/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.schemes; import java.awt.Color; import java.util.ArrayList; import java.util.Enumeration; import java.util.HashMap; import java.util.Hashtable; import java.util.List; import java.util.Map; import java.util.Vector; import jalview.analysis.scoremodels.FeatureScoreModel; import jalview.analysis.scoremodels.PIDScoreModel; import jalview.api.analysis.ScoreModelI; public class ResidueProperties { public static Hashtable scoreMatrices = new Hashtable(); // Stores residue codes/names and colours and other things public static final int[] aaIndex; // aaHash version 2.1.1 and below public static final int[] nucleotideIndex; public static final int[] purinepyrimidineIndex; public static final Map aa3Hash = new HashMap(); public static final Map aa2Triplet = new HashMap(); public static final Map nucleotideName = new HashMap(); static { aaIndex = new int[255]; for (int i = 0; i < 255; i++) { aaIndex[i] = 23; } aaIndex['A'] = 0; aaIndex['R'] = 1; aaIndex['N'] = 2; aaIndex['D'] = 3; aaIndex['C'] = 4; aaIndex['Q'] = 5; aaIndex['E'] = 6; aaIndex['G'] = 7; aaIndex['H'] = 8; aaIndex['I'] = 9; aaIndex['L'] = 10; aaIndex['K'] = 11; aaIndex['M'] = 12; aaIndex['F'] = 13; aaIndex['P'] = 14; aaIndex['S'] = 15; aaIndex['T'] = 16; aaIndex['W'] = 17; aaIndex['Y'] = 18; aaIndex['V'] = 19; aaIndex['B'] = 20; aaIndex['Z'] = 21; aaIndex['X'] = 22; aaIndex['U'] = 22; aaIndex['a'] = 0; aaIndex['r'] = 1; aaIndex['n'] = 2; aaIndex['d'] = 3; aaIndex['c'] = 4; aaIndex['q'] = 5; aaIndex['e'] = 6; aaIndex['g'] = 7; aaIndex['h'] = 8; aaIndex['i'] = 9; aaIndex['l'] = 10; aaIndex['k'] = 11; aaIndex['m'] = 12; aaIndex['f'] = 13; aaIndex['p'] = 14; aaIndex['s'] = 15; aaIndex['t'] = 16; aaIndex['w'] = 17; aaIndex['y'] = 18; aaIndex['v'] = 19; aaIndex['b'] = 20; aaIndex['z'] = 21; aaIndex['x'] = 22; aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also // extend subt. matrices } /** * maximum (gap) index for matrices involving protein alphabet */ public final static int maxProteinIndex = 23; /** * maximum (gap) index for matrices involving nucleotide alphabet */ public final static int maxNucleotideIndex = 10; static { nucleotideIndex = new int[255]; for (int i = 0; i < 255; i++) { nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps. } nucleotideIndex['A'] = 0; nucleotideIndex['a'] = 0; nucleotideIndex['C'] = 1; nucleotideIndex['c'] = 1; nucleotideIndex['G'] = 2; nucleotideIndex['g'] = 2; nucleotideIndex['T'] = 3; nucleotideIndex['t'] = 3; nucleotideIndex['U'] = 4; nucleotideIndex['u'] = 4; nucleotideIndex['I'] = 5; nucleotideIndex['i'] = 5; nucleotideIndex['X'] = 6; nucleotideIndex['x'] = 6; nucleotideIndex['R'] = 7; nucleotideIndex['r'] = 7; nucleotideIndex['Y'] = 8; nucleotideIndex['y'] = 8; nucleotideIndex['N'] = 9; nucleotideIndex['n'] = 9; nucleotideName.put("A", "Adenine"); nucleotideName.put("a", "Adenine"); nucleotideName.put("G", "Guanine"); nucleotideName.put("g", "Guanine"); nucleotideName.put("C", "Cytosine"); nucleotideName.put("c", "Cytosine"); nucleotideName.put("T", "Thymine"); nucleotideName.put("t", "Thymine"); nucleotideName.put("U", "Uracil"); nucleotideName.put("u", "Uracil"); nucleotideName.put("I", "Inosine"); nucleotideName.put("i", "Inosine"); nucleotideName.put("X", "Xanthine"); nucleotideName.put("x", "Xanthine"); nucleotideName.put("R", "Unknown Purine"); nucleotideName.put("r", "Unknown Purine"); nucleotideName.put("Y", "Unknown Pyrimidine"); nucleotideName.put("y", "Unknown Pyrimidine"); nucleotideName.put("N", "Unknown"); nucleotideName.put("n", "Unknown"); nucleotideName.put("W", "Weak nucleotide (A or T)"); nucleotideName.put("w", "Weak nucleotide (A or T)"); nucleotideName.put("S", "Strong nucleotide (G or C)"); nucleotideName.put("s", "Strong nucleotide (G or C)"); nucleotideName.put("M", "Amino (A or C)"); nucleotideName.put("m", "Amino (A or C)"); nucleotideName.put("K", "Keto (G or T)"); nucleotideName.put("k", "Keto (G or T)"); nucleotideName.put("B", "Not A (G or C or T)"); nucleotideName.put("b", "Not A (G or C or T)"); nucleotideName.put("H", "Not G (A or C or T)"); nucleotideName.put("h", "Not G (A or C or T)"); nucleotideName.put("D", "Not C (A or G or T)"); nucleotideName.put("d", "Not C (A or G or T)"); nucleotideName.put("V", "Not T (A or G or C"); nucleotideName.put("v", "Not T (A or G or C"); } static { purinepyrimidineIndex = new int[255]; for (int i = 0; i < 255; i++) { purinepyrimidineIndex[i] = 3; // non-nucleotide symbols are all non-gap // gaps. } purinepyrimidineIndex['A'] = 0; purinepyrimidineIndex['a'] = 0; purinepyrimidineIndex['C'] = 1; purinepyrimidineIndex['c'] = 1; purinepyrimidineIndex['G'] = 0; purinepyrimidineIndex['g'] = 0; purinepyrimidineIndex['T'] = 1; purinepyrimidineIndex['t'] = 1; purinepyrimidineIndex['U'] = 1; purinepyrimidineIndex['u'] = 1; purinepyrimidineIndex['I'] = 2; purinepyrimidineIndex['i'] = 