Label changes as AF recommended

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 3cb11e2..f94ef41 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,16 +21,14 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu viewMenu = new JMenu();
   protected JMenu colourMenu = new JMenu();
   protected JMenu calculateMenu = new JMenu();
-  protected JMenu alignMenu = new JMenu();
+  protected JMenu webService = new JMenu();
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();
-  protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
   protected JMenuItem remove2LeftMenuItem = new JMenuItem();
   protected JMenuItem remove2RightMenuItem = new JMenuItem();
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
-  protected JMenuItem setGapCharMenuItem = new JMenuItem();
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
@@ -42,7 +40,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
   protected JMenuItem clustalAlignMenuItem = new JMenuItem();
-  protected JMenuItem msaAlignMenuItem = new JMenuItem();
   BorderLayout borderLayout1 = new BorderLayout();
   public JLabel statusBar = new JLabel();
   protected JMenu saveAlignmentMenu = new JMenu();
@@ -96,6 +93,10 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem modifyPID = new JMenuItem();
   JMenuItem modifyConservation = new JMenuItem();
   protected JMenu sortByTreeMenu = new JMenu();
+  JMenu jMenu2 = new JMenu();
+  JMenu sort = new JMenu();
+  JMenu calculate = new JMenu();
+  JMenuItem preferences = new JMenuItem();
   public GAlignFrame()
   {
 
@@ -156,7 +157,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.setMnemonic('F');
     fileMenu.setText("File");
     saveAlignmentMenu.setMnemonic('L');
-    saveAlignmentMenu.setText("Save alignment to local file");
+    saveAlignmentMenu.setText("Save");
     closeMenuItem.setMnemonic('C');
     closeMenuItem.setText("Close");
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -170,8 +171,10 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.setText("View");
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
-    alignMenu.setText("Web Service");
+    webService.setText("Web Service");
     selectAllSequenceMenuItem.setText("Select all");
+    selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_A, java.awt.event.KeyEvent.CTRL_MASK, false));
     selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -179,7 +182,10 @@ public class GAlignFrame extends JInternalFrame
         selectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    deselectAllSequenceMenuItem.setText("Clear selection");
+    deselectAllSequenceMenuItem.setText("Deselect All");
+    deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                               getKeyStroke(java.awt.event.
+        KeyEvent.VK_ESCAPE, 0, false));
     deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -187,7 +193,7 @@ public class GAlignFrame extends JInternalFrame
         deselectAllSequenceMenuItem_actionPerformed(e);
       }
     });
-    invertSequenceMenuItem.setText("Invert sequence selection");
+    invertSequenceMenuItem.setText("Invert Selection");
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -195,15 +201,7 @@ public class GAlignFrame extends JInternalFrame
         invertSequenceMenuItem_actionPerformed(e);
       }
     });
-    deselectAllColumnsMenuItem.setText("Deselect all columns");
-    deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        deselectAllColumnsMenuItem_actionPerformed(e);
-      }
-    });
-    remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
+    remove2LeftMenuItem.setText("Remove Left");
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -211,7 +209,7 @@ public class GAlignFrame extends JInternalFrame
         remove2LeftMenuItem_actionPerformed(e);
       }
     });
-    remove2RightMenuItem.setText("Remove sequence -> right of selected column");
+    remove2RightMenuItem.setText("Remove Right");
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -219,7 +217,7 @@ public class GAlignFrame extends JInternalFrame
         remove2RightMenuItem_actionPerformed(e);
       }
     });
-    removeGappedColumnMenuItem.setText("Remove gapped columns");
+    removeGappedColumnMenuItem.setText("Remove Empty Columns");
     removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -227,7 +225,7 @@ public class GAlignFrame extends JInternalFrame
         removeGappedColumnMenuItem_actionPerformed(e);
       }
     });
-    removeAllGapsMenuItem.setText("Remove all gaps");
+    removeAllGapsMenuItem.setText("Remove All Gaps");
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -235,14 +233,6 @@ public class GAlignFrame extends JInternalFrame
         removeAllGapsMenuItem_actionPerformed(e);
       }
     });
-    setGapCharMenuItem.setText("Set gap character to \".\"");
-    setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        setGapCharMenuItem_actionPerformed(e);
-      }
-    });
     viewBoxesMenuItem.setText("Boxes");
     viewBoxesMenuItem.setState(true);
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -261,7 +251,7 @@ public class GAlignFrame extends JInternalFrame
         viewTextMenuItem_actionPerformed(e);
       }
     });
-    sortPairwiseMenuItem.setText("Sort by pairwise identity");
+    sortPairwiseMenuItem.setText("Pairwise Identity");
     sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -269,7 +259,7 @@ public class GAlignFrame extends JInternalFrame
         sortPairwiseMenuItem_actionPerformed(e);
       }
     });
-    sortIDMenuItem.setText("Sort by ID");
+    sortIDMenuItem.setText("ID");
     sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -277,7 +267,7 @@ public class GAlignFrame extends JInternalFrame
         sortIDMenuItem_actionPerformed(e);
       }
     });
-    sortGroupMenuItem.setText("Sort by group");
+    sortGroupMenuItem.setText("Group");
     sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -285,7 +275,7 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-    removeRedundancyMenuItem.setText("Remove redundancy");
+    removeRedundancyMenuItem.setText("Remove Redundancy...");
     removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -293,7 +283,7 @@ public class GAlignFrame extends JInternalFrame
         removeRedundancyMenuItem_actionPerformed(e);
       }
     });
-    pairwiseAlignmentMenuItem.setText("Pairwise alignments");
+    pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
     pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -301,7 +291,7 @@ public class GAlignFrame extends JInternalFrame
         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)
@@ -309,7 +299,7 @@ public class GAlignFrame extends JInternalFrame
         PCAMenuItem_actionPerformed(e);
       }
     });
-    averageDistanceTreeMenuItem.setText("Average distance tree using PID");
+    averageDistanceTreeMenuItem.setText("Average Distance Using % Identity...");
     averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -317,7 +307,7 @@ public class GAlignFrame extends JInternalFrame
         averageDistanceTreeMenuItem_actionPerformed(e);
       }
     });
-    neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
+    neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity...");
     neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -325,7 +315,7 @@ 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)
@@ -333,14 +323,6 @@ public class GAlignFrame extends JInternalFrame
         clustalAlignMenuItem_actionPerformed(e);
       }
     });
-    msaAlignMenuItem.setText("Muscle alignment");
-    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        msaAlignMenuItem_actionPerformed(e);
-      }
-    });
     this.getContentPane().setLayout(borderLayout1);
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
@@ -348,9 +330,9 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText("Status bar");
     outputTextboxMenu.setMnemonic('T');
-    outputTextboxMenu.setText("Output alignment via textbox");
+    outputTextboxMenu.setText("Output to Textbox");
     clustalColour.setSelected(false);
-    clustalColour.setText("Clustalx colours");
+    clustalColour.setText("Clustalx");
     clustalColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -358,7 +340,7 @@ public class GAlignFrame extends JInternalFrame
         clustalColour_actionPerformed(e);
       }
     });
-    zappoColour.setText("Zappo colour scheme");
+    zappoColour.setText("Zappo");
     zappoColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -366,7 +348,7 @@ public class GAlignFrame extends JInternalFrame
         zappoColour_actionPerformed(e);
       }
     });
-    taylorColour.setText("Taylor colour scheme");
+    taylorColour.setText("Taylor");
     taylorColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -374,7 +356,7 @@ public class GAlignFrame extends JInternalFrame
         taylorColour_actionPerformed(e);
       }
     });
-    hydrophobicityColour.setText("By hydrophobicity");
+    hydrophobicityColour.setText("Hydrophobicity");
     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -382,7 +364,7 @@ public class GAlignFrame extends JInternalFrame
         hydrophobicityColour_actionPerformed(e);
       }
     });
-    helixColour.setText("Helix propensity");
+    helixColour.setText("Helix Propensity");
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -390,7 +372,7 @@ public class GAlignFrame extends JInternalFrame
         helixColour_actionPerformed(e);
       }
     });
-    strandColour.setText("Strand propensity");
+    strandColour.setText("Strand Propensity");
     strandColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -398,7 +380,7 @@ public class GAlignFrame extends JInternalFrame
         strandColour_actionPerformed(e);
       }
     });
-    turnColour.setText("Turn propensity");
+    turnColour.setText("Turn Propensity");
     turnColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -406,7 +388,7 @@ public class GAlignFrame extends JInternalFrame
         turnColour_actionPerformed(e);
       }
     });
-    buriedColour.setText("Buried index");
+    buriedColour.setText("Buried Index");
     buriedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -414,7 +396,7 @@ public class GAlignFrame extends JInternalFrame
         buriedColour_actionPerformed(e);
       }
     });
-    userDefinedColour.setText("User defined colours");
+    userDefinedColour.setText("User Defined...");
     userDefinedColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -430,7 +412,7 @@ public class GAlignFrame extends JInternalFrame
         PIDColour_actionPerformed(e);
       }
     });
-    BLOSUM62Colour.setText("BLOSUM62 score");
+    BLOSUM62Colour.setText("BLOSUM62 Score");
     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -438,7 +420,7 @@ public class GAlignFrame extends JInternalFrame
         BLOSUM62Colour_actionPerformed(e);
       }
     });
-    avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
+    avDistanceTreeBlosumMenuItem.setText("Average Distance using BLOSUM62...");
     avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -446,7 +428,7 @@ public class GAlignFrame extends JInternalFrame
         avTreeBlosumMenuItem_actionPerformed(e);
       }
     });
-    njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
+    njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62...");
     njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -455,7 +437,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     annotationPanelMenuItem.setActionCommand("");
-    annotationPanelMenuItem.setText("Annotation Panel");
+    annotationPanelMenuItem.setText("Show Annotations");
     annotationPanelMenuItem.setState(true);
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -464,7 +446,7 @@ public class GAlignFrame extends JInternalFrame
         annotationPanelMenuItem_actionPerformed(e);
       }
     });
-    colourTextMenuItem.setText("Colour text");
+    colourTextMenuItem.setText("Colour Text");
     colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -472,7 +454,7 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
-    htmlMenuItem.setText("Output as HTML");
+    htmlMenuItem.setText("HTML");
     htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -480,7 +462,7 @@ 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)
@@ -491,6 +473,8 @@ 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, java.awt.event.KeyEvent.CTRL_MASK, false));
     undoMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -508,7 +492,7 @@ public class GAlignFrame extends JInternalFrame
         redoMenuItem_actionPerformed(e);
       }
     });
-    conservationMenuItem.setText("By conservation");
+    conservationMenuItem.setText("By Conservation");
     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -525,7 +509,7 @@ public class GAlignFrame extends JInternalFrame
         noColourmenuItem_actionPerformed(e);
       }
     });
-    wrapMenuItem.setText("Wrap alignment");
+    wrapMenuItem.setText("Wrap");
     wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -541,7 +525,7 @@ public class GAlignFrame extends JInternalFrame
         printMenuItem_actionPerformed(e);
       }
     });
-    renderGapsMenuItem.setText("Render gaps");
+    renderGapsMenuItem.setText("Show Gaps");
     renderGapsMenuItem.setState(true);
     renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -550,7 +534,9 @@ public class GAlignFrame extends JInternalFrame
         renderGapsMenuItem_actionPerformed(e);
       }
     });
-    findMenuItem.setText("Find");
+    findMenuItem.setText("Find...");
+    findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
+        event.KeyEvent.VK_F, java.awt.event.KeyEvent.CTRL_MASK, false));
     findMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -560,7 +546,7 @@ public class GAlignFrame extends JInternalFrame
     });
     searchMenu.setText("Search");
 
-    abovePIDThreshold.setText("Above PID threshold");
+    abovePIDThreshold.setText("Above Identity threshold");
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
       public void actionPerformed(ActionEvent e) {
         abovePIDThreshold_actionPerformed(e);
@@ -574,7 +560,7 @@ public class GAlignFrame extends JInternalFrame
         sequenceFeatures_actionPerformed(actionEvent);
       }
     });
-    nucleotideColour.setText("Nucleotide colours");
+    nucleotideColour.setText("Nucleotide");
     nucleotideColour.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -583,7 +569,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     deleteGroups.setSelected(false);
-    deleteGroups.setText("Delete all groups");
+    deleteGroups.setText("Undefine groups");
     deleteGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -592,6 +578,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     copy.setText("Copy");
+    copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_C, java.awt.event.KeyEvent.CTRL_MASK, false));
     copy.setMnemonic(KeyEvent.VK_C);
 
     copy.addActionListener(new java.awt.event.ActionListener()
@@ -602,6 +590,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     cut.setText("Cut");
+    cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
+        KeyEvent.VK_X, java.awt.event.KeyEvent.CTRL_MASK, false));
     cut.setMnemonic(KeyEvent.VK_X);
     cut.addActionListener(new java.awt.event.ActionListener()
     {
@@ -621,6 +611,8 @@ 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, java.awt.event.KeyEvent.CTRL_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -636,7 +628,7 @@ public class GAlignFrame extends JInternalFrame
         pasteThis_actionPerformed(e);
       }
     });
-    applyToAllGroups.setText("Apply colour to all groups");
+    applyToAllGroups.setText("Apply Colour To All Groups");
     applyToAllGroups.setState(true);
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
@@ -653,8 +645,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     createPNG.setActionCommand("Save as PNG Image");
-    createPNG.setText("Save as PNG Image");
-    font.setText("Change Font");
+    createPNG.setText("PNG");
+    font.setText("Font...");
     font.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -662,7 +654,7 @@ public class GAlignFrame extends JInternalFrame
         font_actionPerformed(e);
       }
     });
-    fullSeqId.setText("Show full sequence id");
+    fullSeqId.setText("Show Full Sequence ID");
     fullSeqId.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -670,7 +662,7 @@ public class GAlignFrame extends JInternalFrame
         fullSeqId_actionPerformed(e);
       }
     });
-    epsFile.setText("Save as EPS file");
+    epsFile.setText("EPS");
     epsFile.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -679,14 +671,14 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load assocated tree");
+    LoadtreeMenuItem.setText("Load Assocated Tree");
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
       public void actionPerformed(ActionEvent e)
       {
         LoadtreeMenuItem_actionPerformed(e);
       }
     });
-    jpred.setText("JPred");
+    jpred.setText("JPred...");
     jpred.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -695,7 +687,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     scaleAbove.setVisible(false);
-    scaleAbove.setText("Scale above alignment");
+    scaleAbove.setText("Scale Above");
     scaleAbove.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -705,7 +697,7 @@ public class GAlignFrame extends JInternalFrame
     });
     scaleLeft.setVisible(false);
     scaleLeft.setSelected(true);
-    scaleLeft.setText("Scale left of sequence");
+    scaleLeft.setText("Scale Left");
     scaleLeft.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -715,7 +707,7 @@ public class GAlignFrame extends JInternalFrame
     });
     scaleRight.setVisible(false);
     scaleRight.setSelected(true);
-    scaleRight.setText("Scale right of sequence");
+    scaleRight.setText("Scale Right");
     scaleRight.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -723,7 +715,7 @@ public class GAlignFrame extends JInternalFrame
         scaleRight_actionPerformed(e);
       }
     });
-    modifyPID.setText("Modify PID Threshold");
+    modifyPID.setText("Modify Identity Threshold...");
     modifyPID.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -731,7 +723,7 @@ public class GAlignFrame extends JInternalFrame
         modifyPID_actionPerformed(e);
       }
     });
-    modifyConservation.setText("Modify Conservation Threshold");
+    modifyConservation.setText("Modify Conservation Threshold...");
     modifyConservation.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -739,44 +731,52 @@ public class GAlignFrame extends JInternalFrame
         modifyConservation_actionPerformed(e);
       }
     });
-    sortByTreeMenu.setText("Sort by tree order");
+    sortByTreeMenu.setText("Tree Order");
+    jMenu2.setText("Save as");
+    sort.setText("Sort");
+    calculate.setText("Calculate Tree");
+    preferences.setText("Preferences...");
+    preferences.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        preferences_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
     alignFrameMenuBar.add(viewMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(alignMenu);
     fileMenu.add(saveAlignmentMenu);
+    fileMenu.add(jMenu2);
     fileMenu.add(outputTextboxMenu);
-    fileMenu.add(htmlMenuItem);
-    fileMenu.add(epsFile);
-    fileMenu.add(createPNG);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(LoadtreeMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
+    editMenu.add(undoMenuItem);
+    editMenu.add(redoMenuItem);
+    editMenu.add(cut);
     editMenu.add(copy);
     editMenu.add(jMenu1);
-    editMenu.add(cut);
     editMenu.add(delete);
     editMenu.addSeparator();
-    editMenu.add(undoMenuItem);
-    editMenu.add(redoMenuItem);
-    editMenu.addSeparator();
-    editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(selectAllSequenceMenuItem);
+    editMenu.add(deselectAllSequenceMenuItem);
     editMenu.add(invertSequenceMenuItem);
     editMenu.add(deleteGroups);
     editMenu.addSeparator();
-    editMenu.add(deselectAllColumnsMenuItem);
     editMenu.add(remove2LeftMenuItem);
     editMenu.add(remove2RightMenuItem);
-    editMenu.addSeparator();
     editMenu.add(removeGappedColumnMenuItem);
     editMenu.add(removeAllGapsMenuItem);
-    editMenu.add(setGapCharMenuItem);
+    editMenu.add(removeRedundancyMenuItem);
+    editMenu.addSeparator();
+    editMenu.add(preferences);
+
     searchMenu.add(findMenuItem);
     viewMenu.add(font);
     viewMenu.add(fullSeqId);
@@ -791,11 +791,15 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(colourTextMenuItem);
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
-    viewMenu.add(overviewMenuItem);
     viewMenu.add(sequenceFeatures);
+    viewMenu.addSeparator();
+    viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
     colourMenu.add(noColourmenuItem);
+    colourMenu.addSeparator();
     colourMenu.add(clustalColour);
+    colourMenu.add(BLOSUM62Colour);
+    colourMenu.add(PIDColour);
     colourMenu.add(zappoColour);
     colourMenu.add(taylorColour);
     colourMenu.add(hydrophobicityColour);
@@ -805,32 +809,34 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(userDefinedColour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(BLOSUM62Colour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
-    calculateMenu.add(sortPairwiseMenuItem);
-    calculateMenu.add(sortIDMenuItem);
-    calculateMenu.add(sortGroupMenuItem);
-    calculateMenu.add(sortByTreeMenu);
-    calculateMenu.add(removeRedundancyMenuItem);
+    calculateMenu.add(sort);
+    calculateMenu.add(calculate);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
-    calculateMenu.add(averageDistanceTreeMenuItem);
-    calculateMenu.add(neighbourTreeMenuItem);
-    calculateMenu.add(avDistanceTreeBlosumMenuItem);
-    calculateMenu.add(njTreeBlosumMenuItem);
-    alignMenu.add(clustalAlignMenuItem);
-    alignMenu.add(msaAlignMenuItem);
-    alignMenu.add(jpred);
+    calculateMenu.add(webService);
+    webService.add(clustalAlignMenuItem);
+    webService.add(jpred);
     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)
@@ -849,9 +855,6 @@ public class GAlignFrame extends JInternalFrame
   }
 
 
-
-
-
   protected void closeMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -868,8 +871,6 @@ public class GAlignFrame extends JInternalFrame
   }
 
 
-
-
   protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -885,12 +886,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-
-  protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
   protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -911,14 +906,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-
-
-
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
@@ -942,8 +929,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-
-
   protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
 
@@ -1013,10 +998,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
-  {
 
-  }
 
 
   protected void clustalColour_actionPerformed(ActionEvent e)
@@ -1209,7 +1191,9 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
 
+  }
 
-
-}
+}
\ No newline at end of file