Set startRes 0 for switch to wrap view

[jalview.git] / src / jalview / util / Comparison.java

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