Add nucleotide names

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