From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 18 Mar 2015 20:24:48 +0000 (+0000)
Subject: JAL-845 map 'STOP' codons correctly
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a3ea406406be52a773560fedc4d93f07bfd69f5d;p=jalview.git

JAL-845 map 'STOP' codons correctly
---

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;
       }