Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index f3d9a65..124c7c7 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -32,6 +32,8 @@ import javax.swing.JMenuItem;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.gui.APQHandlers;
+import jalview.gui.Desktop;
 import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -147,10 +149,10 @@ public class GDesktop extends JFrame
      */
     try
     {
-      APQHandlers.setAPQHandlers(this);
+      APQHandlers.setAPQHandlers((Desktop) this);
     } catch (Exception e)
     {
-      System.out.println("Cannot set APQHandlers");
+      jalview.bin.Console.outPrintln("Cannot set APQHandlers");
       // e.printStackTrace();
     } catch (Throwable t)
     {
@@ -191,7 +193,7 @@ public class GDesktop extends JFrame
           inputURLMenuItem_actionPerformed(null);
         } catch (FileFormatException e1)
         {
-          System.err.println("Error loading from URL: " + e1.getMessage());
+          jalview.bin.Console.errPrintln("Error loading from URL: " + e1.getMessage());
         }
       }
     });
@@ -212,7 +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"));
@@ -389,10 +392,6 @@ public class GDesktop extends JFrame
       }
     });
 
-    Float specversion = Platform.isJS() ? Float.valueOf(8)
-            : Float.parseFloat(
-                    System.getProperty("java.specification.version"));
-
     desktopMenubar.add(FileMenu);
     desktopMenubar.add(toolsMenu);
     desktopMenubar.add(HelpMenu);
@@ -404,13 +403,16 @@ public class GDesktop extends JFrame
     FileMenu.add(saveAsState);
     FileMenu.add(loadState);
     FileMenu.addSeparator();
-    FileMenu.add(quit);
-    if (!APQHandlers.setAPQHandlers)
+    if (!APQHandlers.setQuit)
+    {
+      FileMenu.add(quit);
+    }
+    if (!APQHandlers.setAbout)
     {
       HelpMenu.add(aboutMenuItem);
     }
     HelpMenu.add(documentationMenuItem);
-    if (!APQHandlers.setAPQHandlers)
+    if (!APQHandlers.setPreferences)
     {
       toolsMenu.add(preferences);
     }
@@ -519,7 +521,7 @@ public class GDesktop extends JFrame
    */
   protected void quit()
   {
-    // System.out.println("********** GDesktop.quit()");
+    // jalview.bin.Console.outPrintln("********** GDesktop.quit()");
   }
 
   /**