/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
public class ResidueProperties\r
{\r
//Stores residue codes/names and colours and other things\r
- 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
+ public static final int [] aaIndex; // aaHash version 2.1.1 and below\r
+ public static final int [] nucleotideIndex;\r
+ public static final Hashtable aa3Hash = new Hashtable();\r
+ public static final Hashtable aa2Triplet = new Hashtable();\r
+ public static final Hashtable nucleotideName = new Hashtable();\r
\r
- static\r
- {\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("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
{\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
+ aaIndex = new int[132];\r
+ for(int i=0; i<132; i++)\r
+ aaIndex[i] = -1;\r
+\r
+ aaIndex['A'] = 0;\r
+ aaIndex['R'] = 1;\r
+ aaIndex['N'] = 2;\r
+ aaIndex['D'] = 3;\r
+ aaIndex['C'] = 4;\r
+ aaIndex['Q'] = 5;\r
+ aaIndex['E'] = 6;\r
+ aaIndex['G'] = 7;\r
+ aaIndex['H'] = 8;\r
+ aaIndex['I'] = 9;\r
+ aaIndex['L'] = 10;\r
+ aaIndex['K'] = 11;\r
+ aaIndex['M'] = 12;\r
+ aaIndex['F'] = 13;\r
+ aaIndex['P'] = 14;\r
+ aaIndex['S'] = 15;\r
+ aaIndex['T'] = 16;\r
+ aaIndex['W'] = 17;\r
+ aaIndex['Y'] = 18;\r
+ aaIndex['V'] = 19;\r
+ aaIndex['B'] = 20;\r
+ aaIndex['Z'] = 21;\r
+ aaIndex['X'] = 22;\r
+ aaIndex['U'] = 22;\r
+ aaIndex['a'] = 0;\r
+ aaIndex['r'] = 1;\r
+ aaIndex['n'] = 2;\r
+ aaIndex['d'] = 3;\r
+ aaIndex['c'] = 4;\r
+ aaIndex['q'] = 5;\r
+ aaIndex['e'] = 6;\r
+ aaIndex['g'] = 7;\r
+ aaIndex['h'] = 8;\r
+ aaIndex['i'] = 9;\r
+ aaIndex['l'] = 10;\r
+ aaIndex['k'] = 11;\r
+ aaIndex['m'] = 12;\r
+ aaIndex['f'] = 13;\r
+ aaIndex['p'] = 14;\r
+ aaIndex['s'] = 15;\r
+ aaIndex['t'] = 16;\r
+ aaIndex['w'] = 17;\r
+ aaIndex['y'] = 18;\r
+ aaIndex['v'] = 19;\r
+ aaIndex['b'] = 20;\r
+ aaIndex['z'] = 21;\r
+ aaIndex['x'] = 22;\r
+ aaIndex['u'] = 22;\r
+ aaIndex['-'] = 23;\r
+ aaIndex['*'] = 23;\r
+ aaIndex['.'] = 23;\r
+ aaIndex[' '] = 23;\r
}\r
\r
- // These numbers should correspond to the indices in the Color hashes\r
- public static 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
+ nucleotideIndex = new int[132];\r
+ for (int i = 0; i < 132; i++)\r
+ nucleotideIndex[i] = -1;\r
+\r
+ nucleotideIndex['A'] = 0;\r
+ nucleotideIndex['a'] = 0;\r
+ nucleotideIndex['C'] = 1;\r
+ nucleotideIndex['c'] = 1;\r
+ nucleotideIndex['G'] = 2;\r
+ nucleotideIndex['g'] = 2;\r
+ nucleotideIndex['T'] = 3;\r
+ nucleotideIndex['t'] = 3;\r
+ nucleotideIndex['U'] = 4;\r
+ nucleotideIndex['u'] = 4;\r
+ nucleotideIndex['I'] = 5;\r
+ nucleotideIndex['i'] = 5;\r
+ nucleotideIndex['X'] = 6;\r
+ nucleotideIndex['x'] = 6;\r
+ nucleotideIndex['R'] = 7;\r
+ nucleotideIndex['r'] = 7;\r
+ nucleotideIndex['Y'] = 8;\r
+ nucleotideIndex['y'] = 8;\r
+ nucleotideIndex['N'] = 9;\r
+ nucleotideIndex['n'] = 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
+\r
static\r
{\r
aa3Hash.put("ALA", new Integer(0));\r
aa3Hash.put("TRP", new Integer(17));\r
aa3Hash.put("TYR", new Integer(18));\r
aa3Hash.put("VAL", new Integer(19));\r
- aa3Hash.put("B", new Integer(20));\r
- aa3Hash.put("Z", new Integer(21));\r
- aa3Hash.put("X", new Integer(22));\r
+ // IUB Nomenclature for ambiguous peptides\r
+ aa3Hash.put("ASX", new Integer(20)); // "B";\r
+ aa3Hash.put("GLX", new Integer(21)); // X\r
+ aa3Hash.put("XAA", new Integer(22));// X unknown\r
aa3Hash.put("-", new Integer(23));\r
aa3Hash.put("*", new Integer(23));\r
aa3Hash.put(".", new Integer(23));\r
aa3Hash.put(" ", new Integer(23));\r
+ aa3Hash.put("Gap", new Integer(23));\r
}\r
\r
static\r
{\r
aa2Triplet.put("A", "ALA");\r
+ aa2Triplet.put("a", "ALA");\r
aa2Triplet.put("R", "ARG");\r
+ aa2Triplet.put("r", "ARG");\r
aa2Triplet.put("N", "ASN");\r
+ aa2Triplet.put("n", "ASN");\r
aa2Triplet.put("D", "ASP");\r
+ aa2Triplet.put("d", "ASP");\r
aa2Triplet.put("C", "CYS");\r
+ aa2Triplet.put("c", "CYS");\r
aa2Triplet.put("Q", "GLN");\r
+ aa2Triplet.put("q", "GLN");\r
aa2Triplet.put("E", "GLU");\r
+ aa2Triplet.put("e", "GLU");\r
aa2Triplet.put("G", "GLY");\r
+ aa2Triplet.put("g", "GLY");\r
aa2Triplet.put("H", "HIS");\r
+ aa2Triplet.put("h", "HIS");\r
aa2Triplet.put("I", "ILE");\r
+ aa2Triplet.put("i", "ILE");\r
aa2Triplet.put("L", "LEU");\r
+ aa2Triplet.put("l", "LEU");\r
aa2Triplet.put("K", "LYS");\r
+ aa2Triplet.put("k", "LYS");\r
aa2Triplet.put("M", "MET");\r
+ aa2Triplet.put("m", "MET");\r
aa2Triplet.put("F", "PHE");\r
+ aa2Triplet.put("f", "PHE");\r
aa2Triplet.put("P", "PRO");\r
+ aa2Triplet.put("p", "PRO");\r
aa2Triplet.put("S", "SER");\r
+ aa2Triplet.put("s", "SER");\r
aa2Triplet.put("T", "THR");\r
+ aa2Triplet.put("t", "THR");\r
aa2Triplet.put("W", "TRP");\r
+ aa2Triplet.put("w", "TRP");\r
aa2Triplet.put("Y", "TYR");\r
+ aa2Triplet.put("y", "TYR");\r
aa2Triplet.put("V", "VAL");\r
+ aa2Triplet.put("v", "VAL");\r
}\r
\r
- public static String[] aa =\r
+ public static final String[] aa =\r
{\r
"A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",\r
"P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " "\r
};\r
- public static Color midBlue = new Color(100, 100, 255);\r
- public static Vector scaleColours = new Vector();\r
+ public static final Color midBlue = new Color(100, 100, 255);\r
+ public static final Vector scaleColours = new Vector();\r
\r
static\r
{\r
scaleColours.addElement(Color.white);\r
}\r
\r
- public static Color[] taylor =\r
+ public static final Color[] taylor =\r
{\r
new Color(204, 255, 0), // A Greenish-yellowy-yellow\r
new Color(0, 0, 255), // R Blueish-bluey-blue\r
Color.white, // *\r
Color.white // .\r
};\r
- public static Color[] nucleotide =\r
+ public static final Color[] nucleotide =\r
{\r
new Color(100, 247, 63), // A\r
new Color(255, 179, 64), // C\r
new Color(60, 136, 238), // T\r
new Color(60, 136, 238) // U\r
};\r
- public static Color[] color =\r
+ public static final Color[] color =\r
{\r
Color.pink, // A\r
midBlue, // R\r
};\r
\r
// Dunno where I got these numbers from\r
- public static double[] hyd2 =\r
+ public static final double[] hyd2 =\r
{\r
0.62, //A\r
0.29, //R\r
0.0, //Z\r
0.0 //X\r
};\r
- public static double[] helix =\r
+ public static final double[] helix =\r
{\r
1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,\r
1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0\r
};\r
- public static double helixmin = 0.57;\r
- public static double helixmax = 1.51;\r
- public static double[] strand =\r
+ public static final double helixmin = 0.57;\r
+ public static final double helixmax = 1.51;\r
+ public static final double[] strand =\r
{\r
0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,\r
1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0\r
};\r
- public static double strandmin = 0.37;\r
- public static double strandmax = 1.7;\r
- public static double[] turn =\r
+ public static final double strandmin = 0.37;\r
+ public static final double strandmax = 1.7;\r
+ public static final double[] turn =\r
{\r
0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,\r
0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0\r
};\r
- public static double turnmin = 0.47;\r
- public static double turnmax = 1.56;\r
- public static double[] buried =\r
+ public static final double turnmin = 0.47;\r
+ public static final double turnmax = 1.56;\r
+ public static final double[] buried =\r
{\r
1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,\r
0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00\r
};\r
- public static double buriedmin = 0.05;\r
- public static double buriedmax = 4.6;\r
+ public static final double buriedmin = 0.05;\r
+ public static final double buriedmax = 4.6;\r
\r
// This is hydropathy index\r
// Kyte, J., and Doolittle, R.F., J. Mol. Biol.\r
// 1157, 105-132, 1982\r
- public static double[] hyd =\r
+ public static final double[] hyd =\r
{\r
1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9,\r
2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0\r
-8, -8, -8, -8, -8, -8, 1\r
},\r
};\r
- public static Hashtable ssHash = new Hashtable(); // stores the number value of the aa\r
+ public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa\r
\r
static\r
{\r
{\r
1, 1, 1, 1, 1}, // -\r
};\r
- public static Color[] pidColours =\r
+ public static final Color[] pidColours =\r
{\r
midBlue, new Color(153, 153, 255),\r
// Color.lightGray,\r
new Color(204, 204, 255),\r
};\r
- public static float[] pidThresholds =\r
+ public static final float[] pidThresholds =\r
{\r
80, 60, 40, };\r
public static Hashtable codonHash = new Hashtable();\r
Phe.addElement("TTT");\r
}\r
\r
- public static Color[][] groupColors =\r
- {\r
- {\r
- Color.red, Color.red.brighter(), Color.red.brighter().brighter()},\r
- {\r
- Color.orange, Color.orange.brighter(),\r
- Color.orange.brighter().brighter()\r
- },\r
- {\r
- Color.green, Color.green.brighter(), Color.green.brighter().brighter()},\r
- {\r
- Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter()},\r
- {\r
- Color.magenta, Color.magenta.brighter(),\r
- Color.magenta.brighter().brighter()\r
- },\r
- {\r
- Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter()},\r
- {\r
- Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter()},\r
- };\r
\r
//Stores residue codes/names and colours and other things\r
public static Hashtable propHash = new Hashtable();\r
propHash.put("polar", polar);\r
}\r
\r
- public static Hashtable chainColours = new Hashtable();\r
-\r
- static\r
- {\r
- chainColours.put("A", Color.red);\r
- chainColours.put("B", Color.orange);\r
- chainColours.put("C", Color.yellow);\r
- chainColours.put("D", Color.green);\r
- chainColours.put("E", Color.cyan);\r
- chainColours.put("F", Color.blue);\r
- chainColours.put("G", Color.magenta);\r
- chainColours.put("H", Color.pink);\r
- }\r
-\r
private ResidueProperties()\r
{\r
}\r
return hyd;\r
}\r
\r
- public static Hashtable getAAHash()\r
- {\r
- return aaHash;\r
- }\r
-\r
public static Hashtable getAA3Hash()\r
{\r
return aa3Hash;\r
\r
public static int getPAM250(String A1, String A2)\r
{\r
- Integer pog1 = (Integer) aaHash.get(A1);\r
- Integer pog2 = (Integer) aaHash.get(A2);\r
- int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];\r
+ int a = aaIndex[A1.charAt(0)];\r
+ int b = aaIndex[A2.charAt(0)];\r
+\r
+ int pog = ResidueProperties.PAM250[a][b];\r
\r
return pog;\r
}\r
\r
- public static int getBLOSUM62(String A1, String A2)\r
+ public static int getBLOSUM62(char c1, char c2)\r
{\r
int pog = 0;\r
\r
try\r
{\r
- Integer pog1 = (Integer) aaHash.get(A1);\r
- Integer pog2 = (Integer) aaHash.get(A2);\r
- pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];\r
+ int a = aaIndex[c1];\r
+ int b = aaIndex[c2];\r
+\r
+ pog = ResidueProperties.BLOSUM62[a][b];\r
}\r
catch (Exception e)\r
{\r
String key = (String) e.nextElement();\r
Vector tmp = (Vector) codonHash.get(key);\r
\r
- if (tmp.contains(codon))\r
+ if (tmp.contains(codon.toUpperCase()))\r
{\r
return key;\r
}\r
\r
return null;\r
}\r
-\r
- public static Hashtable getChainColours()\r
- {\r
- return chainColours;\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff