JAL-845 map 'STOP' codons correctly

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 337372d..4576881 100644 (file)
--- 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;
       }