X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPromptUserConfig.java;h=507d1f2e9902e701f0c5662ecb9e4088e2c5f76f;hb=87ea83af3e209a8c3a4b19f9530a9c05b4541148;hp=ac15f2b0f248edebd970816b3bc0bf1cd59f6db0;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/PromptUserConfig.java b/src/jalview/gui/PromptUserConfig.java
index ac15f2b..507d1f2 100644
--- a/src/jalview/gui/PromptUserConfig.java
+++ b/src/jalview/gui/PromptUserConfig.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -20,8 +20,6 @@ package jalview.gui;
 import jalview.bin.Cache;
 
 import java.awt.Component;
-import java.io.*;
-import java.net.*;
 
 import javax.swing.*;
 
@@ -200,12 +198,19 @@ public class PromptUserConfig implements Runnable
     }
     try
     {
-      int reply = JOptionPane.showInternalConfirmDialog(
+      int reply = JOptionPane.showConfirmDialog(
               Desktop.desktop, // component,
               dialogText, dialogTitle,
               (allowCancel) ? JOptionPane.YES_NO_CANCEL_OPTION
                       : JOptionPane.YES_NO_OPTION,
               JOptionPane.QUESTION_MESSAGE);
+      // now, ask the desktop to relayer any external windows that might have
+      // been obsured
+      if (Desktop.instance != null)
+      {
+        Desktop.instance.relayerWindows();
+      }
+      // and finish parsing the result
       jalview.bin.Cache.log.debug("Got response : " + reply);
       if (reply == JOptionPane.YES_OPTION)
       {