X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=6c235a46c7328a3ec37febb5f3203d920cde8243;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=22671fb155b97fc0c4e682b41f2113db0e6f094a;hpb=9bea55eea55110a19b17d0127903802013fa60ea;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 22671fb..6c235a4 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,18 +1,33 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
- * AM Waterhouse
- *******************/
-
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.jbgui;
 
-import javax.swing.*;
-import java.awt.event.*;
 import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.gui.*;
+import jalview.schemes.*;
 
-public class GAlignFrame extends JInternalFrame
+public class GAlignFrame
+    extends JInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
   protected JMenu fileMenu = new JMenu();
@@ -29,8 +44,8 @@ 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();
@@ -42,12 +57,13 @@ 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();
@@ -57,21 +73,21 @@ 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 sequenceFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   JMenuItem delete = new JMenuItem();
@@ -80,26 +96,109 @@ public class GAlignFrame extends JInternalFrame
   JMenu jMenu1 = 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 fullSeqId = 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 jnet = new JMenuItem();
+  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
   JMenuItem modifyPID = new JMenuItem();
   JMenuItem modifyConservation = new JMenuItem();
   protected JMenu sortByTreeMenu = new JMenu();
-  JMenu jMenu2 = new JMenu();
-  JMenu sort = new JMenu();
+  protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
   JMenuItem msaAlignMenuItem = new JMenuItem();
+  JMenu jMenu2 = new JMenu();
+  JMenuItem padGapsMenuitem = new JMenuItem();
+  JMenuItem ClustalRealign = new JMenuItem();
+
   public GAlignFrame()
   {
+    ButtonGroup colours = new ButtonGroup();
+    colours.add(noColourmenuItem);
+    colours.add(clustalColour);
+    colours.add(zappoColour);
+    colours.add(taylorColour);
+    colours.add(hydrophobicityColour);
+    colours.add(helixColour);
+    colours.add(strandColour);
+    colours.add(turnColour);
+    colours.add(buriedColour);
+    colours.add(userDefinedColour);
+    colours.add(PIDColour);
+    colours.add(BLOSUM62Colour);
+    colours.add(nucleotideColour);
 
+    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;
+      }
+    }
 
     try
     {
@@ -107,19 +206,13 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       JMenuItem item;
-      // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
-        saveAlignmentMenu.add( item );
-        item.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            saveAs_actionPerformed(e);
-          }
-        });
 
-        item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
+      // dynamically fill save as menu with available formats
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      {
+        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+                             elementAt(
+                                 i));
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -128,36 +221,30 @@ public class GAlignFrame extends JInternalFrame
           }
         });
 
-        outputTextboxMenu.add( item );
+        outputTextboxMenu.add(item);
       }
-
     }
-    catch(Exception e)
+    catch (Exception e)
     {
       e.printStackTrace();
     }
 
-    ButtonGroup colours = new ButtonGroup();
-    colours.add(noColourmenuItem);
-    colours.add(clustalColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(userDefinedColour);
-    colours.add(PIDColour);
-    colours.add(BLOSUM62Colour);
-    colours.add(nucleotideColour);
   }
-  private void jbInit() throws Exception
+
+  private void jbInit()
+      throws Exception
   {
     fileMenu.setMnemonic('F');
     fileMenu.setText("File");
     saveAlignmentMenu.setMnemonic('L');
-    saveAlignmentMenu.setText("Save");
+    saveAlignmentMenu.setText("Save As");
+    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()
@@ -174,8 +261,10 @@ public class GAlignFrame extends JInternalFrame
     webService.setText("Web Service");
     selectAllSequenceMenuItem.setText("Select all");
     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_A, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+        java.awt.event.KeyEvent.VK_A,
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    selectAllSequenceMenuItem.addActionListener(new java.awt.event.
+                                                ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -184,9 +273,10 @@ 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)
       {
@@ -218,7 +308,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     removeGappedColumnMenuItem.setText("Remove Empty Columns");
-    removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeGappedColumnMenuItem.addActionListener(new java.awt.event.
+                                                 ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -251,7 +342,7 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    sortPairwiseMenuItem.setText("Pairwise Identity");
+    sortPairwiseMenuItem.setText("by Pairwise Identity");
     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -259,7 +350,7 @@ public class GAlignFrame extends JInternalFrame
         sortPairwiseMenuItem_actionPerformed(e);
       }
     });
-    sortIDMenuItem.setText("ID");
+    sortIDMenuItem.setText("by ID");
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -267,7 +358,7 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortGroupMenuItem.setText("Group");
+    sortGroupMenuItem.setText("by Group");
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -276,7 +367,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     removeRedundancyMenuItem.setText("Remove Redundancy...");
-    removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+    removeRedundancyMenuItem.addActionListener(new java.awt.event.
+                                               ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -284,14 +376,15 @@ 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)
@@ -299,15 +392,17 @@ 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)
@@ -315,7 +410,7 @@ public class GAlignFrame extends JInternalFrame
         neighbourTreeMenuItem_actionPerformed(e);
       }
     });
-    clustalAlignMenuItem.setText("Clustal Alignment...");
+    clustalAlignMenuItem.setText("Clustal Alignment");
     clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -325,14 +420,29 @@ public class GAlignFrame extends JInternalFrame
     });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
+    alignFrameMenuBar.addAncestorListener(new AncestorListener()
+    {
+      public void ancestorAdded(AncestorEvent event)
+      {
+        alignFrameMenuBar_ancestorAdded(event);
+      }
+
+      public void ancestorRemoved(AncestorEvent event)
+      {
+      }
+
+      public void ancestorMoved(AncestorEvent event)
+      {
+      }
+    });
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText("Status bar");
     outputTextboxMenu.setMnemonic('T');
     outputTextboxMenu.setText("Output to Textbox");
-    clustalColour.setSelected(false);
     clustalColour.setText("Clustalx");
+
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -420,15 +530,17 @@ 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)
@@ -438,7 +550,7 @@ public class GAlignFrame extends JInternalFrame
     });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState(true);
+    annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -462,7 +574,7 @@ 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)
@@ -473,8 +585,9 @@ 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.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)
@@ -501,7 +614,6 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     noColourmenuItem.setText("None");
-    noColourmenuItem.setSelected(true);
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -535,8 +647,9 @@ 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)
@@ -546,9 +659,11 @@ public class GAlignFrame extends JInternalFrame
     });
     searchMenu.setText("Search");
 
-    abovePIDThreshold.setText("Above Identity 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);
       }
     });
@@ -568,7 +683,6 @@ public class GAlignFrame extends JInternalFrame
         nucleotideColour_actionPerformed(e);
       }
     });
-    deleteGroups.setSelected(false);
     deleteGroups.setText("Undefine groups");
     deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
@@ -578,8 +692,9 @@ 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.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()
@@ -590,8 +705,9 @@ 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.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()
     {
@@ -610,9 +726,10 @@ public class GAlignFrame extends JInternalFrame
     });
     jMenu1.setMnemonic('V');
     jMenu1.setText("Paste");
-    pasteNew.setText("to new alignment");
-    pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
-        KeyEvent.VK_V, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    pasteNew.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)
@@ -620,7 +737,7 @@ 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)
@@ -641,10 +758,10 @@ public class GAlignFrame extends JInternalFrame
     {
       public void actionPerformed(ActionEvent e)
       {
-        createPNG_actionPerformed(e);
+        createPNG(null);
       }
     });
-    createPNG.setActionCommand("Save as PNG Image");
+    createPNG.setActionCommand("Save As PNG Image");
     createPNG.setText("PNG");
     font.setText("Font...");
     font.addActionListener(new java.awt.event.ActionListener()
@@ -655,6 +772,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     fullSeqId.setText("Show Full Sequence ID");
+    fullSeqId.setState(true);
     fullSeqId.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -667,19 +785,20 @@ 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() {
+    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()
+    jnet.setText("JNet");
+    jnet.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
@@ -731,16 +850,34 @@ public class GAlignFrame extends JInternalFrame
         modifyConservation_actionPerformed(e);
       }
     });
-    sortByTreeMenu.setText("Tree Order");
-    jMenu2.setText("Save as");
+    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.setText("Muscle Alignment");
+    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
         msaAlignMenuItem_actionPerformed(e);
       }
     });
+    jMenu2.setText("Export");
+    padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        padGapsMenuitem_actionPerformed(e);
+      }
+    });
+    ClustalRealign.setText("Clustal Realign");
+    ClustalRealign.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ClustalRealign_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -761,6 +898,7 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(copy);
     editMenu.add(jMenu1);
     editMenu.add(delete);
+    editMenu.addSeparator();
     editMenu.add(selectAllSequenceMenuItem);
     editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
@@ -771,15 +909,16 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeGappedColumnMenuItem);
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(padGapsMenuitem);
     searchMenu.add(findMenuItem);
     viewMenu.add(font);
-    viewMenu.add(fullSeqId);
     viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
+    viewMenu.add(fullSeqId);
     viewMenu.add(scaleAbove);
     viewMenu.add(scaleLeft);
     viewMenu.add(scaleRight);
-    viewMenu.addSeparator();
     viewMenu.add(viewBoxesMenuItem);
     viewMenu.add(viewTextMenuItem);
     viewMenu.add(colourTextMenuItem);
@@ -789,8 +928,8 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
-    colourMenu.add(noColourmenuItem);
     colourMenu.addSeparator();
+    colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
     colourMenu.add(PIDColour);
@@ -816,383 +955,309 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();
     calculateMenu.add(webService);
     webService.add(clustalAlignMenuItem);
-    webService.add(jpred);
     webService.add(msaAlignMenuItem);
+    webService.add(jnet);
+    webService.add(ClustalRealign);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
     jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
-    jMenu2.add(htmlMenuItem);
-    jMenu2.add(epsFile);
-    jMenu2.add(createPNG);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
-    sort.add(sortByTreeMenu);
     sort.add(sortPairwiseMenuItem);
     calculate.add(averageDistanceTreeMenuItem);
     calculate.add(neighbourTreeMenuItem);
     calculate.add(avDistanceTreeBlosumMenuItem);
     calculate.add(njTreeBlosumMenuItem);
-  }
-
-  protected void saveAs_actionPerformed(ActionEvent e)
-  {
-
+    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 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 clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
-
-
   protected void clustalColour_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 turnColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void buriedColour_actionPerformed(ActionEvent e)
   {
-
   }
 
-
-
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void PIDColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected  void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
   protected void printMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void findMenuItem_actionPerformed(ActionEvent e)
   {
-
   }
 
-
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
-
+  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+  {
   }
 
   public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
   {
-
   }
 
   protected void nucleotideColour_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
-
   }
 
- protected void copy_actionPerformed(ActionEvent e)
+  protected void copy_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 applyToAllGroups_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void createPNG_actionPerformed(ActionEvent e)
+  public void createPNG(java.io.File f)
   {
-
   }
 
   protected void font_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
   {
-
   }
 
-  protected void epsFile_actionPerformed(ActionEvent e)
+  public void createEPS(java.io.File f)
   {
-
   }
 
-  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
-
+  protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+  {
   }
 
   protected void jpred_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
-
   }
 
   protected void preferences_actionPerformed(ActionEvent e)
   {
+  }
+
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)
+  {
   }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  {
+  }
 
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+  {
   }
 
+  protected void ClustalRealign_actionPerformed(ActionEvent e)
+  {
+  }
 }