X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d0327564b480118eb1ca9e9cb92ed8bcd973ebf6;hb=8c4f77adba0521e7dc89dcb77fe2f8b28c62f70d;hp=12dd3a65ac160b45dc02657f48bbcf4f2ff67b23;hpb=f8316a00ebd4f4c9be5d8e41b40b361734b38526;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 12dd3a6..d032756 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,88 +1,153 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.jbgui;
 
-import javax.swing.*;
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.schemes.*;
+import java.awt.BorderLayout;
+
+
+
 
-public class GAlignFrame extends JInternalFrame
+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 fontMenu = new JMenu();
   protected JMenu viewMenu = new JMenu();
   protected JMenu colourMenu = new JMenu();
   protected JMenu calculateMenu = new JMenu();
-  protected JMenu alignMenu = new JMenu();
-  protected JMenuItem groupsMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem groupEditingMenuItem = new JCheckBoxMenuItem();
+  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 deleteSelectedMenuItem = new JMenuItem();
-  protected JMenuItem moveSelectedMenuItem = new JMenuItem();
-  protected JMenuItem copySelectedMenuItem = 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 JMenuItem fontNameMenuItem = new JMenuItem();
-  protected JMenuItem fontSizeMenuItem = new JMenuItem();
-  protected JMenuItem fontStyleMenuItem = 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 sortGroupMenuItem = new JMenuItem();
-  protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
   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();
   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 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 abovePIDColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-  protected JMenuItem conservationColourIncMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
   JMenuItem htmlMenuItem = new JMenuItem();
-  JMenuItem schemeKeyMenuItem = new JMenuItem();
   JMenuItem overviewMenuItem = new JMenuItem();
   protected JMenuItem undoMenuItem = new JMenuItem();
   protected JMenuItem redoMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-  JMenuItem noColourmenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-  JMenuItem pdbTest = new JMenuItem();
+  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
   JMenuItem printMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+  JMenuItem findMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+  JMenuItem deleteGroups = new JMenuItem();
+  JMenuItem delete = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem cut = new JMenuItem();
+  JMenu pasteMenu = new JMenu();
+  JMenuItem pasteNew = new JMenuItem();
+  JMenuItem pasteThis = new JMenuItem();
+  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+  JMenuItem createPNG = new JMenuItem();
+  protected JMenuItem font = new JMenuItem();
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+  JMenuItem epsFile = new JMenuItem();
+  JMenuItem LoadtreeMenuItem = new JMenuItem();
+  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  protected JMenuItem modifyPID = new JMenuItem();
+  protected JMenuItem modifyConservation = new JMenuItem();
+  protected JMenu sortByTreeMenu = new JMenu();
+  protected JMenu sort = new JMenu();
+  JMenu calculate = new JMenu();
+  JMenu jMenu2 = new JMenu();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+  protected ButtonGroup colours = new ButtonGroup();
+  JMenuItem vamsasStore = new JMenuItem();
+  protected JMenuItem showTranslation = new JMenuItem();
+  public JMenuItem featureSettings = new JMenuItem();
+  JMenuItem fetchSequence = new JMenuItem();
+  JMenuItem annotationColour = new JMenuItem();
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = 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();
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+  JMenuItem invertColSel = new JMenuItem();
+  protected JTabbedPane tabbedPane = new JTabbedPane();
+  JMenuItem save = new JMenuItem();
+  JMenuItem jMenuItem1 = new JMenuItem();
+  protected JMenuItem reload = new JMenuItem();
+  JMenuItem newView = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+  JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();
+  JMenu jMenu4 = new JMenu();
+  protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
     try
@@ -90,20 +155,11 @@ public class GAlignFrame extends JInternalFrame
       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)
@@ -112,16 +168,76 @@ public class GAlignFrame extends JInternalFrame
           }
         });
 
-        outputTextboxMenu.add( item );
+        outputTextboxMenu.add(item);
       }
-
     }
-    catch(Exception e)
+    catch (Exception e)
+    {
+    }
+
+    if (!System.getProperty("os.name").startsWith("Mac"))
     {
-      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,
+                      "Remove from default list?",
+                      "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);
     colours.add(taylorColour);
@@ -130,547 +246,999 @@ public class GAlignFrame extends JInternalFrame
     colours.add(strandColour);
     colours.add(turnColour);
     colours.add(buriedColour);
-    colours.add(abovePIDColour);
     colours.add(userDefinedColour);
     colours.add(PIDColour);
     colours.add(BLOSUM62Colour);
+    colours.add(nucleotideColour);
+
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
+
   }
-  private void jbInit() throws Exception
+
+  public void setColourSelected(String defaultColour)
+  {
+
+    if (defaultColour != null)
+    {
+      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
+
+      switch (index)
+      {
+        case ColourSchemeProperty.NONE:
+              noColourmenuItem.setSelected(true);
+              break;
+        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.USER_DEFINED:
+          userDefinedColour.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');
+    saveAs.setText("Save As...");
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));
+    saveAs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        saveAs_actionPerformed(e);
+      }
+    });
     closeMenuItem.setText("Close");
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        closeMenuItem_actionPerformed(e);
+        closeMenuItem_actionPerformed(false);
       }
     });
     editMenu.setText("Edit");
-    fontMenu.setText("Font");
     viewMenu.setText("View");
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
-    alignMenu.setText("Web Service");
-    groupsMenuItem.setText("Groups");
-    groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    webService.setText("Web Service");
+    selectAllSequenceMenuItem.setText("Select All");
+    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_A,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        groupsMenuItem_actionPerformed(e);
+        selectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    groupEditingMenuItem.setText("Group editing mode");
-    groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
+    deselectAllSequenceMenuItem.setText("Deselect All");
+    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                               getKeyStroke(
+        java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
+    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        groupEditingMenuItem_actionPerformed(e);
+        deselectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    selectAllSequenceMenuItem.setText("Select all sequences");
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    invertSequenceMenuItem.setText("Invert Sequence Selection");
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_I,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));
+    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        selectAllSequenceMenuItem_actionPerformed(e);
+        invertSequenceMenuItem_actionPerformed(e);
       }
     });
-    deselectAllSequenceMenuItem.setText("Clear sequence selection");
-    deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    remove2LeftMenuItem.setText("Remove Left");
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        deselectAllSequenceMenuItem_actionPerformed(e);
+        remove2LeftMenuItem_actionPerformed(e);
       }
     });
-    invertSequenceMenuItem.setText("Invert sequence selection");
-    invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    remove2RightMenuItem.setText("Remove Right");
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        invertSequenceMenuItem_actionPerformed(e);
+        remove2RightMenuItem_actionPerformed(e);
+      }
+    });
+    removeGappedColumnMenuItem.setText("Remove Empty Columns");
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                              getKeyStroke(java.awt.event.
+        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+                                                 ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        removeGappedColumnMenuItem_actionPerformed(e);
       }
     });
-    deleteSelectedMenuItem.setText("Delete selected sequences");
-    deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeAllGapsMenuItem.setText("Remove All Gaps");
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_E,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
+    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        deleteSelectedMenuItem_actionPerformed(e);
+        removeAllGapsMenuItem_actionPerformed(e);
       }
     });
-    moveSelectedMenuItem.setText("Move selected sequences to new alignment");
-    moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
+    viewBoxesMenuItem.setText("Boxes");
+    viewBoxesMenuItem.setState(true);
