Added clustalW 'realignment' (primitive)

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 060c387..23c78f3 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -103,6 +103,7 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem msaAlignMenuItem = new JMenuItem();\r
   JMenu jMenu2 = new JMenu();\r
   JMenuItem padGapsMenuitem = new JMenuItem();\r
+  JMenuItem ClustalRealign = new JMenuItem();\r
   public GAlignFrame()\r
   {\r
     ButtonGroup colours = new ButtonGroup();\r
@@ -787,6 +788,14 @@ public class GAlignFrame extends JInternalFrame
         padGapsMenuitem_actionPerformed(e);\r
       }\r
     });\r
+    ClustalRealign.setText("Clustal Realign...");\r
+    ClustalRealign.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        ClustalRealign_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -864,8 +873,9 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();\r
     calculateMenu.add(webService);\r
     webService.add(clustalAlignMenuItem);\r
-    webService.add(jpred);\r
     webService.add(msaAlignMenuItem);\r
+    webService.add(jpred);\r
+    webService.add(ClustalRealign);\r
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
     jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
@@ -1252,4 +1262,9 @@ public class GAlignFrame extends JInternalFrame
 \r
   }\r
 \r
+  protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
 }\r