/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.schemes;\r
\r
-import java.awt.Color;\r
-\r
import java.util.*;\r
\r
-\r
-public class ResidueProperties {\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
-\r
- static {\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
- 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
-\r
- static {\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
- aa3Hash.put("ALA", new Integer(0));\r
- aa3Hash.put("ARG", new Integer(1));\r
- aa3Hash.put("ASN", new Integer(2));\r
- aa3Hash.put("ASP", new Integer(3)); //D\r
- aa3Hash.put("CYS", new Integer(4));\r
- aa3Hash.put("GLN", new Integer(5)); //Q\r
- aa3Hash.put("GLU", new Integer(6)); // E\r
- aa3Hash.put("GLY", new Integer(7));\r
- aa3Hash.put("HIS", new Integer(8));\r
- aa3Hash.put("ILE", new Integer(9));\r
- aa3Hash.put("LEU", new Integer(10));\r
- aa3Hash.put("LYS", new Integer(11));\r
- aa3Hash.put("MET", new Integer(12));\r
- aa3Hash.put("PHE", new Integer(13));\r
- aa3Hash.put("PRO", new Integer(14));\r
- aa3Hash.put("SER", new Integer(15));\r
- aa3Hash.put("THR", new Integer(16));\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
- aa3Hash.put("-", new Integer(23));\r
- aa3Hash.put("*", new Integer(23));\r
- aa3Hash.put(".", new Integer(23));\r
- aa3Hash.put(" ", new Integer(23));\r
- }\r
-\r
- static {\r
- aa2Triplet.put("A", "ALA");\r
- aa2Triplet.put("R", "ARG");\r
- aa2Triplet.put("N", "ASN");\r
- aa2Triplet.put("D", "ASP");\r
- aa2Triplet.put("C", "CYS");\r
- aa2Triplet.put("Q", "GLN");\r
- aa2Triplet.put("E", "GLU");\r
- aa2Triplet.put("G", "GLY");\r
- aa2Triplet.put("H", "HIS");\r
- aa2Triplet.put("I", "ILE");\r
- aa2Triplet.put("L", "LEU");\r
- aa2Triplet.put("K", "LYS");\r
- aa2Triplet.put("M", "MET");\r
- aa2Triplet.put("F", "PHE");\r
- aa2Triplet.put("P", "PRO");\r
- aa2Triplet.put("S", "SER");\r
- aa2Triplet.put("T", "THR");\r
- aa2Triplet.put("W", "TRP");\r
- aa2Triplet.put("Y", "TYR");\r
- aa2Triplet.put("V", "VAL");\r
- }\r
-\r
- public static String[] aa = {\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
-\r
- static {\r
- scaleColours.addElement(new Color(114, 0, 147));\r
- scaleColours.addElement(new Color(156, 0, 98));\r
- scaleColours.addElement(new Color(190, 0, 0));\r
- scaleColours.addElement(Color.red);\r
- scaleColours.addElement(new Color(255, 125, 0));\r
- scaleColours.addElement(Color.orange);\r
- scaleColours.addElement(new Color(255, 194, 85));\r
- scaleColours.addElement(Color.yellow);\r
- scaleColours.addElement(new Color(255, 255, 181));\r
- scaleColours.addElement(Color.white);\r
- }\r
-\r
- public static Color[] taylor = {\r
- new Color(204, 255, 0), // A Greenish-yellowy-yellow\r
- new Color(0, 0, 255), // R Blueish-bluey-blue\r
- new Color(204, 0, 255), // N Blueish-reddy-blue\r
- new Color(255, 0, 0), // D Reddish-reddy-red\r
- new Color(255, 255, 0), // C Yellowish-yellowy-yellow\r
- new Color(255, 0, 204), // Q Reddish-bluey-red\r
- new Color(255, 0, 102), // E Blueish-reddy-red\r
- new Color(255, 153, 0), // G Yellowy-reddy-yellow\r
- new Color(0, 102, 255), // H Greenish-bluey-blue\r
- new Color(102, 255, 0), // I Greenish-yellowy-green\r
- new Color(51, 255, 0), // L Yellowish-greeny-green\r
- new Color(102, 0, 255), // K Reddish-bluey-blue\r
- new Color(0, 255, 0), // M Greenish-greeny-green\r
- new Color(0, 255, 102), // F Blueish-greeny-green\r
- new Color(255, 204, 0), // P Reddish-yellowy-yellow\r
- new Color(255, 51, 0), // S Yellowish-reddy-red\r
- new Color(255, 102, 0), // T Reddish-yellowy-red\r
- new Color(0, 204, 255), // W Blueish-greeny-green\r
- new Color(0, 255, 204), // Y Greenish-bluey-green\r
- new Color(153, 255, 0), // V Yellowish-greeny-yellow\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white // .\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
- public static Color[] color = {\r
- Color.pink, // A\r
- midBlue, // R\r
- Color.green, // N\r
- Color.red, // D\r
- Color.yellow, // C\r
- Color.green, // Q\r
- Color.red, // E\r
- Color.magenta, // G\r
- Color.red, // H\r
- Color.pink, // I\r
- Color.pink, // L\r
- midBlue, // K\r
- Color.pink, // M\r
- Color.orange, // F\r
- Color.magenta, // P\r
- Color.green, // S\r
- Color.green, // T\r
- Color.orange, // W\r
- Color.orange, // Y\r
- Color.pink, // V\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white, // .\r
- Color.white // ' '\r
- };\r
-\r
- // Dunno where I got these numbers from\r
- public static double[] hyd2 = {\r
- 0.62, //A\r
- 0.29, //R\r
- -0.90, //N\r
- -0.74, //D\r
- 1.19, //C\r
- 0.48, //Q\r
- -0.40, //E\r
- 1.38, //G\r
- -1.50, //H\r
- 1.06, //I\r
- 0.64, //L\r
- -0.78, //K\r
- 0.12, //M\r
- -0.85, //F\r
- -2.53, //P\r
- -0.18, //S\r
- -0.05, //T\r
- 1.08, //W\r
- 0.81, //Y\r
- 0.0, //V\r
- 0.26, //B\r
- 0.0, //Z\r
- 0.0 //X\r
- };\r
- public static double[] helix = {\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
- 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
- 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
- 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
-\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
- 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
- };\r
- public static final double hydmax = 4.5;\r
- public static final double hydmin = -3.9;\r
-\r
- //public static final double hydmax = 1.38;\r
- //public static final double hydmin = -2.53;\r
- static final int[][] BLOSUM62 = {\r
- {\r
- 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,\r
- -2, 0, -2, -1, 0, -4\r
- },\r
- {\r
- -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,\r
- -3, -1, 0, -1, -4\r
- },\r
- {\r
- -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,\r
- 3, 0, -1, -4\r
- },\r
- {\r
- -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,\r
- -3, -3, 4, 1, -1, -4\r
- },\r
- {\r
- 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,\r
- -2, -1, -3, -3, -2, -4\r
- },\r
- {\r
- -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,\r
- -2, 0, 3, -1, -4\r
- },\r
- {\r
- -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,\r
- -2, 1, 4, -1, -4\r
- },\r
- {\r
- 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,\r
- -3, -3, -1, -2, -1, -4\r
- },\r
- {\r
- -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,\r
- -3, 0, 0, -1, -4\r
- },\r
- {\r
- -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,\r
- -1, 3, -3, -3, -1, -4\r
- },\r
- {\r
- -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,\r
- -1, 1, -4, -3, -1, -4\r
- },\r
- {\r
- -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,\r
- -2, 0, 1, -1, -4\r
- },\r
- {\r
- -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,\r
- -1, 1, -3, -1, -1, -4\r
- },\r
- {\r
- -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,\r
- -1, -3, -3, -1, -4\r
- },\r
- {\r
- -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,\r
- -4, -3, -2, -2, -1, -2, -4\r
- },\r
- {\r
- 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,\r
- -2, 0, 0, 0, -4\r
- },\r
- {\r
