From 215cda864f5b16592196795281a622b57c493a04 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 5 Aug 2015 18:05:08 +0100
Subject: [PATCH] JAL-1821 JAL-1759 make sure we wait around until the current
 script has finished before starting superposition

---
 src/jalview/gui/AppJmol.java |   18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index a16ea68..7876346 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -748,8 +748,22 @@ public class AppJmol extends StructureViewerBase
         {
           public void run()
           {
-            alignStructs_withAllAlignPanels();
-            // jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+            if (jmb.viewer.isScriptExecuting())
+            {
+              javax.swing.SwingUtilities.invokeLater(this);
+              try
+              {
+                Thread.sleep(5);
+              } catch (InterruptedException q)
+              {
+              }
+              ;
+              return;
+            }
+            else
+            {
+              alignStructs_withAllAlignPanels();
+            }
           }
         });
         alignAddedStructures = false;
-- 
1.7.10.2