListener(new ActionListener()
                 {
+                  @Override
                   public void actionPerformed(ActionEvent evt)
                   {
                     userDefinedColour_actionPerformed(evt);
@@ -235,6 +452,7 @@ public class GAlignFrame
         });
         radioItem.addActionListener(new ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent evt)
           {
             userDefinedColour_actionPerformed(evt);
@@ -257,8 +475,12 @@ public class GAlignFrame
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
-
-    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+    colours.add(purinePyrimidineColour);
+    // colours.add(covariationColour);
+    colours.add(tcoffeeColour);
+    colours.add(RNAInteractionColour);
+    setColourSelected(jalview.bin.Cache
+            .getDefault("DEFAULT_COLOUR", "None"));
 
   }
 
@@ -267,597 +489,989 @@ public class GAlignFrame
 
     if (defaultColour != null)
     {
-      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+      int index = ColourSchemeProperty
+              .getColourIndexFromName(defaultColour);
 
       switch (index)
       {
-        case ColourSchemeProperty.NONE:
-          noColourmenuItem.setSelected(true);
-          break;
-        case ColourSchemeProperty.CLUSTAL:
-          clustalColour.setSelected(true);
+      case ColourSchemeProperty.CLUSTAL:
+        clustalColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.BLOSUM:
-          BLOSUM62Colour.setSelected(true);
+      case ColourSchemeProperty.BLOSUM:
+        BLOSUM62Colour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.PID:
-          PIDColour.setSelected(true);
+      case ColourSchemeProperty.PID:
+        PIDColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.ZAPPO:
-          zappoColour.setSelected(true);
+      case ColourSchemeProperty.ZAPPO:
+        zappoColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.TAYLOR:
-          taylorColour.setSelected(true);
-          break;
+      case ColourSchemeProperty.TAYLOR:
+        taylorColour.setSelected(true);
+        break;
 
-        case ColourSchemeProperty.HYDROPHOBIC:
-          hydrophobicityColour.setSelected(true);
+      case ColourSchemeProperty.HYDROPHOBIC:
+        hydrophobicityColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.HELIX:
-          helixColour.setSelected(true);
+      case ColourSchemeProperty.HELIX:
+        helixColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.STRAND:
-          strandColour.setSelected(true);
+      case ColourSchemeProperty.STRAND:
+        strandColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.TURN:
-          turnColour.setSelected(true);
+      case ColourSchemeProperty.TURN:
+        turnColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.BURIED:
-          buriedColour.setSelected(true);
+      case ColourSchemeProperty.BURIED:
+        buriedColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.NUCLEOTIDE:
-          nucleotideColour.setSelected(true);
+      case ColourSchemeProperty.NUCLEOTIDE:
+        nucleotideColour.setSelected(true);
 
-          break;
+        break;
 
-        case ColourSchemeProperty.USER_DEFINED:
-          userDefinedColour.setSelected(true);
+      case ColourSchemeProperty.TCOFFEE:
+        tcoffeeColour.setSelected(true);
+        break;
+
+      case ColourSchemeProperty.PURINEPYRIMIDINE:
+        purinePyrimidineColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.RNAINTERACTION:
+        RNAInteractionColour.setSelected(true);
+
+        break;
+      /*
+       * case ColourSchemeProperty.COVARIATION:
+       * covariationColour.setSelected(true);
+       * 
+       * break;
+       */
+      case ColourSchemeProperty.USER_DEFINED:
+        userDefinedColour.setSelected(true);
+
+        break;
+      case ColourSchemeProperty.NONE:
+      default:
+        noColourmenuItem.setSelected(true);
+        break;
 