+    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        moveSelectedMenuItem_actionPerformed(e);
+        viewBoxesMenuItem_actionPerformed(e);
       }
     });
-    copySelectedMenuItem.setText("Copy selected sequences to new alignment");
-    copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
+    viewTextMenuItem.setText("Text");
+    viewTextMenuItem.setState(true);
+    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        copySelectedMenuItem_actionPerformed(e);
+        viewTextMenuItem_actionPerformed(e);
       }
     });
-    deselectAllColumnsMenuItem.setText("Deselect all columns");
-    deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    sortPairwiseMenuItem.setText("by Pairwise Identity");
+    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        deselectAllColumnsMenuItem_actionPerformed(e);
+        sortPairwiseMenuItem_actionPerformed(e);
       }
     });
-    remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
-    remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+    sortIDMenuItem.setText("by ID");
+    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        remove2LeftMenuItem_actionPerformed(e);
+        sortIDMenuItem_actionPerformed(e);
       }
     });
-    remove2RightMenuItem.setText("Remove sequence -> right of selected column");
-    remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
+    sortGroupMenuItem.setText("by Group");
+    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        remove2RightMenuItem_actionPerformed(e);
+        sortGroupMenuItem_actionPerformed(e);
       }
     });
-    removeGappedColumnMenuItem.setText("Remove gapped columns");
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeRedundancyMenuItem.setText("Remove Redundancy...");
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeRedundancyMenuItem.addActionListener(new java.awt.event.
+                                               ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        removeGappedColumnMenuItem_actionPerformed(e);
+        removeRedundancyMenuItem_actionPerformed(e);
       }
     });
-    removeAllGapsMenuItem.setText("Remove all gaps");
-    removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        removeAllGapsMenuItem_actionPerformed(e);
+        pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    setGapCharMenuItem.setText("Set gap character to \"-\"");
-    setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
+    PCAMenuItem.setText("Principal Component Analysis");
+    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        setGapCharMenuItem_actionPerformed(e);
+        PCAMenuItem_actionPerformed(e);
       }
     });
-    fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
+    averageDistanceTreeMenuItem.setText(
+        "Average Distance Using % Identity");
+    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        fontNameMenuItem_actionPerformed(e);
+        averageDistanceTreeMenuItem_actionPerformed(e);
       }
     });
-    fontSizeMenuItem.setText("10");
-    fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
+    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        fontSizeMenuItem_actionPerformed(e);
+        neighbourTreeMenuItem_actionPerformed(e);
       }
     });
-    fontStyleMenuItem.setText("Plain");
-    fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
+    this.getContentPane().setLayout(borderLayout1);
+    alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    statusBar.setBackground(Color.white);
+    statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
+    statusBar.setText("Status bar");
+    outputTextboxMenu.setText("Output to Textbox");
+    clustalColour.setText("Clustalx");
+
+    clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        fontStyleMenuItem_actionPerformed(e);
+        clustalColour_actionPerformed(e);
       }
     });
-    viewBoxesMenuItem.setText("Boxes");
-    viewBoxesMenuItem.setState(true);
-    viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+    zappoColour.setText("Zappo");
+    zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        viewBoxesMenuItem_actionPerformed(e);
+        zappoColour_actionPerformed(e);
       }
     });
-    viewTextMenuItem.setText("Text");
-    viewTextMenuItem.setState(true);
-    viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    taylorColour.setText("Taylor");
+    taylorColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        viewTextMenuItem_actionPerformed(e);
+        taylorColour_actionPerformed(e);
       }
     });
-    sortPairwiseMenuItem.setText("Sort by pairwise identity");
-    sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+    hydrophobicityColour.setText("Hydrophobicity");
+    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        sortPairwiseMenuItem_actionPerformed(e);
+        hydrophobicityColour_actionPerformed(e);
       }
     });
-    sortIDMenuItem.setText("Sort by ID");
-    sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+    helixColour.setText("Helix Propensity");
+    helixColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        sortIDMenuItem_actionPerformed(e);
