X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=26e532694dcd370d9bc31f703482a0b3cd452ea4;hb=ef3333028b291ce92bdae34bd2f8487d35d0a0d3;hp=858852425c975760ac820a65c011043ae2ae7636;hpb=dac0affed92bb5dddcbca8fc99cbb2859bd7e579;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8588524..26e5326 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,54 +1,54 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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.gui.*;
+import jalview.schemes.*;
 
-public class GAlignFrame extends JInternalFrame
+public class GAlignFrame
+    extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
   protected JMenu fileMenu = new JMenu();
-  protected JMenuItem saveAsPostscriptMenuItem = new JMenuItem();
   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 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();
@@ -57,50 +57,98 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
   BorderLayout borderLayout1 = new BorderLayout();
   public JLabel statusBar = new JLabel();
-  protected JMenu saveAlignmentMenu = new JMenu();
+  protected JMenuItem saveAlignmentMenu = 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 conservationColour = 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();
-  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();
+  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();
+  JMenu searchMenu = new JMenu();
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+  JMenuItem deleteGroups = new JMenuItem();
+  JMenuItem delete = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem cut = new JMenuItem();
+  JMenu jMenu1 = 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 fullSeqId = new JCheckBoxMenuItem();
+  JMenuItem epsFile = new JMenuItem();
+  JMenuItem LoadtreeMenuItem = new JMenuItem();
+  JMenuItem jnet = new JMenuItem();
+  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  JMenuItem modifyPID = new JMenuItem();
+  JMenuItem modifyConservation = new JMenuItem();
+  protected JMenu sortByTreeMenu = new JMenu();
+  protected JMenu sort = new JMenu();
+  JMenu calculate = new JMenu();
+  JMenuItem msaAlignMenuItem = new JMenuItem();
+  JMenu jMenu2 = new JMenu();
+  JMenuItem padGapsMenuitem = new JMenuItem();
+  JMenuItem ClustalRealign = new JMenuItem();
+
   public GAlignFrame()
   {
+    ButtonGroup colours = new ButtonGroup();
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+    colours.add(nucleotideColour);
+
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
+
     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);
-          }
-        });
 
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
+      // dynamically fill save as menu with available formats
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      {
+        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+                             elementAt(
+                                 i));
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -109,43 +157,104 @@ public class GAlignFrame extends JInternalFrame
           }
         });
 
-        outputTextboxMenu.add( item );
+        outputTextboxMenu.add(item);
       }
-
     }
-    catch(Exception e)
+    catch (Exception e)
     {
-      e.printStackTrace();
     }
 
-    ButtonGroup colours = new ButtonGroup();
-    colours.add(clustalColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(conservationColour);
-    colours.add(abovePIDColour);
-    colours.add(userDefinedColour);
-    colours.add(PIDColour);
-    colours.add(BLOSUM62Colour);
   }
-  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");
-    saveAsPostscriptMenuItem.setMnemonic('P');
-    saveAsPostscriptMenuItem.setText("Save alignment as postscript");
-    saveAsPostscriptMenuItem.addActionListener(new java.awt.event.ActionListener()
+    saveAlignmentMenu.setText("Save As");
+    saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
+    saveAlignmentMenu.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        saveAsPostscriptMenuItem_actionPerformed(e);
+        saveAlignmentMenu_actionPerformed(e);
       }
     });
     closeMenuItem.setMnemonic('C');
@@ -158,46 +267,35 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     editMenu.setText("Edit");
-    fontMenu.setText("Font");
     viewMenu.setText("View");
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
-    alignMenu.setText("Web Service");
-    groupsMenuItem.setEnabled(false);
-    groupsMenuItem.setText("Groups");
-    groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupsMenuItem_actionPerformed(e);
-      }
-    });
-    groupEditingMenuItem.setEnabled(false);
-    groupEditingMenuItem.setText("Group editing mode");
-    groupEditingMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupEditingMenuItem_actionPerformed(e);
-      }
-    });
-    selectAllSequenceMenuItem.setText("Select all sequences");
-    selectAllSequenceMenuItem.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)
       {
         selectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    deselectAllSequenceMenuItem.setText("Clear sequence selection");
-    deselectAllSequenceMenuItem.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)
       {
         deselectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    invertSequenceMenuItem.setText("Invert sequence selection");
+    invertSequenceMenuItem.setText("Invert Selection");
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -205,39 +303,7 @@ public class GAlignFrame extends JInternalFrame
         invertSequenceMenuItem_actionPerformed(e);
       }
     });
-    deleteSelectedMenuItem.setText("Delete selected sequences");
-    deleteSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deleteSelectedMenuItem_actionPerformed(e);
-      }
-    });
-    moveSelectedMenuItem.setText("Move selected sequences to new alignment");
-    moveSelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        moveSelectedMenuItem_actionPerformed(e);
-      }
-    });
-    copySelectedMenuItem.setText("Copy selected sequences to new alignment");
-    copySelectedMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        copySelectedMenuItem_actionPerformed(e);
-      }
-    });
-    deselectAllColumnsMenuItem.setText("Deselect all columns");
-    deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deselectAllColumnsMenuItem_actionPerformed(e);
-      }
-    });
-    remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
+    remove2LeftMenuItem.setText("Remove Left");
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -245,7 +311,7 @@ public class GAlignFrame extends JInternalFrame
         remove2LeftMenuItem_actionPerformed(e);
       }
     });
-    remove2RightMenuItem.setText("Remove sequence -> right of selected column");
+    remove2RightMenuItem.setText("Remove Right");
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -253,15 +319,16 @@ public class GAlignFrame extends JInternalFrame
         remove2RightMenuItem_actionPerformed(e);
       }
     });
-    removeGappedColumnMenuItem.setText("Remove gapped columns");
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeGappedColumnMenuItem.setText("Remove Empty Columns");
+    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+                                                 ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         removeGappedColumnMenuItem_actionPerformed(e);
       }
     });
-    removeAllGapsMenuItem.setText("Remove all gaps");
+    removeAllGapsMenuItem.setText("Remove All Gaps");
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -269,37 +336,6 @@ public class GAlignFrame extends JInternalFrame
         removeAllGapsMenuItem_actionPerformed(e);
       }
     });
-    setGapCharMenuItem.setText("Set gap character to \"-\"");
-    setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        setGapCharMenuItem_actionPerformed(e);
-      }
-    });
-    fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontNameMenuItem_actionPerformed(e);
-      }
-    });
-    fontSizeMenuItem.setText("10");
-    fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontSizeMenuItem_actionPerformed(e);
-      }
-    });
-    fontStyleMenuItem.setText("Plain");
-    fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontStyleMenuItem_actionPerformed(e);
-      }
-    });
     viewBoxesMenuItem.setText("Boxes");
     viewBoxesMenuItem.setState(true);
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -318,7 +354,7 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    sortPairwiseMenuItem.setText("Sort by pairwise identity");
+    sortPairwiseMenuItem.setText("by Pairwise Identity");
     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -326,7 +362,7 @@ public class GAlignFrame extends JInternalFrame
         sortPairwiseMenuItem_actionPerformed(e);
       }
     });
-    sortIDMenuItem.setText("Sort by ID");
+    sortIDMenuItem.setText("by ID");
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -334,7 +370,7 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortGroupMenuItem.setText("Sort by group");
+    sortGroupMenuItem.setText("by Group");
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -342,31 +378,25 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-    sortTreeOrderMenuItem.setText("Sort by tree order");
-    sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        sortTreeOrderMenuItem_actionPerformed(e);
-      }
-    });
-    removeRedundancyMenuItem.setText("Remove redundancy");
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeRedundancyMenuItem.setText("Remove Redundancy...");
+    removeRedundancyMenuItem.addActionListener(new java.awt.event.
+                                               ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         removeRedundancyMenuItem_actionPerformed(e);
       }
     });
-    pairwiseAlignmentMenuItem.setText("Pairwise alignments");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
+    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    PCAMenuItem.setText("Principal component analysis");
+    PCAMenuItem.setText("Principal Component Analysis");
     PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -374,15 +404,17 @@ public class GAlignFrame extends JInternalFrame
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText("Average distance tree using PID");
-    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    averageDistanceTreeMenuItem.setText(
+        "Average Distance Using % Identity");
+    averageDistanceTreeMenuItem.addActionListener(new java.awt.event.
+                                                  ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
         averageDistanceTreeMenuItem_actionPerformed(e);
       }
     });
-    neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
+    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -390,7 +422,7 @@ public class GAlignFrame extends JInternalFrame
         neighbourTreeMenuItem_actionPerformed(e);
       }
     });
-    clustalAlignMenuItem.setText("Clustal alignment");
+    clustalAlignMenuItem.setText("Clustal Alignment");
     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -400,14 +432,29 @@ public class GAlignFrame extends JInternalFrame
     });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    alignFrameMenuBar.addAncestorListener(new AncestorListener()
+    {
+      public void ancestorAdded(AncestorEvent event)
+      {
+        alignFrameMenuBar_ancestorAdded(event);
+      }
+
+      public void ancestorRemoved(AncestorEvent event)
+      {
+      }
+
+      public void ancestorMoved(AncestorEvent event)
+      {
+      }
+    });
     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");
+    outputTextboxMenu.setText("Output to Textbox");
+    clustalColour.setText("Clustalx");
+
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -415,8 +462,7 @@ public class GAlignFrame extends JInternalFrame
         clustalColour_actionPerformed(e);
       }
     });
-    zappoColour.setSelected(true);
-    zappoColour.setText("Zappo colour scheme");
+    zappoColour.setText("Zappo");
     zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -424,7 +470,7 @@ public class GAlignFrame extends JInternalFrame
         zappoColour_actionPerformed(e);
       }
     });
-    taylorColour.setText("Taylor colour scheme");
+    taylorColour.setText("Taylor");
     taylorColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -432,7 +478,7 @@ public class GAlignFrame extends JInternalFrame
         taylorColour_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText("By hydrophobicity");
+    hydrophobicityColour.setText("Hydrophobicity");
     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -440,7 +486,7 @@ public class GAlignFrame extends JInternalFrame
         hydrophobicityColour_actionPerformed(e);
       }
     });
-    helixColour.setText("Helix propensity");
+    helixColour.setText("Helix Propensity");
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -448,7 +494,7 @@ public class GAlignFrame extends JInternalFrame
         helixColour_actionPerformed(e);
       }
     });
-    strandColour.setText("Strand propensity");
+    strandColour.setText("Strand Propensity");
     strandColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -456,7 +502,7 @@ public class GAlignFrame extends JInternalFrame
         strandColour_actionPerformed(e);
       }
     });
-    turnColour.setText("Turn propensity");
+    turnColour.setText("Turn Propensity");
     turnColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -464,7 +510,7 @@ public class GAlignFrame extends JInternalFrame
         turnColour_actionPerformed(e);
       }
     });
-    buriedColour.setText("Buried index");
+    buriedColour.setText("Buried Index");
     buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -472,157 +518,433 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);
       }
     });
-    conservationColour.setEnabled(false);
-    conservationColour.setText("By conservation");
-    conservationColour.addActionListener(new java.awt.event.ActionListener()
+    userDefinedColour.setText("User Defined...");
+    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        conservationColour_actionPerformed(e);
+        userDefinedColour_actionPerformed(e);
       }
     });
-    abovePIDColour.setEnabled(false);
-    abovePIDColour.setText("Above PID threshold only");
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+    PIDColour.setText("Percentage Identity");
+    PIDColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDColour_actionPerformed(e);
+        PIDColour_actionPerformed(e);
       }
     });
-    userDefinedColour.setText("User defined colours");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    BLOSUM62Colour.setText("BLOSUM62 Score");
+    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        userDefinedColour_actionPerformed(e);
+        BLOSUM62Colour_actionPerformed(e);
       }
     });
-    PIDColour.setEnabled(false);
-    PIDColour.setText("By PID");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
+    avDistanceTreeBlosumMenuItem.setText(
+        "Average Distance Using BLOSUM62");
+    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
+        ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        PIDColour_actionPerformed(e);
+        avTreeBlosumMenuItem_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("By BLOSUM62 score");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
+    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        BLOSUM62Colour_actionPerformed(e);
+        njTreeBlosumMenuItem_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    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)
       {
-        avTreeBlosumMenuItem_actionPerformed(e);
+        annotationPanelMenuItem_actionPerformed(e);
       }
     });
-    njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
-    njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    colourTextMenuItem.setText("Colour Text");
+    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        njTreeBlosumMenuItem_actionPerformed(e);
+        colourTextMenuItem_actionPerformed(e);
+      }
+    });
+    htmlMenuItem.setText("HTML");
+    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        htmlMenuItem_actionPerformed(e);
       }
     });
-    conservationColourIncMenuItem.setEnabled(false);
-    conservationColourIncMenuItem.setText("Conservation Colour Increment");
-    conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()
+    overviewMenuItem.setText("Overview Window");
+    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        conservationColourIncMenuItem_actionPerformed(e);
+        overviewMenuItem_actionPerformed(e);
       }
     });
-    consensusGraphMenuItem.setActionCommand("");
-    consensusGraphMenuItem.setText("Consensus graph");
-    consensusGraphMenuItem.setState(true);
-    consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
+    undoMenuItem.setEnabled(false);
+    undoMenuItem.setMnemonic('Z');
+    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)
       {
-        consensusGraphMenuItem_actionPerformed(e);
+        undoMenuItem_actionPerformed(e);
       }
     });
-    colourTextMenuItem.setText("Colour text");
-    colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+    redoMenuItem.setEnabled(false);
+    redoMenuItem.setMnemonic('0');
+    redoMenuItem.setText("Redo");
+    redoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        colourTextMenuItem_actionPerformed(e);
+        redoMenuItem_actionPerformed(e);
       }
     });
-    htmlMenuItem.setText("Output as HTML");
-    htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+    conservationMenuItem.setText("By Conservation");
+    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        htmlMenuItem_actionPerformed(e);
+        conservationMenuItem_actionPerformed(e);
       }
     });
-    schemeKeyMenuItem.setText("Colour Scheme Key");
-    schemeKeyMenuItem.addActionListener(new java.awt.event.ActionListener()
+    noColourmenuItem.setText("None");
+    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        schemeKeyMenuItem_actionPerformed(e);
+        noColourmenuItem_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText("Overview window");
-    overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+    wrapMenuItem.setText("Wrap");
+    wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        overviewMenuItem_actionPerformed(e);
+        wrapMenuItem_actionPerformed(e);
+      }
+    });
+    printMenuItem.setText("Print");
+    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);
+      }
+    });
+    searchMenu.setText("Search");
+
+    abovePIDThreshold.setText("Above Identity Threshold");
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDThreshold_actionPerformed(e);
+      }
+    });
+    sequenceFeatures.setText("Sequence Features");
+    sequenceFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        sequenceFeatures_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.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.setMnemonic(KeyEvent.VK_C);
+
+    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.setMnemonic(KeyEvent.VK_X);
+    cut.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    delete.setText("Delete");
+    delete.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        delete_actionPerformed(e);
+      }
+    });
+    jMenu1.setMnemonic('V');
+    jMenu1.setText("Paste");
+    pasteNew.setText("To New Alignment");
+    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    pasteNew.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteNew_actionPerformed(e);
+      }
+    });
+    pasteThis.setText("Add To This Alignment");
+    pasteThis.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pasteThis_actionPerformed(e);
+      }
+    });
+    applyToAllGroups.setText("Apply Colour To All Groups");
+    applyToAllGroups.setState(true);
+    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);
+      }
+    });
+    fullSeqId.setText("Show Full Sequence ID");
+    fullSeqId.setState(true);
+    fullSeqId.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fullSeqId_actionPerformed(e);
+      }
+    });
+    epsFile.setText("EPS");
+    epsFile.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createEPS(null);
+      }
+    });
+    LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
+    LoadtreeMenuItem.setText("Load Assocated Tree");
+    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        LoadtreeMenuItem_actionPerformed(e);
+      }
+    });
+    jnet.setText("JNet");
+    jnet.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        jpred_actionPerformed(e);
+      }
+    });
+    scaleAbove.setVisible(false);
+    scaleAbove.setText("Scale Above");
+    scaleAbove.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleAbove_actionPerformed(e);
+      }
+    });
+    scaleLeft.setVisible(false);
+    scaleLeft.setSelected(true);
+    scaleLeft.setText("Scale Left");
+    scaleLeft.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleLeft_actionPerformed(e);
+      }
+    });
+    scaleRight.setVisible(false);
+    scaleRight.setSelected(true);
+    scaleRight.setText("Scale Right");
+    scaleRight.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        scaleRight_actionPerformed(e);
+      }
+    });
+    modifyPID.setText("Modify Identity Threshold...");
+    modifyPID.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed(e);
+      }
+    });
+    modifyConservation.setText("Modify Conservation Threshold...");
+    modifyConservation.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed(e);
+      }
+    });
+    sortByTreeMenu.setText("By Tree Order");
+    sort.setText("Sort");
+    calculate.setText("Calculate Tree");
+    msaAlignMenuItem.setText("Muscle Alignment");
+    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        msaAlignMenuItem_actionPerformed(e);
+      }
+    });
+    jMenu2.setText("Export");
+    padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        padGapsMenuitem_actionPerformed(e);
+      }
+    });
+    ClustalRealign.setText("Clustal Realign");
+    ClustalRealign.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ClustalRealign_actionPerformed(e);
       }
     });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(fontMenu);
+    alignFrameMenuBar.add(searchMenu);
     alignFrameMenuBar.add(viewMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(alignMenu);
     fileMenu.add(saveAlignmentMenu);
-    fileMenu.add(saveAsPostscriptMenuItem);
+    fileMenu.add(jMenu2);
     fileMenu.add(outputTextboxMenu);
-    fileMenu.add(htmlMenuItem);
+    fileMenu.add(printMenuItem);
+    fileMenu.addSeparator();
+    fileMenu.add(LoadtreeMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
-    editMenu.add(groupsMenuItem);
-    editMenu.add(groupEditingMenuItem);
+    editMenu.add(undoMenuItem);
+    editMenu.add(redoMenuItem);
+    editMenu.add(cut);
+    editMenu.add(copy);
+    editMenu.add(jMenu1);
+    editMenu.add(delete);
     editMenu.addSeparator();
     editMenu.add(selectAllSequenceMenuItem);
     editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
+    editMenu.add(deleteGroups);
     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);
-    fontMenu.addSeparator();
-    fontMenu.add(colourTextMenuItem);
+    editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(padGapsMenuitem);
+    searchMenu.add(findMenuItem);
+    viewMenu.add(font);
+    viewMenu.addSeparator();
+    viewMenu.add(wrapMenuItem);
+    viewMenu.add(fullSeqId);
+    viewMenu.add(scaleAbove);
+    viewMenu.add(scaleLeft);
+    viewMenu.add(scaleRight);
     viewMenu.add(viewBoxesMenuItem);
     viewMenu.add(viewTextMenuItem);
-    viewMenu.add(consensusGraphMenuItem);
+    viewMenu.add(colourTextMenuItem);
+    viewMenu.add(renderGapsMenuItem);
+    viewMenu.add(annotationPanelMenuItem);
+    viewMenu.add(sequenceFeatures);
+    viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
+    colourMenu.add(applyToAllGroups);
+    colourMenu.addSeparator();
+    colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
     colourMenu.add(zappoColour);
     colourMenu.add(taylorColour);
     colourMenu.add(hydrophobicityColour);
@@ -630,317 +952,324 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(strandColour);
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
+    colourMenu.add(nucleotideColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
-    colourMenu.add(conservationColour);
-    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(conservationMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDThreshold);
+    colourMenu.add(modifyPID);
+    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);
+    calculateMenu.add(webService);
+    webService.add(clustalAlignMenuItem);
+    webService.add(msaAlignMenuItem);
+    webService.add(jnet);
+    webService.add(ClustalRealign);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-  }
-
-  protected void saveAs_actionPerformed(ActionEvent e)
-  {
-
+    jMenu1.add(pasteNew);
+    jMenu1.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);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-
-  }
-
-
-
-  protected void saveAsPostscriptMenuItem_actionPerformed(ActionEvent e)
-  {
-
   }
 
-
   protected void closeMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void groupsMenuItem_actionPerformed(ActionEvent e)
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void groupEditingMenuItem_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 moveSelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void copySelectedMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
-  {
-
   }
 
   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-
-  }
-
-  protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-  protected void fontNameMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
-  {
-
   }
 
-  protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
+  protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
-
-  protected void consensusGraphMenuItem_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 sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
-
-  }
-
-  protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
-  {
-
   }
 
   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void clustalColour_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void zappoColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  protected void taylorColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void helixColour_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void strandColour_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void turnColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void clustalColour_actionPerformed(ActionEvent e)
+  protected void buriedColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
+  protected void PIDColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void printMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void findMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  {
   }
 
-  protected void strandColour_actionPerformed(ActionEvent e)
+  protected void nucleotideColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
+  protected void copy_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void cut_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
+  protected void delete_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void pasteNew_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void conservationColour_actionPerformed(ActionEvent e)
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void createPNG(java.io.File f)
+  {
   }
 
-  protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
- {
+  protected void font_actionPerformed(ActionEvent e)
+  {
+  }
 
- }
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+  }
 
+  public void createEPS(java.io.File f)
+  {
+  }
 
-  protected void abovePIDColour_actionPerformed(ActionEvent e)
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void jpred_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  protected void scaleLeft_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  protected void preferences_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
+  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
   {
+  }
 
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void ClustalRealign_actionPerformed(ActionEvent e)
+  {
+  }
 }