JAL-1517 update copyright to version 2.8.2
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
index 3cb11e2..5f30b57 100755 (executable)
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+ * 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.
+ *  
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.jbgui;
 
-import javax.swing.*;
-import java.awt.event.*;
-import java.awt.*;
+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 alignMenu = 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 deselectAllColumnsMenuItem = new JMenuItem();
+
   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
+
   protected JMenuItem remove2RightMenuItem = new JMenuItem();
+
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
+
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-  protected JMenuItem setGapCharMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+
+  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();
-  protected JMenuItem clustalAlignMenuItem = new JMenuItem();
-  protected JMenuItem msaAlignMenuItem = new JMenuItem();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   public JLabel statusBar = new JLabel();
-  protected JMenu saveAlignmentMenu = new JMenu();
+
+  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 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();
-  protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+
+  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();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem printMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
   JMenuItem findMenuItem = new JMenuItem();
-  JMenu searchMenu = new JMenu();
-  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
-  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+
+  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 jMenu1 = new JMenu();
+
+  JMenu pasteMenu = new JMenu();
+
   JMenuItem pasteNew = new JMenuItem();
+
   JMenuItem pasteThis = new JMenuItem();
-  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+
   JMenuItem createPNG = new JMenuItem();
+
   protected JMenuItem font = new JMenuItem();
-  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
   JMenuItem epsFile = new JMenuItem();
+
   JMenuItem LoadtreeMenuItem = new JMenuItem();
-  JMenuItem jpred = new JMenuItem();
-  protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
-  JMenuItem modifyPID = new JMenuItem();
-  JMenuItem modifyConservation = 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();
-  public GAlignFrame()
-  {
 
+  protected JMenu sort = 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 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 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
     {
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
-      JMenuItem item;
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
-        saveAlignmentMenu.add( item );
-        item.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            saveAs_actionPerformed(e);
-          }
-        });
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      {
+        JMenuItem item = new JMenuItem(
+                jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -127,16 +374,78 @@ public class GAlignFrame extends JInternalFrame
           }
         });
 
-        outputTextboxMenu.add( item );
+        outputTextboxMenu.add(item);
       }
-
+    } catch (Exception e)
+    {
     }
-    catch(Exception e)
+
+    if (!new jalview.util.Platform().isAMac())
     {
-      e.printStackTrace();
+      closeMenuItem.setMnemonic('C');
+      outputTextboxMenu.setMnemonic('T');
+      undoMenuItem.setMnemonic('Z');
+      redoMenuItem.setMnemonic('0');
+      copy.setMnemonic('C');
+      cut.setMnemonic('U');
+      pasteMenu.setMnemonic('P');
+      reload.setMnemonic('R');
     }
 
