From cb03edaa1450e5716bd37ca5cc430a46c245e9db Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 1 Oct 2012 10:56:21 +0100
Subject: [PATCH] JAL-1184 apparent deadlock when launching jalview on w7 -
 attempt to patch

---
 src/jalview/gui/Desktop.java          |   21 +++++++++++++++------
 src/jalview/gui/PromptUserConfig.java |    4 ++--
 2 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index d1e8b6a..50f0095 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -59,6 +59,7 @@ import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.lang.reflect.Constructor;
+import java.lang.reflect.InvocationTargetException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -2616,19 +2617,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * single thread that handles display of dialogs to user.
    */
-  ExecutorService dialogExecutor=null;
+  ExecutorService dialogExecutor=Executors.newSingleThreadExecutor();
   
   /**
    * add another dialog thread to the queue
    * @param prompter
    */
-  public synchronized void addDialogThread(Runnable prompter)
+  public void addDialogThread(final Runnable prompter)
   {
-    if (dialogExecutor==null)
+    dialogExecutor.submit(new Runnable()
     {
-      dialogExecutor = Executors.newSingleThreadExecutor();
-    }
-    dialogExecutor.submit(prompter);
+      public void run()
+      {
+        try
+        {
+          SwingUtilities.invokeAndWait(prompter);
+        } catch (Exception q)
+        {
+          Cache.log.warn("Unexpected Exception in dialog thread.", q);
+        }
+      }
+    });
   }
 
 }
diff --git a/src/jalview/gui/PromptUserConfig.java b/src/jalview/gui/PromptUserConfig.java
index 95d9c69..f05459b 100644
--- a/src/jalview/gui/PromptUserConfig.java
+++ b/src/jalview/gui/PromptUserConfig.java
@@ -200,8 +200,8 @@ public class PromptUserConfig implements Runnable
     }
     try
     {
-      int reply = JOptionPane.showInternalConfirmDialog(
-              Desktop.desktop, // component,
+      int reply = JOptionPane.showConfirmDialog(
+              null, // component,
               dialogText, dialogTitle,
               (allowCancel) ? JOptionPane.YES_NO_CANCEL_OPTION
                       : JOptionPane.YES_NO_OPTION,
-- 
1.7.10.2