X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FComparison.java;h=50472a53ac0851542b951933e39c1927807f3eb5;hb=baa67039bb8cd4236ac4565a62291c0ba6366c07;hp=6c7197ad1ed3717ca0acf0940a707c2421ed8b6f;hpb=21c9c09f36bd0e6dc64628464a2661c6de57d0ce;p=jalview.git

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 6c7197a..50472a5 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -55,8 +55,8 @@ public class Comparison
    */
   public static float compare(SequenceI ii, SequenceI jj, int start, int end)
   {
-    String si = ii.getSequence();
-    String sj = jj.getSequence();
+    String si = ii.getSequenceAsString();
+    String sj = jj.getSequenceAsString();
 
     int ilen = si.length() - 1;
     int jlen = sj.length() - 1;