X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d0327564b480118eb1ca9e9cb92ed8bcd973ebf6;hb=8c4f77adba0521e7dc89dcb77fe2f8b28c62f70d;hp=23c78f3be5a3a65a55c3589f364d5d7137d20c7f;hpb=40c5abaee48533a19613d9566099a92a60e841d4;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 23c78f3..d032756 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,23 +1,36 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.jbgui;
 
-import javax.swing.*;
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
 
-import jalview.gui.Preferences;
-import jalview.schemes.ColourSchemeProperty;
-import javax.swing.event.AncestorListener;
-import javax.swing.event.AncestorEvent;
+import jalview.schemes.*;
+import java.awt.BorderLayout;
 
-public class GAlignFrame extends JInternalFrame
+
+
+
+public class GAlignFrame
+    extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
   protected JMenu fileMenu = new JMenu();
@@ -27,6 +40,7 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu colourMenu = new JMenu();
   protected JMenu calculateMenu = new JMenu();
   protected JMenu webService = new JMenu();
+  protected JMenuItem webServiceNoServices;
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
@@ -34,8 +48,8 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem remove2RightMenuItem = new JMenuItem();
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
   protected JMenuItem removeAllGapsMenuItem = 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();
@@ -44,15 +58,15 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem PCAMenuItem = new JMenuItem();
   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
-  protected JMenuItem clustalAlignMenuItem = new JMenuItem();
   BorderLayout borderLayout1 = new BorderLayout();
   public JLabel statusBar = new JLabel();
-  protected JMenuItem saveAlignmentMenu = new JMenuItem();
+  protected JMenuItem saveAs = new JMenuItem();
   protected JMenu outputTextboxMenu = new JMenu();
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+  protected JRadioButtonMenuItem hydrophobicityColour = new
+      JRadioButtonMenuItem();
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
@@ -62,51 +76,167 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
   JMenuItem njTreeBlosumMenuItem = new JMenuItem();
   JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
   JMenuItem htmlMenuItem = new JMenuItem();
   JMenuItem overviewMenuItem = new JMenuItem();
   protected JMenuItem undoMenuItem = new JMenuItem();
   protected JMenuItem redoMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
   JMenuItem printMenuItem = new JMenuItem();
-  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
   JMenuItem findMenuItem = new JMenuItem();
-  JMenu searchMenu = new JMenu();
-  protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   JMenuItem delete = new JMenuItem();
   JMenuItem copy = new JMenuItem();
   JMenuItem cut = new JMenuItem();
-  JMenu jMenu1 = new JMenu();
+  JMenu pasteMenu = new JMenu();
   JMenuItem pasteNew = new JMenuItem();
   JMenuItem pasteThis = new JMenuItem();
-  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
   JMenuItem createPNG = new JMenuItem();
   protected JMenuItem font = new JMenuItem();
-  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
   JMenuItem epsFile = new JMenuItem();
   JMenuItem LoadtreeMenuItem = new JMenuItem();
-  JMenuItem jpred = new JMenuItem();
-  protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
-  JMenuItem modifyPID = new JMenuItem();
-  JMenuItem modifyConservation = new JMenuItem();
+  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  protected JMenuItem modifyPID = new JMenuItem();
+  protected JMenuItem modifyConservation = new JMenuItem();
   protected JMenu sortByTreeMenu = new JMenu();
   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();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+  protected ButtonGroup colours = new ButtonGroup();
+  JMenuItem vamsasStore = new JMenuItem();
+  protected JMenuItem showTranslation = new JMenuItem();
+  public JMenuItem featureSettings = new JMenuItem();
+  JMenuItem fetchSequence = new JMenuItem();
+  JMenuItem annotationColour = new JMenuItem();
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+  JMenu addSequenceMenu = new JMenu();
+  JMenuItem addFromFile = new JMenuItem();
+  JMenuItem addFromText = new JMenuItem();
+  JMenuItem addFromURL = new JMenuItem();
+  JMenuItem exportAnnotations = new JMenuItem();
+  JMenuItem exportFeatures = new JMenuItem();
+  protected JPanel statusPanel = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
+  JMenu jMenu3 = new JMenu();
+  JMenuItem showAllSeqs = new JMenuItem();
+  JMenuItem showAllColumns = new JMenuItem();
+  JMenu hideMenu = new JMenu();
+  JMenuItem hideSelSequences = new JMenuItem();
+  JMenuItem hideSelColumns = new JMenuItem();
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+  JMenuItem invertColSel = new JMenuItem();
+  protected JTabbedPane tabbedPane = new JTabbedPane();
+  JMenuItem save = new JMenuItem();
+  JMenuItem jMenuItem1 = new JMenuItem();
+  protected JMenuItem reload = new JMenuItem();
+  JMenuItem newView = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+  JCheckBoxMenuItem jCheckBoxMenuItem1 = new JCheckBoxMenuItem();
+  JMenu jMenu4 = new JMenu();
+  protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
   public GAlignFrame()
   {
-    ButtonGroup colours = new ButtonGroup();
+    try
+    {
+      jbInit();
+      setJMenuBar(alignFrameMenuBar);
+
+      // dynamically fill save as menu with available formats
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      {
+        JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            outputText_actionPerformed(e);
+          }
+        });
+
+        outputTextboxMenu.add(item);
+      }
+    }
+    catch (Exception e)
+    {
+    }
+
+    if (!System.getProperty("os.name").startsWith("Mac"))
+    {
+      closeMenuItem.setMnemonic('C');
+      outputTextboxMenu.setMnemonic('T');
+      undoMenuItem.setMnemonic('Z');
+      redoMenuItem.setMnemonic('0');
+      copy.setMnemonic('C');
+      cut.setMnemonic('U');
+      pasteMenu.setMnemonic('P');
+      reload.setMnemonic('R');
+    }
+
+
+    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);
@@ -121,75 +251,109 @@ public class GAlignFrame extends JInternalFrame
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
 
-   noColourmenuItem.setSelected(true);
-   String defaultColour = Preferences.defaultColour;
-   if(defaultColour!=null)
-   {
-   int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
-   switch(index)
-   {
-     case ColourSchemeProperty.CLUSTAL : clustalColour.setSelected(true); break;
-     case ColourSchemeProperty.BLOSUM : BLOSUM62Colour.setSelected(true); break;
-     case ColourSchemeProperty.PID : PIDColour.setSelected(true); break;
-     case ColourSchemeProperty.ZAPPO : zappoColour.setSelected(true); break;
-     case ColourSchemeProperty.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;
-   }
-   }
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
 
 
-    try
+  }
+
+  public void setColourSelected(String defaultColour)
+  {
+
+    if (defaultColour != null)
     {
-      jbInit();
-      setJMenuBar(alignFrameMenuBar);
+      int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
 
-      JMenuItem item;
-      // 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)
-          {
-            outputText_actionPerformed(e);
-          }
-        });
+      switch (index)
+      {
+        case ColourSchemeProperty.NONE:
+              noColourmenuItem.setSelected(true);
+              break;
+        case ColourSchemeProperty.CLUSTAL:
+          clustalColour.setSelected(true);
 
-        outputTextboxMenu.add( item );
-      }
+          break;
 
-    }
-    catch(Exception e)
-    {
-      e.printStackTrace();
+        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
+
+  private void jbInit()
+      throws Exception
   {
-    fileMenu.setMnemonic('F');
     fileMenu.setText("File");
-    saveAlignmentMenu.setMnemonic('L');
-    saveAlignmentMenu.setText("Save As");
-    saveAlignmentMenu.addActionListener(new ActionListener()
+    saveAs.setText("Save As...");
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()| java.awt.event.KeyEvent.SHIFT_MASK, false));
+    saveAs.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        saveAlignmentMenu_actionPerformed(e);
+        saveAs_actionPerformed(e);
       }
     });
-    closeMenuItem.setMnemonic('C');
     closeMenuItem.setText("Close");
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        closeMenuItem_actionPerformed(e);
+        closeMenuItem_actionPerformed(false);
       }
     });
     editMenu.setText("Edit");
@@ -197,10 +361,12 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
     webService.setText("Web Service");
-    selectAllSequenceMenuItem.setText("Select all");
+    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()
+        java.awt.event.KeyEvent.VK_A,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -209,16 +375,20 @@ public class GAlignFrame extends JInternalFrame
     });
     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()
+                                               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 Selection");
+    invertSequenceMenuItem.setText("Invert Sequence Selection");
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_I,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.SHIFT_MASK, false));
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -227,6 +397,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     remove2LeftMenuItem.setText("Remove Left");
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -235,6 +407,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     remove2RightMenuItem.setText("Remove Right");
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_R, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -243,7 +417,11 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     removeGappedColumnMenuItem.setText("Remove Empty Columns");
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                              getKeyStroke(java.awt.event.
+        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+                                                 ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -251,6 +429,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     removeAllGapsMenuItem.setText("Remove All Gaps");
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_E,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -301,7 +482,10 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     removeRedundancyMenuItem.setText("Remove Redundancy...");
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    removeRedundancyMenuItem.addActionListener(new java.awt.event.
+                                               ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -309,14 +493,15 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
-    pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+    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)
@@ -324,15 +509,17 @@ public class GAlignFrame extends JInternalFrame
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
-    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 Using % Identity...");
+    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -340,36 +527,12 @@ 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));
-    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 to Textbox");
     clustalColour.setText("Clustalx");
 
