From 4de8dbdccf508589bec18d9a8af5799531c5807b Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 27 Aug 2010 13:02:02 +0000
Subject: [PATCH] 1.2 compatibility

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |    7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8831bd6..f8fe17b 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -363,7 +363,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         }
       }
     }
-    StringBuffer selcom[] = new StringBuffer[files.length];
+    String[] selcom = new String[files.length];
     // generate select statements to select regions to superimpose structures
     {
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
@@ -371,7 +371,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
         String chainCd = targetC[pdbfnum];
         int lpos = -1;
         boolean run = false;
-        StringBuffer molsel = (selcom[pdbfnum] = new StringBuffer());
+        StringBuffer molsel = new StringBuffer();
         molsel.append("{");
         for (int r = 0; r < matched.length; r++)
         {
@@ -411,8 +411,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
           molsel.append(chainCd);
           molsel.append("}");
         }
+        selcom[pdbfnum] = molsel.toString(); 
         selectioncom.append("((");
-        selectioncom.append(molsel.subSequence(1, molsel.length()-1));
+        selectioncom.append(selcom[pdbfnum].substring(1, selcom[pdbfnum].length()-1));
         selectioncom.append(" )& ");
         selectioncom.append(pdbfnum+1);
         selectioncom.append(".1)");
-- 
1.7.10.2