From 8ae2f185311811757976eeb142b4767c42a9618f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 22 Sep 2005 15:49:21 +0000
Subject: [PATCH] Add nucleotide names

---
 src/jalview/schemes/ResidueProperties.java |   51 ++++++++++++++++++++--------
 1 file changed, 37 insertions(+), 14 deletions(-)

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index a382662..fbaab81 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -29,6 +29,7 @@ public class ResidueProperties
   public static final Hashtable aa3Hash = new Hashtable();
   public static final Hashtable aa2Triplet = new Hashtable();
   public static final Hashtable nucleotideHash = new Hashtable();
+  public static final Hashtable nucleotideName = new Hashtable();
 
   static
   {
@@ -89,27 +90,49 @@ public class ResidueProperties
   static
   {
     nucleotideHash.put("A", new Integer(0));
-    nucleotideHash.put("C", new Integer(1));
-    nucleotideHash.put("G", new Integer(2));
-    nucleotideHash.put("T", new Integer(3));
-    nucleotideHash.put("U", new Integer(4));
     nucleotideHash.put("a", new Integer(0));
+    nucleotideHash.put("C", new Integer(1));
     nucleotideHash.put("c", new Integer(1));
+    nucleotideHash.put("G", new Integer(2));
     nucleotideHash.put("g", new Integer(2));
+    nucleotideHash.put("T", new Integer(3));
     nucleotideHash.put("t", new Integer(3));
+    nucleotideHash.put("U", new Integer(4));
     nucleotideHash.put("u", new Integer(4));
+    nucleotideHash.put("I", new Integer(5));
+    nucleotideHash.put("i", new Integer(5));
+    nucleotideHash.put("X", new Integer(6));
+    nucleotideHash.put("x", new Integer(6));
+    nucleotideHash.put("R", new Integer(7));
+    nucleotideHash.put("r", new Integer(7));
+    nucleotideHash.put("Y", new Integer(8));
+    nucleotideHash.put("y", new Integer(8));
+    nucleotideHash.put("N", new Integer(9));
+    nucleotideHash.put("n", new Integer(9));
+
+
+    nucleotideName.put("A", "Adenine");
+    nucleotideName.put("a", "Adenine");
+    nucleotideName.put("G", "Guanine");
+    nucleotideName.put("g", "Guanine");
+    nucleotideName.put("C", "Cytosine");
+    nucleotideName.put("c", "Cytosine");
+    nucleotideName.put("T", "Thymine");
+    nucleotideName.put("t", "Thymine");
+    nucleotideName.put("U", "Uracil");
+    nucleotideName.put("u", "Uracil");
+    nucleotideName.put("I", "Inosine");
+    nucleotideName.put("i", "Inosine");
+    nucleotideName.put("X", "Xanthine");
+    nucleotideName.put("x", "Xanthine");
+    nucleotideName.put("R", "Unknown Purine");
+    nucleotideName.put("r", "Unknown Purine");
+    nucleotideName.put("Y", "Unknown Pyrimidine");
+    nucleotideName.put("y", "Unknown Pyrimidine");
+    nucleotideName.put("N", "Unknown");
+    nucleotideName.put("n", "Unknown");
   }
 
-  // These numbers should correspond to the indices in the Color hashes
-  public static final Hashtable aaSpecialsHash = new Hashtable();
-
-  static
-  {
-    aaSpecialsHash.put("-", new Integer(23));
-    aaSpecialsHash.put("*", new Integer(24));
-    aaSpecialsHash.put(".", new Integer(25));
-    aaSpecialsHash.put(" ", new Integer(26));
-  }
 
   static
   {
-- 
1.7.10.2