From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 4 Dec 2024 16:32:33 +0000 (+0000)
Subject: JAL-4333 - prophylactically check we have not run out of aligned codons - increase... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Fpatch%2FJAL-4333_translatecodonexception;p=jalview.git

JAL-4333 - prophylactically check we have not run out of aligned codons - increase width if we have..
---

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 9a99b69..a4dc5d0 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -590,10 +590,11 @@ public class Dna
         {
           /*
            * Compare this codon's base positions with those currently aligned to
-           * this column in the translation.
+           * this column in the translation. Always check we've not run out of existing aligned codons !
            */
-          final int compareCodonPos = compareCodonPos(alignedCodon,
-                  alignedCodons[aspos]);
+          final int compareCodonPos = (aspos < alignedCodons.length)
+                  ? compareCodonPos(alignedCodon, alignedCodons[aspos])
+                  : -1;
           switch (compareCodonPos)
           {
           case -1: