From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 6 Sep 2012 14:17:35 +0000 (+0100)
Subject: JAL-1013 - employ index parameter rather than hardcode number for gaps in DNA or... 
X-Git-Tag: Jalview_2_9~326
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=945834b53cf725501cfccb5ca9945c9fb42c0a29;hp=213bb03dc91ef5af6aacbfc641d82420d0bdbb5a;p=jalview.git

JAL-1013 - employ index parameter rather than hardcode number for gaps in DNA or Protein encoding
---

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
     {