Formatting
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
index 6c235a4..1b89d71 100755 (executable)
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -23,7 +23,6 @@ import java.awt.event.*;
 import javax.swing.*;\r
 import javax.swing.event.*;\r
 \r
-import jalview.gui.*;\r
 import jalview.schemes.*;\r
 \r
 public class GAlignFrame\r
@@ -37,6 +36,7 @@ public class GAlignFrame
   protected JMenu colourMenu = new JMenu();\r
   protected JMenu calculateMenu = new JMenu();\r
   protected JMenu webService = new JMenu();\r
+  protected JMenuItem webServiceNoServices;\r
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
@@ -54,10 +54,9 @@ public class GAlignFrame
   protected JMenuItem PCAMenuItem = new JMenuItem();\r
   protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();\r
   protected JMenuItem neighbourTreeMenuItem = new JMenuItem();\r
-  protected JMenuItem clustalAlignMenuItem = new JMenuItem();\r
   BorderLayout borderLayout1 = new BorderLayout();\r
   public JLabel statusBar = new JLabel();\r
-  protected JMenuItem saveAlignmentMenu = new JMenuItem();\r
+  protected JMenuItem saveAs = new JMenuItem();\r
   protected JMenu outputTextboxMenu = new JMenu();\r
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
@@ -85,40 +84,161 @@ public class GAlignFrame
   JMenuItem printMenuItem = new JMenuItem();\r
   public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();\r
   JMenuItem findMenuItem = new JMenuItem();\r
-  JMenu searchMenu = new JMenu();\r
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
-  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
   JMenuItem deleteGroups = new JMenuItem();\r
   JMenuItem delete = new JMenuItem();\r
   JMenuItem copy = new JMenuItem();\r
   JMenuItem cut = new JMenuItem();\r
-  JMenu jMenu1 = new JMenu();\r
+  JMenu pasteMenu = new JMenu();\r
   JMenuItem pasteNew = new JMenuItem();\r
   JMenuItem pasteThis = new JMenuItem();\r
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
   JMenuItem createPNG = new JMenuItem();\r
   protected JMenuItem font = new JMenuItem();\r
-  public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
   JMenuItem epsFile = new JMenuItem();\r
   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
-  JMenuItem jnet = new JMenuItem();\r
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
-  JMenuItem modifyPID = new JMenuItem();\r
-  JMenuItem modifyConservation = new JMenuItem();\r
+  protected JMenuItem modifyPID = new JMenuItem();\r
+  protected JMenuItem modifyConservation = new JMenuItem();\r
   protected JMenu sortByTreeMenu = new JMenu();\r
   protected JMenu sort = new JMenu();\r
   JMenu calculate = new JMenu();\r
-  JMenuItem msaAlignMenuItem = new JMenuItem();\r
   JMenu jMenu2 = new JMenu();\r
-  JMenuItem padGapsMenuitem = new JMenuItem();\r
-  JMenuItem ClustalRealign = new JMenuItem();\r
-\r
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
+  protected ButtonGroup colours = new ButtonGroup();\r
+  JMenuItem vamsasStore = new JMenuItem();\r
+  protected JMenuItem showTranslation = new JMenuItem();\r
+  public JMenuItem featureSettings = new JMenuItem();\r
+  JMenuItem fetchSequence = new JMenuItem();\r
+  JMenuItem annotationColour = new JMenuItem();\r
+  JMenuItem associatedData = new JMenuItem();\r
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
+  JMenu addSequenceMenu = new JMenu();\r
+  JMenuItem addFromFile = new JMenuItem();\r
+  JMenuItem addFromText = new JMenuItem();\r
+  JMenuItem addFromURL = new JMenuItem();\r
+  JMenuItem exportAnnotations = new JMenuItem();\r
+  JMenuItem exportFeatures = new JMenuItem();\r
+  protected JPanel statusPanel = new JPanel();\r
+  GridLayout gridLayout1 = new GridLayout();\r
+  JMenu jMenu3 = new JMenu();\r
+  JMenuItem showAllSeqs = new JMenuItem();\r
+  JMenuItem showAllColumns = new JMenuItem();\r
+  JMenu hideMenu = new JMenu();\r
+  JMenuItem hideSelSequences = new JMenuItem();\r
+  JMenuItem hideSelColumns = new JMenuItem();\r
+  protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
+  JMenuItem invertColSel = new JMenuItem();\r
+  protected JTabbedPane tabbedPane = new JTabbedPane();\r
+  JMenuItem save = new JMenuItem();\r
+  protected JMenuItem reload = new JMenuItem();\r
+  JMenuItem newView = new JMenuItem();\r
+  JMenuItem textColour = new JMenuItem();\r
+  JMenu formatMenu = new JMenu();\r
+  JMenu selectMenu = new JMenu();\r
+  protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();\r
+  protected JMenuItem gatherViews = new JMenuItem();\r
+  protected JMenuItem expandViews = new JMenuItem();\r
+  JMenuItem pageSetup = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
-    ButtonGroup colours = new ButtonGroup();\r
+    try\r
+    {\r
+      jbInit();\r
+      setJMenuBar(alignFrameMenuBar);\r
+\r
+      // dynamically fill save as menu with available formats\r
+      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+      {\r
+        JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.\r
+                                       WRITEABLE_FORMATS[i]);\r
+\r
+        item.addActionListener(new java.awt.event.ActionListener()\r
+        {\r
+          public void actionPerformed(ActionEvent e)\r
+          {\r
+            outputText_actionPerformed(e);\r
+          }\r
+        });\r
+\r
+        outputTextboxMenu.add(item);\r
+      }\r
+    }\r
+    catch (Exception e)\r
+    {\r
+    }\r
+\r
+    if (!System.getProperty("os.name").startsWith("Mac"))\r
+    {\r
+      closeMenuItem.setMnemonic('C');\r
+      outputTextboxMenu.setMnemonic('T');\r
+      undoMenuItem.setMnemonic('Z');\r
+      redoMenuItem.setMnemonic('0');\r
+      copy.setMnemonic('C');\r
+      cut.setMnemonic('U');\r
+      pasteMenu.setMnemonic('P');\r
+      reload.setMnemonic('R');\r
+    }\r
+\r
+    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+    {\r
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+          getUserColourSchemes().keys();\r
+\r
+      while (userColours.hasMoreElements())\r
+      {\r
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(\r
+            userColours.\r
+            nextElement().toString());\r
+        radioItem.setName("USER_DEFINED");\r
+        radioItem.addMouseListener(new MouseAdapter()\r
+        {\r
+          public void mousePressed(MouseEvent evt)\r
+          {\r
+            if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
+            {\r
+              radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
+\r
+              int option = JOptionPane.showInternalConfirmDialog(jalview.gui.\r
+                  Desktop.desktop,\r
+                  "Remove from default list?",\r
+                  "Remove user defined colour",\r
+                  JOptionPane.YES_NO_OPTION);\r
+              if (option == JOptionPane.YES_OPTION)\r
+              {\r
+                jalview.gui.UserDefinedColours.removeColourFromDefaults(\r
+                    radioItem.getText());\r
+                colourMenu.remove(radioItem);\r
+              }\r
+              else\r
+              {\r
+                radioItem.addActionListener(new ActionListener()\r
+                {\r
+                  public void actionPerformed(ActionEvent evt)\r
+                  {\r
+                    userDefinedColour_actionPerformed(evt);\r
+                  }\r
+                });\r
+              }\r
+            }\r
+          }\r
+        });\r
+        radioItem.addActionListener(new ActionListener()\r
+        {\r
+          public void actionPerformed(ActionEvent evt)\r
+          {\r
+            userDefinedColour_actionPerformed(evt);\r
+          }\r
+        });\r
+        colourMenu.insert(radioItem, 15);\r
+        colours.add(radioItem);\r
+      }\r
+    }\r
     colours.add(noColourmenuItem);\r
     colours.add(clustalColour);\r
     colours.add(zappoColour);\r
@@ -133,9 +253,12 @@ public class GAlignFrame
     colours.add(BLOSUM62Colour);\r
     colours.add(nucleotideColour);\r
 \r
-    noColourmenuItem.setSelected(true);\r
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
 \r
-    String defaultColour = Preferences.defaultColour;\r
+  }\r
+\r
+  public void setColourSelected(String defaultColour)\r
+  {\r
 \r
     if (defaultColour != null)\r
     {\r
@@ -143,6 +266,9 @@ public class GAlignFrame
 \r
       switch (index)\r
       {\r
+        case ColourSchemeProperty.NONE:\r
+          noColourmenuItem.setSelected(true);\r
+          break;\r
         case ColourSchemeProperty.CLUSTAL:\r
           clustalColour.setSelected(true);\r
 \r
@@ -163,6 +289,10 @@ public class GAlignFrame
 \r
           break;\r
 \r
+        case ColourSchemeProperty.TAYLOR:\r
+          taylorColour.setSelected(true);\r
+          break;\r
+\r
         case ColourSchemeProperty.HYDROPHOBIC:\r
           hydrophobicityColour.setSelected(true);\r
 \r
@@ -200,58 +330,32 @@ public class GAlignFrame
       }\r
     }\r
 \r
-    try\r
-    {\r
-      jbInit();\r
-      setJMenuBar(alignFrameMenuBar);\r
-\r
-      JMenuItem item;\r
-\r
-      // dynamically fill save as menu with available formats\r
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
-      {\r
-        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
-                             elementAt(\r
-                                 i));\r
-        item.addActionListener(new java.awt.event.ActionListener()\r
-        {\r
-          public void actionPerformed(ActionEvent e)\r
-          {\r
-            outputText_actionPerformed(e);\r
-          }\r
-        });\r
-\r
-        outputTextboxMenu.add(item);\r
-      }\r
-    }\r
-    catch (Exception e)\r
-    {\r
-      e.printStackTrace();\r
-    }\r
-\r
   }\r
 \r
   private void jbInit()\r
       throws Exception\r
   {\r
-    fileMenu.setMnemonic('F');\r
     fileMenu.setText("File");\r
-    saveAlignmentMenu.setMnemonic('L');\r
-    saveAlignmentMenu.setText("Save As");\r
-    saveAlignmentMenu.addActionListener(new ActionListener()\r
+    saveAs.setText("Save As...");\r
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_S,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
+    saveAs.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        saveAlignmentMenu_actionPerformed(e);\r
+        saveAs_actionPerformed(e);\r
       }\r
     });\r
-    closeMenuItem.setMnemonic('C');\r
     closeMenuItem.setText("Close");\r
+    closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        closeMenuItem_actionPerformed(e);\r
+        closeMenuItem_actionPerformed(false);\r
       }\r
     });\r
     editMenu.setText("Edit");\r
@@ -259,7 +363,7 @@ public class GAlignFrame
     colourMenu.setText("Colour");\r
     calculateMenu.setText("Calculate");\r
     webService.setText("Web Service");\r
-    selectAllSequenceMenuItem.setText("Select all");\r
+    selectAllSequenceMenuItem.setText("Select All");\r
     selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_A,\r
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
@@ -283,7 +387,10 @@ public class GAlignFrame
         deselectAllSequenceMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    invertSequenceMenuItem.setText("Invert Selection");\r
+    invertSequenceMenuItem.setText("Invert Sequence Selection");\r
+    invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_I,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -292,6 +399,9 @@ public class GAlignFrame
       }\r
     });\r
     remove2LeftMenuItem.setText("Remove Left");\r
+    remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+        awt.event.KeyEvent.VK_L,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -300,6 +410,9 @@ public class GAlignFrame
       }\r
     });\r
     remove2RightMenuItem.setText("Remove Right");\r
+    remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+        awt.event.KeyEvent.VK_R,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -308,6 +421,9 @@ public class GAlignFrame
       }\r
     });\r
     removeGappedColumnMenuItem.setText("Remove Empty Columns");\r
+    removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.\r
+                                              getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     removeGappedColumnMenuItem.addActionListener(new java.awt.event.\r
                                                  ActionListener()\r
     {\r
@@ -317,6 +433,10 @@ public class GAlignFrame
       }\r
     });\r
     removeAllGapsMenuItem.setText("Remove All Gaps");\r
+    removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_E,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -367,6 +487,9 @@ public class GAlignFrame
       }\r
     });\r
     removeRedundancyMenuItem.setText("Remove Redundancy...");\r
+    removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_D,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     removeRedundancyMenuItem.addActionListener(new java.awt.event.\r
                                                ActionListener()\r
     {\r
@@ -410,36 +533,12 @@ public class GAlignFrame
         neighbourTreeMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    clustalAlignMenuItem.setText("Clustal Alignment");\r
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        clustalAlignMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     this.getContentPane().setLayout(borderLayout1);\r
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
-    alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
-    {\r
-      public void ancestorAdded(AncestorEvent event)\r
-      {\r
-        alignFrameMenuBar_ancestorAdded(event);\r
-      }\r
-\r
-      public void ancestorRemoved(AncestorEvent event)\r
-      {\r
-      }\r
-\r
-      public void ancestorMoved(AncestorEvent event)\r
-      {\r
-      }\r
-    });\r
     statusBar.setBackground(Color.white);\r
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
     statusBar.setText("Status bar");\r
-    outputTextboxMenu.setMnemonic('T');\r
     outputTextboxMenu.setText("Output to Textbox");\r
     clustalColour.setText("Clustalx");\r
 \r
@@ -550,7 +649,8 @@ public class GAlignFrame
     });\r
     annotationPanelMenuItem.setActionCommand("");\r
     annotationPanelMenuItem.setText("Show Annotations");\r
-    annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);\r
+    annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(\r
+        "SHOW_ANNOTATIONS", true));\r
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -583,7 +683,6 @@ public class GAlignFrame
       }\r
     });\r
     undoMenuItem.setEnabled(false);\r
-    undoMenuItem.setMnemonic('Z');\r
     undoMenuItem.setText("Undo");\r
     undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_Z,\r
@@ -596,8 +695,9 @@ public class GAlignFrame
       }\r
     });\r
     redoMenuItem.setEnabled(false);\r
-    redoMenuItem.setMnemonic('0');\r
     redoMenuItem.setText("Redo");\r
+    redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -629,7 +729,9 @@ public class GAlignFrame
         wrapMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    printMenuItem.setText("Print");\r
+    printMenuItem.setText("Print ...");\r
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -657,8 +759,6 @@ public class GAlignFrame
         findMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    searchMenu.setText("Search");\r
-\r
     abovePIDThreshold.setText("Above Identity Threshold");\r
     abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -667,12 +767,12 @@ public class GAlignFrame
         abovePIDThreshold_actionPerformed(e);\r
       }\r
     });\r
-    sequenceFeatures.setText("Sequence Features");\r
-    sequenceFeatures.addActionListener(new ActionListener()\r
+    showSeqFeatures.setText("Show Sequence Features");\r
+    showSeqFeatures.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent actionEvent)\r
       {\r
-        sequenceFeatures_actionPerformed(actionEvent);\r
+        showSeqFeatures_actionPerformed(actionEvent);\r
       }\r
     });\r
     nucleotideColour.setText("Nucleotide");\r
@@ -684,6 +784,8 @@ public class GAlignFrame
       }\r
     });\r
     deleteGroups.setText("Undefine groups");\r
+    deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     deleteGroups.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -695,7 +797,6 @@ public class GAlignFrame
     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_C,\r
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
-    copy.setMnemonic(KeyEvent.VK_C);\r
 \r
     copy.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -708,7 +809,6 @@ public class GAlignFrame
     cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_X,\r
         Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
-    cut.setMnemonic(KeyEvent.VK_X);\r
     cut.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -717,6 +817,8 @@ public class GAlignFrame
       }\r
     });\r
     delete.setText("Delete");\r
+    delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_BACK_SPACE, 0, false));\r
     delete.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -724,12 +826,12 @@ public class GAlignFrame
         delete_actionPerformed(e);\r
       }\r
     });\r
-    jMenu1.setMnemonic('V');\r
-    jMenu1.setText("Paste");\r
+    pasteMenu.setText("Paste");\r
     pasteNew.setText("To New Alignment");\r
     pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_V,\r
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |\r
+        java.awt.event.KeyEvent.SHIFT_MASK, false));\r
     pasteNew.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -738,6 +840,9 @@ public class GAlignFrame
       }\r
     });\r
     pasteThis.setText("Add To This Alignment");\r
+    pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_V,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     pasteThis.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -746,7 +851,6 @@ public class GAlignFrame
       }\r
     });\r
     applyToAllGroups.setText("Apply Colour To All Groups");\r
-    applyToAllGroups.setState(true);\r
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -771,13 +875,14 @@ public class GAlignFrame
         font_actionPerformed(e);\r
       }\r
     });\r
-    fullSeqId.setText("Show Full Sequence ID");\r
-    fullSeqId.setState(true);\r
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+\r
+    seqLimits.setText("Show Sequence Limits");\r
+    seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));\r
+    seqLimits.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        fullSeqId_actionPerformed(e);\r
+        seqLimit_actionPerformed(e);\r
       }\r
     });\r
     epsFile.setText("EPS");\r
@@ -789,7 +894,7 @@ public class GAlignFrame
       }\r
     });\r
     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
-    LoadtreeMenuItem.setText("Load Assocated Tree");\r
+    LoadtreeMenuItem.setText("Load Associated Tree");\r
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -797,14 +902,6 @@ public class GAlignFrame
         LoadtreeMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    jnet.setText("JNet");\r
-    jnet.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        jpred_actionPerformed(e);\r
-      }\r
-    });\r
     scaleAbove.setVisible(false);\r
     scaleAbove.setText("Scale Above");\r
     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
@@ -852,17 +949,26 @@ public class GAlignFrame
     });\r
     sortByTreeMenu.setText("By Tree Order");\r
     sort.setText("Sort");\r
-    calculate.setText("Calculate Tree");\r
-    msaAlignMenuItem.setText("Muscle Alignment");\r
-    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    sort.addMenuListener(new MenuListener()\r
     {\r
-      public void actionPerformed(ActionEvent e)\r
+      public void menuSelected(MenuEvent e)\r
+      {\r
+        buildTreeMenu();\r
+      }\r
+\r
+      public void menuDeselected(MenuEvent e)\r
+      {\r
+      }\r
+\r
+      public void menuCanceled(MenuEvent e)\r
       {\r
-        msaAlignMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    jMenu2.setText("Export");\r
+    calculate.setText("Calculate Tree");\r
+\r
+    jMenu2.setText("Export Image");\r
     padGapsMenuitem.setText("Pad Gaps");\r
+    padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
     padGapsMenuitem.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -870,40 +976,300 @@ public class GAlignFrame
         padGapsMenuitem_actionPerformed(e);\r
       }\r
     });\r
-    ClustalRealign.setText("Clustal Realign");\r
-    ClustalRealign.addActionListener(new ActionListener()\r
+    vamsasStore.setVisible(false);\r
+    vamsasStore.setText("VAMSAS store");\r
+    vamsasStore.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        vamsasStore_actionPerformed(e);\r
+      }\r
+    });\r
+    showTranslation.setText("Translate cDNA");\r
+    showTranslation.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showTranslation_actionPerformed(e);\r
+      }\r
+    });\r
+\r
+    featureSettings.setText("Feature Settings...");\r
+    featureSettings.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        featureSettings_actionPerformed(e);\r
+      }\r
+    });\r
+    fetchSequence.setText("Fetch Sequence(s)...");\r
+    fetchSequence.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        fetchSequence_actionPerformed(e);\r
+      }\r
+    });\r
+\r
+    annotationColour.setText("By Annotation...");\r
+    annotationColour.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        annotationColour_actionPerformed(e);\r
+      }\r
+    });\r
+    associatedData.setText("Load Features / Annotations");\r
+    associatedData.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        associatedData_actionPerformed(e);\r
+      }\r
+    });\r
+    autoCalculate.setText("Autocalculate Consensus");\r
+    autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+    autoCalculate.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        autoCalculate_actionPerformed(e);\r
+      }\r
+    });\r
+    addSequenceMenu.setText("Add Sequences");\r
+    addFromFile.setText("From File");\r
+    addFromFile.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromFile_actionPerformed(e);\r
+      }\r
+    });\r
+    addFromText.setText("From Textbox");\r
+    addFromText.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromText_actionPerformed(e);\r
+      }\r
+    });\r
+    addFromURL.setText("From URL");\r
+    addFromURL.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        addFromURL_actionPerformed(e);\r
+      }\r
+    });\r
+    exportFeatures.setText("Export Features...");\r
+    exportFeatures.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        exportFeatures_actionPerformed(e);\r
+      }\r
+    });\r
+    exportAnnotations.setText("Export Annotations...");\r
+    exportAnnotations.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        exportAnnotations_actionPerformed(e);\r
+      }\r
+    });\r
+    statusPanel.setLayout(gridLayout1);\r
+    jMenu3.setText("Show");\r
+    showAllSeqs.setText("All Sequences");\r
+    showAllSeqs.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showAllSeqs_actionPerformed(e);\r
+      }\r
+    });\r
+    showAllColumns.setText("All Columns");\r
+    showAllColumns.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        showAllColumns_actionPerformed(e);\r
+      }\r
+    });\r
+    hideMenu.setText("Hide");\r
+    hideSelSequences.setText("Selected Sequences");\r
+    hideSelSequences.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hideSelSequences_actionPerformed(e);\r
+      }\r
+    });\r
+    hideSelColumns.setText("Selected Columns");\r
+    hideSelColumns.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hideSelColumns_actionPerformed(e);\r
+      }\r
+    });\r
+    hiddenMarkers.setText("Show Hidden Markers");\r
+    hiddenMarkers.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        hiddenMarkers_actionPerformed(e);\r
+      }\r
+    });\r
+    invertColSel.setText("Invert Column Selection");\r
+    invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_I,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()\r
+        | java.awt.event.KeyEvent.ALT_MASK,\r
+        false));\r
+    invertColSel.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        ClustalRealign_actionPerformed(e);\r
+        invertColSel_actionPerformed(e);\r
       }\r
     });\r
+    tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()\r
+    {\r
+      public void stateChanged(ChangeEvent evt)\r
+      {\r
+        JTabbedPane pane = (JTabbedPane) evt.getSource();\r
+        int sel = pane.getSelectedIndex();\r
+        tabSelectionChanged(sel);\r
+      }\r
+    });\r
+    tabbedPane.addMouseListener(new MouseAdapter()\r
+    {\r
+      public void mousePressed(MouseEvent e)\r
+      {\r
+        tabbedPane_mousePressed(e);\r
+      }\r
+    });\r
+    tabbedPane.addFocusListener(new FocusAdapter()\r
+    {\r
+      public void focusGained(FocusEvent e)\r
+      {\r
+        tabbedPane_focusGained(e);\r
+      }\r
+    });\r
+    save.setText("Save");\r
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+    save.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        save_actionPerformed(e);\r
+      }\r
+    });\r
+    reload.setEnabled(false);\r
+    reload.setText("Reload");\r
+    reload.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        reload_actionPerformed(e);\r
+      }\r
+    });\r
+    newView.setText("New View");\r
+    newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+    newView.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        newView_actionPerformed(e);\r
+      }\r
+    });\r
+    tabbedPane.setToolTipText("<html><i> Right-click to rename tab"\r
+                              +\r
+        "<br> Press X to eXpand tabs, G to reGroup.</i></html>");\r
+    textColour.setText("Text Colour");\r
+    textColour.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        textColour_actionPerformed(e);\r
+      }\r
+    });\r
+    formatMenu.setText("Format");\r
+    selectMenu.setText("Select");\r
+    idRightAlign.setText("Right Align Sequence Id");\r
+    idRightAlign.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        idRightAlign_actionPerformed(e);\r
+      }\r
+    });\r
+    gatherViews.setEnabled(false);\r
+    gatherViews.setText("Gather Views");\r
+    gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_G, 0, false));\r
+    gatherViews.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        gatherViews_actionPerformed(e);\r
+      }\r
+    });\r
+    expandViews.setEnabled(false);\r
+    expandViews.setText("Expand Views");\r
+    expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_X, 0, false));\r
+    expandViews.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        expandViews_actionPerformed(e);\r
+      }\r
+    });\r
+    pageSetup.setText("Page Setup ...");\r
+    pageSetup.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        pageSetup_actionPerformed(e);\r
+      }\r
+    });\r
+\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
-    alignFrameMenuBar.add(searchMenu);\r
+    alignFrameMenuBar.add(selectMenu);\r
     alignFrameMenuBar.add(viewMenu);\r
+    alignFrameMenuBar.add(formatMenu);\r
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
-    fileMenu.add(saveAlignmentMenu);\r
-    fileMenu.add(jMenu2);\r
+    alignFrameMenuBar.add(webService);\r
+    fileMenu.add(fetchSequence);\r
+    fileMenu.add(addSequenceMenu);\r
+    fileMenu.add(reload);\r
+    fileMenu.addSeparator();\r
+    fileMenu.add(vamsasStore);\r
+    fileMenu.add(save);\r
+    fileMenu.add(saveAs);\r
     fileMenu.add(outputTextboxMenu);\r
+    fileMenu.add(pageSetup);\r
     fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
+    fileMenu.add(jMenu2);\r
+    fileMenu.add(exportFeatures);\r
+    fileMenu.add(exportAnnotations);\r
     fileMenu.add(LoadtreeMenuItem);\r
+    fileMenu.add(associatedData);\r
     fileMenu.addSeparator();\r
     fileMenu.add(closeMenuItem);\r
     editMenu.add(undoMenuItem);\r
     editMenu.add(redoMenuItem);\r
     editMenu.add(cut);\r
     editMenu.add(copy);\r
-    editMenu.add(jMenu1);\r
+    editMenu.add(pasteMenu);\r
     editMenu.add(delete);\r
     editMenu.addSeparator();\r
-    editMenu.add(selectAllSequenceMenuItem);\r
-    editMenu.add(deselectAllSequenceMenuItem);\r
-    editMenu.add(invertSequenceMenuItem);\r
-    editMenu.add(deleteGroups);\r
-    editMenu.addSeparator();\r
     editMenu.add(remove2LeftMenuItem);\r
     editMenu.add(remove2RightMenuItem);\r
     editMenu.add(removeGappedColumnMenuItem);\r
@@ -911,23 +1277,21 @@ public class GAlignFrame
     editMenu.add(removeRedundancyMenuItem);\r
     editMenu.addSeparator();\r
     editMenu.add(padGapsMenuitem);\r
-    searchMenu.add(findMenuItem);\r
-    viewMenu.add(font);\r
+    viewMenu.add(newView);\r
+    viewMenu.add(expandViews);\r
+    viewMenu.add(gatherViews);\r
+    viewMenu.addSeparator();\r
+    viewMenu.add(jMenu3);\r
+    viewMenu.add(hideMenu);\r
     viewMenu.addSeparator();\r
-    viewMenu.add(wrapMenuItem);\r
-    viewMenu.add(fullSeqId);\r
-    viewMenu.add(scaleAbove);\r
-    viewMenu.add(scaleLeft);\r
-    viewMenu.add(scaleRight);\r
-    viewMenu.add(viewBoxesMenuItem);\r
-    viewMenu.add(viewTextMenuItem);\r
-    viewMenu.add(colourTextMenuItem);\r
-    viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(annotationPanelMenuItem);\r
-    viewMenu.add(sequenceFeatures);\r
+    viewMenu.addSeparator();\r
+    viewMenu.add(showSeqFeatures);\r
+    viewMenu.add(featureSettings);\r
     viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
     colourMenu.add(applyToAllGroups);\r
+    colourMenu.add(textColour);\r
     colourMenu.addSeparator();\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
@@ -947,23 +1311,23 @@ public class GAlignFrame
     colourMenu.add(modifyConservation);\r
     colourMenu.add(abovePIDThreshold);\r
     colourMenu.add(modifyPID);\r
+    colourMenu.add(annotationColour);\r
     calculateMenu.add(sort);\r
     calculateMenu.add(calculate);\r
     calculateMenu.addSeparator();\r
     calculateMenu.add(pairwiseAlignmentMenuItem);\r
     calculateMenu.add(PCAMenuItem);\r
     calculateMenu.addSeparator();\r
-    calculateMenu.add(webService);\r
-    webService.add(clustalAlignMenuItem);\r
-    webService.add(msaAlignMenuItem);\r
-    webService.add(jnet);\r
-    webService.add(ClustalRealign);\r
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
-    jMenu1.add(pasteNew);\r
-    jMenu1.add(pasteThis);\r
+    calculateMenu.add(showTranslation);\r
+    calculateMenu.add(autoCalculate);\r
+    webServiceNoServices = new JMenuItem("<No Services>");\r
+    webService.add(webServiceNoServices);\r
+    pasteMenu.add(pasteNew);\r
+    pasteMenu.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
     sort.add(sortGroupMenuItem);\r
     sort.add(sortPairwiseMenuItem);\r
+    sort.add(sortByTreeMenu);\r
     calculate.add(averageDistanceTreeMenuItem);\r
     calculate.add(neighbourTreeMenuItem);\r
     calculate.add(avDistanceTreeBlosumMenuItem);\r
@@ -971,17 +1335,72 @@ public class GAlignFrame
     jMenu2.add(htmlMenuItem);\r
     jMenu2.add(epsFile);\r
     jMenu2.add(createPNG);\r
+    addSequenceMenu.add(addFromFile);\r
+    addSequenceMenu.add(addFromText);\r
+    addSequenceMenu.add(addFromURL);\r
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);\r
+    statusPanel.add(statusBar, null);\r
+    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
+    jMenu3.add(showAllColumns);\r
+    jMenu3.add(showAllSeqs);\r
+    hideMenu.add(hideSelColumns);\r
+    hideMenu.add(hideSelSequences);\r
+    formatMenu.add(font);\r
+    formatMenu.addSeparator();\r
+    formatMenu.add(wrapMenuItem);\r
+    formatMenu.add(scaleAbove);\r
+    formatMenu.add(scaleLeft);\r
+    formatMenu.add(scaleRight);\r
+    formatMenu.add(seqLimits);\r
+    formatMenu.add(idRightAlign);\r
+    formatMenu.add(hiddenMarkers);\r
+    formatMenu.add(viewBoxesMenuItem);\r
+    formatMenu.add(viewTextMenuItem);\r
+    formatMenu.add(colourTextMenuItem);\r
+    formatMenu.add(renderGapsMenuItem);\r
+    selectMenu.add(findMenuItem);\r
+    selectMenu.addSeparator();\r
+    selectMenu.add(selectAllSequenceMenuItem);\r
+    selectMenu.add(deselectAllSequenceMenuItem);\r
+    selectMenu.add(invertSequenceMenuItem);\r
+    selectMenu.add(invertColSel);\r
+    selectMenu.add(deleteGroups);\r
   }\r
 \r
   protected void outputText_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
+  public void addFromFile_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void addFromText_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void addFromURL_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void exportFeatures_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void exportAnnotations_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
   protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
-  protected void closeMenuItem_actionPerformed(ActionEvent e)\r
+  protected void closeMenuItem_actionPerformed(boolean b)\r
   {\r
   }\r
 \r
@@ -1085,10 +1504,6 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-  }\r
-\r
   protected void clustalColour_actionPerformed(ActionEvent e)\r
   {\r
   }\r
@@ -1157,7 +1572,7 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
   {\r
   }\r
 \r
@@ -1201,8 +1616,13 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void fullSeqId_actionPerformed(ActionEvent e)\r
+  protected void seqLimit_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
+\r
+  public void seqDBRef_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
   public void createEPS(java.io.File f)\r
@@ -1237,27 +1657,161 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void preferences_actionPerformed(ActionEvent e)\r
+  protected void saveAs_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
-  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+  public void vamsasStore_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+  public void vamsasLoad_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
-  protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+  public void showTranslation_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void featureSettings_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
-  protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+  public void fetchSequence_actionPerformed(ActionEvent e)\r
   {\r
+\r
+  }\r
+\r
+  public void smoothFont_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void annotationColour_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void associatedData_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void autoCalculate_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void showAllSeqs_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void showAllColumns_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hideSelSequences_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hideSelColumns_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void findPdbId_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void enterPdbId_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void pdbFile_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void invertColSel_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void tabSelectionChanged(int sel)\r
+  {\r
+\r
+  }\r
+\r
+  public void tabbedPane_mousePressed(MouseEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void tabbedPane_focusGained(FocusEvent e)\r
+  {\r
+    requestFocus();\r
+  }\r
+\r
+  public void save_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void reload_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void newView_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void textColour_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void idRightAlign_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void expandViews_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void gatherViews_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void buildTreeMenu()\r
+  {\r
+\r
+  }\r
+\r
+  public void pageSetup_actionPerformed(ActionEvent e)\r
+  {\r
+\r
   }\r
 }\r