X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=f5df9993cbaa0a9684997c4e6aa4f33ce2a3e5f3;hb=17bca4a0049fb17668caea440e807d8d8c169a6a;hp=11d1ff3ea212fd11402e1f58d16c4a3cb2f71baa;hpb=a291866e1f09688953bd4eb49a0ab1c9d325d8d6;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 11d1ff3..f5df999 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,47 +1,53 @@
-/********************
- * 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.*;
 
-public class GAlignFrame extends JInternalFrame
+import jalview.schemes.*;
+
+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 JMenu webService = new JMenu();
+  protected JMenuItem webServiceNoServices;
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
-  protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
   protected JMenuItem remove2RightMenuItem = new JMenuItem();
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-  protected JMenuItem setGapCharMenuItem = new JMenuItem();
-  protected 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();
@@ -50,12 +56,13 @@ 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();
@@ -65,22 +72,21 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
   JMenuItem avDistanceTreeBlosumMenuItem = 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 overviewMenuItem = new JMenuItem();
   protected JMenuItem undoMenuItem = new JMenuItem();
   protected JMenuItem redoMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-  JMenuItem pdbTest = new JMenuItem();
+  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
   JMenuItem printMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
   JMenuItem findMenuItem = new JMenuItem();
   JMenu searchMenu = new JMenu();
-  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   JMenuItem delete = new JMenuItem();
@@ -89,6 +95,36 @@ public class GAlignFrame extends JInternalFrame
   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 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 JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
+  //protected JTabbedPane tabbedPane = new JTabbedPane();
+  public JMenuItem featureSettings = new JMenuItem();
+  JMenuItem fetchSequence = new JMenuItem();
+  protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
+  JMenuItem annotationColour = new JMenuItem();
+  JMenuItem fetchSeqFeatures = new JMenuItem();
+
+
+
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
 
@@ -98,20 +134,12 @@ 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);
-          }
-        });
-
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      {
+        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+                             elementAt(
+                                 i));
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -120,16 +148,63 @@ public class GAlignFrame extends JInternalFrame
           }
         });
 
-        outputTextboxMenu.add( item );
+        outputTextboxMenu.add(item);
       }
-
     }
-    catch(Exception e)
+    catch (Exception e)
     {
-      e.printStackTrace();
     }
 
-    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);
@@ -143,13 +218,103 @@ public class GAlignFrame extends JInternalFrame
     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");
+    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)
+      {
+        saveAlignmentMenu_actionPerformed(e);
+      }
+    });
     closeMenuItem.setMnemonic('C');
     closeMenuItem.setText("Close");
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -160,36 +325,35 @@ 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.setText("Groups");
-    groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        groupsMenuItem_actionPerformed(e);
-      }
-    });
+    webService.setText("Web Service");
     selectAllSequenceMenuItem.setText("Select all");
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+    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 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)
@@ -197,15 +361,7 @@ public class GAlignFrame extends JInternalFrame
         invertSequenceMenuItem_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)
@@ -213,7 +369,7 @@ 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)
@@ -221,15 +377,16 @@ 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)
@@ -237,37 +394,6 @@ 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()
@@ -286,7 +412,7 @@ 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)
@@ -294,7 +420,7 @@ 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)
@@ -302,7 +428,7 @@ 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)
@@ -310,31 +436,25 @@ 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)
@@ -342,15 +462,17 @@ 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)
@@ -358,14 +480,6 @@ public class GAlignFrame extends JInternalFrame
         neighbourTreeMenuItem_actionPerformed(e);
       }
     });
-    clustalAlignMenuItem.setText("Clustal alignment");
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalAlignMenuItem_actionPerformed(e);
-      }
-    });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
@@ -373,9 +487,9 @@ public class GAlignFrame extends JInternalFrame
     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)
@@ -383,7 +497,7 @@ public class GAlignFrame extends JInternalFrame
         clustalColour_actionPerformed(e);
       }
     });
-    zappoColour.setText("Zappo colour scheme");
+    zappoColour.setText("Zappo");
     zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -391,7 +505,7 @@ 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)
@@ -399,7 +513,7 @@ 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)
@@ -407,7 +521,7 @@ 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)
@@ -415,7 +529,7 @@ 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)
@@ -423,7 +537,7 @@ 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)
@@ -431,7 +545,7 @@ 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)
@@ -439,7 +553,7 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);
       }
     });
-    userDefinedColour.setText("User defined colours");
+    userDefinedColour.setText("User Defined...");
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -455,7 +569,7 @@ public class GAlignFrame extends JInternalFrame
         PIDColour_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("BLOSUM62 score");
+    BLOSUM62Colour.setText("BLOSUM62 Score");
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -463,15 +577,17 @@ public class GAlignFrame extends JInternalFrame
         BLOSUM62Colour_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
-    avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+    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 tree using BLOSUM62");
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -479,17 +595,17 @@ public class GAlignFrame extends JInternalFrame
         njTreeBlosumMenuItem_actionPerformed(e);
       }
     });
-    consensusGraphMenuItem.setActionCommand("");
-    consensusGraphMenuItem.setText("Consensus graph");
-    consensusGraphMenuItem.setState(true);
-    consensusGraphMenuItem.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)
       {
-        consensusGraphMenuItem_actionPerformed(e);
+        annotationPanelMenuItem_actionPerformed(e);
       }
     });
-    colourTextMenuItem.setText("Colour text");
+    colourTextMenuItem.setText("Colour Text");
     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -497,7 +613,7 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
-    htmlMenuItem.setText("Output as HTML");
+    htmlMenuItem.setText("HTML");
     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -505,7 +621,7 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);
       }
     });
-    overviewMenuItem.setText("Overview window");
+    overviewMenuItem.setText("Overview Window");
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -516,6 +632,9 @@ public class GAlignFrame extends JInternalFrame
     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)
@@ -533,7 +652,7 @@ public class GAlignFrame extends JInternalFrame
         redoMenuItem_actionPerformed(e);
       }
     });
-    conservationMenuItem.setText("By conservation");
+    conservationMenuItem.setText("By Conservation");
     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -542,7 +661,6 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     noColourmenuItem.setText("None");
-    noColourmenuItem.setSelected(true);
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -550,7 +668,7 @@ public class GAlignFrame extends JInternalFrame
         noColourmenuItem_actionPerformed(e);
       }
     });
-    wrapMenuItem.setText("Wrap alignment");
+    wrapMenuItem.setText("Wrap");
     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -558,14 +676,6 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
-    pdbTest.setText("PDB Test Viewer");
-    pdbTest.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pdbTest_actionPerformed(e);
-      }
-    });
     printMenuItem.setText("Print");
     printMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -574,7 +684,7 @@ public class GAlignFrame extends JInternalFrame
         printMenuItem_actionPerformed(e);
       }
     });
-    renderGapsMenuItem.setText("Render gaps");
+    renderGapsMenuItem.setText("Show Gaps");
     renderGapsMenuItem.setState(true);
     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -583,7 +693,10 @@ public class GAlignFrame extends JInternalFrame
         renderGapsMenuItem_actionPerformed(e);
       }
     });
-    findMenuItem.setText("Find");
+    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)
@@ -593,22 +706,23 @@ public class GAlignFrame extends JInternalFrame
     });
     searchMenu.setText("Search");
 
-    abovePIDThreshold.setText("Above PID threshold");
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
+    abovePIDThreshold.setText("Above Identity Threshold");
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    sequenceFeatures.setSelected(true);
-    sequenceFeatures.setText("Sequence Features");
-    sequenceFeatures.addActionListener(new ActionListener()
+    showSeqFeatures.setText("Show Sequence Features");
+    showSeqFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
-        sequenceFeatures_actionPerformed(actionEvent);
+        showSeqFeatures_actionPerformed(actionEvent);
       }
     });
-    nucleotideColour.setText("Nucleotide colours");
+    nucleotideColour.setText("Nucleotide");
     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -616,8 +730,7 @@ public class GAlignFrame extends JInternalFrame
         nucleotideColour_actionPerformed(e);
       }
     });
-    deleteGroups.setSelected(false);
-    deleteGroups.setText("Delete all groups");
+    deleteGroups.setText("Undefine groups");
     deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -626,6 +739,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     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()
@@ -636,6 +752,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     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()
     {
@@ -654,7 +773,10 @@ public class GAlignFrame extends JInternalFrame
     });
     jMenu1.setMnemonic('V');
     jMenu1.setText("Paste");
-    pasteNew.setText("to new alignment");
+    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)
@@ -662,7 +784,7 @@ public class GAlignFrame extends JInternalFrame
         pasteNew_actionPerformed(e);
       }
     });
-    pasteThis.setText("add to this alignment");
+    pasteThis.setText("Add To This Alignment");
     pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -670,55 +792,266 @@ public class GAlignFrame extends JInternalFrame
         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);
+      }
+    });
+
+    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);
+      }
+    });
+    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)
+      {
+        LoadtreeMenuItem_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");
+
+    jMenu2.setText("Export");
+    padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
+    padGapsMenuitem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        padGapsMenuitem_actionPerformed(e);
+      }
+    });
+    vamsasStore.setVisible(false);
+    vamsasStore.setText("VAMSAS store");
+    vamsasStore.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasStore_actionPerformed(e);
+      }
+    });
+    showTranslation.setText("Translate cDNA");
+    showTranslation.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showTranslation_actionPerformed(e);
+      }
+    });
+
+   /* tabbedPane.addChangeListener(new ChangeListener()
+        {
+          public void stateChanged(ChangeEvent ece)
+          {
+
+            tabSelected();
+          }
+        });*/
+    featureSettings.setText("Feature Settings...");
+    featureSettings.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        featureSettings_actionPerformed(e);
+      }
+    });
+    fetchSequence.setText("Fetch Sequence(s)...");
+    fetchSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSequence_actionPerformed(e);
+      }
+    });
+    smoothFont.setText("Smooth Fonts");
+    smoothFont.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        smoothFont_actionPerformed(e);
+      }
+    });
+    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_actionPerformed(e);
+      }
+    });
+    fetchSeqFeatures.setText("Fetch Sequence Features");
+    fetchSeqFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSeqFeatures_actionPerformed(e);
+      }
+    });
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        associatedData_actionPerformed(e);
+      }
+    });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
-    alignFrameMenuBar.add(fontMenu);
     alignFrameMenuBar.add(viewMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(alignMenu);
+    alignFrameMenuBar.add(webService);
+    fileMenu.add(fetchSequence);
+    fileMenu.addSeparator();
+    fileMenu.add(vamsasStore);
     fileMenu.add(saveAlignmentMenu);
+    fileMenu.add(jMenu2);
     fileMenu.add(outputTextboxMenu);
-    fileMenu.add(htmlMenuItem);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    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(jMenu1);
-    editMenu.add(cut);
     editMenu.add(delete);
     editMenu.addSeparator();
-    editMenu.add(undoMenuItem);
-    editMenu.add(redoMenuItem);
-    editMenu.addSeparator();
-    editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(selectAllSequenceMenuItem);
+    editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
     editMenu.add(deleteGroups);
-    editMenu.add(groupsMenuItem);
     editMenu.addSeparator();
-    editMenu.add(deselectAllColumnsMenuItem);
     editMenu.add(remove2LeftMenuItem);
     editMenu.add(remove2RightMenuItem);
-    editMenu.addSeparator();
     editMenu.add(removeGappedColumnMenuItem);
     editMenu.add(removeAllGapsMenuItem);
-    editMenu.add(setGapCharMenuItem);
+    editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(padGapsMenuitem);
     searchMenu.add(findMenuItem);
-    fontMenu.add(fontNameMenuItem);
-    fontMenu.add(fontSizeMenuItem);
-    fontMenu.add(fontStyleMenuItem);
+    viewMenu.add(font);
+    viewMenu.add(smoothFont);
+    viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
+    viewMenu.add(seqLimits);
+    viewMenu.add(scaleAbove);
+    viewMenu.add(scaleLeft);
+    viewMenu.add(scaleRight);
     viewMenu.add(viewBoxesMenuItem);
     viewMenu.add(viewTextMenuItem);
     viewMenu.add(colourTextMenuItem);
     viewMenu.add(renderGapsMenuItem);
-    viewMenu.add(consensusGraphMenuItem);
+    viewMenu.add(annotationPanelMenuItem);
+    viewMenu.addSeparator();
+    viewMenu.add(fetchSeqFeatures);
+    viewMenu.add(showSeqFeatures);
+    viewMenu.add(featureSettings);
+    viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
-    viewMenu.add(sequenceFeatures);
+    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);
@@ -728,369 +1061,362 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(userDefinedColour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(BLOSUM62Colour);
     colourMenu.addSeparator();
-    colourMenu.add(abovePIDThreshold);
     colourMenu.add(conservationMenuItem);
-    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);
+    calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
+    webServiceNoServices=new JMenuItem("<No Services>");
+    webService.add(webServiceNoServices);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
+  //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
     jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
-  }
-
-  protected void saveAs_actionPerformed(ActionEvent e)
-  {
-
+    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 closeMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-
-  }
-
-
-  protected void groupsMenuItem_actionPerformed(ActionEvent e)
-  {
-
   }
 
-
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void invertSequenceMenuItem_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 clustalColour_actionPerformed(ActionEvent e)
+  {
+  }
 
-
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+  protected void zappoColour_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 clustalColour_actionPerformed(ActionEvent e)
+  protected void turnColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void buriedColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
+  protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void PIDColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
+  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  protected void printMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
+  protected void findMenuItem_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void strandColour_actionPerformed(ActionEvent e)
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
   {
+  }
 
+  protected void nucleotideColour_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
+  protected void deleteGroups_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void copy_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
+  protected void cut_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void delete_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void pasteNew_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void pasteThis_actionPerformed(ActionEvent e)
+  {
+  }
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
   {
+  }
 
+  public void createPNG(java.io.File f)
+  {
   }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
+  protected void font_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void seqLimit_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  public void seqDBRef_actionPerformed(ActionEvent e)
   {
 
   }
 
 
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  public void createEPS(java.io.File f)
   {
-
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void pdbTest_actionPerformed(ActionEvent e)
+  protected void jpred_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void printMenuItem_actionPerformed(ActionEvent e)
+  protected void scaleLeft_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void findMenuItem_actionPerformed(ActionEvent e)
+
+
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
   }
 
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+  public void vamsasStore_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  public void vamsasLoad_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void deleteGroups_actionPerformed(ActionEvent e)
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
 
   }
 
- protected void copy_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
-
-  protected void cut_actionPerformed(ActionEvent e)
+  public void smoothFont_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  public void annotationColour_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
+  public void associatedData_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
 
-
+  }
 }