X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGDesktop.java;h=3343c8879338cb001c5f6d1e1f15b20a1507ee68;hb=b364e1e6d199002069dab615d1007799b5bb71e1;hp=459835d67d3f09f260d387bd031f8ed71a5fcb12;hpb=f9574ab683df8d0c9dfda092c9005ca773c38e55;p=jalview.git

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 459835d..3343c88 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -32,6 +32,7 @@ import javax.swing.JMenuItem;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.gui.Desktop;
 import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -213,7 +214,8 @@ public class GDesktop extends JFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        quit();
+        if (Desktop.instance != null)
+          Desktop.instance.desktopQuit();
       }
     });
     aboutMenuItem.setText(MessageManager.getString("label.about"));
@@ -401,7 +403,10 @@ public class GDesktop extends JFrame
     FileMenu.add(saveAsState);
     FileMenu.add(loadState);
     FileMenu.addSeparator();
-    FileMenu.add(quit);
+    if (!APQHandlers.setQuit)
+    {
+      FileMenu.add(quit);
+    }
     if (!APQHandlers.setAbout)
     {
       HelpMenu.add(aboutMenuItem);