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