From e75315ad5faf541f6943e9395c81a078369f2f63 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 12 Oct 2023 10:54:02 +0100
Subject: [PATCH] JAL-629 null check and neatening code

---
 src/jalview/gui/JvOptionPane.java |   22 +++++++++++++---------
 1 file changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java
index 0a7c49e..8edab03 100644
--- a/src/jalview/gui/JvOptionPane.java
+++ b/src/jalview/gui/JvOptionPane.java
@@ -859,8 +859,9 @@ public class JvOptionPane extends JOptionPane
           break NOTNULL;
         }
 
-        // run through buttons for initialValue first so can set a final
-        // timeoutThreadF
+        // run through buttons for initialValue first so we can set (and start)
+        // a final timeoutThreadF to include (and interrupt) in the button
+        // actions
         Thread timeoutThread = null;
         for (int i = 0; i < options.length; i++)
         {
@@ -868,11 +869,10 @@ public class JvOptionPane extends JOptionPane
           JButton jb = buttons[i];
           if (o.equals(initialValue))
           {
-            initialValueButton = jb;
-            if (timeout > 0 && initialValueButton != null
-                    && initialValueButton instanceof JButton)
+            if (timeout > 0 && jb != null && jb instanceof JButton)
             {
-              Runnable timeoutClose = () -> {
+              // after timeout ms click the default button
+              timeoutThread = new Thread(() -> {
                 try
                 {
                   Thread.sleep(timeout);
@@ -882,13 +882,17 @@ public class JvOptionPane extends JOptionPane
                           "Dialog timeout interrupted.  Probably a button pressed.");
                 }
                 jb.doClick();
-              };
-              timeoutThread = new Thread(timeoutClose);
+              });
             }
+            initialValueButton = jb;
+            break;
           }
         }
         final Thread timeoutThreadF = timeoutThread;
-        timeoutThreadF.start();
+        if (timeoutThreadF != null)
+        {
+          timeoutThreadF.start();
+        }
 
         int[] buttonActions = { JOptionPane.YES_OPTION,
             JOptionPane.NO_OPTION, JOptionPane.CANCEL_OPTION };
-- 
1.7.10.2