-          break;
       }
     }
 
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
-    fileMenu.setText("File");
-    saveAs.setText("Save As...");
-    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
+    fileMenu.setText(MessageManager.getString("action.file"));
+    saveAs.setText(MessageManager.getString("action.save_as") + "...");
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
     saveAs.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         saveAs_actionPerformed(e);
       }
     });
-    closeMenuItem.setText("Close");
-    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    closeMenuItem.setText(MessageManager.getString("action.close"));
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_W, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         closeMenuItem_actionPerformed(false);
       }
     });
-    editMenu.setText("Edit");
-    viewMenu.setText("View");
-    colourMenu.setText("Colour");
-    calculateMenu.setText("Calculate");
-    webService.setText("Web Service");
-    selectAllSequenceMenuItem.setText("Select All");
-    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_A,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
-                                                ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        selectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    deselectAllSequenceMenuItem.setText("Deselect All");
-    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
-                                               getKeyStroke(
-        java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
-                                                  ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deselectAllSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    invertSequenceMenuItem.setText("Invert Sequence Selection");
-    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_I,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        invertSequenceMenuItem_actionPerformed(e);
-      }
-    });
-    remove2LeftMenuItem.setText("Remove Left");
-    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_L,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2LeftMenuItem_actionPerformed(e);
-      }
-    });
-    remove2RightMenuItem.setText("Remove Right");
-    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_R,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        remove2RightMenuItem_actionPerformed(e);
-      }
-    });
-    removeGappedColumnMenuItem.setText("Remove Empty Columns");
-    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
-                                              getKeyStroke(java.awt.event.
-        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
-                                                 ActionListener()
+    editMenu.setText(MessageManager.getString("action.edit"));
+    viewMenu.setText(MessageManager.getString("action.view"));
+    colourMenu.setText(MessageManager.getString("action.colour"));
+    calculateMenu.setText(MessageManager.getString("action.calculate"));
+    webService.setText(MessageManager.getString("action.web_service"));
+    selectAllSequenceMenuItem.setText(MessageManager
+            .getString("action.select_all"));
+    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_A, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                selectAllSequenceMenuItem_actionPerformed(e);
+              }
+            });
+    deselectAllSequenceMenuItem.setText(MessageManager
+            .getString("action.deselect_all"));
+    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+    deselectAllSequenceMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                deselectAllSequenceMenuItem_actionPerformed(e);
+              }
+            });
+    invertSequenceMenuItem.setText(MessageManager
+            .getString("action.invert_sequence_selection"));
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_I, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    invertSequenceMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                invertSequenceMenuItem_actionPerformed(e);
+              }
+            });
+    grpsFromSelection.setText(MessageManager
+            .getString("action.make_groups_selection"));
+    grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        removeGappedColumnMenuItem_actionPerformed(e);
+        makeGrpsFromSelection_actionPerformed(e);
       }
     });
-    removeAllGapsMenuItem.setText("Remove All Gaps");
-    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_E,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
-    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    expandAlignment.setText(MessageManager
+            .getString("action.view_flanking_regions"));
+    expandAlignment.setToolTipText(MessageManager
+            .getString("label.view_flanking_regions"));
+    expandAlignment.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        removeAllGapsMenuItem_actionPerformed(e);
+        expand_newalign(e);
       }
     });
-    viewBoxesMenuItem.setText("Boxes");
+    remove2LeftMenuItem.setText(MessageManager
+            .getString("action.remove_left"));
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    remove2LeftMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                remove2LeftMenuItem_actionPerformed(e);
+              }
+            });
+    remove2RightMenuItem.setText(MessageManager
+            .getString("action.remove_right"));
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    remove2RightMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                remove2RightMenuItem_actionPerformed(e);
+              }
+            });
+    removeGappedColumnMenuItem.setText(MessageManager
+            .getString("action.remove_empty_columns"));
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeGappedColumnMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                removeGappedColumnMenuItem_actionPerformed(e);
+              }
+            });
+    removeAllGapsMenuItem.setText(MessageManager
+            .getString("action.remove_all_gaps"));
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_E, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
+    removeAllGapsMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                removeAllGapsMenuItem_actionPerformed(e);
+              }
+            });
+    justifyLeftMenuItem.setText(MessageManager
+            .getString("action.left_justify_alignment"));
+    justifyLeftMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                justifyLeftMenuItem_actionPerformed(e);
+              }
+            });
+    justifyRightMenuItem.setText(MessageManager
+            .getString("action.right_justify_alignment"));
+    justifyRightMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                justifyRightMenuItem_actionPerformed(e);
+              }
+            });
+    viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
     viewBoxesMenuItem.setState(true);
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         viewBoxesMenuItem_actionPerformed(e);
       }
     });
-    viewTextMenuItem.setText("Text");
+    viewTextMenuItem.setText(MessageManager.getString("action.text"));
     viewTextMenuItem.setState(true);
     viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    sortPairwiseMenuItem.setText("by Pairwise Identity");
-    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortPairwiseMenuItem_actionPerformed(e);
-      }
-    });
-    sortIDMenuItem.setText("by ID");
+    showNonconservedMenuItem.setText(MessageManager
+            .getString("label.show_non_conversed"));
+    showNonconservedMenuItem.setState(false);
+    showNonconservedMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                showUnconservedMenuItem_actionPerformed(e);
+              }
+            });
+    sortPairwiseMenuItem.setText(MessageManager
+            .getString("action.by_pairwise_id"));
+    sortPairwiseMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                sortPairwiseMenuItem_actionPerformed(e);
+              }
+            });
+    sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortGroupMenuItem.setText("by Group");
+    sortLengthMenuItem
+            .setText(MessageManager.getString("action.by_length"));
+    sortLengthMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                sortLengthMenuItem_actionPerformed(e);
+              }
+            });
+    sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-    removeRedundancyMenuItem.setText("Remove Redundancy...");
-    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_D,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.
-                                               ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        removeRedundancyMenuItem_actionPerformed(e);
-      }
-    });
-    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
-                                                ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pairwiseAlignmentMenuItem_actionPerformed(e);
-      }
-    });
-    PCAMenuItem.setText("Principal Component Analysis");
+    removeRedundancyMenuItem.setText(MessageManager
+            .getString("action.remove_redundancy").concat("..."));
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_D, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeRedundancyMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                removeRedundancyMenuItem_actionPerformed(e);
+              }
+            });
+    pairwiseAlignmentMenuItem.setText(MessageManager
+            .getString("action.pairwise_alignment"));
+    pairwiseAlignmentMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                pairwiseAlignmentMenuItem_actionPerformed(e);
+              }
+            });
+    PCAMenuItem.setText(MessageManager
+            .getString("label.principal_component_analysis"));
     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText(
-        "Average Distance Using % Identity");
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
-                                                  ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
-    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
+    averageDistanceTreeMenuItem.setText(MessageManager
+            .getString("label.average_distance_identity"));
+    averageDistanceTreeMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                averageDistanceTreeMenuItem_actionPerformed(e);
+              }
+            });
+    neighbourTreeMenuItem.setText(MessageManager
+            .getString("label.neighbour_joining_identity"));
+    neighbourTreeMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                neighbourTreeMenuItem_actionPerformed(e);
+              }
+            });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
-    statusBar.setText("Status bar");
-    outputTextboxMenu.setText("Output to Textbox");
-    clustalColour.setText("Clustalx");
+    statusBar.setText(MessageManager.getString("label.status_bar"));
+    outputTextboxMenu.setText(MessageManager
+            .getString("label.out_to_textbox"));
+    clustalColour.setText(MessageManager.getString("label.clustalx"));
 
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         clustalColour_actionPerformed(e);
       }
     });
-    zappoColour.setText("Zappo");
+    zappoColour.setText(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         zappoColour_actionPerformed(e);
       }
     });
-    taylorColour.setText("Taylor");
+    taylorColour.setText(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         taylorColour_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
-    helixColour.setText("Helix Propensity");
+    hydrophobicityColour.setText(MessageManager
+            .getString("label.hydrophobicity"));
+    hydrophobicityColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                hydrophobicityColour_actionPerformed(e);
+              }
+            });
+    helixColour.setText(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         helixColour_actionPerformed(e);
       }
     });
-    strandColour.setText("Strand Propensity");
+    strandColour.setText(MessageManager
+            .getString("label.strand_propensity"));
     strandColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         strandColour_actionPerformed(e);
       }
     });
-    turnColour.setText("Turn Propensity");
+    turnColour.setText(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         turnColour_actionPerformed(e);
       }
     });
-    buriedColour.setText("Buried Index");
+    buriedColour.setText(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         buriedColour_actionPerformed(e);
       }
     });
-    userDefinedColour.setText("User Defined...");
+    userDefinedColour.setText(MessageManager
+            .getString("action.user_defined"));
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         userDefinedColour_actionPerformed(e);
       }
     });
-    PIDColour.setText("Percentage Identity");
+    PIDColour
+            .setText(MessageManager.getString("label.percentage_identity"));
     PIDColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         PIDColour_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("BLOSUM62 Score");
+    BLOSUM62Colour
+            .setText(MessageManager.getString("label.blosum62_score"));
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         BLOSUM62Colour_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText(
-        "Average Distance Using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
-        ActionListener()
+    nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        avTreeBlosumMenuItem_actionPerformed(e);
+        nucleotideColour_actionPerformed(e);
       }
     });
-    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
-    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    purinePyrimidineColour.setText(MessageManager
+            .getString("label.purine_pyrimidine"));
+    purinePyrimidineColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                purinePyrimidineColour_actionPerformed(e);
+              }
+            });
+
+    RNAInteractionColour.setText("RNA Interaction type");
+    RNAInteractionColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                RNAInteractionColour_actionPerformed(e);
+              }
+            });
+    /*
+     * covariationColour.setText("Covariation");
+     * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+     * public void actionPerformed(ActionEvent e) {
+     * covariationColour_actionPerformed(e); } });
+     */
+
+    avDistanceTreeBlosumMenuItem.setText(MessageManager
+            .getString("label.average_distance_bloslum62"));
+    avDistanceTreeBlosumMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                avTreeBlosumMenuItem_actionPerformed(e);
+              }
+            });
+    njTreeBlosumMenuItem.setText(MessageManager
+            .getString("label.neighbour_blosum62"));
+    njTreeBlosumMenuItem
+            .addActionListener(new java.awt.event.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.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        njTreeBlosumMenuItem_actionPerformed(e);
+        annotationPanelMenuItem_actionPerformed(e);
       }
     });
-    annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
-        "SHOW_ANNOTATIONS", true));
-    annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
+    /*
+     * Show/hide all annotations only enabled if annotation panel is shown
+     */
+    showAllAnnotations.setText(MessageManager
+            .getString("label.show_all_annotations"));
+    showAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    showAllAnnotations.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        annotationPanelMenuItem_actionPerformed(e);
+        showAllAnnotations_actionPerformed();
       }
     });
-    colourTextMenuItem.setText("Colour Text");
-    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    hideAllAnnotations.setText(MessageManager
+            .getString("label.hide_all_annotations"));
+    hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    hideAllAnnotations.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        colourTextMenuItem_actionPerformed(e);
+        hideAllAnnotations_actionPerformed();
       }
     });
-    htmlMenuItem.setText("HTML");
+    colourTextMenuItem.setText(MessageManager
+            .getString("label.colour_text"));
+    colourTextMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                colourTextMenuItem_actionPerformed(e);
+              }
+            });
+    htmlMenuItem.setText(MessageManager.getString("label.html"));
     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         htmlMenuItem_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText("Overview Window");
+    overviewMenuItem.setText(MessageManager
+            .getString("label.overview_window"));
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         overviewMenuItem_actionPerformed(e);
       }
     });
     undoMenuItem.setEnabled(false);
-    undoMenuItem.setText("Undo");
+    undoMenuItem.setText(MessageManager.getString("action.undo"));
     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_Z,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         undoMenuItem_actionPerformed(e);
       }
     });
     redoMenuItem.setEnabled(false);
-    redoMenuItem.setText("Redo");
-    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    redoMenuItem.setText(MessageManager.getString("action.redo"));
+    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         redoMenuItem_actionPerformed(e);
       }
     });
-    conservationMenuItem.setText("By Conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    conservationMenuItem.setText(MessageManager
+            .getString("action.by_conservation"));
+    conservationMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                conservationMenuItem_actionPerformed(e);
+              }
+            });
+    noColourmenuItem.setText(MessageManager.getString("label.none"));
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed(e);
+      }
+    });
+    wrapMenuItem.setText(MessageManager.getString("label.wrap"));
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        wrapMenuItem_actionPerformed(e);
+      }
+    });
+    printMenuItem.setText(MessageManager.getString("action.print") + "...");
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_P, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        printMenuItem_actionPerformed(e);
+      }
+    });
+    renderGapsMenuItem
+            .setText(MessageManager.getString("action.show_gaps"));
+    renderGapsMenuItem.setState(true);
+    renderGapsMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                renderGapsMenuItem_actionPerformed(e);
+              }
+            });
+    findMenuItem.setText(MessageManager.getString("action.find"));
+    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_F, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.find_tip")));
+    findMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        findMenuItem_actionPerformed(e);
+      }
+    });
+    abovePIDThreshold.setText(MessageManager
+            .getString("label.above_identity_threshold"));
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDThreshold_actionPerformed(e);
+      }
+    });
+    showSeqFeatures.setText(MessageManager
+            .getString("label.show_sequence_features"));
+    showSeqFeatures.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        showSeqFeatures_actionPerformed(actionEvent);
+      }
+    });
+    /*
+     * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+     * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
+     * void actionPerformed(ActionEvent actionEvent) {
+     * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
+     */
+    showDbRefsMenuitem.setText(MessageManager
+            .getString("label.show_database_refs"));
+    showDbRefsMenuitem.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showDbRefs_actionPerformed(e);
+      }
+
+    });
+    showNpFeatsMenuitem.setText(MessageManager
+            .getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showNpFeats_actionPerformed(e);
+      }
+
+    });
+    showGroupConservation.setText(MessageManager
+            .getString("label.group_conservation"));
+    showGroupConservation.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showGroupConservation_actionPerformed(e);
+      }
+
+    });
+
+    showGroupConsensus.setText(MessageManager
+            .getString("label.group_consensus"));
+    showGroupConsensus.addActionListener(new ActionListener()
     {
+
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed(e);
+        showGroupConsensus_actionPerformed(e);
       }
+
     });
-    noColourmenuItem.setText("None");
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    showConsensusHistogram.setText(MessageManager
+            .getString("label.show_consensus_histogram"));
+    showConsensusHistogram.addActionListener(new ActionListener()
     {
+
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        noColourmenuItem_actionPerformed(e);
+        showConsensusHistogram_actionPerformed(e);
       }
+
     });
-    wrapMenuItem.setText("Wrap");
-    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showSequenceLogo.setText(MessageManager
+            .getString("label.show_consensus_logo"));
+    showSequenceLogo.addActionListener(new ActionListener()
     {
+
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        wrapMenuItem_actionPerformed(e);
+        showSequenceLogo_actionPerformed(e);
       }
+
     });
-    printMenuItem.setText("Print ...");
-    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    normaliseSequenceLogo.setText(MessageManager
+            .getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo.addActionListener(new ActionListener()
     {
+
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        printMenuItem_actionPerformed(e);
+        normaliseSequenceLogo_actionPerformed(e);
       }
+
     });
-    renderGapsMenuItem.setText("Show Gaps");
-    renderGapsMenuItem.setState(true);
-    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    applyAutoAnnotationSettings.setText(MessageManager
+            .getString("label.apply_all_groups"));
+    applyAutoAnnotationSettings.setState(false);
+    applyAutoAnnotationSettings.setVisible(true);
+    applyAutoAnnotationSettings.addActionListener(new ActionListener()
     {
+
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        renderGapsMenuItem_actionPerformed(e);
+        applyAutoAnnotationSettings_actionPerformed(e);
       }
+
     });
-    findMenuItem.setText("Find...");
-    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_F,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    findMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        findMenuItem_actionPerformed(e);
+        nucleotideColour_actionPerformed(e);
       }
     });
-    abovePIDThreshold.setText("Above Identity Threshold");
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+
+    tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
+    tcoffeeColour.setEnabled(false);
+    tcoffeeColour.addActionListener(new ActionListener()
     {
+
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed(e);
+        tcoffeeColorScheme_actionPerformed(e);
       }
     });
-    showSeqFeatures.setText("Show Sequence Features");
-    showSeqFeatures.addActionListener(new ActionListener()
+
+    deleteGroups
+            .setText(MessageManager.getString("action.undefine_groups"));
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
-      public void actionPerformed(ActionEvent actionEvent)
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
-        showSeqFeatures_actionPerformed(actionEvent);
+        deleteGroups_actionPerformed(e);
       }
     });
-    nucleotideColour.setText("Nucleotide");
-    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    createGroup.setText(MessageManager.getString("action.create_groups"));
+    createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    createGroup.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        nucleotideColour_actionPerformed(e);
+        createGroup_actionPerformed(e);
       }
     });
-    deleteGroups.setText("Undefine groups");
-    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    deleteGroups.addActionListener(new java.awt.event.ActionListener()
+    unGroup.setText(MessageManager.getString("action.remove_group"));
+    unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
+    unGroup.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        deleteGroups_actionPerformed(e);
+        unGroup_actionPerformed(e);
       }
     });
-    copy.setText("Copy");
+    copy.setText(MessageManager.getString("action.copy"));
     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_C,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
 
     copy.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         copy_actionPerformed(e);
       }
     });
-    cut.setText("Cut");
+    cut.setText(MessageManager.getString("action.cut"));
     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_X,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     cut.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cut_actionPerformed(e);
       }
     });
-    delete.setText("Delete");
-    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_BACK_SPACE, 0, false));
+    delete.setText(MessageManager.getString("action.delete"));
     delete.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         delete_actionPerformed(e);
       }
     });
-    pasteMenu.setText("Paste");
-    pasteNew.setText("To New Alignment");
+    pasteMenu.setText(MessageManager.getString("action.paste"));
+    pasteNew.setText(MessageManager.getString("label.to_new_alignment"));
     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_V,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
-        java.awt.event.KeyEvent.SHIFT_MASK, false));
+            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.SHIFT_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pasteNew_actionPerformed(e);
       }
     });
-    pasteThis.setText("Add To This Alignment");
+    pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
     pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_V,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pasteThis_actionPerformed(e);
       }
     });
-    applyToAllGroups.setText("Apply Colour To All Groups");
+    applyToAllGroups.setText(MessageManager
+            .getString("label.apply_colour_to_all_groups"));
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         applyToAllGroups_actionPerformed(e);
@@ -865,26 +1479,31 @@ public class GAlignFrame
     });
     createPNG.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         createPNG(null);
       }
     });
-    createPNG.setActionCommand("Save As PNG Image");
+    createPNG.setActionCommand(MessageManager
+            .getString("label.save_png_image"));
     createPNG.setText("PNG");
-    font.setText("Font...");
+    font.setText(MessageManager.getString("action.font"));
     font.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         font_actionPerformed(e);
       }
     });
 
-    seqLimits.setText("Show Sequence Limits");
+    seqLimits.setText(MessageManager
+            .getString("label.show_sequence_limits"));
     seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
     seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         seqLimit_actionPerformed(e);
@@ -893,24 +1512,30 @@ public class GAlignFrame
     epsFile.setText("EPS");
     epsFile.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         createEPS(null);
       }
     });
-    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load Associated Tree");
+    LoadtreeMenuItem.setActionCommand(MessageManager
+            .getString("label.load_tree_for_sequence_set"));
+    LoadtreeMenuItem.setText(MessageManager
+            .getString("label.load_associated_tree"));
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         LoadtreeMenuItem_actionPerformed(e);
       }
     });
+
     scaleAbove.setVisible(false);
-    scaleAbove.setText("Scale Above");
+    scaleAbove.setText(MessageManager.getString("action.scale_above"));
     scaleAbove.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         scaleAbove_actionPerformed(e);
@@ -918,9 +1543,10 @@ public class GAlignFrame
     });
     scaleLeft.setVisible(false);
     scaleLeft.setSelected(true);
-    scaleLeft.setText("Scale Left");
+    scaleLeft.setText(MessageManager.getString("action.scale_left"));
     scaleLeft.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         scaleLeft_actionPerformed(e);
@@ -928,249 +1554,411 @@ public class GAlignFrame
     });
     scaleRight.setVisible(false);
     scaleRight.setSelected(true);
-    scaleRight.setText("Scale Right");
+    scaleRight.setText(MessageManager.getString("action.scale_right"));
     scaleRight.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         scaleRight_actionPerformed(e);
       }
     });
-    modifyPID.setText("Modify Identity Threshold...");
-    modifyPID.addActionListener(new java.awt.event.ActionListener()
+    centreColumnLabelsMenuItem.setVisible(true);
+    centreColumnLabelsMenuItem.setState(false);
+    centreColumnLabelsMenuItem.setText(MessageManager
+            .getString("label.centre_column_labels"));
+    centreColumnLabelsMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                centreColumnLabels_actionPerformed(e);
+              }
+            });
+    followHighlightMenuItem.setVisible(true);
+    followHighlightMenuItem.setState(true);
+    followHighlightMenuItem.setText(MessageManager
+            .getString("label.automatic_scrolling"));
+    followHighlightMenuItem.addActionListener(new ActionListener()
     {
+
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        modifyPID_actionPerformed(e);
+        followHighlight_actionPerformed();
       }
+
     });
-    modifyConservation.setText("Modify Conservation Threshold...");
-    modifyConservation.addActionListener(new java.awt.event.ActionListener()
+
+    modifyPID.setText(MessageManager
+            .getString("label.modify_identity_thereshold"));
+    modifyPID.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        modifyConservation_actionPerformed(e);
+        modifyPID_actionPerformed(e);
       }
     });
-    sortByTreeMenu.setText("By Tree Order");
-    sort.setText("Sort");
+    modifyConservation.setText(MessageManager
+            .getString("label.modify_conservation_thereshold"));
+    modifyConservation
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                modifyConservation_actionPerformed(e);
+              }
+            });
+    sortByTreeMenu
+            .setText(MessageManager.getString("action.by_tree_order"));
+    sort.setText(MessageManager.getString("action.sort"));
     sort.addMenuListener(new MenuListener()
     {
+      @Override
       public void menuSelected(MenuEvent e)
       {
         buildTreeMenu();
       }
 
+      @Override
       public void menuDeselected(MenuEvent e)
       {
       }
 
+      @Override
       public void menuCanceled(MenuEvent e)
       {
       }
     });
-    sortByAnnotScore.setText("by Score");
+    sortByAnnotScore.setText(MessageManager
+            .getString("label.sort_by_score"));
     sort.add(sortByAnnotScore);
-    sortByAnnotScore.addMenuListener(
-            new javax.swing.event.MenuListener() {
-              
-                public void menuCanceled(MenuEvent e)
-                {
-                }
+    sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+    {
 
-                public void menuDeselected(MenuEvent e)
-                {
-                }
+      @Override
+      public void menuCanceled(MenuEvent e)
+      {
+      }
 
-                public void menuSelected(MenuEvent e)
-                {
-                  buildSortByAnnotationScoresMenu();
-                }
-              }
-              );
+      @Override
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      @Override
+      public void menuSelected(MenuEvent e)
+      {
+        buildSortByAnnotationScoresMenu();
+      }
+    });
     sortByAnnotScore.setVisible(false);
-    
-    calculate.setText("Calculate Tree");
 