- 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,\r
- -2, 0, -1, -1, 0, -4\r
- },\r
- {\r
- -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,\r
- 11, 2, -3, -4, -3, -2, -4\r
- },\r
- {\r
- -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,\r
- 7, -1, -3, -2, -1, -4\r
- },\r
- {\r
- 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,\r
- -1, 4, -3, -2, -1, -4\r
- },\r
- {\r
- -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,\r
- -3, 4, 1, -1, -4\r
- },\r
- {\r
- -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,\r
- -2, 1, 4, -1, -4\r
- },\r
- {\r
- 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,\r
- -1, -1, -1, -1, -1, -4\r
- },\r
- {\r
- -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,\r
- -4, -4, -4, -4, -4, -4, 1\r
- },\r
- };\r
- static final int[][] PAM250 = {\r
- {\r
- 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,\r
- 0, 0, 0, -8\r
- },\r
- {\r
- -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,\r
- -2, -1, 0, -1, -8\r
- },\r
- {\r
- 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,\r
- 2, 1, 0, -8\r
- },\r
- {\r
- 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,\r
- 3, 3, -1, -8\r
- },\r
- {\r
- -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,\r
- -8, 0, -2, -4, -5, -3, -8\r
- },\r
- {\r
- 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,\r
- -2, 1, 3, -1, -8\r
- },\r
- {\r
- 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,\r
- 3, 3, -1, -8\r
- },\r
- {\r
- 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,\r
- -1, 0, 0, -1, -8\r
- },\r
- {\r
- -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,\r
- -2, 1, 2, -1, -8\r
- },\r
- {\r
- -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,\r
- -1, 4, -2, -2, -1, -8\r
- },\r
- {\r
- -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,\r
- -1, 2, -3, -3, -1, -8\r
- },\r
- {\r
- -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,\r
- 1, 0, -1, -8\r
- },\r
- {\r
- -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,\r
- 2, -2, -2, -1, -8\r
- },\r
- {\r
- -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,\r
- -1, -4, -5, -2, -8\r
- },\r
- {\r
- 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,\r
- -1, -1, 0, -1, -8\r
- },\r
- {\r
- 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,\r
- 0, 0, 0, -8\r
- },\r
- {\r
- 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,\r
- 0, -1, 0, -8\r
- },\r
- {\r
- -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,\r
- 0, -6, -5, -6, -4, -8\r
- },\r
- {\r
- -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,\r
- 10, -2, -3, -4, -2, -8\r
- },\r
- {\r
- 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,\r
- -2, 4, -2, -2, -1, -8\r
- },\r
- {\r
- 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,\r
- 3, 2, -1, -8\r
- },\r
- {\r
- 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,\r
- 2, 3, -1, -8\r
- },\r
- {\r
- 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,\r
- -2, -1, -1, -1, -1, -8\r
- },\r
- {\r
- -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,\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
-\r
- static {\r
- ssHash.put("H", Color.magenta);\r
- ssHash.put("E", Color.yellow);\r
- ssHash.put("-", Color.white);\r
- ssHash.put(".", Color.white);\r
- ssHash.put("S", Color.cyan);\r
- ssHash.put("T", Color.blue);\r
- ssHash.put("G", Color.pink);\r
- ssHash.put("I", Color.pink);\r
- ssHash.put("B", Color.yellow);\r
- }\r
-\r
- static final int[][] DNA = {\r
- { 5, -4, -4, -4, 1 }, // C\r
- { -4, 5, -4, -4, 1 }, // T\r
- { -4, -4, 5, -4, 1 }, // A\r
- { -4, -4, -4, 5, 1 }, // G\r
- { 1, 1, 1, 1, 1 }, // -\r
- };\r
- public static Color[] pidColours = {\r
- midBlue, new Color(153, 153, 255), \r
- // Color.lightGray,\r
- new Color(204, 204, 255),\r
- };\r
- public static float[] pidThresholds = { 80, 60, 40, };\r
- public static Hashtable codonHash = new Hashtable();\r
- public static Vector Lys = new Vector();\r
- public static Vector Asn = new Vector();\r
- public static Vector Gln = new Vector();\r
- public static Vector His = new Vector();\r
- public static Vector Glu = new Vector();\r
- public static Vector Asp = new Vector();\r
- public static Vector Tyr = new Vector();\r
- public static Vector Thr = new Vector();\r
- public static Vector Pro = new Vector();\r
- public static Vector Ala = new Vector();\r
- public static Vector Ser = new Vector();\r
- public static Vector Arg = new Vector();\r
- public static Vector Gly = new Vector();\r
- public static Vector Trp = new Vector();\r
- public static Vector Cys = new Vector();\r
- public static Vector Ile = new Vector();\r
- public static Vector Met = new Vector();\r
- public static Vector Leu = new Vector();\r
- public static Vector Val = new Vector();\r
- public static Vector Phe = new Vector();\r
- public static Vector STOP = new Vector();\r
-\r
- static {\r
- codonHash.put("K", Lys);\r
- codonHash.put("N", Asn);\r
- codonHash.put("Q", Gln);\r
- codonHash.put("H", His);\r
- codonHash.put("E", Glu);\r
- codonHash.put("D", Asp);\r
- codonHash.put("Y", Tyr);\r
- codonHash.put("T", Thr);\r
- codonHash.put("P", Pro);\r
- codonHash.put("A", Ala);\r
- codonHash.put("S", Ser);\r
- codonHash.put("R", Arg);\r
- codonHash.put("G", Gly);\r
- codonHash.put("W", Trp);\r
- codonHash.put("C", Cys);\r
- codonHash.put("I", Ile);\r
- codonHash.put("M", Met);\r
- codonHash.put("L", Leu);\r
- codonHash.put("V", Val);\r
- codonHash.put("F", Phe);\r
- codonHash.put("STOP", STOP);\r
- }\r
-\r
- public static Hashtable codonHash2 = new Hashtable();\r
-\r
- static {\r
- codonHash2.put("AAA", "K");\r
- codonHash2.put("AAG", "K");\r
- codonHash2.put("AAC", "N");\r
- codonHash2.put("AAT", "N");\r
-\r
- codonHash2.put("CAA", "E");\r
- codonHash2.put("CAG", "E");\r
- codonHash2.put("CAC", "H");\r
- codonHash2.put("CAT", "H");\r
-\r
- codonHash2.put("GAA", "Q");\r
- codonHash2.put("GAG", "Q");\r
- codonHash2.put("GAC", "D");\r
- codonHash2.put("GAT", "D");\r
-\r
- codonHash2.put("TAC", "Y");\r
- codonHash2.put("TAT", "Y");\r
-\r
- codonHash2.put("ACA", "T");\r
- codonHash2.put("AAG", "T");\r
- codonHash2.put("ACC", "T");\r
- codonHash2.put("ACT", "T");\r
-\r
- codonHash2.put("CCA", "P");\r
- codonHash2.put("CCG", "P");\r
- codonHash2.put("CCC", "P");\r
- codonHash2.put("CCT", "P");\r
-\r
- codonHash2.put("GCA", "A");\r
- codonHash2.put("GCG", "A");\r
- codonHash2.put("GCC", "A");\r
- codonHash2.put("GCT", "A");\r
-\r
- codonHash2.put("TCA", "S");\r
- codonHash2.put("TCG", "S");\r
- codonHash2.put("TCC", "S");\r
- codonHash2.put("TCT", "S");\r
- codonHash2.put("AGC", "S");\r
- codonHash2.put("AGT", "S");\r
-\r
- codonHash2.put("AGA", "R");\r
- codonHash2.put("AGG", "R");\r
- codonHash2.put("CGA", "R");\r
- codonHash2.put("CGG", "R");\r
- codonHash2.put("CGC", "R");\r
- codonHash2.put("CGT", "R");\r
-\r
- codonHash2.put("GGA", "G");\r
- codonHash2.put("GGG", "G");\r
- codonHash2.put("GGC", "G");\r
- codonHash2.put("GGT", "G");\r
-\r
- codonHash2.put("TGA", "*");\r
- codonHash2.put("TAA", "*");\r
- codonHash2.put("TAG", "*");\r
-\r
- codonHash2.put("TGG", "W");\r
-\r
- codonHash2.put("TGC", "C");\r
- codonHash2.put("TGT", "C");\r
-\r
- codonHash2.put("ATA", "I");\r
- codonHash2.put("ATC", "I");\r
- codonHash2.put("ATT", "I");\r
-\r
- codonHash2.put("ATG", "M");\r
-\r
- codonHash2.put("CTA", "L");\r
- codonHash2.put("CTG", "L");\r
- codonHash2.put("CTC", "L");\r
- codonHash2.put("CTT", "L");\r
- codonHash2.put("TTA", "L");\r
- codonHash2.put("TTG", "L");\r
-\r
- codonHash2.put("GTA", "V");\r
- codonHash2.put("GTG", "V");\r
- codonHash2.put("GTC", "V");\r
- codonHash2.put("GTT", "V");\r
-\r
- codonHash2.put("TTC", "F");\r
- codonHash2.put("TTT", "F");\r
- }\r
-\r
- static {\r
- Lys.addElement("AAA");\r
- Lys.addElement("AAG");\r
- Asn.addElement("AAC");\r
- Asn.addElement("AAT");\r
-\r
- Gln.addElement("CAA");\r
- Gln.addElement("CAG");\r
- His.addElement("CAC");\r
- His.addElement("CAT");\r
-\r
- Glu.addElement("GAA");\r
- Glu.addElement("GAG");\r
- Asp.addElement("GAC");\r
- Asp.addElement("GAT");\r
-\r
- Tyr.addElement("TAC");\r
- Tyr.addElement("TAT");\r
-\r
- Thr.addElement("ACA");\r
- Thr.addElement("ACG");\r
- Thr.addElement("ACC");\r
- Thr.addElement("ACT");\r
-\r
- Pro.addElement("CCA");\r
- Pro.addElement("CCG");\r
- Pro.addElement("CCC");\r
- Pro.addElement("CCT");\r
-\r
- Ala.addElement("GCA");\r
- Ala.addElement("GCG");\r
- Ala.addElement("GCC");\r
- Ala.addElement("GCT");\r
-\r
- Ser.addElement("TCA");\r
- Ser.addElement("TCG");\r
- Ser.addElement("TCC");\r
- Ser.addElement("TCT");\r
- Ser.addElement("AGC");\r
- Ser.addElement("AGT");\r
-\r
- Arg.addElement("AGA");\r
- Arg.addElement("AGG");\r
- Arg.addElement("CGA");\r
- Arg.addElement("CGG");\r
- Arg.addElement("CGC");\r
- Arg.addElement("CGT");\r
-\r
- Gly.addElement("GGA");\r
- Gly.addElement("GGG");\r
- Gly.addElement("GGC");\r
- Gly.addElement("GGT");\r
-\r
- STOP.addElement("TGA");\r
- STOP.addElement("TAA");\r
- STOP.addElement("TAG");\r
-\r
- Trp.addElement("TGG");\r
-\r
- Cys.addElement("TGC");\r
- Cys.addElement("TGT");\r
-\r
- Ile.addElement("ATA");\r
- Ile.addElement("ATC");\r
- Ile.addElement("ATT");\r
-\r
- Met.addElement("ATG");\r
-\r
- Leu.addElement("CTA");\r
- Leu.addElement("CTG");\r
- Leu.addElement("CTC");\r
- Leu.addElement("CTT");\r
- Leu.addElement("TTA");\r
- Leu.addElement("TTG");\r
-\r
- Val.addElement("GTA");\r
- Val.addElement("GTG");\r
- Val.addElement("GTC");\r
- Val.addElement("GTT");\r
-\r
- Phe.addElement("TTC");\r
- Phe.addElement("TTT");\r
- }\r
-\r
- public static Color[][] groupColors = {\r
- { Color.red, Color.red.brighter(), Color.red.brighter().brighter() },\r
- {\r
- Color.orange, Color.orange.brighter(),\r
- Color.orange.brighter().brighter()\r
- },\r
- { Color.green, Color.green.brighter(), Color.green.brighter().brighter() },\r
- { Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter() },\r
- {\r
- Color.magenta, Color.magenta.brighter(),\r
- Color.magenta.brighter().brighter()\r
- },\r
- { Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter() },\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
- public static Hashtable hydrophobic = new Hashtable();\r
- public static Hashtable polar = new Hashtable();\r
- public static Hashtable small = new Hashtable();\r
- public static Hashtable positive = new Hashtable();\r
- public static Hashtable negative = new Hashtable();\r
- public static Hashtable charged = new Hashtable();\r
- public static Hashtable aromatic = new Hashtable();\r
- public static Hashtable aliphatic = new Hashtable();\r
- public static Hashtable tiny = new Hashtable();\r
- public static Hashtable proline = new Hashtable();\r
-\r
- static {\r
- hydrophobic.put("I", new Integer(1));\r
- hydrophobic.put("L", new Integer(1));\r
- hydrophobic.put("V", new Integer(1));\r
- hydrophobic.put("C", new Integer(1));\r
- hydrophobic.put("A", new Integer(1));\r
- hydrophobic.put("G", new Integer(1));\r
- hydrophobic.put("M", new Integer(1));\r
- hydrophobic.put("F", new Integer(1));\r
- hydrophobic.put("Y", new Integer(1));\r
- hydrophobic.put("W", new Integer(1));\r
- hydrophobic.put("H", new Integer(1));\r
- hydrophobic.put("K", new Integer(1));\r
- hydrophobic.put("X", new Integer(1));\r
- hydrophobic.put("-", new Integer(1));\r
- hydrophobic.put("*", new Integer(1));\r
- hydrophobic.put("R", new Integer(0));\r
- hydrophobic.put("E", new Integer(0));\r
- hydrophobic.put("Q", new Integer(0));\r
- hydrophobic.put("D", new Integer(0));\r
- hydrophobic.put("N", new Integer(0));\r
- hydrophobic.put("S", new Integer(0));\r
- hydrophobic.put("T", new Integer(0));\r
- hydrophobic.put("P", new Integer(0));\r
- }\r
-\r
- static {\r
- polar.put("Y", new Integer(1));\r
- polar.put("W", new Integer(1));\r
- polar.put("H", new Integer(1));\r
- polar.put("K", new Integer(1));\r
- polar.put("R", new Integer(1));\r
- polar.put("E", new Integer(1));\r
- polar.put("Q", new Integer(1));\r
- polar.put("D", new Integer(1));\r
- polar.put("N", new Integer(1));\r
- polar.put("S", new Integer(1));\r
- polar.put("T", new Integer(1));\r
- polar.put("X", new Integer(1));\r
- polar.put("-", new Integer(1));\r
- polar.put("*", new Integer(1));\r
- polar.put("I", new Integer(0));\r
- polar.put("L", new Integer(0));\r
- polar.put("V", new Integer(0));\r
- polar.put("C", new Integer(0));\r
- polar.put("A", new Integer(0));\r
- polar.put("G", new Integer(0));\r
- polar.put("M", new Integer(0));\r
- polar.put("F", new Integer(0));\r
- polar.put("P", new Integer(0));\r
- }\r
-\r
- static {\r
- small.put("I", new Integer(0));\r
- small.put("L", new Integer(0));\r
- small.put("V", new Integer(1));\r
- small.put("C", new Integer(1));\r
- small.put("A", new Integer(1));\r
- small.put("G", new Integer(1));\r
- small.put("M", new Integer(0));\r
- small.put("F", new Integer(0));\r
- small.put("Y", new Integer(0));\r
- small.put("W", new Integer(0));\r
- small.put("H", new Integer(0));\r
- small.put("K", new Integer(0));\r
- small.put("R", new Integer(0));\r
- small.put("E", new Integer(0));\r
- small.put("Q", new Integer(0));\r
- small.put("D", new Integer(1));\r
- small.put("N", new Integer(1));\r
- small.put("S", new Integer(1));\r
- small.put("T", new Integer(1));\r
- small.put("P", new Integer(1));\r
- small.put("-", new Integer(1));\r
- small.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- positive.put("I", new Integer(0));\r
- positive.put("L", new Integer(0));\r
- positive.put("V", new Integer(0));\r
- positive.put("C", new Integer(0));\r
- positive.put("A", new Integer(0));\r
- positive.put("G", new Integer(0));\r
- positive.put("M", new Integer(0));\r
- positive.put("F", new Integer(0));\r
- positive.put("Y", new Integer(0));\r
- positive.put("W", new Integer(0));\r
- positive.put("H", new Integer(1));\r
- positive.put("K", new Integer(1));\r
- positive.put("R", new Integer(1));\r
- positive.put("E", new Integer(0));\r
- positive.put("Q", new Integer(0));\r
- positive.put("D", new Integer(0));\r
- positive.put("N", new Integer(0));\r