-    ButtonGroup colours = new ButtonGroup();
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+                userColours.nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+        {
+          public void mousePressed(MouseEvent evt)
+          {
+            if (evt.isControlDown()
+                    || SwingUtilities.isRightMouseButton(evt))
+            {
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+              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());
+                colourMenu.remove(radioItem);
+              }
+              else
+              {
+                radioItem.addActionListener(new ActionListener()
+                {
+                  public void actionPerformed(ActionEvent evt)
+                  {
+                    userDefinedColour_actionPerformed(evt);
+                  }
+                });
+              }
+            }
+          }
+        });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.insert(radioItem, 15);
+        colours.add(radioItem);
+      }
+    }
     colours.add(noColourmenuItem);
     colours.add(clustalColour);
     colours.add(zappoColour);
@@ -150,652 +459,1463 @@ public class GAlignFrame extends JInternalFrame
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
+    colours.add(purinePyrimidineColour);
+    // colours.add(covariationColour);
+    colours.add(tcoffeeColour);
+    colours.add(RNAInteractionColour);
+    setColourSelected(jalview.bin.Cache
+            .getDefault("DEFAULT_COLOUR", "None"));
+
+  }
+
+  public void setColourSelected(String defaultColour)
+  {
+
+    if (defaultColour != null)
+    {
+      int index = ColourSchemeProperty
+              .getColourIndexFromName(defaultColour);
+
+      switch (index)
+      {
+      case ColourSchemeProperty.CLUSTAL:
+        clustalColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.BLOSUM:
+        BLOSUM62Colour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.PID:
+        PIDColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.ZAPPO:
+        zappoColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.TAYLOR:
+        taylorColour.setSelected(true);
+        break;
+
+      case ColourSchemeProperty.HYDROPHOBIC:
+        hydrophobicityColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.HELIX:
+        helixColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.STRAND:
+        strandColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.TURN:
+        turnColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.BURIED:
+        buriedColour.setSelected(true);
+
+        break;
+
+      case ColourSchemeProperty.NUCLEOTIDE:
+        nucleotideColour.setSelected(true);
+
+        break;
+
+      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;
+
+      }
+    }
+
   }
+
   private void jbInit() throws Exception
   {
-    fileMenu.setMnemonic('F');
-    fileMenu.setText("File");
-    saveAlignmentMenu.setMnemonic('L');
-    saveAlignmentMenu.setText("Save alignment to local file");
-    closeMenuItem.setMnemonic('C');
-    closeMenuItem.setText("Close");
+    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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveAs_actionPerformed(e);
+      }
+    });
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        closeMenuItem_actionPerformed(e);
+        closeMenuItem_actionPerformed(false);
+      }
+    });
+    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()
+            {
+              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()
+            {
+              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()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                invertSequenceMenuItem_actionPerformed(e);
+              }
+            });
+    grpsFromSelection.setText(MessageManager.getString("action.make_groups_selection"));
+    grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        makeGrpsFromSelection_actionPerformed(e);
+      }
+    });
+    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)
+      {
+        expand_newalign(e);
+      }
+    });
+    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()
+            {
+              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()
+            {
+              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()
+            {
+              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()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                removeAllGapsMenuItem_actionPerformed(e);
+              }
+            });
+    justifyLeftMenuItem.setText(MessageManager.getString("action.left_justify_alignment"));
+    justifyLeftMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                justifyLeftMenuItem_actionPerformed(e);
+              }
+            });
+    justifyRightMenuItem.setText(MessageManager.getString("action.right_justify_alignment"));
+    justifyRightMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                justifyRightMenuItem_actionPerformed(e);
+              }
+            });
+    viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
+    viewBoxesMenuItem.setState(true);
+    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        viewBoxesMenuItem_actionPerformed(e);
+      }
+    });
+    viewTextMenuItem.setText(MessageManager.getString("action.text"));
+    viewTextMenuItem.setState(true);
+    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        viewTextMenuItem_actionPerformed(e);
+      }
+    });
+    showNonconservedMenuItem.setText(MessageManager.getString("label.show_non_conversed"));
+    showNonconservedMenuItem.setState(false);
+    showNonconservedMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                showUnconservedMenuItem_actionPerformed(e);
+              }
+            });
+    sortPairwiseMenuItem.setText(MessageManager.getString("action.by_pairwise_id"));
+    sortPairwiseMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                sortPairwiseMenuItem_actionPerformed(e);
+              }
+            });
+    sortIDMenuItem.setText(MessageManager.getString("action.by_id"));
+    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortIDMenuItem_actionPerformed(e);
+      }
+    });
+    sortLengthMenuItem.setText(MessageManager.getString("action.by_length"));
+    sortLengthMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                sortLengthMenuItem_actionPerformed(e);
+              }
+            });
+    sortGroupMenuItem.setText(MessageManager.getString("action.by_group"));
+    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sortGroupMenuItem_actionPerformed(e);
+      }
+    });
+    removeRedundancyMenuItem.setText(MessageManager.getString("action.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(MessageManager.getString("action.pairwise_alignment"));
+    pairwiseAlignmentMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                pairwiseAlignmentMenuItem_actionPerformed(e);
+              }
+            });
+    PCAMenuItem.setText(MessageManager.getString("label.principal_component_analysis"));
+    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PCAMenuItem_actionPerformed(e);
+      }
+    });
+    averageDistanceTreeMenuItem
+            .setText(MessageManager.getString("label.average_distance_identity"));
+    averageDistanceTreeMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                averageDistanceTreeMenuItem_actionPerformed(e);
+              }
+            });
+    neighbourTreeMenuItem.setText(MessageManager.getString("label.neighbour_joining_identity"));
+    neighbourTreeMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              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(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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        clustalColour_actionPerformed(e);
+      }
+    });
+    zappoColour.setText(MessageManager.getString("label.zappo"));
+    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zappoColour_actionPerformed(e);
+      }
+    });
+    taylorColour.setText(MessageManager.getString("label.taylor"));
+    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        taylorColour_actionPerformed(e);
+      }
+    });
+    hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+    hydrophobicityColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                hydrophobicityColour_actionPerformed(e);
+              }
+            });
+    helixColour.setText(MessageManager.getString("label.helix_propensity"));
+    helixColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        helixColour_actionPerformed(e);
+      }
+    });
+    strandColour.setText(MessageManager.getString("label.strand_propensity"));
+    strandColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        strandColour_actionPerformed(e);
+      }
+    });
+    turnColour.setText(MessageManager.getString("label.turn_propensity"));
+    turnColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        turnColour_actionPerformed(e);
+      }
+    });
+    buriedColour.setText(MessageManager.getString("label.buried_index"));
+    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        buriedColour_actionPerformed(e);
+      }
+    });
+    userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        userDefinedColour_actionPerformed(e);
+      }
+    });
+    PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PIDColour_actionPerformed(e);
+      }
+    });
+    BLOSUM62Colour.setText(MessageManager.getString("label.blosum62_score"));
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        BLOSUM62Colour_actionPerformed(e);
+      }
+    });
+    nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideColour_actionPerformed(e);
+      }
+    });
+
+    purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+    purinePyrimidineColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                purinePyrimidineColour_actionPerformed(e);
+              }
+            });
+    
+    RNAInteractionColour.setText("RNA Interaction type");
+    RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+            {
+              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()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                avTreeBlosumMenuItem_actionPerformed(e);
+              }
+            });
+    njTreeBlosumMenuItem.setText(MessageManager.getString("label.neighbour_blosum62"));
+    njTreeBlosumMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                njTreeBlosumMenuItem_actionPerformed(e);
+              }
+            });
+    annotationPanelMenuItem.setActionCommand("");
+    annotationPanelMenuItem.setText(MessageManager.getString("label.show_annotations"));
+    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
+            "SHOW_ANNOTATIONS", true));
+    annotationPanelMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                annotationPanelMenuItem_actionPerformed(e);
+              }
+            });
+    colourTextMenuItem.setText(MessageManager.getString("label.colour_text"));
+    colourTextMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                colourTextMenuItem_actionPerformed(e);
+              }
+            });
+    htmlMenuItem.setText(MessageManager.getString("label.html"));
+    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        htmlMenuItem_actionPerformed(e);
+      }
+    });
+    overviewMenuItem.setText(MessageManager.getString("label.overview_window"));
+    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        overviewMenuItem_actionPerformed(e);
+      }
+    });
+    undoMenuItem.setEnabled(false);
+    undoMenuItem.setText(MessageManager.getString("action.undo"));
+    undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_Z, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        undoMenuItem_actionPerformed(e);
+      }
+    });
+    redoMenuItem.setEnabled(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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        redoMenuItem_actionPerformed(e);
+      }
+    });
+    conservationMenuItem.setText(MessageManager.getString("action.by_conservation"));
+    conservationMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                conservationMenuItem_actionPerformed(e);
+              }
+            });
+    noColourmenuItem.setText(MessageManager.getString("label.none"));
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed(e);
       }
     });
-    editMenu.setText("Edit");
-    viewMenu.setText("View");
-    colourMenu.setText("Colour");
-    calculateMenu.setText("Calculate");
-    alignMenu.setText("Web Service");
-    selectAllSequenceMenuItem.setText("Select all");
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    wrapMenuItem.setText(MessageManager.getString("label.wrap"));
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        selectAllSequenceMenuItem_actionPerformed(e);
+        wrapMenuItem_actionPerformed(e);
       }
     });
-    deselectAllSequenceMenuItem.setText("Clear selection");
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        deselectAllSequenceMenuItem_actionPerformed(e);
+        printMenuItem_actionPerformed(e);
       }
     });
-    invertSequenceMenuItem.setText("Invert sequence selection");
-    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    renderGapsMenuItem.setText(MessageManager.getString("action.show_gaps"));
+    renderGapsMenuItem.setState(true);
+    renderGapsMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              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.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        invertSequenceMenuItem_actionPerformed(e);
+        findMenuItem_actionPerformed(e);
       }
     });
-    deselectAllColumnsMenuItem.setText("Deselect all columns");
-    deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    abovePIDThreshold.setText(MessageManager.getString("label.above_identity_threshold"));
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        deselectAllColumnsMenuItem_actionPerformed(e);
+        abovePIDThreshold_actionPerformed(e);
       }
     });
-    remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
-    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showSeqFeatures.setText(MessageManager.getString("label.show_sequence_features"));
+    showSeqFeatures.addActionListener(new ActionListener()
     {
-      public void actionPerformed(ActionEvent e)
+      public void actionPerformed(ActionEvent actionEvent)
       {
-        remove2LeftMenuItem_actionPerformed(e);
+        showSeqFeatures_actionPerformed(actionEvent);
       }
     });
-    remove2RightMenuItem.setText("Remove sequence -> right of selected column");
-    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
+    /*
+     * 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()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        remove2RightMenuItem_actionPerformed(e);
+        showDbRefs_actionPerformed(e);
       }
+
     });
-    removeGappedColumnMenuItem.setText("Remove gapped columns");
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showNpFeatsMenuitem.setText(MessageManager.getString("label.show_non_positional_features"));
+    showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        removeGappedColumnMenuItem_actionPerformed(e);
+        showNpFeats_actionPerformed(e);
       }
+
     });
-    removeAllGapsMenuItem.setText("Remove all gaps");
-    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showGroupConservation.setText(MessageManager.getString("label.group_conservation"));
+    showGroupConservation.addActionListener(new ActionListener()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        removeAllGapsMenuItem_actionPerformed(e);
+        showGroupConservation_actionPerformed(e);
       }
+
     });
-    setGapCharMenuItem.setText("Set gap character to \".\"");
-    setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    showGroupConsensus.setText(MessageManager.getString("label.group_consensus"));
+    showGroupConsensus.addActionListener(new ActionListener()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        setGapCharMenuItem_actionPerformed(e);
+        showGroupConsensus_actionPerformed(e);
       }
+
     });
-    viewBoxesMenuItem.setText("Boxes");
-    viewBoxesMenuItem.setState(true);
-    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showConsensusHistogram.setText(MessageManager.getString("label.show_consensus_histogram"));
+    showConsensusHistogram.addActionListener(new ActionListener()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        viewBoxesMenuItem_actionPerformed(e);
+        showConsensusHistogram_actionPerformed(e);
       }
+
     });
-    viewTextMenuItem.setText("Text");
-    viewTextMenuItem.setState(true);
-    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showSequenceLogo.setText(MessageManager.getString("label.show_consensus_logo"));
+    showSequenceLogo.addActionListener(new ActionListener()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        viewTextMenuItem_actionPerformed(e);
+        showSequenceLogo_actionPerformed(e);
       }
+
     });
-    sortPairwiseMenuItem.setText("Sort by pairwise identity");
-    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+    normaliseSequenceLogo.setText(MessageManager.getString("label.norm_consensus_logo"));
+    normaliseSequenceLogo.addActionListener(new ActionListener()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        sortPairwiseMenuItem_actionPerformed(e);
+        normaliseSequenceLogo_actionPerformed(e);
       }
+
     });
-    sortIDMenuItem.setText("Sort by ID");
-    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+    applyAutoAnnotationSettings.setText(MessageManager.getString("label.apply_all_groups"));
+    applyAutoAnnotationSettings.setState(false);
+    applyAutoAnnotationSettings.setVisible(true);
+    applyAutoAnnotationSettings.addActionListener(new ActionListener()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        sortIDMenuItem_actionPerformed(e);
+        applyAutoAnnotationSettings_actionPerformed(e);
       }
+
     });
-    sortGroupMenuItem.setText("Sort by group");
-    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        sortGroupMenuItem_actionPerformed(e);
+        nucleotideColour_actionPerformed(e);
       }
     });
-    removeRedundancyMenuItem.setText("Remove redundancy");
-    removeRedundancyMenuItem.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)
       {
-        removeRedundancyMenuItem_actionPerformed(e);
+        tcoffeeColorScheme_actionPerformed(e);
       }
     });
-    pairwiseAlignmentMenuItem.setText("Pairwise alignments");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.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 e)
       {
-        pairwiseAlignmentMenuItem_actionPerformed(e);
+        deleteGroups_actionPerformed(e);
       }
     });
-    PCAMenuItem.setText("Principal component analysis");
-    PCAMenuItem.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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        PCAMenuItem_actionPerformed(e);
+        createGroup_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText("Average distance tree using PID");
-    averageDistanceTreeMenuItem.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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        averageDistanceTreeMenuItem_actionPerformed(e);
+        unGroup_actionPerformed(e);
       }
     });
-    neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
-    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    copy.setText(MessageManager.getString("action.copy"));
+    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+
+    copy.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        neighbourTreeMenuItem_actionPerformed(e);
+        copy_actionPerformed(e);
       }
     });
-    clustalAlignMenuItem.setText("Clustal alignment");
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    cut.setText(MessageManager.getString("action.cut"));
+    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_X, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    cut.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        clustalAlignMenuItem_actionPerformed(e);
+        cut_actionPerformed(e);
       }
     });
-    msaAlignMenuItem.setText("Muscle alignment");
-    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    delete.setText(MessageManager.getString("action.delete"));
+    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false));
+    delete.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        msaAlignMenuItem_actionPerformed(e);
+        delete_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.setMnemonic('T');
-    outputTextboxMenu.setText("Output alignment via textbox");
-    clustalColour.setSelected(false);
-    clustalColour.setText("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    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));
+    pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        clustalColour_actionPerformed(e);
+        pasteNew_actionPerformed(e);
       }
     });
-    zappoColour.setText("Zappo colour scheme");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    pasteThis.setText(MessageManager.getString("label.to_this_alignment"));
+    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_V, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        zappoColour_actionPerformed(e);
+        pasteThis_actionPerformed(e);
       }
     });
-    taylorColour.setText("Taylor colour scheme");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    applyToAllGroups.setText(MessageManager.getString("label.apply_colour_to_all_groups"));
+    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        taylorColour_actionPerformed(e);
+        applyToAllGroups_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText("By hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+    createPNG.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        hydrophobicityColour_actionPerformed(e);
+        createPNG(null);
       }
     });
-    helixColour.setText("Helix propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
+    createPNG.setActionCommand(MessageManager.getString("label.save_png_image"));
+    createPNG.setText("PNG");
+    font.setText(MessageManager.getString("action.font"));
+    font.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        helixColour_actionPerformed(e);
+        font_actionPerformed(e);
       }
     });
-    strandColour.setText("Strand propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
+
+    seqLimits.setText(MessageManager.getString("label.show_sequence_limits"));
+    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+    seqLimits.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        strandColour_actionPerformed(e);
+        seqLimit_actionPerformed(e);
       }
     });
-    turnColour.setText("Turn propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
+    epsFile.setText("EPS");
+    epsFile.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        turnColour_actionPerformed(e);
+        createEPS(null);
       }
     });
-    buriedColour.setText("Buried index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        buriedColour_actionPerformed(e);
+        LoadtreeMenuItem_actionPerformed(e);
       }
     });
-    userDefinedColour.setText("User defined colours");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+
+    scaleAbove.setVisible(false);
+    scaleAbove.setText(MessageManager.getString("action.scale_above"));
+    scaleAbove.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        userDefinedColour_actionPerformed(e);
+        scaleAbove_actionPerformed(e);
       }
     });
-    PIDColour.setText("Percentage Identity");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    scaleLeft.setVisible(false);
+    scaleLeft.setSelected(true);
+    scaleLeft.setText(MessageManager.getString("action.scale_left"));
+    scaleLeft.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        PIDColour_actionPerformed(e);
+        scaleLeft_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("BLOSUM62 score");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    scaleRight.setVisible(false);
+    scaleRight.setSelected(true);
+    scaleRight.setText(MessageManager.getString("action.scale_right"));
+    scaleRight.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        BLOSUM62Colour_actionPerformed(e);
+        scaleRight_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.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()
+            {
+              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()
     {
+
       public void actionPerformed(ActionEvent e)
       {
-        avTreeBlosumMenuItem_actionPerformed(e);
+        followHighlight_actionPerformed();
       }
+
     });
-    njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
-    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    modifyPID.setText(MessageManager.getString("label.modify_identity_thereshold"));
+    modifyPID.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        njTreeBlosumMenuItem_actionPerformed(e);
+        modifyPID_actionPerformed(e);
       }
     });
-    annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText("Annotation Panel");
-    annotationPanelMenuItem.setState(true);
-    annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
+    modifyConservation.setText(MessageManager.getString("label.modify_conservation_thereshold"));
+    modifyConservation
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              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()
+    {
+      public void menuSelected(MenuEvent e)
+      {
+        buildTreeMenu();
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+    });
+    sortByAnnotScore.setText(MessageManager.getString("label.sort_by_score"));
+    sort.add(sortByAnnotScore);
+    sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener()
+    {
+
+      public void menuCanceled(MenuEvent e)
+      {
+      }
+
+      public void menuDeselected(MenuEvent e)
+      {
+      }
+
+      public void menuSelected(MenuEvent e)
+      {
+        buildSortByAnnotationScoresMenu();
+      }
+    });
+    sortByAnnotScore.setVisible(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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        annotationPanelMenuItem_actionPerformed(e);
+        padGapsMenuitem_actionPerformed(e);
       }
     });
-    colourTextMenuItem.setText("Colour text");
-    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    vamsasStore.setVisible(false);
+    vamsasStore.setText(MessageManager.getString("label.vamsas_store"));
+    vamsasStore.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        colourTextMenuItem_actionPerformed(e);
+        vamsasStore_actionPerformed(e);
       }
     });
-    htmlMenuItem.setText("Output as HTML");
-    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showTranslation.setText(MessageManager.getString("label.translate_cDNA"));
+    showTranslation.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        htmlMenuItem_actionPerformed(e);
+        showTranslation_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText("Overview window");
-    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    extractScores.setText(MessageManager.getString("label.extract_scores") + "...");
+    extractScores.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        overviewMenuItem_actionPerformed(e);
+        extractScores_actionPerformed(e);
       }
     });
-    undoMenuItem.setEnabled(false);
-    undoMenuItem.setMnemonic('Z');
-    undoMenuItem.setText("Undo");
-    undoMenuItem.addActionListener(new java.awt.event.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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        undoMenuItem_actionPerformed(e);
+        featureSettings_actionPerformed(e);
       }
     });
-    redoMenuItem.setEnabled(false);
-    redoMenuItem.setMnemonic('0');
-    redoMenuItem.setText("Redo");
-    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    fetchSequence.setText(MessageManager.getString("label.fetch_sequences"));
+    fetchSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        redoMenuItem_actionPerformed(e);
+        fetchSequence_actionPerformed(e);
       }
     });
-    conservationMenuItem.setText("By conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    annotationColour.setText(MessageManager.getString("action.by_annotation"));
+    annotationColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed(e);
+        annotationColour_actionPerformed(e);
       }
     });
-    noColourmenuItem.setText("None");
-    noColourmenuItem.setSelected(true);
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    rnahelicesColour.setText(MessageManager.getString("action.by_rna_helixes"));
+    rnahelicesColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        noColourmenuItem_actionPerformed(e);
+        rnahelicesColour_actionPerformed(e);
       }
     });
-    wrapMenuItem.setText("Wrap alignment");
-    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    associatedData.setText(MessageManager.getString("label.load_features_annotations"));
+    associatedData.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        wrapMenuItem_actionPerformed(e);
+        associatedData_actionPerformed(e);
       }
     });
-    printMenuItem.setText("Print");
-    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    autoCalculate.setText(MessageManager.getString("label.autocalculate_consensus"));
+    autoCalculate.setState(jalview.bin.Cache.getDefault(
+            "AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        printMenuItem_actionPerformed(e);
+        autoCalculate_actionPerformed(e);
       }
     });
-    renderGapsMenuItem.setText("Render gaps");
-    renderGapsMenuItem.setState(true);
-    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        renderGapsMenuItem_actionPerformed(e);
+        sortByTreeOption_actionPerformed(e);
       }
     });
-    findMenuItem.setText("Find");
-    findMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        findMenuItem_actionPerformed(e);
+        listenToViewSelections_actionPerformed(e);
       }
     });
-    searchMenu.setText("Search");
 
-    abovePIDThreshold.setText("Above PID threshold");
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
-        abovePIDThreshold_actionPerformed(e);
+    addSequenceMenu.setText(MessageManager.getString("label.add_sequences"));
+    addFromFile.setText(MessageManager.getString("label.from_file"));
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
       }
     });
-    sequenceFeatures.setText("Sequence Features");
-    sequenceFeatures.addActionListener(new ActionListener()
+    addFromText.setText(MessageManager.getString("label.from_textbox"));
+    addFromText.addActionListener(new ActionListener()
     {
-      public void actionPerformed(ActionEvent actionEvent)
+      public void actionPerformed(ActionEvent e)
       {
-        sequenceFeatures_actionPerformed(actionEvent);
+        addFromText_actionPerformed(e);
       }
     });
-    nucleotideColour.setText("Nucleotide colours");
-    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    addFromURL.setText(MessageManager.getString("label.from_url"));
+    addFromURL.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        nucleotideColour_actionPerformed(e);
+        addFromURL_actionPerformed(e);
       }
     });
-    deleteGroups.setSelected(false);
-    deleteGroups.setText("Delete all groups");
-    deleteGroups.addActionListener(new java.awt.event.ActionListener()
+    exportFeatures.setText(MessageManager.getString("label.export_features"));
+    exportFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        deleteGroups_actionPerformed(e);
+        exportFeatures_actionPerformed(e);
       }
     });
-    copy.setText("Copy");
-    copy.setMnemonic(KeyEvent.VK_C);
-
-    copy.addActionListener(new java.awt.event.ActionListener()
+    exportAnnotations.setText(MessageManager.getString("label.export_annotations"));
+    exportAnnotations.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        copy_actionPerformed(e);
+        exportAnnotations_actionPerformed(e);
       }
     });
-    cut.setText("Cut");
-    cut.setMnemonic(KeyEvent.VK_X);
-    cut.addActionListener(new java.awt.event.ActionListener()
+    statusPanel.setLayout(gridLayout1);
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        showAllSeqs_actionPerformed(e);
       }
     });
-    delete.setText("Delete");
-    delete.addActionListener(new java.awt.event.ActionListener()
+    showAllColumns.setText(MessageManager.getString("label.all_columns"));
+    showAllColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+    showAllColumns.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        delete_actionPerformed(e);
+        showAllColumns_actionPerformed(e);
       }
     });
-    jMenu1.setMnemonic('V');
-    jMenu1.setText("Paste");
-    pasteNew.setText("to new alignment");
-    pasteNew.addActionListener(new java.awt.event.ActionListener()
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        pasteNew_actionPerformed(e);
+        hideSelSequences_actionPerformed(e);
       }
     });
-    pasteThis.setText("add to this alignment");
-    pasteThis.addActionListener(new java.awt.event.ActionListener()
+    hideSelColumns.setText(MessageManager.getString("label.selected_columns"));
+    hideSelColumns.setToolTipText(MessageManager.getString("label.toggle_columns_visibility"));
+    hideSelColumns.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        pasteThis_actionPerformed(e);
+        hideSelColumns_actionPerformed(e);
       }
     });
-    applyToAllGroups.setText("Apply colour to all groups");
-    applyToAllGroups.setState(true);
-    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+    hideAllSelection.setText(MessageManager.getString("label.selected_region"));
+    hideAllSelection.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        applyToAllGroups_actionPerformed(e);
+        hideAllSelection_actionPerformed(e);
       }
     });
-    createPNG.addActionListener(new java.awt.event.ActionListener()
+    // TODO: should be hidden if no selection exists.
+    hideAllButSelection.setText(MessageManager.getString("label.all_but_selected_region"));
+    hideAllButSelection.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        createPNG_actionPerformed(e);
+        hideAllButSelection_actionPerformed(e);
       }
     });
-    createPNG.setActionCommand("Save as PNG Image");
-    createPNG.setText("Save as PNG Image");
-    font.setText("Change Font");
-    font.addActionListener(new java.awt.event.ActionListener()
+    showAllhidden.setText(MessageManager.getString("label.all_sequences_columns"));
+    showAllhidden
+            .setToolTipText(MessageManager.getString("label.toggles_visibility_hidden_selected_regions"));
+    showAllhidden.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        font_actionPerformed(e);
+        showAllhidden_actionPerformed(e);
       }
     });
-    fullSeqId.setText("Show full sequence id");
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+    hiddenMarkers.setText(MessageManager.getString("action.show_hidden_markers"));
+    hiddenMarkers.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        fullSeqId_actionPerformed(e);
+        hiddenMarkers_actionPerformed(e);
       }
     });
-    epsFile.setText("Save as EPS file");
-    epsFile.addActionListener(new java.awt.event.ActionListener()
+    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()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertColSel_actionPerformed(e);
+      }
+    });
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        JTabbedPane pane = (JTabbedPane) evt.getSource();
+        int sel = pane.getSelectedIndex();
+        tabSelectionChanged(sel);
+      }
+    });
+    tabbedPane.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        tabbedPane_mousePressed(e);
+      }
+    });
+    tabbedPane.addFocusListener(new FocusAdapter()
+    {
+      public void focusGained(FocusEvent e)
+      {
+        tabbedPane_focusGained(e);
+      }
+    });
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        epsFile_actionPerformed(e);
+        save_actionPerformed(e);
       }
     });
-    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load assocated tree");
-    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+    reload.setEnabled(false);
+    reload.setText(MessageManager.getString("action.reload"));
+    reload.addActionListener(new ActionListener()
+    {
       public void actionPerformed(ActionEvent e)
       {
-        LoadtreeMenuItem_actionPerformed(e);
+        reload_actionPerformed(e);
       }
     });
-    jpred.setText("JPred");
-    jpred.addActionListener(new java.awt.event.ActionListener()
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        jpred_actionPerformed(e);
+        newView_actionPerformed(e);
       }
     });
-    scaleAbove.setVisible(false);
-    scaleAbove.setText("Scale above alignment");
-    scaleAbove.addActionListener(new java.awt.event.ActionListener()
+    tabbedPane.setToolTipText("<html><i>" + MessageManager.getString("label.rename_tab_eXpand_reGroup") + "</i></html>");
+    textColour.setText(MessageManager.getString("label.colour_text") + "...");
+    textColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        scaleAbove_actionPerformed(e);
+        textColour_actionPerformed(e);
       }
     });
-    scaleLeft.setVisible(false);
-    scaleLeft.setSelected(true);
-    scaleLeft.setText("Scale left of sequence");
-    scaleLeft.addActionListener(new java.awt.event.ActionListener()
+    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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        scaleLeft_actionPerformed(e);
+        idRightAlign_actionPerformed(e);
       }
     });
-    scaleRight.setVisible(false);
-    scaleRight.setSelected(true);
-    scaleRight.setText("Scale right of sequence");
-    scaleRight.addActionListener(new java.awt.event.ActionListener()
+    gatherViews.setEnabled(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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        scaleRight_actionPerformed(e);
+        gatherViews_actionPerformed(e);
       }
     });
-    modifyPID.setText("Modify PID Threshold");
-    modifyPID.addActionListener(new java.awt.event.ActionListener()
+    expandViews.setEnabled(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()
     {
       public void actionPerformed(ActionEvent e)
       {
-        modifyPID_actionPerformed(e);
+        expandViews_actionPerformed(e);
       }
     });
-    modifyConservation.setText("Modify Conservation Threshold");
-    modifyConservation.addActionListener(new java.awt.event.ActionListener()
+    pageSetup.setText(MessageManager.getString("action.page_setup") + "...");
+    pageSetup.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        modifyConservation_actionPerformed(e);
+        pageSetup_actionPerformed(e);
+      }
+    });
+    alignmentProperties.setText(MessageManager.getString("label.alignment_props") + "...");
+    alignmentProperties.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        alignmentProperties();
       }
     });
-    sortByTreeMenu.setText("Sort by tree order");
+    tooltipSettingsMenu.setText(MessageManager.getString("label.sequence_id_tooltip"));
+    autoAnnMenu.setText(MessageManager.getString("label.autocalculated_annotation"));
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(searchMenu);
+    alignFrameMenuBar.add(selectMenu);
     alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(alignMenu);
-    fileMenu.add(saveAlignmentMenu);
+    alignFrameMenuBar.add(webService);
+    fileMenu.add(fetchSequence);
+    fileMenu.add(addSequenceMenu);
+    fileMenu.add(reload);
+    fileMenu.addSeparator();
+    fileMenu.add(vamsasStore);
+    fileMenu.add(save);
+    fileMenu.add(saveAs);
     fileMenu.add(outputTextboxMenu);
-    fileMenu.add(htmlMenuItem);
-    fileMenu.add(epsFile);
-    fileMenu.add(createPNG);
+    fileMenu.add(pageSetup);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    fileMenu.add(jMenu2);
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
-    editMenu.add(copy);
-    editMenu.add(jMenu1);
-    editMenu.add(cut);
-    editMenu.add(delete);
-    editMenu.addSeparator();
     editMenu.add(undoMenuItem);
     editMenu.add(redoMenuItem);
+    editMenu.add(cut);
+    editMenu.add(copy);
+    editMenu.add(pasteMenu);
+    editMenu.add(delete);
     editMenu.addSeparator();
-    editMenu.add(deselectAllSequenceMenuItem);
-    editMenu.add(selectAllSequenceMenuItem);
-    editMenu.add(invertSequenceMenuItem);
-    editMenu.add(deleteGroups);
-    editMenu.addSeparator();
-    editMenu.add(deselectAllColumnsMenuItem);
     editMenu.add(remove2LeftMenuItem);
     editMenu.add(remove2RightMenuItem);
-    editMenu.addSeparator();
     editMenu.add(removeGappedColumnMenuItem);
     editMenu.add(removeAllGapsMenuItem);
-    editMenu.add(setGapCharMenuItem);
-    searchMenu.add(findMenuItem);
-    viewMenu.add(font);
-    viewMenu.add(fullSeqId);
+    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);
+    viewMenu.add(gatherViews);
     viewMenu.addSeparator();
-    viewMenu.add(wrapMenuItem);
-    viewMenu.add(scaleAbove);
-    viewMenu.add(scaleLeft);
-    viewMenu.add(scaleRight);
+    viewMenu.add(jMenu3);
+    viewMenu.add(hideMenu);
     viewMenu.addSeparator();
-    viewMenu.add(viewBoxesMenuItem);
-    viewMenu.add(viewTextMenuItem);
-    viewMenu.add(colourTextMenuItem);
-    viewMenu.add(renderGapsMenuItem);
+    viewMenu.add(followHighlightMenuItem);
     viewMenu.add(annotationPanelMenuItem);
+    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(showSeqFeaturesHeight);
+
+    viewMenu.add(openFeatureSettings);
+    tooltipSettingsMenu.add(showDbRefsMenuitem);
+    tooltipSettingsMenu.add(showNpFeatsMenuitem);
+    viewMenu.add(tooltipSettingsMenu);
+    viewMenu.addSeparator();
+    viewMenu.add(alignmentProperties);
+    viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
-    viewMenu.add(sequenceFeatures);
     colourMenu.add(applyToAllGroups);
+    colourMenu.add(textColour);
+    colourMenu.addSeparator();
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
     colourMenu.add(zappoColour);
     colourMenu.add(taylorColour);
     colourMenu.add(hydrophobicityColour);
@@ -804,412 +1924,731 @@ public class GAlignFrame extends JInternalFrame
     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.add(PIDColour);
-    colourMenu.add(BLOSUM62Colour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
-    calculateMenu.add(sortPairwiseMenuItem);
-    calculateMenu.add(sortIDMenuItem);
-    calculateMenu.add(sortGroupMenuItem);
-    calculateMenu.add(sortByTreeMenu);
-    calculateMenu.add(removeRedundancyMenuItem);
+    colourMenu.add(annotationColour);
+    colourMenu.add(rnahelicesColour);  
+    calculateMenu.add(sort);
+    calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
-    calculateMenu.add(averageDistanceTreeMenuItem);
-    calculateMenu.add(neighbourTreeMenuItem);
-    calculateMenu.add(avDistanceTreeBlosumMenuItem);
-    calculateMenu.add(njTreeBlosumMenuItem);
-    alignMenu.add(clustalAlignMenuItem);
-    alignMenu.add(msaAlignMenuItem);
-    alignMenu.add(jpred);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-    jMenu1.add(pasteNew);
-    jMenu1.add(pasteThis);
+    calculateMenu.add(showTranslation);
+    calculateMenu.add(showProducts);
+    calculateMenu.add(autoCalculate);
+    calculateMenu.add(sortByTree);
+    calculateMenu.addSeparator();
+    calculateMenu.add(extractScores);
+    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);
+    jMenu2.add(htmlMenuItem);
+    jMenu2.add(epsFile);
+    jMenu2.add(createPNG);
+    addSequenceMenu.add(addFromFile);
+    addSequenceMenu.add(addFromText);
+    addSequenceMenu.add(addFromURL);
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
+    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);
+    formatMenu.add(scaleAbove);
+    formatMenu.add(scaleLeft);
+    formatMenu.add(scaleRight);
+    formatMenu.add(seqLimits);
+    formatMenu.add(idRightAlign);
+    formatMenu.add(hiddenMarkers);
+    formatMenu.add(viewBoxesMenuItem);
+    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 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 saveAs_actionPerformed(ActionEvent e)
+  protected void hideAllButSelection_actionPerformed(ActionEvent e)
   {
+    // TODO Auto-generated method stub
 
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  protected void hideAllSelection_actionPerformed(ActionEvent e)
   {
+    // TODO Auto-generated method stub
 
   }
 
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  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 closeMenuItem_actionPerformed(ActionEvent e)
+  protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
+    // TODO Auto-generated method stub
 
   }
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  protected void showGroupConsensus_actionPerformed(ActionEvent e)
   {
+    // TODO Auto-generated method stub
 
   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  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 selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  }
+
+  protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
+    // TODO Auto-generated method stub
 
   }
 
-  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
   {
+    // TODO Auto-generated method stub
 
   }
 
-  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+  protected void followHighlight_actionPerformed()
   {
+    // TODO Auto-generated method stub
 
   }
 
+  protected void showNpFeats_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
 
-  protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
+  protected void showDbRefs_actionPerformed(ActionEvent e)
   {
+    // TODO Auto-generated method stub
 
   }
 
-  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  protected void centreColumnLabels_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void showProducts_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  protected void buildSortByAnnotationScoresMenu()
   {
+  }
 
+  protected void extractScores_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+  protected void outputText_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+  public void addFromText_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
+  public void addFromURL_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
 
+  }
 
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
 
+  }
 
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void closeMenuItem_actionPerformed(boolean b)
+  {
   }
 
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+  protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void overviewMenuItem_actionPerformed(ActionEvent e)
+  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void overviewMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
   protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
   protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+  protected void PCAMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
+  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void clustalColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+  protected void zappoColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void taylorColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void helixColour_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void strandColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  protected void turnColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void buriedColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
+  }
+
+  protected void PIDColour_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+  {
+  }
+  
+  protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+  {
+  }
+  
 
+  /*
+   * protected void covariationColour_actionPerformed(ActionEvent e) { }
+   */
 
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  protected void printMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void findMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void clustalColour_actionPerformed(ActionEvent e)
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
+  {
   }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
+  protected void nucleotideColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
+  }
+  
+  protected void createGroup_actionPerformed(ActionEvent e)
+  {
+  }
+  
+  protected void unGroup_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void cut_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  protected void pasteNew_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void createPNG(java.io.File f)
+  {
   }
 
-  protected void strandColour_actionPerformed(ActionEvent e)
+  protected void font_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void seqLimit_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
+  public void seqDBRef_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
+  public void createEPS(java.io.File f)
+  {
+  }
+
+  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)
+  {
 
+  }
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  /**
+   * 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 PIDColour_actionPerformed(ActionEvent e)
+  protected void jpred_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void scaleAbove_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleLeft_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  protected void scaleRight_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void modifyPID_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  public void vamsasStore_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void vamsasLoad_actionPerformed(ActionEvent e)
+  {
 
-  protected void printMenuItem_actionPerformed(ActionEvent e)
+  }
+
+  public void showTranslation_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void findMenuItem_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  public void rnahelicesColour_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
+  public void associatedData_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void deleteGroups_actionPerformed(ActionEvent e)
+  public void autoCalculate_actionPerformed(ActionEvent e)
   {
 
   }
 
- protected void copy_actionPerformed(ActionEvent e)
+  public void sortByTreeOption_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
 
-  protected void cut_actionPerformed(ActionEvent e)
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  public void hideSelSequences_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
+  public void hideSelColumns_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  public void findPdbId_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
+  public void enterPdbId_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void font_actionPerformed(ActionEvent e)
+  public void pdbFile_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  public void invertColSel_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
+  public void tabSelectionChanged(int sel)
   {
 
   }
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+  public void tabbedPane_mousePressed(MouseEvent e)
+  {
+
+  }
 
+  public void tabbedPane_focusGained(FocusEvent e)
+  {
+    requestFocus();
   }
 
-  protected void jpred_actionPerformed(ActionEvent e)
+  public void save_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleAbove_actionPerformed(ActionEvent e)
+  public void reload_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleLeft_actionPerformed(ActionEvent e)
+  public void newView_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleRight_actionPerformed(ActionEvent e)
+  public void textColour_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
+  public void idRightAlign_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
+  public void expandViews_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void gatherViews_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void buildTreeMenu()
   {
 
   }
 
+  public void pageSetup_actionPerformed(ActionEvent e)
+  {
+
+  }
 
+  public void alignmentProperties()
+  {
 
+  }
 
+  protected void expand_newalign(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }