X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;fp=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=02b3f41f35a8397cd8ad1a0f5d018d2a22432da2;hb=cfd38a33612b73a5b050c9f19d0fb0d81a7b646a;hp=65fd1100b8e8a7f2cdc33f1d1a90f80aaa3076bf;hpb=de9592c0781569ccefd4c115bb36524d6c9deaab;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 65fd110..02b3f41 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -890,7 +890,8 @@ public class AlignSeq
         pdbpos++;
       }
 
-      if (allowmismatch || c1 == c2)
+      // ignore case differences
+      if (allowmismatch || (c1 == c2) || (Math.abs(c2-c1)==('a'-'A')))
       {
         // extend mapping interval
         if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos)