From 0696ddbefc131556c89fa28161d1a85bc1b8195c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 12 Nov 2008 11:11:53 +0000
Subject: [PATCH] gracefully translate ambigous nucleotides as 'X'

---
 src/jalview/schemes/ResidueProperties.java |   10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 77938dd..ff73050 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1138,8 +1138,14 @@ public class ResidueProperties
     return null;
   }
 
-  public static String codonTranslate(String codon)
+  public static String codonTranslate(String lccodon)
   {
+    String codon=lccodon.toUpperCase();
+    // all base ambiguity codes yield an 'X' amino acid residue
+    if (codon.indexOf('X')>-1 || codon.indexOf('N')>-1)
+    {
+      return "X";
+    }
     Enumeration e = codonHash.keys();
 
     while (e.hasMoreElements())
@@ -1147,7 +1153,7 @@ public class ResidueProperties
       String key = (String) e.nextElement();
       Vector tmp = (Vector) codonHash.get(key);
 
-      if (tmp.contains(codon.toUpperCase()))
+      if (tmp.contains(codon))
       {
         return key;
       }
-- 
1.7.10.2