From 970bedebd2260e55bd1e584ee511d5e3990a5ce5 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sat, 4 Apr 2009 11:35:24 +0000
Subject: [PATCH] rejigged jmol check thread to run prior to data loading
 thread to avoid classloader race condition in java 1.6_10
 (Sillitoe/Clegg/CATH issue)

---
 src/jalview/bin/JalviewLite.java |   15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 9226dc4..9a09df4 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -599,7 +599,7 @@ public class JalviewLite extends Applet
      * State variable: format of file source
      */
     String format;
-
+    String _file;
     JalviewLite applet;
     private void dbgMsg(String msg)
     {
@@ -635,14 +635,10 @@ public class JalviewLite extends Applet
       dbgMsg("Protocol identified as '" + protocol + "'");
       return file;
     }
-
+    
     public LoadingThread(String _file, JalviewLite _applet)
     {
-      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
-      file = setProtocolState(_file);
-
-      format = new jalview.io.IdentifyFile().Identify(file, protocol);
-      dbgMsg("File identified as '" + format + "'");
+      this._file=_file;
       applet = _applet;
     }
 
@@ -660,6 +656,11 @@ public class JalviewLite extends Applet
 
     private void startLoading()
     {
+      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+      file = setProtocolState(_file);
+
+      format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      dbgMsg("File identified as '" + format + "'");
       dbgMsg("Loading started.");
       Alignment al = null;
       try
-- 
1.7.10.2