From e02b02024dfd55916e3d96e7ae2166478b8a6688 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 3 Aug 2015 15:44:19 +0100
Subject: [PATCH] JAL-1821 avoid race condition when multiple structures
 loaded in Jmol where getFiles() returns {null} and
 waitUntilLoad times out rather than performs superposition

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |   11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index c7496df..abd742e 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -259,8 +259,17 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public void superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
+    while (viewer.isScriptExecuting())
+    {
+      try
+      {
+        Thread.sleep(10);
+      } catch (InterruptedException i)
+      {
+      }
+      ;
+    }
     String[] files = getPdbFile();
-
     if (!waitForFileLoad(files))
     {
       return;
-- 
1.7.10.2