-    jMenu2.setText("Export Image");
-    padGapsMenuitem.setText("Pad Gaps");
-    padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    calculateTree
+            .setText(MessageManager.getString("action.calculate_tree"));
+
+    jMenu2.setText(MessageManager.getString("label.export_image"));
+    padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
+    padGapsMenuitem.setState(jalview.bin.Cache
+            .getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         padGapsMenuitem_actionPerformed(e);
       }
     });
     vamsasStore.setVisible(false);
-    vamsasStore.setText("VAMSAS store");
+    vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
     vamsasStore.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         vamsasStore_actionPerformed(e);
       }
     });
-    showTranslation.setText("Translate cDNA");
+    showTranslation.setText(MessageManager
+            .getString("label.translate_cDNA"));
     showTranslation.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showTranslation_actionPerformed(e);
       }
     });
-    extractScores.setText("Extract Scores...");
+    extractScores.setText(MessageManager.getString("label.extract_scores")
+            + "...");
     extractScores.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         extractScores_actionPerformed(e);
       }
     });
-    extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based score extraction
-    showProducts.setText("Get Cross References");
-    /*showProducts.addActionListener(new ActionListener()
-    {
-
-      public void actionPerformed(ActionEvent e)
-      {
-        showProducts_actionPerformed(e);
-      }
-    });*/
-    featureSettings.setText("Feature Settings...");
-    featureSettings.addActionListener(new ActionListener()
+    extractScores.setVisible(true); // JBPNote: TODO: make gui for regex based
+    // score extraction
+    showProducts.setText(MessageManager.getString("label.get_cross_refs"));
+    /*
+     * showProducts.addActionListener(new ActionListener() {
+     * 
+     * public void actionPerformed(ActionEvent e) {
+     * showProducts_actionPerformed(e); } });
+     */
+    openFeatureSettings.setText(MessageManager
+            .getString("label.feature_settings"));
+    openFeatureSettings.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         featureSettings_actionPerformed(e);
       }
     });
-    fetchSequence.setText("Fetch Sequence(s)...");
+    fetchSequence
+            .setText(MessageManager.getString("label.fetch_sequences"));
     fetchSequence.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         fetchSequence_actionPerformed(e);
       }
     });
 
-    annotationColour.setText("By Annotation...");
+    annotationColour.setText(MessageManager
+            .getString("action.by_annotation"));
     annotationColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         annotationColour_actionPerformed(e);
       }
     });
-    associatedData.setText("Load Features / Annotations");
+
+    rnahelicesColour.setText(MessageManager
+            .getString("action.by_rna_helixes"));
+    rnahelicesColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        rnahelicesColour_actionPerformed(e);
+      }
+    });
+
+    associatedData.setText(MessageManager
+            .getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         associatedData_actionPerformed(e);
       }
     });
-    autoCalculate.setText("Autocalculate Consensus");
-    autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.setText(MessageManager
+            .getString("label.autocalculate_consensus"));
+    autoCalculate.setState(jalview.bin.Cache.getDefault(
+            "AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         autoCalculate_actionPerformed(e);
       }
     });
-    addSequenceMenu.setText("Add Sequences");
-    addFromFile.setText("From File");
+    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()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortByTreeOption_actionPerformed(e);
+      }
+    });
+
+    listenToViewSelections.setText(MessageManager
+            .getString("label.listen_for_selections"));
+    listenToViewSelections
+            .setToolTipText("<html>"
+                    + MessageManager
+                            .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+    listenToViewSelections.setState(false);
+    listenToViewSelections.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        listenToViewSelections_actionPerformed(e);
+      }
+    });
+
+    addSequenceMenu
+            .setText(MessageManager.getString("label.add_sequences"));
+    addFromFile.setText(MessageManager.getString("label.from_file"));
     addFromFile.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         addFromFile_actionPerformed(e);
       }
     });
-    addFromText.setText("From Textbox");
+    addFromText.setText(MessageManager.getString("label.from_textbox"));
     addFromText.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         addFromText_actionPerformed(e);
       }
     });
-    addFromURL.setText("From URL");
+    addFromURL.setText(MessageManager.getString("label.from_url"));
     addFromURL.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         addFromURL_actionPerformed(e);
       }
     });
-    exportFeatures.setText("Export Features...");
+    exportFeatures.setText(MessageManager
+            .getString("label.export_features"));
     exportFeatures.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         exportFeatures_actionPerformed(e);
       }
     });
-    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.setText(MessageManager
+            .getString("label.export_annotations"));
     exportAnnotations.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         exportAnnotations_actionPerformed(e);
       }
     });
     statusPanel.setLayout(gridLayout1);
-    jMenu3.setText("Show");
-    showAllSeqs.setText("All Sequences");
+    jMenu3.setText(MessageManager.getString("action.show"));
+    showAllSeqs.setText(MessageManager.getString("label.all_sequences"));
+    showAllSeqs.setToolTipText(MessageManager
+            .getString("label.toggle_sequence_visibility"));
     showAllSeqs.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showAllSeqs_actionPerformed(e);
       }
     });
-    showAllColumns.setText("All Columns");
+    showAllColumns.setText(MessageManager.getString("label.all_columns"));
+    showAllColumns.setToolTipText(MessageManager
+            .getString("label.toggle_columns_visibility"));
     showAllColumns.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showAllColumns_actionPerformed(e);
       }
     });
-    hideMenu.setText("Hide");
-    hideSelSequences.setText("Selected Sequences");
+    hideMenu.setText(MessageManager.getString("action.hide"));
+    hideSelSequences.setText(MessageManager
+            .getString("label.selected_sequences"));
+    hideSelSequences.setToolTipText(MessageManager
+            .getString("label.toggle_sequence_visibility"));
     hideSelSequences.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hideSelSequences_actionPerformed(e);
       }
     });
-    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.setText(MessageManager
+            .getString("label.selected_columns"));
+    hideSelColumns.setToolTipText(MessageManager
+            .getString("label.toggle_columns_visibility"));
     hideSelColumns.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hideSelColumns_actionPerformed(e);
       }
     });
-    hiddenMarkers.setText("Show Hidden Markers");
+    hideAllSelection.setText(MessageManager
+            .getString("label.selected_region"));
+    hideAllSelection.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideAllSelection_actionPerformed(e);
+      }
+    });
+    // TODO: should be hidden if no selection exists.
+    hideAllButSelection.setText(MessageManager
+            .getString("label.all_but_selected_region"));
+    hideAllButSelection.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hideAllButSelection_actionPerformed(e);
+      }
+    });
+    showAllhidden.setText(MessageManager
+            .getString("label.all_sequences_columns"));
+    showAllhidden.setToolTipText(MessageManager
+            .getString("label.toggles_visibility_hidden_selected_regions"));
+    showAllhidden.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllhidden_actionPerformed(e);
+      }
+    });
+    hiddenMarkers.setText(MessageManager
+            .getString("action.show_hidden_markers"));
     hiddenMarkers.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         hiddenMarkers_actionPerformed(e);
       }
     });
-    invertColSel.setText("Invert Column Selection");
-    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_I,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-        | java.awt.event.KeyEvent.ALT_MASK,
-        false));
+    invertColSel.setText(MessageManager
+            .getString("action.invert_column_selection"));
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_I, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask()
+                    | java.awt.event.KeyEvent.ALT_MASK, false));
     invertColSel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         invertColSel_actionPerformed(e);
@@ -1178,6 +1966,7 @@ public class GAlignFrame
     });
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         JTabbedPane pane = (JTabbedPane) evt.getSource();
@@ -1187,6 +1976,7 @@ public class GAlignFrame
     });
     tabbedPane.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         tabbedPane_mousePressed(e);
@@ -1194,100 +1984,119 @@ public class GAlignFrame
     });
     tabbedPane.addFocusListener(new FocusAdapter()
     {
+      @Override
       public void focusGained(FocusEvent e)
       {
         tabbedPane_focusGained(e);
       }
     });
-    save.setText("Save");
-    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    save.setText(MessageManager.getString("action.save"));
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_S, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     save.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         save_actionPerformed(e);
       }
     });
     reload.setEnabled(false);
-    reload.setText("Reload");
+    reload.setText(MessageManager.getString("action.reload"));
     reload.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         reload_actionPerformed(e);
       }
     });
-    newView.setText("New View");
-    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    newView.setText(MessageManager.getString("action.new_view"));
+    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_T, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
     newView.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         newView_actionPerformed(e);
       }
     });
-    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
-                              +
-        "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
-    textColour.setText("Colour Text ...");
+    tabbedPane.setToolTipText("<html><i>"
+            + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+            + "</i></html>");
+    textColour.setText(MessageManager.getString("label.colour_text")
+            + "...");
     textColour.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         textColour_actionPerformed(e);
       }
     });
-    formatMenu.setText("Format");
-    selectMenu.setText("Select");
-    idRightAlign.setText("Right Align Sequence Id");
+    formatMenu.setText(MessageManager.getString("action.format"));
+    selectMenu.setText(MessageManager.getString("action.select"));
+    idRightAlign.setText(MessageManager
+            .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         idRightAlign_actionPerformed(e);
       }
     });
     gatherViews.setEnabled(false);
-    gatherViews.setText("Gather Views");
-    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_G, 0, false));
+    gatherViews.setText(MessageManager.getString("action.gather_views"));
+    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_G, 0, false));
     gatherViews.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         gatherViews_actionPerformed(e);
       }
     });
     expandViews.setEnabled(false);
-    expandViews.setText("Expand Views");
-    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_X, 0, false));
+    expandViews.setText(MessageManager.getString("action.expand_views"));
+    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_X, 0, false));
     expandViews.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         expandViews_actionPerformed(e);
       }
     });
-    pageSetup.setText("Page Setup ...");
+    pageSetup
+            .setText(MessageManager.getString("action.page_setup") + "...");
     pageSetup.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         pageSetup_actionPerformed(e);
       }
     });
-    alignmentProperties.setText("Alignment Properties...");
+    alignmentProperties.setText(MessageManager
+            .getString("label.alignment_props") + "...");
     alignmentProperties.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         alignmentProperties();
       }
     });
-
+    tooltipSettingsMenu.setText(MessageManager
+            .getString("label.sequence_id_tooltip"));
+    autoAnnMenu.setText(MessageManager
+            .getString("label.autocalculated_annotation"));
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(selectMenu);
@@ -1327,6 +2136,11 @@ public class GAlignFrame
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
+    // dont add these yet in the CVS build - they cannot be undone!
+    // Excluded from Jalview 2.5 release - undo needs to be implemented.
+    // editMenu.add(justifyLeftMenuItem);
+    // editMenu.add(justifyRightMenuItem);
+    // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
     viewMenu.add(newView);
     viewMenu.add(expandViews);
@@ -1335,10 +2149,26 @@ public class GAlignFrame
     viewMenu.add(jMenu3);
     viewMenu.add(hideMenu);
     viewMenu.addSeparator();
+    viewMenu.add(followHighlightMenuItem);
     viewMenu.add(annotationPanelMenuItem);
+    viewMenu.add(showAllAnnotations);
+    viewMenu.add(hideAllAnnotations);
+    autoAnnMenu.add(applyAutoAnnotationSettings);
+    autoAnnMenu.add(showConsensusHistogram);
+    autoAnnMenu.add(showSequenceLogo);
+    autoAnnMenu.add(normaliseSequenceLogo);
+    autoAnnMenu.addSeparator();
+    autoAnnMenu.add(showGroupConservation);
+    autoAnnMenu.add(showGroupConsensus);
+    viewMenu.add(autoAnnMenu);
     viewMenu.addSeparator();
     viewMenu.add(showSeqFeatures);
-    viewMenu.add(featureSettings);
+    // viewMenu.add(showSeqFeaturesHeight);
+
+    viewMenu.add(openFeatureSettings);
+    tooltipSettingsMenu.add(showDbRefsMenuitem);
+    tooltipSettingsMenu.add(showNpFeatsMenuitem);
+    viewMenu.add(tooltipSettingsMenu);
     viewMenu.addSeparator();
     viewMenu.add(alignmentProperties);
     viewMenu.addSeparator();
@@ -1358,6 +2188,10 @@ public class GAlignFrame
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
+    colourMenu.add(purinePyrimidineColour);
+    colourMenu.add(RNAInteractionColour);
+    // colourMenu.add(covariationColour);
+    colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
@@ -1365,8 +2199,9 @@ public class GAlignFrame
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
+    colourMenu.add(rnahelicesColour);
     calculateMenu.add(sort);
-    calculateMenu.add(calculate);
+    calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
@@ -1374,20 +2209,19 @@ public class GAlignFrame
     calculateMenu.add(showTranslation);
     calculateMenu.add(showProducts);
     calculateMenu.add(autoCalculate);
+    calculateMenu.add(sortByTree);
     calculateMenu.addSeparator();
     calculateMenu.add(extractScores);
-    webServiceNoServices = new JMenuItem("<No Services>");
+    webServiceNoServices = new JMenuItem(
+            MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
+    sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
     sort.add(sortByTreeMenu);
-    calculate.add(averageDistanceTreeMenuItem);
-    calculate.add(neighbourTreeMenuItem);
-    calculate.add(avDistanceTreeBlosumMenuItem);
-    calculate.add(njTreeBlosumMenuItem);
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
@@ -1399,8 +2233,12 @@ public class GAlignFrame
     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
     jMenu3.add(showAllColumns);
     jMenu3.add(showAllSeqs);
+    jMenu3.add(showAllhidden);
     hideMenu.add(hideSelColumns);
     hideMenu.add(hideSelSequences);
+    hideMenu.add(hideAllSelection);
+    hideMenu.add(hideAllButSelection);
+
     formatMenu.add(font);
     formatMenu.addSeparator();
     formatMenu.add(wrapMenuItem);
@@ -1414,19 +2252,166 @@ public class GAlignFrame
     formatMenu.add(viewTextMenuItem);
     formatMenu.add(colourTextMenuItem);
     formatMenu.add(renderGapsMenuItem);
+    formatMenu.add(centreColumnLabelsMenuItem);
+    formatMenu.add(showNonconservedMenuItem);
     selectMenu.add(findMenuItem);
     selectMenu.addSeparator();
     selectMenu.add(selectAllSequenceMenuItem);
     selectMenu.add(deselectAllSequenceMenuItem);
     selectMenu.add(invertSequenceMenuItem);
     selectMenu.add(invertColSel);
+    selectMenu.add(createGroup);
+    selectMenu.add(unGroup);
+    selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
+    calculateMenu.add(expandAlignment);
+    // TODO - determine if the listenToViewSelections button is needed : see bug
+    // JAL-574
+    // selectMenu.addSeparator();
+    // selectMenu.add(listenToViewSelections);
   }
 
-  protected void showProducts_actionPerformed(ActionEvent e)
+  /**
+   * Action on clicking Show all annotations.
+   */
+  protected void showAllAnnotations_actionPerformed()
+  {
+    setAllAnnotationsVisibility(true);
+  }
+
+  /**
+   * Action on clicking Hide all annotations.
+   */
+  protected void hideAllAnnotations_actionPerformed()
+  {
+    setAllAnnotationsVisibility(false);
+  }
+
+  /**
+   * Set the visibility of all annotations to true or false.
+   * 
+   * @param visible
+   */
+  protected void setAllAnnotationsVisibility(boolean visible)
+  {
+
+  }
+
+  protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void listenToViewSelections_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showAllhidden_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void hideAllButSelection_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void hideAllSelection_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showSequenceLogo_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showGroupConsensus_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showGroupConservation_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showSeqFeaturesHeight_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void followHighlight_actionPerformed()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showNpFeats_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showDbRefs_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
-    
+
+  }
+
+  protected void centreColumnLabels_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void showProducts_actionPerformed(ActionEvent e)
+  {
   }
 
   protected void buildSortByAnnotationScoresMenu()
@@ -1542,6 +2527,10 @@ public class GAlignFrame
   {
   }
 
+  protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -1618,6 +2607,18 @@ public class GAlignFrame
   {
   }
 
+  protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /*
+   * protected void covariationColour_actionPerformed(ActionEvent e) { }
+   */
+
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -1654,6 +2655,14 @@ public class GAlignFrame
   {
   }
 
+  protected void createGroup_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void unGroup_actionPerformed(ActionEvent e)
+  {
+  }
+
   protected void copy_actionPerformed(ActionEvent e)
   {
   }
@@ -1701,6 +2710,33 @@ public class GAlignFrame
 
   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
+
+  }
+
+  /**
+   * Template method to handle the 'load T-Coffee scores' menu event.
+   * <p>
+   * Subclasses override this method to provide a custom action.
+   * 
+   * @param event
+   *          The raised event
+   */
+  protected void loadScores_actionPerformed(ActionEvent event)
+  {
+
+  }
+
+  /**
+   * Template method to handle the 'Color T-Coffee scores' menu event.
+   * <p>
+   * Subclasses override this method to provide a custom action.
+   * 
+   * @param event
+   *          The raised event
+   */
+  protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+  {
+
   }
 
   protected void jpred_actionPerformed(ActionEvent e)
@@ -1770,6 +2806,11 @@ public class GAlignFrame
 
   }
 
+  public void rnahelicesColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   public void associatedData_actionPerformed(ActionEvent e)
   {
 
@@ -1780,6 +2821,11 @@ public class GAlignFrame
 
   }
 
+  public void sortByTreeOption_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   public void showAllSeqs_actionPerformed(ActionEvent e)
   {
 
@@ -1879,7 +2925,7 @@ public class GAlignFrame
   {
 
   }
-  
+
   public void pageSetup_actionPerformed(ActionEvent e)
   {
 
@@ -1889,4 +2935,10 @@ public class GAlignFrame
   {
 
   }
+
+  protected void expand_newalign(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
 }