merge from 2_4_Release branch

[jalview.git] / src / jalview / jbgui / GDesktop.java

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index aa86809..a8e2ef5 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -25,40 +25,66 @@ import javax.swing.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class GDesktop
-    extends JFrame
+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();
+
   protected JMenu VamsasStMenu = 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();
+
   protected JMenu toolsMenu = new JMenu();
+
   JMenuItem preferences = new JMenuItem();
+
   JMenuItem saveState = new JMenuItem();
+
   JMenuItem loadState = new JMenuItem();
+
   JMenu inputMenu = new JMenu();
+
   protected JMenuItem vamsasStart = new JMenuItem();
+
   protected JMenuItem vamsasImport = new JMenuItem();
+
   protected JMenuItem vamsasSave = new JMenuItem();
+
   JMenuItem inputSequence = new JMenuItem();
+
   protected JMenuItem vamsasStop = new JMenuItem();
+
   JMenuItem closeAll = new JMenuItem();
+
   JMenuItem raiseRelated = new JMenuItem();
+
   JMenuItem minimizeAssociated = new JMenuItem();
+
   protected JCheckBoxMenuItem showMemusage = new JCheckBoxMenuItem();
+
   JMenuItem garbageCollect = new JMenuItem();
 
   /**
@@ -70,8 +96,7 @@ public class GDesktop
     {
       jbInit();
       this.setJMenuBar(desktopMenubar);
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -92,11 +117,11 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
    */
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     FileMenu.setText("File");
     HelpMenu.setText("Help");
@@ -105,16 +130,17 @@ public class GDesktop
     VamsasStMenu.setText("Connect to");
     VamsasStMenu.setToolTipText("Join an existing vamsas session");
     inputLocalFileMenuItem.setText("from File");
-    inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_O,
-        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
-    inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        inputLocalFileMenuItem_actionPerformed(null);
-      }
-    });
+    inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_O, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask(), false));
+    inputLocalFileMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                inputLocalFileMenuItem_actionPerformed(null);
+              }
+            });
     inputURLMenuItem.setText("from URL");
     inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -124,13 +150,14 @@ public class GDesktop
       }
     });
     inputTextboxMenuItem.setText("from Textbox");
-    inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        inputTextboxMenuItem_actionPerformed(null);
-      }
-    });
+    inputTextboxMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                inputTextboxMenuItem_actionPerformed(null);
+              }
+            });
     quit.setText("Quit");
     quit.addActionListener(new java.awt.event.ActionListener()
     {
@@ -148,15 +175,16 @@ public class GDesktop
       }
     });
     documentationMenuItem.setText("Documentation");
-    documentationMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
-        java.awt.event.KeyEvent.VK_F1, 0, false));
-    documentationMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        documentationMenuItem_actionPerformed(e);
-      }
-    });
+    documentationMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0, false));
+    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...");
@@ -300,19 +328,19 @@ public class GDesktop
     windowMenu.add(raiseRelated);
     windowMenu.add(minimizeAssociated);
     windowMenu.addSeparator();
-    //    inputMenu.add(vamsasLoad);
+    // inputMenu.add(vamsasLoad);
   }
 
   protected void showMemusage_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void garbageCollect_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   protected void vamsasStMenu_actionPerformed()
@@ -325,30 +353,34 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
-  protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.
-      AlignViewport av)
+  protected void inputLocalFileMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av)
   {
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
-  protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)
+  protected void inputURLMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av)
   {
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
-  protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport
-      av)
+  protected void inputTextboxMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av)
   {
   }
 
@@ -361,8 +393,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void aboutMenuItem_actionPerformed(ActionEvent e)
   {
@@ -370,8 +403,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void documentationMenuItem_actionPerformed(ActionEvent e)
   {
@@ -379,8 +413,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void SaveState_actionPerformed(ActionEvent e)
   {
@@ -388,8 +423,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void preferences_actionPerformed(ActionEvent e)
   {
@@ -397,8 +433,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void saveState_actionPerformed(ActionEvent e)
   {
@@ -406,8 +443,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void loadState_actionPerformed(ActionEvent e)
   {
@@ -415,8 +453,9 @@ public class GDesktop
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void loadJalviewAlign_actionPerformed(ActionEvent e)
   {