- positive.put("S", new Integer(0));\r
- positive.put("T", new Integer(0));\r
- positive.put("P", new Integer(0));\r
- positive.put("-", new Integer(1));\r
- positive.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- negative.put("I", new Integer(0));\r
- negative.put("L", new Integer(0));\r
- negative.put("V", new Integer(0));\r
- negative.put("C", new Integer(0));\r
- negative.put("A", new Integer(0));\r
- negative.put("G", new Integer(0));\r
- negative.put("M", new Integer(0));\r
- negative.put("F", new Integer(0));\r
- negative.put("Y", new Integer(0));\r
- negative.put("W", new Integer(0));\r
- negative.put("H", new Integer(0));\r
- negative.put("K", new Integer(0));\r
- negative.put("R", new Integer(0));\r
- negative.put("E", new Integer(1));\r
- negative.put("Q", new Integer(0));\r
- negative.put("D", new Integer(1));\r
- negative.put("N", new Integer(0));\r
- negative.put("S", new Integer(0));\r
- negative.put("T", new Integer(0));\r
- negative.put("P", new Integer(0));\r
- negative.put("-", new Integer(1));\r
- negative.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- charged.put("I", new Integer(0));\r
- charged.put("L", new Integer(0));\r
- charged.put("V", new Integer(0));\r
- charged.put("C", new Integer(0));\r
- charged.put("A", new Integer(0));\r
- charged.put("G", new Integer(0));\r
- charged.put("M", new Integer(0));\r
- charged.put("F", new Integer(0));\r
- charged.put("Y", new Integer(0));\r
- charged.put("W", new Integer(0));\r
- charged.put("H", new Integer(1));\r
- charged.put("K", new Integer(1));\r
- charged.put("R", new Integer(1));\r
- charged.put("E", new Integer(1));\r
- charged.put("Q", new Integer(0));\r
- charged.put("D", new Integer(1));\r
- charged.put("N", new Integer(1));\r
- charged.put("S", new Integer(0));\r
- charged.put("T", new Integer(0));\r
- charged.put("P", new Integer(0));\r
- charged.put("-", new Integer(1));\r
- charged.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- aromatic.put("I", new Integer(0));\r
- aromatic.put("L", new Integer(0));\r
- aromatic.put("V", new Integer(0));\r
- aromatic.put("C", new Integer(0));\r
- aromatic.put("A", new Integer(0));\r
- aromatic.put("G", new Integer(0));\r
- aromatic.put("M", new Integer(0));\r
- aromatic.put("F", new Integer(1));\r
- aromatic.put("Y", new Integer(1));\r
- aromatic.put("W", new Integer(1));\r
- aromatic.put("H", new Integer(1));\r
- aromatic.put("K", new Integer(0));\r
- aromatic.put("R", new Integer(0));\r
- aromatic.put("E", new Integer(0));\r
- aromatic.put("Q", new Integer(0));\r
- aromatic.put("D", new Integer(0));\r
- aromatic.put("N", new Integer(0));\r
- aromatic.put("S", new Integer(0));\r
- aromatic.put("T", new Integer(0));\r
- aromatic.put("P", new Integer(0));\r
- aromatic.put("-", new Integer(1));\r
- aromatic.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- aliphatic.put("I", new Integer(1));\r
- aliphatic.put("L", new Integer(1));\r
- aliphatic.put("V", new Integer(1));\r
- aliphatic.put("C", new Integer(0));\r
- aliphatic.put("A", new Integer(0));\r
- aliphatic.put("G", new Integer(0));\r
- aliphatic.put("M", new Integer(0));\r
- aliphatic.put("F", new Integer(0));\r
- aliphatic.put("Y", new Integer(0));\r
- aliphatic.put("W", new Integer(0));\r
- aliphatic.put("H", new Integer(0));\r
- aliphatic.put("K", new Integer(0));\r
- aliphatic.put("R", new Integer(0));\r
- aliphatic.put("E", new Integer(0));\r
- aliphatic.put("Q", new Integer(0));\r
- aliphatic.put("D", new Integer(0));\r
- aliphatic.put("N", new Integer(0));\r
- aliphatic.put("S", new Integer(0));\r
- aliphatic.put("T", new Integer(0));\r
- aliphatic.put("P", new Integer(0));\r
- aliphatic.put("-", new Integer(1));\r
- aliphatic.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- tiny.put("I", new Integer(0));\r
- tiny.put("L", new Integer(0));\r
- tiny.put("V", new Integer(0));\r
- tiny.put("C", new Integer(0));\r
- tiny.put("A", new Integer(1));\r
- tiny.put("G", new Integer(1));\r
- tiny.put("M", new Integer(0));\r
- tiny.put("F", new Integer(0));\r
- tiny.put("Y", new Integer(0));\r
- tiny.put("W", new Integer(0));\r
- tiny.put("H", new Integer(0));\r
- tiny.put("K", new Integer(0));\r
- tiny.put("R", new Integer(0));\r
- tiny.put("E", new Integer(0));\r
- tiny.put("Q", new Integer(0));\r
- tiny.put("D", new Integer(0));\r
- tiny.put("N", new Integer(0));\r
- tiny.put("S", new Integer(1));\r
- tiny.put("T", new Integer(0));\r
- tiny.put("P", new Integer(0));\r
- tiny.put("-", new Integer(1));\r
- tiny.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- proline.put("I", new Integer(0));\r
- proline.put("L", new Integer(0));\r
- proline.put("V", new Integer(0));\r
- proline.put("C", new Integer(0));\r
- proline.put("A", new Integer(0));\r
- proline.put("G", new Integer(0));\r
- proline.put("M", new Integer(0));\r
- proline.put("F", new Integer(0));\r
- proline.put("Y", new Integer(0));\r
- proline.put("W", new Integer(0));\r
- proline.put("H", new Integer(0));\r
- proline.put("K", new Integer(0));\r
- proline.put("R", new Integer(0));\r
- proline.put("E", new Integer(0));\r
- proline.put("Q", new Integer(0));\r
- proline.put("D", new Integer(0));\r
- proline.put("N", new Integer(0));\r
- proline.put("S", new Integer(0));\r
- proline.put("T", new Integer(0));\r
- proline.put("P", new Integer(1));\r
- proline.put("-", new Integer(1));\r
- proline.put("*", new Integer(1));\r
- }\r
-\r
- static {\r
- propHash.put("hydrophobic", hydrophobic);\r
- propHash.put("small", small);\r
- propHash.put("positive", positive);\r
- propHash.put("negative", negative);\r
- propHash.put("charged", charged);\r
- propHash.put("aromatic", aromatic);\r
- propHash.put("aliphatic", aliphatic);\r
- propHash.put("tiny", tiny);\r
- propHash.put("proline", proline);\r
- propHash.put("polar", polar);\r
- }\r
-\r
- public static Hashtable chainColours = new Hashtable();\r
-\r
- static {\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
- public static double getHydmax() {\r
- return hydmax;\r
- }\r
-\r
- public static double getHydmin() {\r
- return hydmin;\r
+import java.awt.*;\r
+\r
+public class ResidueProperties\r
+{\r
+ //Stores residue codes/names and colours and other things\r
+ public static final Hashtable aaHash = new Hashtable(); // stores the number value of the aa\r
+ 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
+ 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("U", 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("u", 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("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
+\r
+ static\r
+ {\r
+ aa3Hash.put("ALA", new Integer(0));\r
+ aa3Hash.put("ARG", new Integer(1));\r
+ aa3Hash.put("ASN", new Integer(2));\r
+ aa3Hash.put("ASP", new Integer(3)); //D\r
+ aa3Hash.put("CYS", new Integer(4));\r
+ aa3Hash.put("GLN", new Integer(5)); //Q\r
+ aa3Hash.put("GLU", new Integer(6)); // E\r
+ aa3Hash.put("GLY", new Integer(7));\r
+ aa3Hash.put("HIS", new Integer(8));\r
+ aa3Hash.put("ILE", new Integer(9));\r
+ aa3Hash.put("LEU", new Integer(10));\r
+ aa3Hash.put("LYS", new Integer(11));\r
+ aa3Hash.put("MET", new Integer(12));\r
+ aa3Hash.put("PHE", new Integer(13));\r
+ aa3Hash.put("PRO", new Integer(14));\r
+ aa3Hash.put("SER", new Integer(15));\r
+ aa3Hash.put("THR", new Integer(16));\r
+ aa3Hash.put("TRP", new Integer(17));\r
+ aa3Hash.put("TYR", new Integer(18));\r
+ aa3Hash.put("VAL", new Integer(19));\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
+ }\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 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 final Color midBlue = new Color(100, 100, 255);\r
+ public static final Vector scaleColours = new Vector();\r
+\r
+ static\r
+ {\r
+ scaleColours.addElement(new Color(114, 0, 147));\r
+ scaleColours.addElement(new Color(156, 0, 98));\r
+ scaleColours.addElement(new Color(190, 0, 0));\r
+ scaleColours.addElement(Color.red);\r
+ scaleColours.addElement(new Color(255, 125, 0));\r
+ scaleColours.addElement(Color.orange);\r
+ scaleColours.addElement(new Color(255, 194, 85));\r
+ scaleColours.addElement(Color.yellow);\r
+ scaleColours.addElement(new Color(255, 255, 181));\r
+ scaleColours.addElement(Color.white);\r
+ }\r
+\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
+ new Color(204, 0, 255), // N Blueish-reddy-blue\r
+ new Color(255, 0, 0), // D Reddish-reddy-red\r
+ new Color(255, 255, 0), // C Yellowish-yellowy-yellow\r
+ new Color(255, 0, 204), // Q Reddish-bluey-red\r
+ new Color(255, 0, 102), // E Blueish-reddy-red\r
+ new Color(255, 153, 0), // G Yellowy-reddy-yellow\r
+ new Color(0, 102, 255), // H Greenish-bluey-blue\r
+ new Color(102, 255, 0), // I Greenish-yellowy-green\r
+ new Color(51, 255, 0), // L Yellowish-greeny-green\r
+ new Color(102, 0, 255), // K Reddish-bluey-blue\r
+ new Color(0, 255, 0), // M Greenish-greeny-green\r
+ new Color(0, 255, 102), // F Blueish-greeny-green\r
+ new Color(255, 204, 0), // P Reddish-yellowy-yellow\r
+ new Color(255, 51, 0), // S Yellowish-reddy-red\r
+ new Color(255, 102, 0), // T Reddish-yellowy-red\r
+ new Color(0, 204, 255), // W Blueish-greeny-green\r
+ new Color(0, 255, 204), // Y Greenish-bluey-green\r
+ new Color(153, 255, 0), // V Yellowish-greeny-yellow\r
+ Color.white, // B\r
+ Color.white, // Z\r
+ Color.white, // X\r
+ Color.white, // -\r
+ Color.white, // *\r
+ Color.white // .\r
+ };\r
+ public static final Color[] nucleotide =\r
+ {\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
+ public static final Color[] color =\r
+ {\r
+ Color.pink, // A\r
+ midBlue, // R\r
+ Color.green, // N\r
+ Color.red, // D\r
+ Color.yellow, // C\r
+ Color.green, // Q\r
+ Color.red, // E\r
+ Color.magenta, // G\r
+ Color.red, // H\r
+ Color.pink, // I\r
+ Color.pink, // L\r
+ midBlue, // K\r
+ Color.pink, // M\r
+ Color.orange, // F\r
+ Color.magenta, // P\r
+ Color.green, // S\r
+ Color.green, // T\r
+ Color.orange, // W\r
+ Color.orange, // Y\r
+ Color.pink, // V\r
+ Color.white, // B\r
+ Color.white, // Z\r
+ Color.white, // X\r
+ Color.white, // -\r
+ Color.white, // *\r
+ Color.white, // .\r
+ Color.white // ' '\r
+ };\r
+\r
+ // Dunno where I got these numbers from\r
+ public static final double[] hyd2 =\r
+ {\r
+ 0.62, //A\r
+ 0.29, //R\r
+ -0.90, //N\r
+ -0.74, //D\r
+ 1.19, //C\r
+ 0.48, //Q\r
+ -0.40, //E\r
+ 1.38, //G\r
+ -1.50, //H\r
+ 1.06, //I\r
+ 0.64, //L\r
+ -0.78, //K\r
+ 0.12, //M\r
+ -0.85, //F\r
+ -2.53, //P\r
+ -0.18, //S\r
+ -0.05, //T\r
+ 1.08, //W\r
+ 0.81, //Y\r
+ 0.0, //V\r
+ 0.26, //B\r
+ 0.0, //Z\r
+ 0.0 //X\r
+ };\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 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 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 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 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 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
+ };\r
+ public static final double hydmax = 4.5;\r
+ public static final double hydmin = -3.9;\r
+\r
+ //public static final double hydmax = 1.38;\r
+ //public static final double hydmin = -2.53;\r
+ static final int[][] BLOSUM62 =\r
+ {\r
+ {\r
+ 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,\r
+ -2, 0, -2, -1, 0, -4\r
+ },\r
+ {\r
+ -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2,\r
+ -3, -1, 0, -1, -4\r
+ },\r
+ {\r
+ -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3,\r
+ 3, 0, -1, -4\r
+ },\r
+ {\r
+ -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,\r
+ -3, -3, 4, 1, -1, -4\r
+ },\r
+ {\r
+ 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2,\r
+ -2, -1, -3, -3, -2, -4\r
+ },\r
+ {\r
+ -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,\r
+ -2, 0, 3, -1, -4\r
+ },\r
+ {\r
+ -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,\r
+ -2, 1, 4, -1, -4\r
+ },\r
+ {\r
+ 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,\r
+ -3, -3, -1, -2, -1, -4\r
+ },\r
+ {\r
+ -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2,\r
+ -3, 0, 0, -1, -4\r
+ },\r
+ {\r
+ -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,\r
+ -1, 3, -3, -3, -1, -4\r
+ },\r
+ {\r
+ -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,\r
+ -1, 1, -4, -3, -1, -4\r
+ },\r
+ {\r
+ -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2,\r
+ -2, 0, 1, -1, -4\r
+ },\r
+ {\r
+ -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,\r
+ -1, 1, -3, -1, -1, -4\r
+ },\r
+ {\r
+ -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3,\r
+ -1, -3, -3, -1, -4\r
+ },\r
+ {\r
+ -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,\r
+ -4, -3, -2, -2, -1, -2, -4\r
+ },\r
+ {\r
+ 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,\r
+ -2, 0, 0, 0, -4\r
+ },\r
+ {\r
+ 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,\r
+ -2, 0, -1, -1, 0, -4\r
+ },\r
+ {\r
+ -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,\r
+ 11, 2, -3, -4, -3, -2, -4\r
+ },\r
+ {\r
+ -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2,\r
+ 7, -1, -3, -2, -1, -4\r
+ },\r
+ {\r
+ 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,\r
+ -1, 4, -3, -2, -1, -4\r
+ },\r
+ {\r
+ -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3,\r
+ -3, 4, 1, -1, -4\r
+ },\r
+ {\r
+ -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,\r
+ -2, 1, 4, -1, -4\r
+ },\r
+ {\r
+ 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2,\r
+ -1, -1, -1, -1, -1, -4\r
+ },\r
+ {\r
+ -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,\r
+ -4, -4, -4, -4, -4, -4, 1\r
+ },\r
+ };\r
+ static final int[][] PAM250 =\r
+ {\r
+ {\r
+ 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0,\r
+ 0, 0, 0, -8\r
+ },\r
+ {\r
+ -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,\r
+ -2, -1, 0, -1, -8\r
+ },\r
+ {\r
+ 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,\r
+ 2, 1, 0, -8\r
+ },\r
+ {\r
+ 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2,\r
+ 3, 3, -1, -8\r
+ },\r
+ {\r
+ -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,\r
+ -8, 0, -2, -4, -5, -3, -8\r
+ },\r
+ {\r
+ 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,\r
+ -2, 1, 3, -1, -8\r
+ },\r
+ {\r
+ 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2,\r
+ 3, 3, -1, -8\r
+ },\r
+ {\r
+ 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,\r
+ -1, 0, 0, -1, -8\r
+ },\r
+ {\r
+ -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,\r
+ -2, 1, 2, -1, -8\r
+ },\r
+ {\r
+ -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,\r
+ -1, 4, -2, -2, -1, -8\r
+ },\r
+ {\r
+ -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,\r
+ -1, 2, -3, -3, -1, -8\r
+ },\r
+ {\r
+ -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2,\r
+ 1, 0, -1, -8\r
+ },\r
+ {\r
+ -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2,\r
+ 2, -2, -2, -1, -8\r
+ },\r
+ {\r
+ -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7,\r
+ -1, -4, -5, -2, -8\r
+ },\r
+ {\r
+ 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,\r
+ -1, -1, 0, -1, -8\r
+ },\r
+ {\r
+ 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1,\r
+ 0, 0, 0, -8\r
+ },\r
+ {\r
+ 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0,\r
+ 0, -1, 0, -8\r
+ },\r
+ {\r
+ -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17,\r
+ 0, -6, -5, -6, -4, -8\r
+ },\r
+ {\r
+ -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,\r
+ 10, -2, -3, -4, -2, -8\r
+ },\r
+ {\r
+ 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,\r
+ -2, 4, -2, -2, -1, -8\r
+ },\r
+ {\r
+ 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2,\r
+ 3, 2, -1, -8\r
+ },\r
+ {\r
+ 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2,\r
+ 2, 3, -1, -8\r
+ },\r
+ {\r
+ 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,\r
+ -2, -1, -1, -1, -1, -8\r
+ },\r
+ {\r
+ -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,\r
+ -8, -8, -8, -8, -8, -8, 1\r
+ },\r
+ };\r
+ public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa\r
+\r
+ static\r
+ {\r
+ ssHash.put("H", Color.magenta);\r
+ ssHash.put("E", Color.yellow);\r
+ ssHash.put("-", Color.white);\r
+ ssHash.put(".", Color.white);\r
+ ssHash.put("S", Color.cyan);\r
+ ssHash.put("T", Color.blue);\r
+ ssHash.put("G", Color.pink);\r
+ ssHash.put("I", Color.pink);\r
+ ssHash.put("B", Color.yellow);\r
+ }\r
+\r
+ static final int[][] DNA =\r
+ {\r
+ {\r
+ 5, -4, -4, -4, 1}, // C\r
+ {\r
+ -4, 5, -4, -4, 1}, // T\r
+ {\r
+ -4, -4, 5, -4, 1}, // A\r
+ {\r
+ -4, -4, -4, 5, 1}, // G\r
+ {\r
+ 1, 1, 1, 1, 1}, // -\r
+ };\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 final float[] pidThresholds =\r
+ {\r
+ 80, 60, 40, };\r
+ public static Hashtable codonHash = new Hashtable();\r
+ public static Vector Lys = new Vector();\r
+ public static Vector Asn = new Vector();\r
+ public static Vector Gln = new Vector();\r
+ public static Vector His = new Vector();\r
+ public static Vector Glu = new Vector();\r
+ public static Vector Asp = new Vector();\r
+ public static Vector Tyr = new Vector();\r
+ public static Vector Thr = new Vector();\r
+ public static Vector Pro = new Vector();\r
+ public static Vector Ala = new Vector();\r
+ public static Vector Ser = new Vector();\r
+ public static Vector Arg = new Vector();\r
+ public static Vector Gly = new Vector();\r
+ public static Vector Trp = new Vector();\r
+ public static Vector Cys = new Vector();\r
+ public static Vector Ile = new Vector();\r
+ public static Vector Met = new Vector();\r
+ public static Vector Leu = new Vector();\r
+ public static Vector Val = new Vector();\r
+ public static Vector Phe = new Vector();\r
+ public static Vector STOP = new Vector();\r
+\r
+ static\r
+ {\r
+ codonHash.put("K", Lys);\r
+ codonHash.put("N", Asn);\r
+ codonHash.put("Q", Gln);\r
+ codonHash.put("H", His);\r
+ codonHash.put("E", Glu);\r
+ codonHash.put("D", Asp);\r
+ codonHash.put("Y", Tyr);\r
+ codonHash.put("T", Thr);\r
+ codonHash.put("P", Pro);\r
+ codonHash.put("A", Ala);\r
+ codonHash.put("S", Ser);\r
+ codonHash.put("R", Arg);\r
+ codonHash.put("G", Gly);\r
+ codonHash.put("W", Trp);\r
+ codonHash.put("C", Cys);\r
+ codonHash.put("I", Ile);\r
+ codonHash.put("M", Met);\r
+ codonHash.put("L", Leu);\r
+ codonHash.put("V", Val);\r
+ codonHash.put("F", Phe);\r
+ codonHash.put("STOP", STOP);\r
+ }\r
+\r
+ public static Hashtable codonHash2 = new Hashtable();\r
+\r
+ static\r
+ {\r
+ codonHash2.put("AAA", "K");\r
+ codonHash2.put("AAG", "K");\r
+ codonHash2.put("AAC", "N");\r
+ codonHash2.put("AAT", "N");\r
+\r
+ codonHash2.put("CAA", "E");\r
+ codonHash2.put("CAG", "E");\r
+ codonHash2.put("CAC", "H");\r
+ codonHash2.put("CAT", "H");\r
+\r
+ codonHash2.put("GAA", "Q");\r
+ codonHash2.put("GAG", "Q");\r
+ codonHash2.put("GAC", "D");\r
+ codonHash2.put("GAT", "D");\r
+\r
+ codonHash2.put("TAC", "Y");\r
+ codonHash2.put("TAT", "Y");\r
+\r
+ codonHash2.put("ACA", "T");\r
+ codonHash2.put("AAG", "T");\r
+ codonHash2.put("ACC", "T");\r
+ codonHash2.put("ACT", "T");\r
+\r
+ codonHash2.put("CCA", "P");\r
+ codonHash2.put("CCG", "P");\r
+ codonHash2.put("CCC", "P");\r
+ codonHash2.put("CCT", "P");\r
+\r
+ codonHash2.put("GCA", "A");\r
+ codonHash2.put("GCG", "A");\r
+ codonHash2.put("GCC", "A");\r
+ codonHash2.put("GCT", "A");\r
+\r
+ codonHash2.put("TCA", "S");\r
+ codonHash2.put("TCG", "S");\r
+ codonHash2.put("TCC", "S");\r
+ codonHash2.put("TCT", "S");\r
+ codonHash2.put("AGC", "S");\r
+ codonHash2.put("AGT", "S");\r
+\r
+ codonHash2.put("AGA", "R");\r
+ codonHash2.put("AGG", "R");\r
+ codonHash2.put("CGA", "R");\r
+ codonHash2.put("CGG", "R");\r
+ codonHash2.put("CGC", "R");\r
+ codonHash2.put("CGT", "R");\r
+\r
+ codonHash2.put("GGA", "G");\r
+ codonHash2.put("GGG", "G");\r
+ codonHash2.put("GGC", "G");\r
+ codonHash2.put("GGT", "G");\r
+\r
+ codonHash2.put("TGA", "*");\r
+ codonHash2.put("TAA", "*");\r
+ codonHash2.put("TAG", "*");\r
+\r
+ codonHash2.put("TGG", "W");\r
+\r
+ codonHash2.put("TGC", "C");\r
+ codonHash2.put("TGT", "C");\r
+\r
+ codonHash2.put("ATA", "I");\r
+ codonHash2.put("ATC", "I");\r
+ codonHash2.put("ATT", "I");\r
+\r
+ codonHash2.put("ATG", "M");\r
+\r
+ codonHash2.put("CTA", "L");\r
+ codonHash2.put("CTG", "L");\r
+ codonHash2.put("CTC", "L");\r
+ codonHash2.put("CTT", "L");\r
+ codonHash2.put("TTA", "L");\r
+ codonHash2.put("TTG", "L");\r
+\r
+ codonHash2.put("GTA", "V");\r
+ codonHash2.put("GTG", "V");\r
+ codonHash2.put("GTC", "V");\r
+ codonHash2.put("GTT", "V");\r
+\r
+ codonHash2.put("TTC", "F");\r
+ codonHash2.put("TTT", "F");\r
+ }\r
+\r
+ static\r
+ {\r
+ Lys.addElement("AAA");\r
+ Lys.addElement("AAG");\r
+ Asn.addElement("AAC");\r
+ Asn.addElement("AAT");\r
+\r
+ Gln.addElement("CAA");\r
+ Gln.addElement("CAG");\r
+ His.addElement("CAC");\r
+ His.addElement("CAT");\r
+\r
+ Glu.addElement("GAA");\r
+ Glu.addElement("GAG");\r
+ Asp.addElement("GAC");\r
+ Asp.addElement("GAT");\r
+\r
+ Tyr.addElement("TAC");\r
+ Tyr.addElement("TAT");\r
+\r
+ Thr.addElement("ACA");\r
+ Thr.addElement("ACG");\r
+ Thr.addElement("ACC");\r
+ Thr.addElement("ACT");\r
+\r
+ Pro.addElement("CCA");\r
