From 9194c4500128ee9d624c9a185770093c8620696a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 4 Jun 2015 15:07:41 +0100
Subject: [PATCH] JAL-1747 close all windows on Quit (+small bug fix)

---
 src/jalview/gui/Desktop.java |   37 +++++++++++++++++++------------------
 1 file changed, 19 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 1228965..e8d7ffd 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,22 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -100,6 +84,22 @@ import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+
 /**
  * Jalview Desktop
  * 
@@ -1166,7 +1166,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       dialogExecutor.shutdownNow();
     }
-
+    closeAll_actionPerformed(null);
     System.exit(0);
   }
 
@@ -2522,7 +2522,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
-    if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+    if (progressBarHandlers == null
+            || !progressBars.containsKey(new Long(id)))
     {
       throw new Error(
               MessageManager
-- 
1.7.10.2