X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=95acf914f9a803be5ce1d6bfe9ce1ce459a3f2f7;hb=9218eaf932c0847b83e9886f5c06d70a0bc7808e;hp=aa0297ec8f617757123297affe9214864d8429ca;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index aa0297e..95acf91 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -28,6 +28,7 @@ public class ResidueProperties {
   public static Hashtable aaHash = new Hashtable();  // stores the number value of the aa
   public static Hashtable aa3Hash = new Hashtable();
   public static Hashtable aa2Triplet = new Hashtable();
+  public static Hashtable nucleotideHash = new Hashtable();
 
   static {
     aaHash.put("A", new Integer(0));
@@ -53,12 +54,43 @@ public class ResidueProperties {
     aaHash.put("B", new Integer(20));
     aaHash.put("Z", new Integer(21));
     aaHash.put("X", new Integer(22));
+    aaHash.put("a", new Integer(0));
+    aaHash.put("r", new Integer(1));
+    aaHash.put("n", new Integer(2));
+    aaHash.put("d", new Integer(3));
+    aaHash.put("c", new Integer(4));
+    aaHash.put("q", new Integer(5));
+    aaHash.put("e", new Integer(6));
+    aaHash.put("g", new Integer(7));
+    aaHash.put("h", new Integer(8));
+    aaHash.put("i", new Integer(9));
+    aaHash.put("l", new Integer(10));
+    aaHash.put("k", new Integer(11));
+    aaHash.put("m", new Integer(12));
+    aaHash.put("f", new Integer(13));
+    aaHash.put("p", new Integer(14));
+    aaHash.put("s", new Integer(15));
+    aaHash.put("t", new Integer(16));
+    aaHash.put("w", new Integer(17));
+    aaHash.put("y", new Integer(18));
+    aaHash.put("v", new Integer(19));
+    aaHash.put("b", new Integer(20));
+    aaHash.put("z", new Integer(21));
+    aaHash.put("x", new Integer(22));
     aaHash.put("-", new Integer(23));
     aaHash.put("*", new Integer(23));
     aaHash.put(".", new Integer(23));
     aaHash.put(" ", new Integer(23));
   }
 
+  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));
+  }
+
   // These numbers should correspond to the indices in the Color hashes
   public static Hashtable aaSpecialsHash = new Hashtable();
   static {
@@ -168,6 +200,14 @@ public class ResidueProperties {
     Color.white          // .
   };
 
+  public static Color[] nucleotide = {
+      new Color(100,247,63),          // A
+      new Color(255,179,64),          // C
+      new Color(235,65,60),           // G
+      new Color(60,136,238),          // T
+      new Color(60,136,238)           // U
+  };
+
   public static Color[] color = {
     Color.pink,          // A
     midBlue,             // R