X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=86bf7216d14c0e2dc6705f3fd7a04084f9f76951;hb=b71ca98d05f8848fa3170d606b7b8a8ef6d274f4;hp=369721d8c2b325fa0d4bec3a20ce73f9824906f3;hpb=5f2df50328b5b4e3ca082b8bf27360aaabc69e3a;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 369721d..86bf721 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -620,7 +620,10 @@ public class AlignSeq
       {
         if ((i + (j * len)) < astr1.length())
         {
-          if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+          boolean sameChar = Comparison.isSameResidue(
+                  astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
+                  false);
+          if (sameChar
                   && !jalview.util.Comparison.isGap(astr1.charAt(i
                           + (j * len))))
           {
@@ -663,8 +666,7 @@ public class AlignSeq
     }
 
     pid = pid / (aseq1.length - count) * 100;
-    output = output.append(new Format("Percentage ID = %2.2f\n")
-            .form(pid));
+    output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
     try
     {
       os.print(output.toString());