@@ -460,15 +623,17 @@ public class GAlignFrame extends JInternalFrame
         BLOSUM62Colour_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText("Average Distance 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 using BLOSUM62...");
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -478,7 +643,7 @@ public class GAlignFrame extends JInternalFrame
     });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState( jalview.gui.Preferences.showAnnotation );
+    annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -502,7 +667,7 @@ 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)
@@ -511,10 +676,10 @@ 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.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)
@@ -523,8 +688,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     redoMenuItem.setEnabled(false);
-    redoMenuItem.setMnemonic('0');
     redoMenuItem.setText("Redo");
+    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     redoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -557,6 +723,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     printMenuItem.setText("Print");
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     printMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -574,8 +742,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     findMenuItem.setText("Find...");
-    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
-        event.KeyEvent.VK_F, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    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)
@@ -583,20 +752,20 @@ public class GAlignFrame extends JInternalFrame
         findMenuItem_actionPerformed(e);
       }
     });
-    searchMenu.setText("Search");
-
     abovePIDThreshold.setText("Above Identity Threshold");
-    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
-      public void actionPerformed(ActionEvent e) {
+    abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    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");
@@ -608,6 +777,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     deleteGroups.setText("Undefine groups");
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -616,9 +787,9 @@ 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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_C,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
 
