From a4ca9e8e125bd9cbfde7abe66029793980c83139 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 17 Dec 2010 14:24:26 +0000
Subject: [PATCH] 1.1 compat

---
 src/jalview/datamodel/ColumnSelection.java |   13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 589c19b..3b46c47 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1227,9 +1227,16 @@ public class ColumnSelection
         int diff = origseq.getLength() - sq.length();
         while (diff > 0)
         {
-          sq = sq
-                  + ((diff >= sb.length()) ? sb.toString() : sb
-                          .substring(0, diff));
+          //sq = sq
+          //        + ((diff >= sb.length()) ? sb.toString() : sb
+          //                .substring(0, diff));
+          if (diff>=sb.length()) {
+            sq+=sb.toString();
+          } else {
+            char[] buf = new char[diff];
+            sb.getChars(0, diff, buf, 0);
+            sq+=buf.toString();
+          }
           diff = origseq.getLength() - sq.length();
         }
       }
-- 
1.7.10.2