+        helixColour_actionPerformed(e);
       }
     });
-    sortGroupMenuItem.setText("Sort by group");
-    sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    strandColour.setText("Strand Propensity");
+    strandColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        sortGroupMenuItem_actionPerformed(e);
+        strandColour_actionPerformed(e);
       }
     });
-    sortTreeOrderMenuItem.setText("Sort by tree order");
-    sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
+    turnColour.setText("Turn Propensity");
+    turnColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        sortTreeOrderMenuItem_actionPerformed(e);
+        turnColour_actionPerformed(e);
       }
     });
-    removeRedundancyMenuItem.setText("Remove redundancy");
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+    buriedColour.setText("Buried Index");
+    buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        removeRedundancyMenuItem_actionPerformed(e);
+        buriedColour_actionPerformed(e);
+      }
+    });
+    userDefinedColour.setText("User Defined...");
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        userDefinedColour_actionPerformed(e);
+      }
+    });
+    PIDColour.setText("Percentage Identity");
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        PIDColour_actionPerformed(e);
+      }
+    });
+    BLOSUM62Colour.setText("BLOSUM62 Score");
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        BLOSUM62Colour_actionPerformed(e);
+      }
+    });
+    avDistanceTreeBlosumMenuItem.setText(
+        "Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
+        ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        avTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
+    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        njTreeBlosumMenuItem_actionPerformed(e);
+      }
+    });
+    annotationPanelMenuItem.setActionCommand("");
+    annotationPanelMenuItem.setText("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("Colour Text");
+    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        colourTextMenuItem_actionPerformed(e);
+      }
+    });
+    htmlMenuItem.setText("HTML");
+    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        htmlMenuItem_actionPerformed(e);
+      }
+    });
+    overviewMenuItem.setText("Overview Window");
+    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        overviewMenuItem_actionPerformed(e);
+      }
+    });
+    undoMenuItem.setEnabled(false);
+    undoMenuItem.setText("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("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("By Conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(e);
+      }
+    });
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        noColourmenuItem_actionPerformed(e);
+      }
+    });
+    wrapMenuItem.setText("Wrap");
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        wrapMenuItem_actionPerformed(e);
+      }
+    });
+    printMenuItem.setText("Print");
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        printMenuItem_actionPerformed(e);
+      }
+    });
+    renderGapsMenuItem.setText("Show Gaps");
+    renderGapsMenuItem.setState(true);
+    renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        renderGapsMenuItem_actionPerformed(e);
+      }
+    });
+    findMenuItem.setText("Find...");
+    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_F,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    findMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        findMenuItem_actionPerformed(e);
+      }
+    });
+    abovePIDThreshold.setText("Above Identity Threshold");
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDThreshold_actionPerformed(e);
+      }
+    });
+    showSeqFeatures.setText("Show Sequence Features");
+    showSeqFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        showSeqFeatures_actionPerformed(actionEvent);
+      }
+    });
+    nucleotideColour.setText("Nucleotide");
+    nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        nucleotideColour_actionPerformed(e);
+      }
+    });
+    deleteGroups.setText("Undefine groups");
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    deleteGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        deleteGroups_actionPerformed(e);
+      }
+    });
+    copy.setText("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)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+    cut.setText("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)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    delete.setText("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)
+      {
+        delete_actionPerformed(e);
+      }
+    });
+    pasteMenu.setText("Paste");
+    pasteNew.setText("To New Alignment");
+    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.ALT_MASK, false));
+    pasteNew.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteNew_actionPerformed(e);
+      }
+    });
+    pasteThis.setText("Add 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)
+      {
+        pasteThis_actionPerformed(e);
+      }
+    });
+    applyToAllGroups.setText("Apply Colour To All Groups");
+    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyToAllGroups_actionPerformed(e);
+      }
+    });
+    createPNG.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createPNG(null);
+      }
+    });
+    createPNG.setActionCommand("Save As PNG Image");
+    createPNG.setText("PNG");
+    font.setText("Font...");
+    font.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        font_actionPerformed(e);
+      }
+    });
+
+    seqLimits.setText("Show Sequence Limits");
+    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));
+    seqLimits.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        seqLimit_actionPerformed(e);
+      }
+    });
+    epsFile.setText("EPS");
+    epsFile.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createEPS(null);
       }
     });
-    pairwiseAlignmentMenuItem.setText("Pairwise alignments");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
+    LoadtreeMenuItem.setText("Load Associated Tree");
+    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        pairwiseAlignmentMenuItem_actionPerformed(e);
+        LoadtreeMenuItem_actionPerformed(e);
       }
     });
-    PCAMenuItem.setText("Principal component analysis");
-    PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+    scaleAbove.setVisible(false);
+    scaleAbove.setText("Scale Above");
+    scaleAbove.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        PCAMenuItem_actionPerformed(e);
+        scaleAbove_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText("Average distance tree using PID");
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    scaleLeft.setVisible(false);
+    scaleLeft.setSelected(true);
+    scaleLeft.setText("Scale Left");
+    scaleLeft.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        averageDistanceTreeMenuItem_actionPerformed(e);
+        scaleLeft_actionPerformed(e);
       }
     });
-    neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
-    neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    scaleRight.setVisible(false);
+    scaleRight.setSelected(true);
+    scaleRight.setText("Scale Right");
+    scaleRight.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        neighbourTreeMenuItem_actionPerformed(e);
+        scaleRight_actionPerformed(e);
       }
     });
-    clustalAlignMenuItem.setText("Clustal alignment");
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    modifyPID.setText("Modify Identity Threshold...");
+    modifyPID.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        clustalAlignMenuItem_actionPerformed(e);
+        modifyPID_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.setEnabled(false);
-    clustalColour.setSelected(false);
-    clustalColour.setText("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
+    modifyConservation.setText("Modify Conservation Threshold...");
+    modifyConservation.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        clustalColour_actionPerformed(e);
+        modifyConservation_actionPerformed(e);
       }
     });
-    zappoColour.setSelected(true);
-    zappoColour.setText("Zappo colour scheme");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
+    sortByTreeMenu.setText("By Tree Order");
+    sort.setText("Sort");
+    calculate.setText("Calculate Tree");
+
+    jMenu2.setText("Export Image");
+    padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        zappoColour_actionPerformed(e);
+        padGapsMenuitem_actionPerformed(e);
       }
     });
-    taylorColour.setText("Taylor colour scheme");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
+    vamsasStore.setVisible(false);
+    vamsasStore.setText("VAMSAS store");
+    vamsasStore.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        taylorColour_actionPerformed(e);
+        vamsasStore_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText("By hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+    showTranslation.setText("Translate cDNA");
+    showTranslation.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        hydrophobicityColour_actionPerformed(e);
+        showTranslation_actionPerformed(e);
       }
     });
-    helixColour.setText("Helix propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
+
+
+    featureSettings.setText("Feature Settings...");
+    featureSettings.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        helixColour_actionPerformed(e);
+        featureSettings_actionPerformed(e);
       }
     });
-    strandColour.setText("Strand propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
+    fetchSequence.setText("Fetch Sequence(s)...");
+    fetchSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        strandColour_actionPerformed(e);
+        fetchSequence_actionPerformed(e);
       }
     });
-    turnColour.setText("Turn propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
+
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        turnColour_actionPerformed(e);
+        annotationColour_actionPerformed(e);
       }
     });
