From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 28 Jan 2021 16:56:55 +0000 (+0000)
Subject: JAL-3806 more lax allowance (3 positions) for stop codon
X-Git-Tag: Release_2_11_1_4~6^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=855af27bbb88788ac9c1ee9872a43fbb333ae380;p=jalview.git

JAL-3806 more lax allowance (3 positions) for stop codon
---

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 6faf7a6..6ccc0fc 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -171,8 +171,8 @@ public class AlignedCodonFrame
 
       if (length != -1)
       {
-        // add 1 to mapped length to allow for a mapped stop codon
-        if (length + 1 >= (mend - mstart + 1))
+        // add 3 to mapped length to allow for a mapped stop codon
+        if (length + 3 >= (mend - mstart + 1))
         {
           return true;
         }