X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=457688160ac3a62cbde7005e3be741c0563d0d7e;hb=a3ea406406be52a773560fedc4d93f07bfd69f5d;hp=337372db221bc2009cdc5dd341c7293ae7087bac;hpb=330289271fe2239a59fa318d6b2b19fdd319f8a4;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 337372d..4576881 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -445,7 +445,7 @@ public class AlignmentUtils
        * ? allow X in protein to match untranslatable in dna ?
        */
       final char aaRes = aaSeqChars[aaResidue];
-      if (translated == null && aaRes == 'X')
+      if ((translated == null || "STOP".equals(translated)) && aaRes == 'X')
       {
         continue;
       }