X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=d0327564b480118eb1ca9e9cb92ed8bcd973ebf6;hb=8c4f77adba0521e7dc89dcb77fe2f8b28c62f70d;hp=8aa5159c513a23e422650bc3ed8b8e9cb15e2428;hpb=7bc213bae5828287329a3490faba291706599b03;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8aa5159..d032756 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -21,10 +21,14 @@ package jalview.jbgui;
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
+import javax.swing.event.*;
 
 import jalview.schemes.*;
 import java.awt.BorderLayout;
 
+
+
+
 public class GAlignFrame
     extends JInternalFrame
 {
@@ -54,10 +58,9 @@ public class GAlignFrame
   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();
@@ -85,7 +88,6 @@ public class GAlignFrame
   JMenuItem printMenuItem = new JMenuItem();
   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
   JMenuItem findMenuItem = new JMenuItem();
-  JMenu searchMenu = new JMenu();
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
@@ -93,7 +95,7 @@ public class GAlignFrame
   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();
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
@@ -117,7 +119,6 @@ public class GAlignFrame
   protected JMenuItem showTranslation = new JMenuItem();
   public JMenuItem featureSettings = new JMenuItem();
   JMenuItem fetchSequence = new JMenuItem();
-  protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
   JMenuItem annotationColour = new JMenuItem();
   JMenuItem associatedData = new JMenuItem();
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
@@ -132,26 +133,33 @@ public class GAlignFrame
   JMenu jMenu3 = new JMenu();
   JMenuItem showAllSeqs = new JMenuItem();
   JMenuItem showAllColumns = new JMenuItem();
-  JMenu jMenu4 = new JMenu();
+  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()
   {
-
-
     try
     {
       jbInit();
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size()-1; i++)
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
       {
-        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
-                             elementAt(
-                                 i));
+        JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
         item.addActionListener(new java.awt.event.ActionListener()
         {
           public void actionPerformed(ActionEvent e)
@@ -167,6 +175,18 @@ public class GAlignFrame
     {
     }
 
+    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)
     {
@@ -314,26 +334,26 @@ public class GAlignFrame
   private void jbInit()
       throws Exception
   {
-    fileMenu.setMnemonic('F');
     fileMenu.setText("File");
-    saveAlignmentMenu.setMnemonic('L');
-    saveAlignmentMenu.setText("Save As");
-    saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
-        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
-    saveAlignmentMenu.addActionListener(new ActionListener()
+    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");
@@ -341,7 +361,7 @@ public class GAlignFrame
     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));
@@ -365,7 +385,10 @@ public class GAlignFrame
         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)
@@ -374,6 +397,8 @@ public class GAlignFrame
       }
     });
     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)
@@ -382,6 +407,8 @@ public class GAlignFrame
       }
     });
     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)
@@ -390,6 +417,9 @@ public class GAlignFrame
       }
     });
     removeGappedColumnMenuItem.setText("Remove Empty Columns");
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
+                                              getKeyStroke(java.awt.event.
+        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeGappedColumnMenuItem.addActionListener(new java.awt.event.
                                                  ActionListener()
     {
@@ -399,6 +429,9 @@ public class GAlignFrame
       }
     });
     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)
@@ -449,6 +482,8 @@ public class GAlignFrame
       }
     });
     removeRedundancyMenuItem.setText("Remove Redundancy...");
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+        java.awt.event.KeyEvent.VK_D, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
     removeRedundancyMenuItem.addActionListener(new java.awt.event.
                                                ActionListener()
     {
@@ -498,7 +533,6 @@ public class GAlignFrame
     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");
 
@@ -642,7 +676,6 @@ public class GAlignFrame
       }
     });
     undoMenuItem.setEnabled(false);
-    undoMenuItem.setMnemonic('Z');
     undoMenuItem.setText("Undo");
     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
         java.awt.event.KeyEvent.VK_Z,
@@ -655,8 +688,9 @@ public class GAlignFrame
       }
     });
     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)
@@ -689,6 +723,8 @@ public class GAlignFrame
       }
     });
     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)
@@ -716,8 +752,6 @@ public class GAlignFrame
         findMenuItem_actionPerformed(e);
       }
     });
-    searchMenu.setText("Search");
-
     abovePIDThreshold.setText("Above Identity Threshold");
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
     {
@@ -743,6 +777,8 @@ public class GAlignFrame
       }
     });
     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)
@@ -754,7 +790,6 @@ public class GAlignFrame
     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()
     {
@@ -767,7 +802,6 @@ public class GAlignFrame
     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
         java.awt.event.KeyEvent.VK_X,
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    cut.setMnemonic(KeyEvent.VK_X);
     cut.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -776,6 +810,8 @@ public class GAlignFrame
       }
     });
     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)
@@ -783,12 +819,11 @@ public class GAlignFrame
         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));
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()|java.awt.event.KeyEvent.ALT_MASK, false));
     pasteNew.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -797,6 +832,9 @@ public class GAlignFrame
       }
     });
     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)
@@ -805,7 +843,6 @@ public class GAlignFrame
       }
     });
     applyToAllGroups.setText("Apply Colour To All Groups");
-    applyToAllGroups.setState(true);
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -906,7 +943,7 @@ public class GAlignFrame
     sort.setText("Sort");
     calculate.setText("Calculate Tree");
 
-    jMenu2.setText("Export");
+    jMenu2.setText("Export Image");
     padGapsMenuitem.setText("Pad Gaps");
     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
@@ -934,14 +971,7 @@ public class GAlignFrame
       }
     });
 
-   /* tabbedPane.addChangeListener(new ChangeListener()
-        {
-          public void stateChanged(ChangeEvent ece)
-          {
 
-            tabSelected();
-          }
-        });*/
     featureSettings.setText("Feature Settings...");
     featureSettings.addActionListener(new ActionListener()
     {
@@ -958,15 +988,7 @@ public class GAlignFrame
         fetchSequence_actionPerformed(e);
       }
     });
-    smoothFont.setText("Smooth Fonts");
-    smoothFont.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        smoothFont_actionPerformed(e);
-      }
-    });
-    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
+
     annotationColour.setText("By Annotation...");
     annotationColour.addActionListener(new ActionListener()
     {
@@ -1051,7 +1073,7 @@ public class GAlignFrame
         showAllColumns_actionPerformed(e);
       }
     });
-    jMenu4.setText("Hide");
+    hideMenu.setText("Hide");
     hideSelSequences.setText("Selected Sequences");
     hideSelSequences.addActionListener(new ActionListener()
     {
@@ -1068,8 +1090,7 @@ public class GAlignFrame
         hideSelColumns_actionPerformed(e);
       }
     });
-    hiddenMarkers.setText("Hidden Markers");
-    hiddenMarkers.setState(true);
+    hiddenMarkers.setText("Show Hidden Markers");
     hiddenMarkers.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1077,23 +1098,109 @@ public class GAlignFrame
         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)
+      {
+        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);
     alignFrameMenuBar.add(webService);
-    fileMenu.add(addSequenceMenu);
     fileMenu.add(fetchSequence);
+    fileMenu.add(addSequenceMenu);
+    fileMenu.add(reload);
     fileMenu.addSeparator();
     fileMenu.add(vamsasStore);
-    fileMenu.add(saveAlignmentMenu);
-    fileMenu.add(jMenu2);
+    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);
@@ -1104,14 +1211,9 @@ public class GAlignFrame
     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);
@@ -1119,23 +1221,11 @@ public class GAlignFrame
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
-    searchMenu.add(findMenuItem);
-    viewMenu.add(font);
-    viewMenu.add(smoothFont);
+    viewMenu.add(newView);
     viewMenu.addSeparator();
     viewMenu.add(jMenu3);
-    viewMenu.add(jMenu4);
-    viewMenu.add(hiddenMarkers);
+    viewMenu.add(hideMenu);
     viewMenu.addSeparator();
-    viewMenu.add(wrapMenuItem);
-    viewMenu.add(seqLimits);
-    viewMenu.add(scaleAbove);
-    viewMenu.add(scaleLeft);
-    viewMenu.add(scaleRight);
-    viewMenu.add(viewBoxesMenuItem);
-    viewMenu.add(viewTextMenuItem);
-    viewMenu.add(colourTextMenuItem);
-    viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
     viewMenu.add(showSeqFeatures);
@@ -1143,6 +1233,7 @@ public class GAlignFrame
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
     colourMenu.add(applyToAllGroups);
+    colourMenu.add(textColour);
     colourMenu.addSeparator();
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
@@ -1172,8 +1263,8 @@ public class GAlignFrame
     calculateMenu.add(showTranslation);
     calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
-    webService.add(webServiceNoServices);jMenu1.add(pasteNew);
-    jMenu1.add(pasteThis);
+    webService.add(webServiceNoServices);pasteMenu.add(pasteNew);
+    pasteMenu.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
@@ -1189,10 +1280,31 @@ public class GAlignFrame
     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);
-    jMenu4.add(hideSelColumns);
-    jMenu4.add(hideSelSequences);
+    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)
@@ -1228,7 +1340,7 @@ public class GAlignFrame
   {
   }
 
-  protected void closeMenuItem_actionPerformed(ActionEvent e)
+  protected void closeMenuItem_actionPerformed(boolean b)
   {
   }
 
@@ -1488,7 +1600,7 @@ public class GAlignFrame
 
 
 
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  protected void saveAs_actionPerformed(ActionEvent e)
   {
   }
 
@@ -1582,4 +1694,49 @@ public class GAlignFrame
   {
 
   }
+
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void tabSelectionChanged(int sel)
+  {
+
+  }
+
+  public void tabbedPane_mousePressed(MouseEvent e)
+  {
+
+  }
+
+  public void tabbedPane_focusGained(FocusEvent e)
+  {
+    requestFocus();
+  }
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void reload_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void newView_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void textColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void idRightAlign_actionPerformed(ActionEvent e)
+  {
+
+  }
 }