From f7a97ef025c498c19fdcc37d9fc0506d511d18dd Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 22 May 2007 21:17:26 +0000
Subject: [PATCH] fixed jalview 2.3 bug where gapped aligned codons were
 always translated as inserted residues rather than aligned
 with eachother

---
 src/jalview/analysis/Dna.java |    1 +
 1 file changed, 1 insertion(+)

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 5096ae8..48d03b3 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -116,6 +116,7 @@ public class Dna {
                 newSeq[sq].insertCharAt(aspos, gapCharacter);
               }
               System.arraycopy(codons, aspos, codons, aspos+1, aslen-aspos);
+              codons[aspos]=null; // clear so new codon position can be marked.
               findpos=false;
               break;
             case +1:
-- 
1.7.10.2