From 945834b53cf725501cfccb5ca9945c9fb42c0a29 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 6 Sep 2012 15:17:35 +0100
Subject: [PATCH] JAL-1013 - employ index parameter rather than hardcode
 number for gaps in DNA or Protein encoding

---
 src/jalview/analysis/AlignSeq.java |    4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index bb4796f..5d28fc3 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -382,13 +382,13 @@ public class AlignSeq
     {
       intToStr = pep;
       charToInt = ResidueProperties.aaIndex;
-      defInt = 23;
+      defInt = ResidueProperties.maxProteinIndex;
     }
     else if (type.equals(AlignSeq.DNA))
     {
       intToStr = dna;
       charToInt = ResidueProperties.nucleotideIndex;
-      defInt = 4;
+      defInt = ResidueProperties.maxNucleotideIndex;
     }
     else
     {
-- 
1.7.10.2