2; purinepyrimidineIndex['X'] = 2; purinepyrimidineIndex['x'] = 2; purinepyrimidineIndex['R'] = 0; purinepyrimidineIndex['r'] = 0; purinepyrimidineIndex['Y'] = 1; purinepyrimidineIndex['y'] = 1; purinepyrimidineIndex['N'] = 2; purinepyrimidineIndex['n'] = 2; } static { aa3Hash.put("ALA", new Integer(0)); aa3Hash.put("ARG", new Integer(1)); aa3Hash.put("ASN", new Integer(2)); aa3Hash.put("ASP", new Integer(3)); // D aa3Hash.put("CYS", new Integer(4)); aa3Hash.put("GLN", new Integer(5)); // Q aa3Hash.put("GLU", new Integer(6)); // E aa3Hash.put("GLY", new Integer(7)); aa3Hash.put("HIS", new Integer(8)); aa3Hash.put("ILE", new Integer(9)); aa3Hash.put("LEU", new Integer(10)); aa3Hash.put("LYS", new Integer(11)); aa3Hash.put("MET", new Integer(12)); aa3Hash.put("PHE", new Integer(13)); aa3Hash.put("PRO", new Integer(14)); aa3Hash.put("SER", new Integer(15)); aa3Hash.put("THR", new Integer(16)); aa3Hash.put("TRP", new Integer(17)); aa3Hash.put("TYR", new Integer(18)); aa3Hash.put("VAL", new Integer(19)); // IUB Nomenclature for ambiguous peptides aa3Hash.put("ASX", new Integer(20)); // "B"; aa3Hash.put("GLX", new Integer(21)); // X aa3Hash.put("XAA", new Integer(22)); // X unknown aa3Hash.put("-", new Integer(23)); aa3Hash.put("*", new Integer(23)); aa3Hash.put(".", new Integer(23)); aa3Hash.put(" ", new Integer(23)); aa3Hash.put("Gap", new Integer(23)); } static { aa2Triplet.put("A", "ALA"); aa2Triplet.put("a", "ALA"); aa2Triplet.put("R", "ARG"); aa2Triplet.put("r", "ARG"); aa2Triplet.put("N", "ASN"); aa2Triplet.put("n", "ASN"); aa2Triplet.put("D", "ASP"); aa2Triplet.put("d", "ASP"); aa2Triplet.put("C", "CYS"); aa2Triplet.put("c", "CYS"); aa2Triplet.put("Q", "GLN"); aa2Triplet.put("q", "GLN"); aa2Triplet.put("E", "GLU"); aa2Triplet.put("e", "GLU"); aa2Triplet.put("G", "GLY"); aa2Triplet.put("g", "GLY"); aa2Triplet.put("H", "HIS"); aa2Triplet.put("h", "HIS"); aa2Triplet.put("I", "ILE"); aa2Triplet.put("i", "ILE"); aa2Triplet.put("L", "LEU"); aa2Triplet.put("l", "LEU"); aa2Triplet.put("K", "LYS"); aa2Triplet.put("k", "LYS"); aa2Triplet.put("M", "MET"); aa2Triplet.put("m", "MET"); aa2Triplet.put("F", "PHE"); aa2Triplet.put("f", "PHE"); aa2Triplet.put("P", "PRO"); aa2Triplet.put("p", "PRO"); aa2Triplet.put("S", "SER"); aa2Triplet.put("s", "SER"); aa2Triplet.put("T", "THR"); aa2Triplet.put("t", "THR"); aa2Triplet.put("W", "TRP"); aa2Triplet.put("w", "TRP"); aa2Triplet.put("Y", "TYR"); aa2Triplet.put("y", "TYR"); aa2Triplet.put("V", "VAL"); aa2Triplet.put("v", "VAL"); } public static final String[] aa = { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " }; public static final Color midBlue = new Color(100, 100, 255); public static final Vector scaleColours = new Vector(); static { scaleColours.addElement(new Color(114, 0, 147)); scaleColours.addElement(new Color(156, 0, 98)); scaleColours.addElement(new Color(190, 0, 0)); scaleColours.addElement(Color.red); scaleColours.addElement(new Color(255, 125, 0)); scaleColours.addElement(Color.orange); scaleColours.addElement(new Color(255, 194, 85)); scaleColours.addElement(Color.yellow); scaleColours.addElement(new Color(255, 255, 181)); scaleColours.addElement(Color.white); } public static final Color[] taylor = { new Color(204, 255, 0), // A Greenish-yellowy-yellow new Color(0, 0, 255), // R Blueish-bluey-blue new Color(204, 0, 255), // N Blueish-reddy-blue new Color(255, 0, 0), // D Reddish-reddy-red new Color(255, 255, 0), // C Yellowish-yellowy-yellow new Color(255, 0, 204), // Q Reddish-bluey-red new Color(255, 0, 102), // E Blueish-reddy-red new Color(255, 153, 0), // G Yellowy-reddy-yellow new Color(0, 102, 255), // H Greenish-bluey-blue new Color(102, 255, 0), // I Greenish-yellowy-green new Color(51, 255, 0), // L Yellowish-greeny-green new Color(102, 0, 255), // K Reddish-bluey-blue new Color(0, 255, 0), // M Greenish-greeny-green new Color(0, 255, 102), // F Blueish-greeny-green new Color(255, 204, 0), // P Reddish-yellowy-yellow new Color(255, 51, 0), // S Yellowish-reddy-red new Color(255, 102, 0), // T Reddish-yellowy-red new Color(0, 204, 255), // W Blueish-greeny-green new Color(0, 255, 204), // Y Greenish-bluey-green new Color(153, 255, 0), // V Yellowish-greeny-yellow Color.white, // B Color.white, // Z Color.white, // X Color.white, // - Color.white, // * Color.white // . }; public static final 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 Color.white, // I (inosine) Color.white, // X (xanthine) Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap }; // Added for PurinePyrimidineColourScheme public static final Color[] purinepyrimidine = { new Color(255, 131, 250), // A, G, R purines purplish/orchid new Color(64, 224, 208), // C,U, T, Y pyrimidines turquoise Color.white, // all other nucleotides Color.white // Gap }; // Zappo public static final Color[] zappo = { Color.pink, // A midBlue, // R Color.green, // N Color.red, // D Color.yellow, // C Color.green, // Q Color.red, // E Color.magenta, // G midBlue,// Color.red, // H Color.pink, // I Color.pink, // L midBlue, // K Color.pink, // M Color.orange, // F Color.magenta, // P Color.green, // S Color.green, // T Color.orange, // W Color.orange, // Y Color.pink, // V Color.white, // B Color.white, // Z Color.white, // X Color.white, // - Color.white, // * Color.white, // . Color.white // ' ' }; // Dunno where I got these numbers from public static final double[] hyd2 = { 0.62, // A 0.29, // R -0.90, // N -0.74, // D 1.19, // C 0.48, // Q -0.40, // E 1.38, // G -1.50, // H 1.06, // I 0.64, // L -0.78, // K 0.12, // M -0.85, // F -2.53, // P -0.18, // S -0.05, // T 1.08, // W 0.81, // Y 0.0, // V 0.26, // B 0.0, // Z 0.0 // X }; public static final double[] helix = { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16, 1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 }; public static final double helixmin = 0.57; public static final double helixmax = 1.51; public static final double[] strand = { 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74, 1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 }; public static final double strandmin = 0.37; public static final double strandmax = 1.7; public static final double[] turn = { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01, 0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0, 0 }; public static final double turnmin = 0.47; public static final double turnmax = 1.56; public static final double[] buried = { 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, 0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00 }; public static final double buriedmin = 0.05; public static final double buriedmax = 4.6; // This is hydropathy index // Kyte, J., and Doolittle, R.F., J. Mol. Biol. // 1157, 105-132, 1982 public static final double[] hyd = { 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, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 }; public static final double hydmax = 4.5; public static final double hydmin = -3.9; // public static final double hydmax = 1.38; // public static final double hydmin = -2.53; private static final int[][] BLOSUM62 = { { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4 }, { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4 }, { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4 }, { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4 }, { 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4 }, { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4 }, { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4 }, { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4 }, { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4 }, { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4 }, { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4 }, { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4 }, { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4 }, { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4 }, { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4 }, { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4 }, { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4 }, { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4 }, { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4 }, { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4 }, { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4 }, { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4 }, { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4 }, { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1 }, }; static final int[][] PAM250 = { { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0, 0, 0, 0, -8 }, { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, -2, -1, 0, -1, -8 }, { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, 2, 1, 0, -8 }, { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8 }, { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, -8, 0, -2, -4, -5, -3, -8 }, { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, -2, 1, 3, -1, -8 }, { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2, 3, 3, -1, -8 }, { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, -1, 0, 0, -1, -8 }, { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, -2, 1, 2, -1, -8 }, { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, -1, 4, -2, -2, -1, -8 }, { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, -1, 2, -3, -3, -1, -8 }, { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2, 1, 0, -1, -8 }, { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2, 2, -2, -2, -1, -8 }, { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7, -1, -4, -5, -2, -8 }, { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, -1, -1, 0, -1, -8 }, { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1, 0, 0, 0, -8 }, { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0, 0, -1, 0, -8 }, { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17, 0, -6, -5, -6, -4, -8 }, { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, 10, -2, -3, -4, -2, -8 }, { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, -2, 4, -2, -2, -1, -8 }, { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2, 3, 2, -1, -8 }, { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2, 2, 3, -1, -8 }, { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, -2, -1, -1, -1, -1, -8 }, { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, 1 }, }; public static final Hashtable ssHash = new Hashtable(); // stores the number // value of the aa static { ssHash.put("H", Color.magenta); ssHash.put("E", Color.yellow); ssHash.put("-", Color.white); ssHash.put(".", Color.white); ssHash.put("S", Color.cyan); ssHash.put("T", Color.blue); ssHash.put("G", Color.pink); ssHash.put("I", Color.pink); ssHash.put("B", Color.yellow); } /* * new Color(60, 136, 238), // U Color.white, // I Color.white, // X * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap */ // JBPNote: patch matrix for T/U equivalence when working with DNA or RNA. // Will equate sequences if working with mixed nucleotide sets. // treats T and U identically. R and Y weak equivalence with AG and CTU. // N matches any other base weakly // static final int[][] DNA = { { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A { -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C { -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // U { 1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1 }, // I { 1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1 }, // X { 1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1 }, // R { -8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1 }, // Y { 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1 }, // N { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }, // - }; /** * register matrices in list */ static { scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0)); scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0)); scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1)); } public static final Color[] pidColours = { midBlue, new Color(153, 153, 255), // Color.lightGray, new Color(204, 204, 255), }; public static final float[] pidThresholds = { 80, 60, 40, }; public static Map> codonHash = new HashMap>(); private static List Lys = new ArrayList(); private static List Asn = new ArrayList(); private static List Gln = new ArrayList(); private static List His = new ArrayList(); private static List Glu = new ArrayList(); private static List Asp = new ArrayList(); private static List Tyr = new ArrayList(); private static List Thr = new ArrayList(); private static List Pro = new ArrayList(); private static List Ala = new ArrayList(); private static List Ser = new ArrayList(); private static List Arg = new ArrayList(); private static List Gly = new ArrayList(); private static List Trp = new ArrayList(); private static List Cys = new ArrayList(); private static List Ile = new ArrayList(); private static List Met = new ArrayList(); private static List Leu = new ArrayList(); private static List Val = new ArrayList(); private static List Phe = new ArrayList(); public static List STOP = new ArrayList(); public static String START = "ATG"; static { codonHash.put("K", Lys); codonHash.put("N", Asn); codonHash.put("Q", Gln); codonHash.put("H", His); codonHash.put("E", Glu); codonHash.put("D", Asp); codonHash.put("Y", Tyr); codonHash.put("T", Thr); codonHash.put("P", Pro); codonHash.put("A", Ala); codonHash.put("S", Ser); codonHash.put("R", Arg); codonHash.put("G", Gly); codonHash.put("W", Trp); codonHash.put("C", Cys); codonHash.put("I", Ile); codonHash.put("M", Met); codonHash.put("L", Leu); codonHash.put("V", Val); codonHash.put("F", Phe); codonHash.put("STOP", STOP); } /** * Nucleotide Ambiguity Codes */ public static final Map ambiguityCodes = new Hashtable(); /** * Codon triplets with additional symbols for unambiguous codons that include * ambiguity codes */ public static final Hashtable codonHash2 = new Hashtable(); /** * all ambiguity codes for a given base */ public final static Hashtable> _ambiguityCodes = new Hashtable>(); static { /* * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html */ ambiguityCodes.put("R", new String[] { "A", "G" }); ambiguityCodes.put("Y", new String[] { "T", "C" }); ambiguityCodes.put("W", new String[] { "A", "T" }); ambiguityCodes.put("S", new String[] { "G", "C" }); ambiguityCodes.put("M", new String[] { "A", "C" }); ambiguityCodes.put("K", new String[] { "G", "T" }); ambiguityCodes.put("H", new String[] { "A", "T", "C" }); ambiguityCodes.put("B", new String[] { "G", "T", "C" }); ambiguityCodes.put("V", new String[] { "G", "A", "C" }); ambiguityCodes.put("D", new String[] { "G", "A", "T" }); ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" }); // Now