-    buriedColour.setText("Buried index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        buriedColour_actionPerformed(e);
+        associatedData_actionPerformed(e);
       }
     });
-    abovePIDColour.setEnabled(false);
-    abovePIDColour.setText("Above PID threshold only");
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDColour_actionPerformed(e);
+        autoCalculate_actionPerformed(e);
       }
     });
-    userDefinedColour.setText("User defined colours");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        userDefinedColour_actionPerformed(e);
+        addFromFile_actionPerformed(e);
       }
     });
-    PIDColour.setEnabled(false);
-    PIDColour.setText("By PID");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        PIDColour_actionPerformed(e);
+        addFromText_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("By BLOSUM62 score");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        BLOSUM62Colour_actionPerformed(e);
+        addFromURL_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        avTreeBlosumMenuItem_actionPerformed(e);
+        exportFeatures_actionPerformed(e);
       }
     });
-    njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
-    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        njTreeBlosumMenuItem_actionPerformed(e);
+        exportAnnotations_actionPerformed(e);
       }
     });
-    conservationColourIncMenuItem.setEnabled(false);
-    conservationColourIncMenuItem.setText("Conservation Colour Increment");
-    conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        conservationColourIncMenuItem_actionPerformed(e);
+        showAllSeqs_actionPerformed(e);
       }
     });
-    consensusGraphMenuItem.setActionCommand("");
-    consensusGraphMenuItem.setText("Consensus graph");
-    consensusGraphMenuItem.setState(true);
-    consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
+    showAllColumns.setText("All Columns");
+    showAllColumns.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        consensusGraphMenuItem_actionPerformed(e);
+        showAllColumns_actionPerformed(e);
       }
     });
-    colourTextMenuItem.setText("Colour text");
-    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    hideMenu.setText("Hide");
+    hideSelSequences.setText("Selected Sequences");
+    hideSelSequences.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        colourTextMenuItem_actionPerformed(e);
+        hideSelSequences_actionPerformed(e);
       }
     });
-    htmlMenuItem.setText("Output as HTML");
-    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        htmlMenuItem_actionPerformed(e);
+        hideSelColumns_actionPerformed(e);
       }
     });
-    schemeKeyMenuItem.setText("Colour Scheme Key");
-    schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
+    hiddenMarkers.setText("Show Hidden Markers");
+    hiddenMarkers.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        schemeKeyMenuItem_actionPerformed(e);
+        hiddenMarkers_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText("Overview window");
-    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    invertColSel.setText("Invert Column Selection");
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    invertColSel.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        overviewMenuItem_actionPerformed(e);
+        invertColSel_actionPerformed(e);
       }
     });
-    undoMenuItem.setEnabled(false);
-    undoMenuItem.setMnemonic('Z');
-    undoMenuItem.setText("Undo");
-    undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
-      public void actionPerformed(ActionEvent e)
+        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)
       {
-        undoMenuItem_actionPerformed(e);
+        tabbedPane_mousePressed(e);
       }
     });
-    redoMenuItem.setEnabled(false);
-    redoMenuItem.setMnemonic('0');
-    redoMenuItem.setText("Redo");
-    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+    tabbedPane.addFocusListener(new FocusAdapter()
     {
-      public void actionPerformed(ActionEvent e)
+      public void focusGained(FocusEvent e)
       {
-        redoMenuItem_actionPerformed(e);
+        tabbedPane_focusGained(e);
       }
     });
-    conservationMenuItem.setText("By conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+    save.setText("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)
       {
-        conservationMenuItem_actionPerformed(e);
+        save_actionPerformed(e);
       }
     });
-    noColourmenuItem.setText("None");
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+    reload.setEnabled(false);
+    reload.setText("Reload");
+    reload.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        noColourmenuItem_actionPerformed(e);
+        reload_actionPerformed(e);
       }
     });
-    wrapMenuItem.setEnabled(false);
-    wrapMenuItem.setText("Wrap alignment");
-    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+    newView.setText("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)
       {
-        wrapMenuItem_actionPerformed(e);
+        newView_actionPerformed(e);
       }
     });
-    pdbTest.setText("PDB Test Viewer");
-    pdbTest.addActionListener(new java.awt.event.ActionListener()
+    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
+                              +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        pdbTest_actionPerformed(e);
+        textColour_actionPerformed(e);
       }
     });
-    printMenuItem.setText("Print");
-    printMenuItem.addActionListener(new java.awt.event.ActionListener()
+    jMenu1.setText("Format");
+    jCheckBoxMenuItem1.setText("Right Align Ids");
+    jMenu4.setText("Select");
+    idRightAlign.setText("Right Align Sequence Id");
+    idRightAlign.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        printMenuItem_actionPerformed(e);
+        idRightAlign_actionPerformed(e);
       }
     });
+
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(fontMenu);
+    alignFrameMenuBar.add(jMenu4);
     alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(jMenu1);
     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(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(undoMenuItem);
     editMenu.add(redoMenuItem);
+    editMenu.add(cut);
+    editMenu.add(copy);
+    editMenu.add(pasteMenu);
+    editMenu.add(delete);
     editMenu.addSeparator();
-    editMenu.add(groupsMenuItem);
-    editMenu.add(groupEditingMenuItem);
-    editMenu.addSeparator();
-    editMenu.add(selectAllSequenceMenuItem);
-    editMenu.add(deselectAllSequenceMenuItem);
-    editMenu.add(invertSequenceMenuItem);
-    editMenu.addSeparator();
-    editMenu.add(copySelectedMenuItem);
-    editMenu.add(moveSelectedMenuItem);
-    editMenu.add(deleteSelectedMenuItem);
-    editMenu.addSeparator();
-    editMenu.add(deselectAllColumnsMenuItem);
     editMenu.add(remove2LeftMenuItem);
     editMenu.add(remove2RightMenuItem);
-    editMenu.addSeparator();
     editMenu.add(removeGappedColumnMenuItem);
     editMenu.add(removeAllGapsMenuItem);
-    editMenu.add(setGapCharMenuItem);
-    fontMenu.add(fontNameMenuItem);
-    fontMenu.add(fontSizeMenuItem);
-    fontMenu.add(fontStyleMenuItem);
-    viewMenu.add(wrapMenuItem);
-    viewMenu.add(viewBoxesMenuItem);
-    viewMenu.add(viewTextMenuItem);
-    viewMenu.add(colourTextMenuItem);
-    viewMenu.add(consensusGraphMenuItem);
+    editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(padGapsMenuitem);
+    viewMenu.add(newView);
+    viewMenu.addSeparator();
+    viewMenu.add(jMenu3);
+    viewMenu.add(hideMenu);
+    viewMenu.addSeparator();
+    viewMenu.add(annotationPanelMenuItem);
+    viewMenu.addSeparator();
+    viewMenu.add(showSeqFeatures);
+    viewMenu.add(featureSettings);
+    viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
+    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);
@@ -678,347 +1246,497 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(strandColour);
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
-    colourMenu.add(conservationColourIncMenuItem);
-    colourMenu.addSeparator();
-    colourMenu.add(abovePIDColour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(BLOSUM62Colour);
-    colourMenu.addSeparator();
-    colourMenu.add(schemeKeyMenuItem);
-    calculateMenu.add(sortPairwiseMenuItem);
-    calculateMenu.add(sortIDMenuItem);
-    calculateMenu.add(sortGroupMenuItem);
-    calculateMenu.add(sortTreeOrderMenuItem);
-    calculateMenu.add(removeRedundancyMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
+    calculateMenu.add(sort);
+    calculateMenu.add(calculate);
     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(pdbTest);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
+    calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
+    webServiceNoServices=new JMenuItem("<No Services>");
+    webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
+    sort.add(sortIDMenuItem);
+    sort.add(sortGroupMenuItem);
+    sort.add(sortPairwiseMenuItem);
+    calculate.add(averageDistanceTreeMenuItem);
+    calculate.add(neighbourTreeMenuItem);
+    calculate.add(avDistanceTreeBlosumMenuItem);
+    calculate.add(njTreeBlosumMenuItem);
+    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);
+    hideMenu.add(hideSelColumns);
+    hideMenu.add(hideSelSequences);
+    jMenu1.add(font);
+    jMenu1.addSeparator();
+    jMenu1.add(wrapMenuItem);
+    jMenu1.add(scaleAbove);
+    jMenu1.add(scaleLeft);
+    jMenu1.add(scaleRight);
+    jMenu1.add(seqLimits);
+    jMenu1.add(idRightAlign);
+    jMenu1.add(hiddenMarkers);
+    jMenu1.add(viewBoxesMenuItem);
+    jMenu1.add(viewTextMenuItem);
+    jMenu1.add(colourTextMenuItem);
+    jMenu1.add(renderGapsMenuItem);
+    jMenu4.add(findMenuItem);
+    jMenu4.addSeparator();
+    jMenu4.add(selectAllSequenceMenuItem);
+    jMenu4.add(deselectAllSequenceMenuItem);
+    jMenu4.add(invertSequenceMenuItem);
+    jMenu4.add(invertColSel);
+    jMenu4.add(deleteGroups);
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  protected void outputText_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void outputText_actionPerformed(ActionEvent e)
+  public void addFromFile_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  public void addFromText_actionPerformed(ActionEvent e)
   {
 
   }
 
-
-
-
-
-  protected void closeMenuItem_actionPerformed(ActionEvent e)
+  public void addFromURL_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  public void exportFeatures_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  public void exportAnnotations_actionPerformed(ActionEvent e)
   {
 
   }
 
-
-  protected void groupsMenuItem_actionPerformed(ActionEvent e)
+  protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void closeMenuItem_actionPerformed(boolean b)
+  {
   }
 
-  protected void groupEditingMenuItem_actionPerformed(ActionEvent e)
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void deleteSelectedMenuItem_actionPerformed(ActionEvent e)
+  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void moveSelectedMenuItem_actionPerformed(ActionEvent e)
+  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void copySelectedMenuItem_actionPerformed(ActionEvent e)
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
+  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+  protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void overviewMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void PCAMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
+  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void fontNameMenuItem_actionPerformed(ActionEvent e)
+  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void clustalColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
+  protected void zappoColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void taylorColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
+  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void helixColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  protected void strandColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void turnColour_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void buriedColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void PIDColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+  protected void printMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void findMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
   {
+  }
 
+  protected void nucleotideColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void overviewMenuItem_actionPerformed(ActionEvent e)
+  protected void deleteGroups_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void copy_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+  protected void cut_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void delete_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+  protected void pasteNew_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void createPNG(java.io.File f)
+  {
   }
 
-  protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
+  protected void font_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void seqLimit_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+  public void seqDBRef_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+
+  public void createEPS(java.io.File f)
   {
+  }
 
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
+  protected void jpred_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+  protected void scaleLeft_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
   }
 
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+
+  protected void saveAs_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+
+  public void vamsasStore_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void vamsasLoad_actionPerformed(ActionEvent e)
+  {
 
+  }
 
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
 
+  }
 
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
+  public void smoothFont_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
+  public void annotationColour_actionPerformed(ActionEvent e)
   {
 
   }
 
 
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  public void associatedData_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
+  public void autoCalculate_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void strandColour_actionPerformed(ActionEvent e)
+  public void showAllSeqs_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
+  public void showAllColumns_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
+  public void hideSelSequences_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
 
-  protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
+  }
 
- }
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
 
+  }
 
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
+  public void findPdbId_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void enterPdbId_actionPerformed(ActionEvent e)
+  {
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  }
+
+  public void pdbFile_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
+  public void invertColSel_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  public void tabSelectionChanged(int sel)
   {
 
   }
 
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
+  public void tabbedPane_mousePressed(MouseEvent e)
   {
 
   }
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  public void tabbedPane_focusGained(FocusEvent e)
+  {
+    requestFocus();
+  }
+
+  public void save_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  public void reload_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pdbTest_actionPerformed(ActionEvent e)
+  public void newView_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void printMenuItem_actionPerformed(ActionEvent e)
+  public void textColour_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+
+  }
 }