accelerators, save menu item
authoramwaterhouse <Andrew Waterhouse>
Mon, 6 Nov 2006 13:59:56 +0000 (13:59 +0000)
committeramwaterhouse <Andrew Waterhouse>
Mon, 6 Nov 2006 13:59:56 +0000 (13:59 +0000)
src/jalview/gui/AlignFrame.java
src/jalview/jbgui/GAlignFrame.java
src/jalview/jbgui/GDesktop.java

index 189c5c0..f82efb5 100755 (executable)
@@ -60,6 +60,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
 
+  public String fileName = null;
+
   private int treeCount = 0;
 
   /**
@@ -571,12 +573,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
   }
 
+
+  public void save_actionPerformed(ActionEvent e)
+  {
+    if(fileName==null || currentFileFormat==null)
+      saveAs_actionPerformed(null);
+    else
+      saveAlignment(fileName, currentFileFormat);
+  }
+
   /**
    * DOCUMENT ME!
    *
    * @param e DOCUMENT ME!
    */
-  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
+  public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
         getProperty( "LAST_DIRECTORY"),
@@ -597,7 +608,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
         currentFileFormat = chooser.getSelectedFormat();
-
         if (currentFileFormat == null)
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -608,13 +618,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
           return;
         }
 
+        fileName = chooser.getSelectedFile().getPath();
+
       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
                                     currentFileFormat);
 
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
 
-      saveAlignment(choice, currentFileFormat);
+      saveAlignment(fileName, currentFileFormat);
     }
   }
 
@@ -632,6 +643,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
       new Jalview2XML().SaveAlignment(this, file, shortName);
 
+      statusBar.setText("Successfully saved to file: "
+                          +fileName+" in "
+                          +format +" format.");
+
+
       // USE Jalview2XML to save this file
       return true;
     }
@@ -670,6 +686,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         out.print(output);
         out.close();
         this.setTitle(file);
+        statusBar.setText("Successfully saved to file: "
+                          +fileName+" in "
+                          +format +" format.");
         return true;
       }
       catch (Exception ex)
@@ -821,8 +840,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         }
       //  alignPanels = null;
       }
-      else
-        System.out.println("null one here");
+    //  else
+     //   System.out.println("null one here");
 
