editMenuPadGaps and sortByTree/sort items

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b4cd276..9af1ee9 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -98,10 +98,11 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem modifyPID = new JMenuItem();\r
   JMenuItem modifyConservation = new JMenuItem();\r
   protected JMenu sortByTreeMenu = new JMenu();\r
   JMenuItem modifyPID = new JMenuItem();\r
   JMenuItem modifyConservation = new JMenuItem();\r
   protected JMenu sortByTreeMenu = new JMenu();\r

-  JMenu sort = new JMenu();\r
+  protected JMenu sort = new JMenu();\r

   JMenu calculate = new JMenu();\r
   JMenuItem msaAlignMenuItem = new JMenuItem();\r
   JMenu jMenu2 = new JMenu();\r
   JMenu calculate = new JMenu();\r
   JMenuItem msaAlignMenuItem = new JMenuItem();\r
   JMenu jMenu2 = new JMenu();\r

+  JMenuItem padGapsMenuitem = new JMenuItem();\r

   public GAlignFrame()\r
   {\r
     ButtonGroup colours = new ButtonGroup();\r
   public GAlignFrame()\r
   {\r
     ButtonGroup colours = new ButtonGroup();\r

@@ -778,6 +779,14 @@ public class GAlignFrame extends JInternalFrame
       }\r
     });\r
     jMenu2.setText("Export");\r
       }\r
     });\r
     jMenu2.setText("Export");\r

+    padGapsMenuitem.setText("Pad Gaps");\r
+    padGapsMenuitem.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        padGapsMenuitem_actionPerformed(e);\r
+      }\r
+    });\r

     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r

@@ -809,6 +818,8 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeGappedColumnMenuItem);\r
     editMenu.add(removeAllGapsMenuItem);\r
     editMenu.add(removeRedundancyMenuItem);\r
     editMenu.add(removeGappedColumnMenuItem);\r
     editMenu.add(removeAllGapsMenuItem);\r
     editMenu.add(removeRedundancyMenuItem);\r

+    editMenu.addSeparator();\r
+    editMenu.add(padGapsMenuitem);\r

     searchMenu.add(findMenuItem);\r
     viewMenu.add(font);\r
     viewMenu.addSeparator();\r
     searchMenu.add(findMenuItem);\r
     viewMenu.add(font);\r
     viewMenu.addSeparator();\r

@@ -859,7 +870,6 @@ public class GAlignFrame extends JInternalFrame
     jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
     jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r

-    sort.add(sortByTreeMenu);\r

     sort.add(sortGroupMenuItem);\r
     sort.add(sortPairwiseMenuItem);\r
     calculate.add(averageDistanceTreeMenuItem);\r
     sort.add(sortGroupMenuItem);\r
     sort.add(sortPairwiseMenuItem);\r
     calculate.add(averageDistanceTreeMenuItem);\r

@@ -1227,12 +1237,17 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
 \r
   }\r
 \r

-  public void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+  {\r
+\r
+  }\r
+\r
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r

   {\r
 \r
   }\r
 \r
   {\r
 \r
   }\r
 \r

-  public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r

   {\r
 \r
   }\r
   {\r
 \r
   }\r