X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=d0fc9277f5c5bbda923b5b7f0acc4d695c5f11de;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=0bcbd5b2eb61e958cb4a1992ffd55f17d012820e;hpb=c5b266dbd1a12ac4b5e0a070b10fa707a73cd889;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 0bcbd5b..d0fc927 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -1181,9 +1181,16 @@ public class ColumnSelection
                 sq = sq + sb;
                 while ((diff = spos + offset - sq.length() - 1) > 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();
+                  }
                 }
               }
               sq += sb.toString();
@@ -1220,9 +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();
         }
       }