From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 20 Jul 2016 08:05:29 +0000 (+0100)
Subject: JAL-2023 JAL-1681 fixed bug in computing '+' for co-modal codons
X-Git-Tag: Release_2_10_0~125^2~12
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=331cf6c6db133ff63d426b8ab6ad6aed8f0e33c5

JAL-2023 JAL-1681 fixed bug in computing '+' for co-modal codons
---

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 3d61b11..fb49541 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -624,8 +624,11 @@ public class AAFrequency
       String modalCodon = String.valueOf(CodingUtils
               .decodeCodon(modalCodonEncoded));
       if (sortedCodonCounts.length > 1
-              && sortedCodonCounts[codons.length - 2] == modalCodonEncoded)
+              && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
       {
+        /*
+         * two or more codons share the modal count
+         */
         modalCodon = "+";
       }
       float pid = sortedCodonCounts[sortedCodonCounts.length - 1] * 100