JAL-1747 close all windows on Quit (+small bug fix)

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 5f45dc1..e8d7ffd 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -169,6 +169,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private static final int THREE = 3;
 
+  private static AlignFrame currentAlignFrame;
+
   public static jalview.ws.jws1.Discoverer discoverer;
 
   public static Object[] jalviewClipboard;
@@ -1022,6 +1024,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
                 format);
+        // viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled());
+        // AlignFrame af = viewport.getAlignPanel().alignFrame;
+        // if (af != null)
+        // {
+        // af.changeColour(JSONFile.getColourScheme());
+        // af.setMenusForViewport();
+        // }
       }
       else
       {
@@ -1157,7 +1166,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       dialogExecutor.shutdownNow();
     }
-
+    closeAll_actionPerformed(null);
     System.exit(0);
   }
 
@@ -2513,7 +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
@@ -3073,4 +3083,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     myTopFrame.setDisplayedView(myTopFrame.alignPanel);
 
   }
+
+  // public static AlignFrame getCurrentAlignFrame()
+  // {
+  // return currentAlignFrame;
+  // }
+  //
+  // public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  // {
+  // Desktop.currentAlignFrame = currentAlignFrame;
+  // }
+
+
 }