From a3ea406406be52a773560fedc4d93f07bfd69f5d Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 18 Mar 2015 20:24:48 +0000 Subject: [PATCH] JAL-845 map 'STOP' codons correctly --- src/jalview/analysis/AlignmentUtils.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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; } -- 1.7.10.2