     copy.addActionListener(new java.awt.event.ActionListener()
     {
@@ -628,9 +799,9 @@ 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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_X,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     cut.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -639,6 +810,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     delete.setText("Delete");
+    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_BACK_SPACE, 0, false));
     delete.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -646,11 +819,11 @@ public class GAlignFrame extends JInternalFrame
         delete_actionPerformed(e);
       }
     });
-    jMenu1.setMnemonic('V');
-    jMenu1.setText("Paste");
+    pasteMenu.setText("Paste");
     pasteNew.setText("To New Alignment");
-    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.ALT_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -659,6 +832,9 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     pasteThis.setText("Add To This Alignment");
+    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_V,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     pasteThis.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -667,7 +843,6 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     applyToAllGroups.setText("Apply Colour To All Groups");
-    applyToAllGroups.setState(true);
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -679,7 +854,7 @@ public class GAlignFrame extends JInternalFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        createPNG_actionPerformed(e);
+        createPNG(null);
       }
     });
     createPNG.setActionCommand("Save As PNG Image");
@@ -692,13 +867,14 @@ public class GAlignFrame extends JInternalFrame
         font_actionPerformed(e);
       }
     });
-    fullSeqId.setText("Show Full Sequence ID");
-    fullSeqId.setState(true);
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+    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)
       {
-        fullSeqId_actionPerformed(e);
+        seqLimit_actionPerformed(e);
       }
     });
     epsFile.setText("EPS");
@@ -706,23 +882,16 @@ public class GAlignFrame extends JInternalFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        epsFile_actionPerformed(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);
-      }
-    });
-    jpred.setText("JPred...");
-    jpred.addActionListener(new java.awt.event.ActionListener()
+    LoadtreeMenuItem.setText("Load Associated Tree");
+    LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        jpred_actionPerformed(e);
+        LoadtreeMenuItem_actionPerformed(e);
       }
     });
     scaleAbove.setVisible(false);
@@ -773,14 +942,10 @@ public class GAlignFrame extends JInternalFrame
     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");
+
+    jMenu2.setText("Export Image");
     padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -788,40 +953,267 @@ public class GAlignFrame extends JInternalFrame
         padGapsMenuitem_actionPerformed(e);
       }
     });
-    ClustalRealign.setText("Clustal Realign...");
-    ClustalRealign.addActionListener(new ActionListener()
+    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);
+      }
+    });
+
+
+    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);
+      }
+    });
+
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_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);
+      }
+    });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportFeatures_actionPerformed(e);
+      }
+    });
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportAnnotations_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
+    jMenu3.setText("Show");
+    showAllSeqs.setText("All Sequences");
+    showAllSeqs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllSeqs_actionPerformed(e);
+      }
+    });
+    showAllColumns.setText("All Columns");
+    showAllColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showAllColumns_actionPerformed(e);
+      }
+    });
+    hideMenu.setText("Hide");
+    hideSelSequences.setText("Selected Sequences");
+    hideSelSequences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelSequences_actionPerformed(e);
+      }
+    });
+    hideSelColumns.setText("Selected Columns");
+    hideSelColumns.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hideSelColumns_actionPerformed(e);
+      }
+    });
+    hiddenMarkers.setText("Show Hidden Markers");
+    hiddenMarkers.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hiddenMarkers_actionPerformed(e);
+      }
+    });
+    invertColSel.setText("Invert Column Selection");
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_I, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    invertColSel.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        invertColSel_actionPerformed(e);
+      }
+    });
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+    {
+        public void stateChanged(ChangeEvent evt)
+        {
+            JTabbedPane pane = (JTabbedPane)evt.getSource();
+            int sel = pane.getSelectedIndex();
+            tabSelectionChanged(sel);
+        }
+    });
+    tabbedPane.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        tabbedPane_mousePressed(e);
+      }
+    });
+    tabbedPane.addFocusListener(new FocusAdapter()
+    {
+      public void focusGained(FocusEvent e)
+      {
+        tabbedPane_focusGained(e);
+      }
+    });
+    save.setText("Save");
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    save.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        ClustalRealign_actionPerformed(e);
+        save_actionPerformed(e);
       }
     });
+    reload.setEnabled(false);
+    reload.setText("Reload");
+    reload.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        reload_actionPerformed(e);
+      }
+    });
+    newView.setText("New View");
+    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    newView.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        newView_actionPerformed(e);
+      }
+    });
+    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
+                              +"<br> Press X to eXpand tabs, G to reGroup.</i></html>");
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed(e);
+      }
+    });
+    jMenu1.setText("Format");
+    jCheckBoxMenuItem1.setText("Right Align Ids");
+    jMenu4.setText("Select");
+    idRightAlign.setText("Right Align Sequence Id");
+    idRightAlign.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        idRightAlign_actionPerformed(e);
+      }
+    });
+
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
-    alignFrameMenuBar.add(searchMenu);
+    alignFrameMenuBar.add(jMenu4);
     alignFrameMenuBar.add(viewMenu);
+    alignFrameMenuBar.add(jMenu1);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    fileMenu.add(saveAlignmentMenu);
-    fileMenu.add(jMenu2);
+    alignFrameMenuBar.add(webService);
+    fileMenu.add(fetchSequence);
+    fileMenu.add(addSequenceMenu);
+    fileMenu.add(reload);
+    fileMenu.addSeparator();
+    fileMenu.add(vamsasStore);
+    fileMenu.add(save);
+    fileMenu.add(saveAs);
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    fileMenu.add(jMenu2);
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
     editMenu.add(redoMenuItem);
     editMenu.add(cut);
     editMenu.add(copy);
-    editMenu.add(jMenu1);
+    editMenu.add(pasteMenu);
     editMenu.add(delete);
     editMenu.addSeparator();
-    editMenu.add(selectAllSequenceMenuItem);
-    editMenu.add(deselectAllSequenceMenuItem);
-    editMenu.add(invertSequenceMenuItem);
-    editMenu.add(deleteGroups);
-    editMenu.addSeparator();
     editMenu.add(remove2LeftMenuItem);
     editMenu.add(remove2RightMenuItem);
     editMenu.add(removeGappedColumnMenuItem);
@@ -829,23 +1221,19 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
-    searchMenu.add(findMenuItem);
-    viewMenu.add(font);
+    viewMenu.add(newView);
+    viewMenu.addSeparator();
+    viewMenu.add(jMenu3);
+    viewMenu.add(hideMenu);
     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(colourTextMenuItem);
-    viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
-    viewMenu.add(sequenceFeatures);
+    viewMenu.addSeparator();
+    viewMenu.add(showSeqFeatures);
+    viewMenu.add(featureSettings);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
+    colourMenu.add(textColour);
     colourMenu.addSeparator();
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
@@ -865,20 +1253,18 @@ public class GAlignFrame extends JInternalFrame
     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(webService);
-    webService.add(clustalAlignMenuItem);
-    webService.add(msaAlignMenuItem);
-    webService.add(jpred);
-    webService.add(ClustalRealign);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-    jMenu1.add(pasteNew);
-    jMenu1.add(pasteThis);
+    calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
+    webServiceNoServices=new JMenuItem("<No Services>");
+    webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
@@ -889,382 +1275,468 @@ public class GAlignFrame extends JInternalFrame
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
+    addSequenceMenu.add(addFromFile);
+    addSequenceMenu.add(addFromText);
+    addSequenceMenu.add(addFromURL);
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
+    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+    jMenu3.add(showAllColumns);
+    jMenu3.add(showAllSeqs);
+    hideMenu.add(hideSelColumns);
+    hideMenu.add(hideSelSequences);
+    jMenu1.add(font);
+    jMenu1.addSeparator();
+    jMenu1.add(wrapMenuItem);
+    jMenu1.add(scaleAbove);
+    jMenu1.add(scaleLeft);
+    jMenu1.add(scaleRight);
+    jMenu1.add(seqLimits);
+    jMenu1.add(idRightAlign);
+    jMenu1.add(hiddenMarkers);
+    jMenu1.add(viewBoxesMenuItem);
+    jMenu1.add(viewTextMenuItem);
+    jMenu1.add(colourTextMenuItem);
+    jMenu1.add(renderGapsMenuItem);
+    jMenu4.add(findMenuItem);
+    jMenu4.addSeparator();
+    jMenu4.add(selectAllSequenceMenuItem);
+    jMenu4.add(deselectAllSequenceMenuItem);
+    jMenu4.add(invertSequenceMenuItem);
+    jMenu4.add(invertColSel);
+    jMenu4.add(deleteGroups);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
+  }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  public void addFromText_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
 
-  protected void closeMenuItem_actionPerformed(ActionEvent e)
+  public void exportFeatures_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  public void exportAnnotations_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  protected void htmlMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void closeMenuItem_actionPerformed(boolean b)
   {
+  }
 
+  protected void redoMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void undoMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void colourTextMenuItem_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 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 printMenuItem_actionPerformed(ActionEvent e)
+  protected void jpred_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleAbove_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+  protected void scaleLeft_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void scaleRight_actionPerformed(ActionEvent e)
+  {
   }
 
-  protected void findMenuItem_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed(ActionEvent e)
   {
+  }
 
+  protected void modifyConservation_actionPerformed(ActionEvent e)
+  {
   }
 
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
 
+  protected void saveAs_actionPerformed(ActionEvent e)
+  {
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
+
+  public void vamsasStore_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void deleteGroups_actionPerformed(ActionEvent e)
+  public void vamsasLoad_actionPerformed(ActionEvent e)
   {
 
   }
 
- protected void copy_actionPerformed(ActionEvent e)
+  public void showTranslation_actionPerformed(ActionEvent e)
   {
 
   }
 
-
-  protected void cut_actionPerformed(ActionEvent e)
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void delete_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pasteNew_actionPerformed(ActionEvent e)
+  public void smoothFont_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void pasteThis_actionPerformed(ActionEvent e)
+  public void annotationColour_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+
+  public void associatedData_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
+  public void autoCalculate_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void font_actionPerformed(ActionEvent e)
+  public void showAllSeqs_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  public void showAllColumns_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
+  public void hideSelSequences_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
 
   }
 
-  protected void jpred_actionPerformed(ActionEvent e)
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleAbove_actionPerformed(ActionEvent e)
+  public void findPdbId_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleLeft_actionPerformed(ActionEvent e)
+  public void enterPdbId_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void scaleRight_actionPerformed(ActionEvent e)
+  public void pdbFile_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
+  public void invertColSel_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
+  public void tabSelectionChanged(int sel)
   {
 
   }
 
-  protected void preferences_actionPerformed(ActionEvent e)
+  public void tabbedPane_mousePressed(MouseEvent e)
   {
 
   }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
-
+  public void tabbedPane_focusGained(FocusEvent e)
+  {
+    requestFocus();
   }
 
-  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+  public void save_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  public void reload_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  public void newView_actionPerformed(ActionEvent e)
   {
 
   }
 
-  protected void ClustalRealign_actionPerformed(ActionEvent e)
+  public void textColour_actionPerformed(ActionEvent e)
   {
 
   }
 
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+
+  }
 }