+ Pro.addElement("CCG");\r
+ Pro.addElement("CCC");\r
+ Pro.addElement("CCT");\r
+\r
+ Ala.addElement("GCA");\r
+ Ala.addElement("GCG");\r
+ Ala.addElement("GCC");\r
+ Ala.addElement("GCT");\r
+\r
+ Ser.addElement("TCA");\r
+ Ser.addElement("TCG");\r
+ Ser.addElement("TCC");\r
+ Ser.addElement("TCT");\r
+ Ser.addElement("AGC");\r
+ Ser.addElement("AGT");\r
+\r
+ Arg.addElement("AGA");\r
+ Arg.addElement("AGG");\r
+ Arg.addElement("CGA");\r
+ Arg.addElement("CGG");\r
+ Arg.addElement("CGC");\r
+ Arg.addElement("CGT");\r
+\r
+ Gly.addElement("GGA");\r
+ Gly.addElement("GGG");\r
+ Gly.addElement("GGC");\r
+ Gly.addElement("GGT");\r
+\r
+ STOP.addElement("TGA");\r
+ STOP.addElement("TAA");\r
+ STOP.addElement("TAG");\r
+\r
+ Trp.addElement("TGG");\r
+\r
+ Cys.addElement("TGC");\r
+ Cys.addElement("TGT");\r
+\r
+ Ile.addElement("ATA");\r
+ Ile.addElement("ATC");\r
+ Ile.addElement("ATT");\r
+\r
+ Met.addElement("ATG");\r
+\r
+ Leu.addElement("CTA");\r
+ Leu.addElement("CTG");\r
+ Leu.addElement("CTC");\r
+ Leu.addElement("CTT");\r
+ Leu.addElement("TTA");\r
+ Leu.addElement("TTG");\r
+\r
+ Val.addElement("GTA");\r
+ Val.addElement("GTG");\r
+ Val.addElement("GTC");\r
+ Val.addElement("GTT");\r
+\r
+ Phe.addElement("TTC");\r
+ Phe.addElement("TTT");\r
+ }\r
+\r
+\r
+ //Stores residue codes/names and colours and other things\r
+ public static Hashtable propHash = new Hashtable();\r
+ public static Hashtable hydrophobic = new Hashtable();\r
+ public static Hashtable polar = new Hashtable();\r
+ public static Hashtable small = new Hashtable();\r
+ public static Hashtable positive = new Hashtable();\r
+ public static Hashtable negative = new Hashtable();\r
+ public static Hashtable charged = new Hashtable();\r
+ public static Hashtable aromatic = new Hashtable();\r
+ public static Hashtable aliphatic = new Hashtable();\r
+ public static Hashtable tiny = new Hashtable();\r
+ public static Hashtable proline = new Hashtable();\r
+\r
+ static\r
+ {\r
+ hydrophobic.put("I", new Integer(1));\r
+ hydrophobic.put("L", new Integer(1));\r
+ hydrophobic.put("V", new Integer(1));\r
+ hydrophobic.put("C", new Integer(1));\r
+ hydrophobic.put("A", new Integer(1));\r
+ hydrophobic.put("G", new Integer(1));\r
+ hydrophobic.put("M", new Integer(1));\r
+ hydrophobic.put("F", new Integer(1));\r
+ hydrophobic.put("Y", new Integer(1));\r
+ hydrophobic.put("W", new Integer(1));\r
+ hydrophobic.put("H", new Integer(1));\r
+ hydrophobic.put("K", new Integer(1));\r
+ hydrophobic.put("X", new Integer(1));\r
+ hydrophobic.put("-", new Integer(1));\r
+ hydrophobic.put("*", new Integer(1));\r
+ hydrophobic.put("R", new Integer(0));\r
+ hydrophobic.put("E", new Integer(0));\r
+ hydrophobic.put("Q", new Integer(0));\r
+ hydrophobic.put("D", new Integer(0));\r
+ hydrophobic.put("N", new Integer(0));\r
+ hydrophobic.put("S", new Integer(0));\r
+ hydrophobic.put("T", new Integer(0));\r
+ hydrophobic.put("P", new Integer(0));\r
+ }\r
+\r
+ static\r
+ {\r
+ polar.put("Y", new Integer(1));\r
+ polar.put("W", new Integer(1));\r
+ polar.put("H", new Integer(1));\r
+ polar.put("K", new Integer(1));\r
+ polar.put("R", new Integer(1));\r
+ polar.put("E", new Integer(1));\r
+ polar.put("Q", new Integer(1));\r
+ polar.put("D", new Integer(1));\r
+ polar.put("N", new Integer(1));\r
+ polar.put("S", new Integer(1));\r
+ polar.put("T", new Integer(1));\r
+ polar.put("X", new Integer(1));\r
+ polar.put("-", new Integer(1));\r
+ polar.put("*", new Integer(1));\r
+ polar.put("I", new Integer(0));\r
+ polar.put("L", new Integer(0));\r
+ polar.put("V", new Integer(0));\r
+ polar.put("C", new Integer(0));\r
+ polar.put("A", new Integer(0));\r
+ polar.put("G", new Integer(0));\r
+ polar.put("M", new Integer(0));\r
+ polar.put("F", new Integer(0));\r
+ polar.put("P", new Integer(0));\r
+ }\r
+\r
+ static\r
+ {\r
+ small.put("I", new Integer(0));\r
+ small.put("L", new Integer(0));\r
+ small.put("V", new Integer(1));\r
+ small.put("C", new Integer(1));\r
+ small.put("A", new Integer(1));\r
+ small.put("G", new Integer(1));\r
+ small.put("M", new Integer(0));\r
+ small.put("F", new Integer(0));\r
+ small.put("Y", new Integer(0));\r
+ small.put("W", new Integer(0));\r
+ small.put("H", new Integer(0));\r
+ small.put("K", new Integer(0));\r
+ small.put("R", new Integer(0));\r
+ small.put("E", new Integer(0));\r
+ small.put("Q", new Integer(0));\r
+ small.put("D", new Integer(1));\r
+ small.put("N", new Integer(1));\r
+ small.put("S", new Integer(1));\r
+ small.put("T", new Integer(1));\r
+ small.put("P", new Integer(1));\r
+ small.put("-", new Integer(1));\r
+ small.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ positive.put("I", new Integer(0));\r
+ positive.put("L", new Integer(0));\r
+ positive.put("V", new Integer(0));\r
+ positive.put("C", new Integer(0));\r
+ positive.put("A", new Integer(0));\r
+ positive.put("G", new Integer(0));\r
+ positive.put("M", new Integer(0));\r
+ positive.put("F", new Integer(0));\r
+ positive.put("Y", new Integer(0));\r
+ positive.put("W", new Integer(0));\r
+ positive.put("H", new Integer(1));\r
+ positive.put("K", new Integer(1));\r
+ positive.put("R", new Integer(1));\r
+ positive.put("E", new Integer(0));\r
+ positive.put("Q", new Integer(0));\r
+ positive.put("D", new Integer(0));\r
+ positive.put("N", new Integer(0));\r
+ positive.put("S", new Integer(0));\r
+ positive.put("T", new Integer(0));\r
+ positive.put("P", new Integer(0));\r
+ positive.put("-", new Integer(1));\r
+ positive.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ negative.put("I", new Integer(0));\r
+ negative.put("L", new Integer(0));\r
+ negative.put("V", new Integer(0));\r
+ negative.put("C", new Integer(0));\r
+ negative.put("A", new Integer(0));\r
+ negative.put("G", new Integer(0));\r
+ negative.put("M", new Integer(0));\r
+ negative.put("F", new Integer(0));\r
+ negative.put("Y", new Integer(0));\r
+ negative.put("W", new Integer(0));\r
+ negative.put("H", new Integer(0));\r
+ negative.put("K", new Integer(0));\r
+ negative.put("R", new Integer(0));\r
+ negative.put("E", new Integer(1));\r
+ negative.put("Q", new Integer(0));\r
+ negative.put("D", new Integer(1));\r
+ negative.put("N", new Integer(0));\r
+ negative.put("S", new Integer(0));\r
+ negative.put("T", new Integer(0));\r
+ negative.put("P", new Integer(0));\r
+ negative.put("-", new Integer(1));\r
+ negative.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ charged.put("I", new Integer(0));\r
+ charged.put("L", new Integer(0));\r
+ charged.put("V", new Integer(0));\r
+ charged.put("C", new Integer(0));\r
+ charged.put("A", new Integer(0));\r
+ charged.put("G", new Integer(0));\r
+ charged.put("M", new Integer(0));\r
+ charged.put("F", new Integer(0));\r
+ charged.put("Y", new Integer(0));\r
+ charged.put("W", new Integer(0));\r
+ charged.put("H", new Integer(1));\r
+ charged.put("K", new Integer(1));\r
+ charged.put("R", new Integer(1));\r
+ charged.put("E", new Integer(1));\r
+ charged.put("Q", new Integer(0));\r
+ charged.put("D", new Integer(1));\r
+ charged.put("N", new Integer(1));\r
+ charged.put("S", new Integer(0));\r
+ charged.put("T", new Integer(0));\r
+ charged.put("P", new Integer(0));\r
+ charged.put("-", new Integer(1));\r
+ charged.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ aromatic.put("I", new Integer(0));\r
+ aromatic.put("L", new Integer(0));\r
+ aromatic.put("V", new Integer(0));\r
+ aromatic.put("C", new Integer(0));\r
+ aromatic.put("A", new Integer(0));\r
+ aromatic.put("G", new Integer(0));\r
+ aromatic.put("M", new Integer(0));\r
+ aromatic.put("F", new Integer(1));\r
+ aromatic.put("Y", new Integer(1));\r
+ aromatic.put("W", new Integer(1));\r
+ aromatic.put("H", new Integer(1));\r
+ aromatic.put("K", new Integer(0));\r
+ aromatic.put("R", new Integer(0));\r
+ aromatic.put("E", new Integer(0));\r
+ aromatic.put("Q", new Integer(0));\r
+ aromatic.put("D", new Integer(0));\r
+ aromatic.put("N", new Integer(0));\r
+ aromatic.put("S", new Integer(0));\r
+ aromatic.put("T", new Integer(0));\r
+ aromatic.put("P", new Integer(0));\r
+ aromatic.put("-", new Integer(1));\r
+ aromatic.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ aliphatic.put("I", new Integer(1));\r
+ aliphatic.put("L", new Integer(1));\r
+ aliphatic.put("V", new Integer(1));\r
+ aliphatic.put("C", new Integer(0));\r
+ aliphatic.put("A", new Integer(0));\r
+ aliphatic.put("G", new Integer(0));\r
+ aliphatic.put("M", new Integer(0));\r
+ aliphatic.put("F", new Integer(0));\r
+ aliphatic.put("Y", new Integer(0));\r
+ aliphatic.put("W", new Integer(0));\r
+ aliphatic.put("H", new Integer(0));\r
+ aliphatic.put("K", new Integer(0));\r
+ aliphatic.put("R", new Integer(0));\r
+ aliphatic.put("E", new Integer(0));\r
+ aliphatic.put("Q", new Integer(0));\r
+ aliphatic.put("D", new Integer(0));\r
+ aliphatic.put("N", new Integer(0));\r
+ aliphatic.put("S", new Integer(0));\r
+ aliphatic.put("T", new Integer(0));\r
+ aliphatic.put("P", new Integer(0));\r
+ aliphatic.put("-", new Integer(1));\r
+ aliphatic.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ tiny.put("I", new Integer(0));\r
+ tiny.put("L", new Integer(0));\r
+ tiny.put("V", new Integer(0));\r
+ tiny.put("C", new Integer(0));\r
+ tiny.put("A", new Integer(1));\r
+ tiny.put("G", new Integer(1));\r
+ tiny.put("M", new Integer(0));\r
+ tiny.put("F", new Integer(0));\r
+ tiny.put("Y", new Integer(0));\r
+ tiny.put("W", new Integer(0));\r
+ tiny.put("H", new Integer(0));\r
+ tiny.put("K", new Integer(0));\r
+ tiny.put("R", new Integer(0));\r
+ tiny.put("E", new Integer(0));\r
+ tiny.put("Q", new Integer(0));\r
+ tiny.put("D", new Integer(0));\r
+ tiny.put("N", new Integer(0));\r
+ tiny.put("S", new Integer(1));\r
+ tiny.put("T", new Integer(0));\r
+ tiny.put("P", new Integer(0));\r
+ tiny.put("-", new Integer(1));\r
+ tiny.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ proline.put("I", new Integer(0));\r
+ proline.put("L", new Integer(0));\r
+ proline.put("V", new Integer(0));\r
+ proline.put("C", new Integer(0));\r
+ proline.put("A", new Integer(0));\r
+ proline.put("G", new Integer(0));\r
+ proline.put("M", new Integer(0));\r
+ proline.put("F", new Integer(0));\r
+ proline.put("Y", new Integer(0));\r
+ proline.put("W", new Integer(0));\r
+ proline.put("H", new Integer(0));\r
+ proline.put("K", new Integer(0));\r
+ proline.put("R", new Integer(0));\r
+ proline.put("E", new Integer(0));\r
+ proline.put("Q", new Integer(0));\r
+ proline.put("D", new Integer(0));\r
+ proline.put("N", new Integer(0));\r
+ proline.put("S", new Integer(0));\r
+ proline.put("T", new Integer(0));\r
+ proline.put("P", new Integer(1));\r
+ proline.put("-", new Integer(1));\r
+ proline.put("*", new Integer(1));\r
+ }\r
+\r
+ static\r
+ {\r
+ propHash.put("hydrophobic", hydrophobic);\r
+ propHash.put("small", small);\r
+ propHash.put("positive", positive);\r
+ propHash.put("negative", negative);\r
+ propHash.put("charged", charged);\r
+ propHash.put("aromatic", aromatic);\r
+ propHash.put("aliphatic", aliphatic);\r
+ propHash.put("tiny", tiny);\r
+ propHash.put("proline", proline);\r
+ propHash.put("polar", polar);\r
+ }\r
+\r
+ private ResidueProperties()\r
+ {\r
+ }\r
+\r
+ public static double getHydmax()\r
+ {\r
+ return hydmax;\r
+ }\r
+\r
+ public static double getHydmin()\r
+ {\r
+ return hydmin;\r
+ }\r
+\r
+ public static double[] getHyd()\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
+\r
+ public static int[][] getDNA()\r
+ {\r
+ return ResidueProperties.DNA;\r
+ }\r
+\r
+ public static int[][] getBLOSUM62()\r
+ {\r
+ return ResidueProperties.BLOSUM62;\r
+ }\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
+\r
+ return pog;\r
+ }\r
+\r
+ public static int getBLOSUM62(String A1, String A2)\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
}\r
-\r
- public static double[] getHyd() {\r
- return hyd;\r
+ catch (Exception e)\r
+ {\r
+ //System.out.println("Unknown residue in " + A1 + " " + A2);\r
}\r
\r
- public static Hashtable getAAHash() {\r
- return aaHash;\r
- }\r
+ return pog;\r
+ }\r
\r
- public static Hashtable getAA3Hash() {\r
- return aa3Hash;\r
+ public static Vector getCodons(String res)\r
+ {\r
+ if (codonHash.containsKey(res))\r
+ {\r
+ return (Vector) codonHash.get(res);\r
}\r
\r
- public static int[][] getDNA() {\r
- return ResidueProperties.DNA;\r
- }\r
+ return null;\r
+ }\r
\r
- public static int[][] getBLOSUM62() {\r
- return ResidueProperties.BLOSUM62;\r
- }\r
+ public static String codonTranslate(String codon)\r
+ {\r
+ Enumeration e = codonHash.keys();\r
\r
- public static int getPAM250(String A1, String A2) {\r
- Integer pog1 = (Integer) aaHash.get(A1);\r
- Integer pog2 = (Integer) aaHash.get(A2);\r
- int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];\r
+ while (e.hasMoreElements())\r
+ {\r
+ String key = (String) e.nextElement();\r
+ Vector tmp = (Vector) codonHash.get(key);\r
\r
- return pog;\r
+ if (tmp.contains(codon.toUpperCase()))\r
+ {\r
+ return key;\r
+ }\r
}\r
\r
- public static int getBLOSUM62(String A1, String A2) {\r
- int pog = 0;\r
-\r
- try {\r
- Integer pog1 = (Integer) aaHash.get(A1);\r
- Integer pog2 = (Integer) aaHash.get(A2);\r
- pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];\r
- } catch (Exception e) {\r
- //System.out.println("Unknown residue in " + A1 + " " + A2);\r
- }\r
-\r
- return pog;\r
- }\r
-\r
- public static Vector getCodons(String res) {\r
- if (codonHash.containsKey(res)) {\r
- return (Vector) codonHash.get(res);\r
- }\r
-\r
- return null;\r
- }\r
-\r
- public static String codonTranslate(String codon) {\r
- Enumeration e = codonHash.keys();\r
-\r
- while (e.hasMoreElements()) {\r
- String key = (String) e.nextElement();\r
- Vector tmp = (Vector) codonHash.get(key);\r
-\r
- if (tmp.contains(codon)) {\r
- return key;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-\r
- public static Hashtable getChainColours() {\r
- return chainColours;\r
- }\r
+ return null;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff