From f6b699b87c2666f105973aa0be80e2dc62ed39e6 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Mon, 1 Oct 2012 12:15:10 +0100
Subject: [PATCH] JAL-1183 dialog thread is only started after the
 splashscreen goes away

---
 src/jalview/gui/Desktop.java      |   22 ++++++++++++++++++++++
 src/jalview/gui/SplashScreen.java |    1 +
 2 files changed, 23 insertions(+)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 50f0095..d357e4f 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -67,6 +67,7 @@ import java.util.StringTokenizer;
 import java.util.Vector;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
+import java.util.concurrent.Semaphore;
 
 import javax.swing.DefaultDesktopManager;
 import javax.swing.DesktopManager;
@@ -2618,6 +2619,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * single thread that handles display of dialogs to user.
    */
   ExecutorService dialogExecutor=Executors.newSingleThreadExecutor();
+  /**
+   * flag indicating if dialogExecutor should try to acquire a permit
+   */
+  private volatile boolean dialogPause=true;
+  /**
+   * pause the queue 
+   */
+  private java.util.concurrent.Semaphore block=new Semaphore(0);
   
   /**
    * add another dialog thread to the queue
@@ -2629,6 +2638,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       public void run()
       {
+        if (dialogPause) {
+          try { block.acquire(); } catch (InterruptedException x){};
+        }
+        if (instance==null)
+        {
+          return;
+        }
         try
         {
           SwingUtilities.invokeAndWait(prompter);
@@ -2640,4 +2656,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     });
   }
 
+  public void startDialogQueue()
+  {
+    // set the flag so we don't pause waiting for another permit and semaphore the current task to begin
+    dialogPause=false;
+    block.release();
+  }
 }
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 15914df..6fcb6a0 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -197,6 +197,7 @@ public class SplashScreen extends JPanel implements Runnable, HyperlinkListener
     }
 
     closeSplash();
+    Desktop.instance.startDialogQueue();
   }
 
   /**
-- 
1.7.10.2