     //  alignPanel = null;
     //  viewport = null;
index cbe888a..304134c 100755 (executable)
@@ -61,7 +61,7 @@ public class GAlignFrame
   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
@@ -142,6 +142,7 @@ public class GAlignFrame
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();\r
   JMenuItem invertColSel = new JMenuItem();\r
   protected JTabbedPane tabbedPane = new JTabbedPane();\r
+  JMenuItem save = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
     try\r
@@ -316,21 +317,21 @@ public class GAlignFrame
   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.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
-        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
-    saveAlignmentMenu.addActionListener(new ActionListener()\r
+    saveAs.setText("Save As ...");\r
+    saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_S, java.awt.event.KeyEvent.ALT_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, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     closeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -650,8 +651,6 @@ public class GAlignFrame
       }\r
     });\r
     overviewMenuItem.setText("Overview Window");\r
-    overviewMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
-        event.KeyEvent.VK_O, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -709,6 +708,8 @@ public class GAlignFrame
       }\r
     });\r
     printMenuItem.setText("Print");\r
+    printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
+        event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -927,10 +928,8 @@ public class GAlignFrame
     sort.setText("Sort");\r
     calculate.setText("Calculate Tree");\r
 \r
-    jMenu2.setText("Export");\r
+    jMenu2.setText("Export Image");\r
     padGapsMenuitem.setText("Pad Gaps");\r
-    padGapsMenuitem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.\r
-        event.KeyEvent.VK_P, java.awt.event.KeyEvent.CTRL_MASK, false));\r
     padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));\r
     padGapsMenuitem.addActionListener(new ActionListener()\r
     {\r
@@ -1125,6 +1124,16 @@ public class GAlignFrame
         tabbedPane_focusGained(e);\r
       }\r
     });\r
+    save.setText("Save");\r
+    save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.\r
+        KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
+    save.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        save_actionPerformed(e);\r
+      }\r
+    });\r
 \r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
@@ -1137,11 +1146,12 @@ public class GAlignFrame
     fileMenu.add(fetchSequence);\r
     fileMenu.addSeparator();\r
     fileMenu.add(vamsasStore);\r
-    fileMenu.add(saveAlignmentMenu);\r
-    fileMenu.add(jMenu2);\r
+    fileMenu.add(save);\r
+    fileMenu.add(saveAs);\r
     fileMenu.add(outputTextboxMenu);\r
     fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
+    fileMenu.add(jMenu2);\r
     fileMenu.add(exportFeatures);\r
     fileMenu.add(exportAnnotations);\r
     fileMenu.add(LoadtreeMenuItem);\r
@@ -1538,7 +1548,7 @@ public class GAlignFrame
 \r
 \r
 \r
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+  protected void saveAs_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
@@ -1652,4 +1662,9 @@ public class GAlignFrame
   {\r
     requestFocus();\r
   }\r
+\r
+  public void save_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
 }\r
index fea3c5c..16b4950 100755 (executable)
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GDesktop extends JFrame
-{
-    protected static JMenu windowMenu = new JMenu();
-    JMenuBar DesktopMenubar = new JMenuBar();
-    JMenu FileMenu = new JMenu();
-    JMenu HelpMenu = new JMenu();
-    protected JMenu VamsasMenu = new JMenu();
-    JMenuItem inputLocalFileMenuItem = new JMenuItem();
-    JMenuItem inputURLMenuItem = new JMenuItem();
-    JMenuItem inputTextboxMenuItem = new JMenuItem();
-    JMenuItem quit = new JMenuItem();
-    JMenuItem aboutMenuItem = new JMenuItem();
-    JMenuItem documentationMenuItem = new JMenuItem();
-    FlowLayout flowLayout1 = new FlowLayout();
-    JMenu toolsMenu = new JMenu();
-    JMenuItem preferences = new JMenuItem();
-    JMenuItem saveState = new JMenuItem();
-    JMenuItem loadState = new JMenuItem();
-    JMenu jMenu1 = new JMenu();
-  protected JMenuItem vamsasLoad = new JMenuItem();
-  JMenuItem inputSequence = new JMenuItem();
-  protected JMenuItem vamsasStop = new JMenuItem();
-
-  /**
-     * Creates a new GDesktop object.
-     */
-    public GDesktop()
-    {
-        try
-        {
-            jbInit();
-            this.setJMenuBar(DesktopMenubar);
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
-    {
-        FileMenu.setMnemonic('F');
-        FileMenu.setText("File");
-        HelpMenu.setText("Help");
-        VamsasMenu.setText("Vamsas");
-        VamsasMenu.setMnemonic('V');
-        VamsasMenu.setToolTipText("Share data with other vamsas applications.");
-        inputLocalFileMenuItem.setMnemonic('L');
-        inputLocalFileMenuItem.setText("from File");
-        inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    inputLocalFileMenuItem_actionPerformed(null);
-                }
-            });
-        inputURLMenuItem.setMnemonic('U');
-        inputURLMenuItem.setText("from URL");
-        inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    inputURLMenuItem_actionPerformed(null);
-                }
-            });
-        inputTextboxMenuItem.setMnemonic('C');
-        inputTextboxMenuItem.setText("from Textbox");
-        inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    inputTextboxMenuItem_actionPerformed(null);
-                }
-            });
-        quit.setMnemonic('Q');
-        quit.setText("Quit");
-        quit.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    quit();
-                }
-            });
-        aboutMenuItem.setText("About");
-        aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    aboutMenuItem_actionPerformed(e);
-                }
-            });
-        documentationMenuItem.setText("Documentation");
-        documentationMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    documentationMenuItem_actionPerformed(e);
-                }
-            });
-        this.getContentPane().setLayout(flowLayout1);
-        windowMenu.setText("Window");
-        preferences.setText("Preferences...");
-        preferences.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    preferences_actionPerformed(e);
-                }
-            });
-        toolsMenu.setText("Tools");
-        saveState.setMnemonic('S');
-        saveState.setText("Save Project");
-        saveState.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    saveState_actionPerformed(e);
-                }
-            });
-        loadState.setMnemonic('L');
-        loadState.setText("Load Project");
-        loadState.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    loadState_actionPerformed(e);
-                }
-            });
-        jMenu1.setMnemonic('I');
-        jMenu1.setText("Input Alignment");
-    vamsasLoad.setText("Start Vamsas Session...");
-    vamsasLoad.setVisible(false);
-    vamsasLoad.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        vamsasLoad_actionPerformed(e);
-      }
-    });
-    inputSequence.setText("Fetch Sequence(s)...");
-    inputSequence.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        inputSequence_actionPerformed(e);
-      }
-    });
-    vamsasStop.setText("Stop Vamsas Session");
-    vamsasStop.setVisible(false);
-    vamsasStop.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        vamsasStop_actionPerformed(e);
-      }
-    });    DesktopMenubar.add(FileMenu);
-        DesktopMenubar.add(toolsMenu);
-        VamsasMenu.setVisible(false);
-        DesktopMenubar.add(VamsasMenu);
-        DesktopMenubar.add(HelpMenu);
-        DesktopMenubar.add(windowMenu);
-    FileMenu.add(jMenu1);
-    FileMenu.add(inputSequence);
-    FileMenu.addSeparator();
-        FileMenu.add(saveState);
-        FileMenu.add(loadState);
-        FileMenu.addSeparator();
-        FileMenu.add(quit);
-        HelpMenu.add(aboutMenuItem);
-        HelpMenu.add(documentationMenuItem);
-        VamsasMenu.add(vamsasLoad);
-        VamsasMenu.add(vamsasStop);
-        toolsMenu.add(preferences);
-        jMenu1.add(inputLocalFileMenuItem);
-        jMenu1.add(inputURLMenuItem);
-        jMenu1.add(inputTextboxMenuItem);
-       //    jMenu1.add(vamsasLoad);
-  }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    protected void quit()
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void aboutMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void documentationMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void SaveState_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void preferences_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveState_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadState_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadJalviewAlign_actionPerformed(ActionEvent e)
-    {
-    }
-
-  public void vamsasLoad_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void inputSequence_actionPerformed(ActionEvent e)
-  {
-
-  }
-  public void vamsasStop_actionPerformed(ActionEvent e)
-  {
-
-       }
-}
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2006 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
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
+package jalview.jbgui;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.*;\r
+\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class GDesktop extends JFrame\r
+{\r
+    protected static JMenu windowMenu = new JMenu();\r
+    JMenuBar DesktopMenubar = new JMenuBar();\r
+    JMenu FileMenu = new JMenu();\r
+    JMenu HelpMenu = new JMenu();\r
+    protected JMenu VamsasMenu = new JMenu();\r
+    JMenuItem inputLocalFileMenuItem = new JMenuItem();\r
+    JMenuItem inputURLMenuItem = new JMenuItem();\r
+    JMenuItem inputTextboxMenuItem = new JMenuItem();\r
+    JMenuItem quit = new JMenuItem();\r
+    JMenuItem aboutMenuItem = new JMenuItem();\r
+    JMenuItem documentationMenuItem = new JMenuItem();\r
+    FlowLayout flowLayout1 = new FlowLayout();\r
+    JMenu toolsMenu = new JMenu();\r
+    JMenuItem preferences = new JMenuItem();\r
+    JMenuItem saveState = new JMenuItem();\r
+    JMenuItem loadState = new JMenuItem();\r
+    JMenu jMenu1 = new JMenu();\r
+  protected JMenuItem vamsasLoad = new JMenuItem();\r
+  JMenuItem inputSequence = new JMenuItem();\r
+  protected JMenuItem vamsasStop = new JMenuItem();\r
+\r
+  /**\r
+     * Creates a new GDesktop object.\r
+     */\r
+    public GDesktop()\r
+    {\r
+        try\r
+        {\r
+            jbInit();\r
+            this.setJMenuBar(DesktopMenubar);\r
+        }\r
+        catch (Exception e)\r
+        {\r
+            e.printStackTrace();\r
+        }\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @throws Exception DOCUMENT ME!\r
+     */\r
+    private void jbInit() throws Exception\r
+    {\r
+        FileMenu.setMnemonic('F');\r
+        FileMenu.setText("File");\r
+        HelpMenu.setText("Help");\r
+        VamsasMenu.setText("Vamsas");\r
+        VamsasMenu.setMnemonic('V');\r
+        VamsasMenu.setToolTipText("Share data with other vamsas applications.");\r
+        inputLocalFileMenuItem.setMnemonic('L');\r
+        inputLocalFileMenuItem.setText("from File");\r
+    inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+        java.awt.event.KeyEvent.VK_O, java.awt.event.KeyEvent.CTRL_MASK, false));\r
+    inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    inputLocalFileMenuItem_actionPerformed(null);\r
+                }\r
+            });\r
+        inputURLMenuItem.setMnemonic('U');\r
+        inputURLMenuItem.setText("from URL");\r
+        inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    inputURLMenuItem_actionPerformed(null);\r
+                }\r
+            });\r
+        inputTextboxMenuItem.setMnemonic('C');\r
+        inputTextboxMenuItem.setText("from Textbox");\r
+        inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    inputTextboxMenuItem_actionPerformed(null);\r
+                }\r
+            });\r
+        quit.setMnemonic('Q');\r
+        quit.setText("Quit");\r
+        quit.addActionListener(new java.awt.event.ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    quit();\r
+                }\r
+            });\r
+        aboutMenuItem.setText("About");\r
+        aboutMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    aboutMenuItem_actionPerformed(e);\r
+                }\r
+            });\r
+        documentationMenuItem.setText("Documentation");\r
+        documentationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    documentationMenuItem_actionPerformed(e);\r
+                }\r
+            });\r
+        this.getContentPane().setLayout(flowLayout1);\r
+        windowMenu.setText("Window");\r
+        preferences.setText("Preferences...");\r
+        preferences.addActionListener(new ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    preferences_actionPerformed(e);\r
+                }\r
+            });\r
+        toolsMenu.setText("Tools");\r
+        saveState.setMnemonic('S');\r
+        saveState.setText("Save Project");\r
+        saveState.addActionListener(new ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    saveState_actionPerformed(e);\r
+                }\r
+            });\r
+        loadState.setMnemonic('L');\r
+        loadState.setText("Load Project");\r
+        loadState.addActionListener(new ActionListener()\r
+            {\r
+                public void actionPerformed(ActionEvent e)\r
+                {\r
+                    loadState_actionPerformed(e);\r
+                }\r
+            });\r
+        jMenu1.setMnemonic('I');\r
+        jMenu1.setText("Input Alignment");\r
+    vamsasLoad.setText("Start Vamsas Session...");\r
+    vamsasLoad.setVisible(false);\r
+    vamsasLoad.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        vamsasLoad_actionPerformed(e);\r
+      }\r
+    });\r
+    inputSequence.setText("Fetch Sequence(s)...");\r
+    inputSequence.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        inputSequence_actionPerformed(e);\r
+      }\r
+    });\r
+    vamsasStop.setText("Stop Vamsas Session");\r
+    vamsasStop.setVisible(false);\r
+    vamsasStop.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        vamsasStop_actionPerformed(e);\r
+      }\r
+    });    DesktopMenubar.add(FileMenu);\r
+        DesktopMenubar.add(toolsMenu);\r
+        VamsasMenu.setVisible(false);\r
+        DesktopMenubar.add(VamsasMenu);\r
+        DesktopMenubar.add(HelpMenu);\r
+        DesktopMenubar.add(windowMenu);\r
+    FileMenu.add(jMenu1);\r
+    FileMenu.add(inputSequence);\r
+    FileMenu.addSeparator();\r
+        FileMenu.add(saveState);\r
+        FileMenu.add(loadState);\r
+        FileMenu.addSeparator();\r
+        FileMenu.add(quit);\r
+        HelpMenu.add(aboutMenuItem);\r
+        HelpMenu.add(documentationMenuItem);\r
+        VamsasMenu.add(vamsasLoad);\r
+        VamsasMenu.add(vamsasStop);\r
+        toolsMenu.add(preferences);\r
+        jMenu1.add(inputLocalFileMenuItem);\r
+        jMenu1.add(inputURLMenuItem);\r
+        jMenu1.add(inputTextboxMenuItem);\r
+       //    jMenu1.add(vamsasLoad);\r
+  }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     */\r
+    protected void quit()\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    protected void aboutMenuItem_actionPerformed(ActionEvent e)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    protected void documentationMenuItem_actionPerformed(ActionEvent e)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    public void SaveState_actionPerformed(ActionEvent e)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    protected void preferences_actionPerformed(ActionEvent e)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    public void saveState_actionPerformed(ActionEvent e)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    public void loadState_actionPerformed(ActionEvent e)\r
+    {\r
+    }\r
+\r
+    /**\r
+     * DOCUMENT ME!\r
+     *\r
+     * @param e DOCUMENT ME!\r
+     */\r
+    public void loadJalviewAlign_actionPerformed(ActionEvent e)\r
+    {\r
+    }\r
+\r
+  public void vamsasLoad_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void inputSequence_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+  public void vamsasStop_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+       }\r
+}\r