X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=86bf7216d14c0e2dc6705f3fd7a04084f9f76951;hb=34d5dfb25731d7d797177cadfce954258ae90991;hp=f7e8f2ebe26d9fc58f28be41f5f534103c91a311;hpb=1e943acf589b7393c666204f533d2ebce28d7471;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index f7e8f2e..86bf721 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -620,7 +620,7 @@ public class AlignSeq
       {
         if ((i + (j * len)) < astr1.length())
         {
-          boolean sameChar = Comparison.compareChars(
+          boolean sameChar = Comparison.isSameResidue(
                   astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
                   false);
           if (sameChar