build codon translation table codonHash2.put("AAA", "K"); codonHash2.put("AAG", "K"); codonHash2.put("AAC", "N"); codonHash2.put("AAT", "N"); codonHash2.put("CAA", "Q"); codonHash2.put("CAG", "Q"); codonHash2.put("CAC", "H"); codonHash2.put("CAT", "H"); codonHash2.put("GAA", "E"); codonHash2.put("GAG", "E"); codonHash2.put("GAC", "D"); codonHash2.put("GAT", "D"); codonHash2.put("TAC", "Y"); codonHash2.put("TAT", "Y"); codonHash2.put("ACA", "T"); codonHash2.put("ACC", "T"); codonHash2.put("ACT", "T"); codonHash2.put("ACG", "T"); codonHash2.put("CCA", "P"); codonHash2.put("CCG", "P"); codonHash2.put("CCC", "P"); codonHash2.put("CCT", "P"); codonHash2.put("GCA", "A"); codonHash2.put("GCG", "A"); codonHash2.put("GCC", "A"); codonHash2.put("GCT", "A"); codonHash2.put("TCA", "S"); codonHash2.put("TCG", "S"); codonHash2.put("TCC", "S"); codonHash2.put("TCT", "S"); codonHash2.put("AGC", "S"); codonHash2.put("AGT", "S"); codonHash2.put("AGA", "R"); codonHash2.put("AGG", "R"); codonHash2.put("CGA", "R"); codonHash2.put("CGG", "R"); codonHash2.put("CGC", "R"); codonHash2.put("CGT", "R"); codonHash2.put("GGA", "G"); codonHash2.put("GGG", "G"); codonHash2.put("GGC", "G"); codonHash2.put("GGT", "G"); codonHash2.put("TGA", "*"); codonHash2.put("TAA", "*"); codonHash2.put("TAG", "*"); codonHash2.put("TGG", "W"); codonHash2.put("TGC", "C"); codonHash2.put("TGT", "C"); codonHash2.put("ATA", "I"); codonHash2.put("ATC", "I"); codonHash2.put("ATT", "I"); codonHash2.put("ATG", "M"); codonHash2.put("CTA", "L"); codonHash2.put("CTG", "L"); codonHash2.put("CTC", "L"); codonHash2.put("CTT", "L"); codonHash2.put("TTA", "L"); codonHash2.put("TTG", "L"); codonHash2.put("GTA", "V"); codonHash2.put("GTG", "V"); codonHash2.put("GTC", "V"); codonHash2.put("GTT", "V"); codonHash2.put("TTC", "F"); codonHash2.put("TTT", "F"); buildAmbiguityCodonSet(); } /** * programmatic generation of codons including ambiguity codes */ public static void buildAmbiguityCodonSet() { if (_ambiguityCodes.size() > 0) { System.err .println("Ignoring multiple calls to buildAmbiguityCodonSet"); return; } // Invert the ambiguity code set for (Map.Entry acode : ambiguityCodes.entrySet()) { for (String r : acode.getValue()) { List codesfor = _ambiguityCodes.get(r); if (codesfor == null) { _ambiguityCodes.put(r, codesfor = new ArrayList()); } if (!codesfor.contains(acode.getKey())) { codesfor.add(acode.getKey()); } else { System.err .println("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + acode.getKey() + " in residue " + r); } } } // and programmatically add in the ambiguity codes that yield the same amino // acid String[] unambcodons = codonHash2.keySet().toArray( new String[codonHash2.size()]); for (String codon : unambcodons) { String residue = codonHash2.get(codon); String acodon[][] = new String[codon.length()][]; for (int i = 0, iSize = codon.length(); i < iSize; i++) { String _ac = "" + codon.charAt(i); List acodes = _ambiguityCodes.get(_ac); if (acodes != null) { acodon[i] = acodes.toArray(new String[acodes.size()]); } else { acodon[i] = new String[] {}; } } // enumerate all combinations and test for veracity of translation int tpos[] = new int[codon.length()], cpos[] = new int[codon.length()]; for (int i = 0; i < tpos.length; i++) { tpos[i] = -1; } tpos[acodon.length - 1] = 0; int ipos, j; while (tpos[0] < acodon[0].length) { // make all codons for this combination char allres[][] = new char[tpos.length][]; String _acodon = ""; char _anuc; for (ipos = 0; ipos < tpos.length; ipos++) { if (acodon[ipos].length == 0 || tpos[ipos] < 0) { _acodon += codon.charAt(ipos); allres[ipos] = new char[] { codon.charAt(ipos) }; } else { _acodon += acodon[ipos][tpos[ipos]]; String[] altbase = ambiguityCodes.get(acodon[ipos][tpos[ipos]]); allres[ipos] = new char[altbase.length]; j = 0; for (String ab : altbase) { allres[ipos][j++] = ab.charAt(0); } } } // test all codons for this combination for (ipos = 0; ipos < cpos.length; ipos++) { cpos[ipos] = 0; } boolean valid = true; do { String _codon = ""; for (j = 0; j < cpos.length; j++) { _codon += allres[j][cpos[j]]; } String tr = codonHash2.get(_codon); if (valid = (tr != null && tr.equals(residue))) { // advance to next combination ipos = acodon.length - 1; while (++cpos[ipos] >= allres[ipos].length && ipos > 0) { cpos[ipos] = 0; ipos--; } } } while (valid && cpos[0] < allres[0].length); if (valid) { // Add this to the set of codons we will translate // System.out.println("Adding ambiguity codon: " + _acodon + " for " // + residue); codonHash2.put(_acodon, residue); } else { // System.err.println("Rejecting ambiguity codon: " + _acodon // + " for " + residue); } // next combination ipos = acodon.length - 1; while (++tpos[ipos] >= acodon[ipos].length && ipos > 0) { tpos[ipos] = -1; ipos--; } } } } static { Lys.add("AAA"); Lys.add("AAG"); Asn.add("AAC"); Asn.add("AAT"); Gln.add("CAA"); Gln.add("CAG"); His.add("CAC"); His.add("CAT"); Glu.add("GAA"); Glu.add("GAG"); Asp.add("GAC"); Asp.add("GAT"); Tyr.add("TAC"); Tyr.add("TAT"); Thr.add("ACA"); Thr.add("ACG"); Thr.add("ACC"); Thr.add("ACT"); Pro.add("CCA"); Pro.add("CCG"); Pro.add("CCC"); Pro.add("CCT"); Ala.add("GCA"); Ala.add("GCG"); Ala.add("GCC"); Ala.add("GCT"); Ser.add("TCA"); Ser.add("TCG"); Ser.add("TCC"); Ser.add("TCT"); Ser.add("AGC"); Ser.add("AGT"); Arg.add("AGA"); Arg.add("AGG"); Arg.add("CGA"); Arg.add("CGG"); Arg.add("CGC"); Arg.add("CGT"); Gly.add("GGA"); Gly.add("GGG"); Gly.add("GGC"); Gly.add("GGT"); STOP.add("TGA"); STOP.add("TAA"); STOP.add("TAG"); Trp.add("TGG"); Cys.add("TGC"); Cys.add("TGT"); Ile.add("ATA"); Ile.add("ATC"); Ile.add("ATT"); Met.add("ATG"); Leu.add("CTA"); Leu.add("CTG"); Leu.add("CTC"); Leu.add("CTT"); Leu.add("TTA"); Leu.add("TTG"); Val.add("GTA"); Val.add("GTG"); Val.add("GTC"); Val.add("GTT"); Phe.add("TTC"); Phe.add("TTT"); } // Stores residue codes/names and colours and other things public static Hashtable propHash = new Hashtable(); public static Hashtable hydrophobic = new Hashtable(); public static Hashtable polar = new Hashtable(); public static Hashtable small = new Hashtable(); public static Hashtable positive = new Hashtable(); public static Hashtable negative = new Hashtable(); public static Hashtable charged = new Hashtable(); public static Hashtable aromatic = new Hashtable(); public static Hashtable aliphatic = new Hashtable(); public static Hashtable tiny = new Hashtable(); public static Hashtable proline = new Hashtable(); static { hydrophobic.put("I", new Integer(1)); hydrophobic.put("L", new Integer(1)); hydrophobic.put("V", new Integer(1)); hydrophobic.put("C", new Integer(1)); hydrophobic.put("A", new Integer(1)); hydrophobic.put("G", new Integer(1)); hydrophobic.put("M", new Integer(1)); hydrophobic.put("F", new Integer(1)); hydrophobic.put("Y", new Integer(1)); hydrophobic.put("W", new Integer(1)); hydrophobic.put("H", new Integer(1)); hydrophobic.put("K", new Integer(1)); hydrophobic.put("X", new Integer(1)); hydrophobic.put("-", new Integer(1)); hydrophobic.put("*", new Integer(1)); hydrophobic.put("R", new Integer(0)); hydrophobic.put("E", new Integer(0)); hydrophobic.put("Q", new Integer(0)); hydrophobic.put("D", new Integer(0)); hydrophobic.put("N", new Integer(0)); hydrophobic.put("S", new Integer(0)); hydrophobic.put("T", new Integer(0)); hydrophobic.put("P", new Integer(0)); } static { polar.put("Y", new Integer(1)); polar.put("W", new Integer(1)); polar.put("H", new Integer(1)); polar.put("K", new Integer(1)); polar.put("R", new Integer(1)); polar.put("E", new Integer(1)); polar.put("Q", new Integer(1)); polar.put("D", new Integer(1)); polar.put("N", new Integer(1)); polar.put("S", new Integer(1)); polar.put("T", new Integer(1)); polar.put("X", new Integer(1)); polar.put("-", new Integer(1)); polar.put("*", new Integer(1)); polar.put("I", new Integer(0)); polar.put("L", new Integer(0)); polar.put("V", new Integer(0)); polar.put("C", new Integer(0)); polar.put("A", new Integer(0)); polar.put("G", new Integer(0)); polar.put("M", new Integer(0)); polar.put("F", new Integer(0)); polar.put("P", new Integer(0)); } static { small.put("I", new Integer(0)); small.put("L", new Integer(0)); small.put("V", new Integer(1)); small.put("C", new Integer(1)); small.put("A", new Integer(1)); small.put("G", new Integer(1)); small.put("M", new Integer(0)); small.put("F", new Integer(0)); small.put("Y", new Integer(0)); small.put("W", new Integer(0)); small.put("H", new Integer(0)); small.put("K", new Integer(0)); small.put("R", new Integer(0)); small.put("E", new Integer(0)); small.put("Q", new Integer(0)); small.put("D", new Integer(1)); small.put("N", new Integer(1)); small.put("S", new Integer(1)); small.put("T", new Integer(1)); small.put("P", new Integer(1)); small.put("-", new Integer(1)); small.put("*", new Integer(1)); } static { positive.put("I", new Integer(0)); positive.put("L", new Integer(0)); positive.put("V", new Integer(0)); positive.put("C", new Integer(0)); positive.put("A", new Integer(0)); positive.put("G", new Integer(0)); positive.put("M", new Integer(0)); positive.put("F", new Integer(0)); positive.put("Y", new Integer(0)); positive.put("W", new Integer(0)); positive.put("H", new Integer(1)); positive.put("K", new Integer(1)); positive.put("R", new Integer(1)); positive.put("E", new Integer(0)); positive.put("Q", new Integer(0)); positive.put("D", new Integer(0)); positive.put("N", new Integer(0)); positive.put("S", new Integer(0)); positive.put("T", new Integer(0)); positive.put("P", new Integer(0)); positive.put("-", new Integer(1)); positive.put("*", new Integer(1)); } static { negative.put("I", new Integer(0)); negative.put("L", new Integer(0)); negative.put("V", new Integer(0)); negative.put("C", new Integer(0)); negative.put("A", new Integer(0)); negative.put("G", new Integer(0)); negative.put("M", new Integer(0)); negative.put("F", new Integer(0)); negative.put("Y", new Integer(0)); negative.put("W", new Integer(0)); negative.put("H", new Integer(0)); negative.put("K", new Integer(0)); negative.put("R", new Integer(0)); negative.put("E", new Integer(1)); negative.put("Q", new Integer(0)); negative.put("D", new Integer(1)); negative.put("N", new Integer(0)); negative.put("S", new Integer(0)); negative.put("T", new Integer(0)); negative.put("P", new Integer(0)); negative.put("-", new Integer(1)); negative.put("*", new Integer(1)); } static { charged.put("I", new Integer(0)); charged.put("L", new Integer(0)); charged.put("V", new Integer(0)); charged.put("C", new Integer(0)); charged.put("A", new Integer(0)); charged.put("G", new Integer(0)); charged.put("M", new Integer(0)); charged.put("F", new Integer(0)); charged.put("Y", new Integer(0)); charged.put("W", new Integer(0)); charged.put("H", new Integer(1)); charged.put("K", new Integer(1)); charged.put("R", new Integer(1)); charged.put("E", new Integer(1)); charged.put("Q", new Integer(0)); charged.put("D", new Integer(1)); charged.put("N", new Integer(0)); // Asparagine is polar but not charged. // Alternative would be charged and // negative (in basic form)? charged.put("S", new Integer(0)); charged.put("T", new Integer(0)); charged.put("P", new Integer(0)); charged.put("-", new Integer(1)); charged.put("*", new Integer(1)); } static { aromatic.put("I", new Integer(0)); aromatic.put("L", new Integer(0)); aromatic.put("V", new Integer(0)); aromatic.put("C", new Integer(0)); aromatic.put("A", new Integer(0)); aromatic.put("G", new Integer(0)); aromatic.put("M", new Integer(0)); aromatic.put("F", new Integer(1)); aromatic.put("Y", new Integer(1)); aromatic.put("W", new Integer(1)); aromatic.put("H", new Integer(1)); aromatic.put("K", new Integer(0)); aromatic.put("R", new Integer(0)); aromatic.put("E", new Integer(0)); aromatic.put("Q", new Integer(0)); aromatic.put("D", new Integer(0)); aromatic.put("N", new Integer(0)); aromatic.put("S", new Integer(0)); aromatic.put("T", new Integer(0)); aromatic.put("P", new Integer(0)); aromatic.put("-", new Integer(1)); aromatic.put("*", new Integer(1)); } static { aliphatic.put("I", new Integer(1)); aliphatic.put("L", new Integer(1)); aliphatic.put("V", new Integer(1)); aliphatic.put("C", new Integer(0)); aliphatic.put("A", new Integer(0)); aliphatic.put("G", new Integer(0)); aliphatic.put("M", new Integer(0)); aliphatic.put("F", new Integer(0)); aliphatic.put("Y", new Integer(0)); aliphatic.put("W", new Integer(0)); aliphatic.put("H", new Integer(0)); aliphatic.put("K", new Integer(0)); aliphatic.put("R", new Integer(0)); aliphatic.put("E", new Integer(0)); aliphatic.put("Q", new Integer(0)); aliphatic.put("D", new Integer(0)); aliphatic.put("N", new Integer(0)); aliphatic.put("S", new Integer(0)); aliphatic.put("T", new Integer(0)); aliphatic.put("P", new Integer(0)); aliphatic.put("-", new Integer(1)); aliphatic.put("*", new Integer(1)); } static { tiny.put("I", new Integer(0)); tiny.put("L", new Integer(0)); tiny.put("V", new Integer(0)); tiny.put("C", new Integer(0)); tiny.put("A", new Integer(1)); tiny.put("G", new Integer(1)); tiny.put("M", new Integer(0)); tiny.put("F", new Integer(0)); tiny.put("Y", new Integer(0)); tiny.put("W", new Integer(0)); tiny.put("H", new Integer(0)); tiny.put("K", new Integer(0)); tiny.put("R", new Integer(0)); tiny.put("E", new Integer(0)); tiny.put("Q", new Integer(0)); tiny.put("D", new Integer(0)); tiny.put("N", new Integer(0)); tiny.put("S", new Integer(1)); tiny.put("T", new Integer(0)); tiny.put("P", new Integer(0)); tiny.put("-", new Integer(1)); tiny.put("*", new Integer(1)); } static { proline.put("I", new Integer(0)); proline.put("L", new Integer(0)); proline.put("V", new Integer(0)); proline.put("C", new Integer(0)); proline.put("A", new Integer(0)); proline.put("G", new Integer(0)); proline.put("M", new Integer(0)); proline.put("F", new Integer(0)); proline.put("Y", new Integer(0)); proline.put("W", new Integer(0)); proline.put("H", new Integer(0)); proline.put("K", new Integer(0)); proline.put("R", new Integer(0)); proline.put("E", new Integer(0)); proline.put("Q", new Integer(0)); proline.put("D", new Integer(0)); proline.put("N", new Integer(0)); proline.put("S", new Integer(0)); proline.put("T", new Integer(0)); proline.put("P", new Integer(1)); proline.put("-", new Integer(1)); proline.put("*", new Integer(1)); } static { propHash.put("hydrophobic", hydrophobic); propHash.put("small", small); propHash.put("positive", positive); propHash.put("negative", negative); propHash.put("charged", charged); propHash.put("aromatic", aromatic); propHash.put("aliphatic", aliphatic); propHash.put("tiny", tiny); propHash.put("proline", proline); propHash.put("polar", polar); } static { int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex], propMatrixPos = new int[maxProteinIndex][maxProteinIndex], propMatrixEpos = new int[maxProteinIndex][maxProteinIndex]; for (int i = 0; i < maxProteinIndex; i++) { int maxF = 0, maxP = 0, maxEP = 0; String ic = ""; if (aa.length > i) { ic += aa[i]; } else { ic = "-"; } for (int j = i + 1; j < maxProteinIndex; j++) { String jc = ""; if (aa.length > j) { jc += aa[j]; } else { jc = "-"; } propMatrixF[i][j] = 0; propMatrixPos[i][j] = 0; propMatrixEpos[i][j] = 0; for (Enumeration en = propHash.keys(); en .hasMoreElements();) { String ph = en.nextElement(); Map pph = (Map) propHash .get(ph); if (pph.get(ic) != null && pph.get(jc) != null) { int icp = pph.get(ic).intValue(), jcp = pph.get(jc).intValue(); // Still working on these definitions. propMatrixPos[i][j] += icp == jcp && icp > 0 ? 2 : 0; propMatrixPos[j][i] += icp == jcp && icp > 0 ? 2 : 0; propMatrixF[i][j] += icp == jcp ? 2 : 0; propMatrixF[j][i] += icp == jcp ? 2 : 0; propMatrixEpos[i][j] += icp == jcp ? (1 + icp * 2) : 0; propMatrixEpos[j][i] += icp == jcp ? (1 + icp * 2) : 0; } } if (maxF < propMatrixF[i][j]) { maxF = propMatrixF[i][j]; } if (maxP < propMatrixPos[i][j]) { maxP = propMatrixPos[i][j]; } if (maxEP < propMatrixEpos[i][j]) { maxEP = propMatrixEpos[i][j]; } } propMatrixF[i][i] = maxF; propMatrixPos[i][i] = maxP; propMatrixEpos[i][i] = maxEP; } // JAL-1512 comment out physicochemical score matrices for 2.8.1 release // scoreMatrices.put("Conservation Pos", new // ScoreMatrix("Conservation Pos",propMatrixPos,0)); // scoreMatrices.put("Conservation Both", new // ScoreMatrix("Conservation Both",propMatrixF,0)); // scoreMatrices.put("Conservation EnhPos", new // ScoreMatrix("Conservation EnhPos",propMatrixEpos,0)); scoreMatrices.put("PID", new PIDScoreModel()); scoreMatrices.put("Displayed Features", new FeatureScoreModel()); } private ResidueProperties() { } public static double getHydmax() { return hydmax; } public static double getHydmin() { return hydmin; } public static double[] getHyd() { return hyd; } public static Map getAA3Hash() { return aa3Hash; } public static int[][] getDNA() { return ResidueProperties.DNA; } public static int[][] getBLOSUM62() { return ResidueProperties.BLOSUM62; } public static int getPAM250(String A1, String A2) { return getPAM250(A1.charAt(0), A2.charAt(0)); } public static int getBLOSUM62(char c1, char c2) { int pog = 0; try { int a = aaIndex[c1]; int b = aaIndex[c2]; pog = ResidueProperties.BLOSUM62[a][b]; } catch (Exception e) { // System.out.println("Unknown residue in " + A1 + " " + A2); } return pog; } public static Vector getCodons(String res) { if (codonHash.containsKey(res)) { return (Vector) codonHash.get(res); } return null; } public static String codonTranslate(String lccodon) { if (false) { return _codonTranslate(lccodon); } String cdn = codonHash2.get(lccodon.toUpperCase()); if (cdn != null && cdn.equals("*")) { return "STOP"; } return cdn; } public static String _codonTranslate(String lccodon) { String codon = lccodon.toUpperCase(); // all base ambiguity codes yield an 'X' amino acid residue if (codon.indexOf('X') > -1 || codon.indexOf('N') > -1) { return "X"; } for (String key : codonHash.keySet()) { if (codonHash.get(key).contains(codon)) { return key; } } return null; } public static int[][] getDefaultPeptideMatrix() { return ResidueProperties.getBLOSUM62(); } public static int[][] getDefaultDnaMatrix() { return ResidueProperties.getDNA(); } /** * get a ScoreMatrix based on its string name * * @param pwtype * @return matrix in scoreMatrices with key pwtype or null */ public static ScoreMatrix getScoreMatrix(String pwtype) { Object val = scoreMatrices.get(pwtype); if (val != null && val instanceof ScoreMatrix) { return (ScoreMatrix) val; } return null; } /** * get a ScoreModel based on its string name * * @param pwtype * @return scoremodel of type pwtype or null */ public static ScoreModelI getScoreModel(String pwtype) { return scoreMatrices.get(pwtype); } public static int getPAM250(char c, char d) { int a = aaIndex[c]; int b = aaIndex[d]; int pog = ResidueProperties.PAM250[a][b]; return pog; } public static Hashtable toDssp3State; static { toDssp3State = new Hashtable(); toDssp3State.put("H", "H"); toDssp3State.put("E", "E"); toDssp3State.put("C", " "); toDssp3State.put(" ", " "); toDssp3State.put("T", " "); toDssp3State.put("B", "E"); toDssp3State.put("G", "H"); toDssp3State.put("I", "H"); toDssp3State.put("X", " "); } /** * translate from other dssp secondary structure alphabets to 3-state * * @param ssstring * @return ssstring as a three-state secondary structure assignment. */ public static String getDssp3state(String ssstring) { if (ssstring == null) { return null; } StringBuffer ss = new StringBuffer(); for (int i = 0; i < ssstring.length(); i++) { String ssc = ssstring.substring(i, i + 1); if (toDssp3State.containsKey(ssc)) { ss.append((String) toDssp3State.get(ssc)); } else { ss.append(" "); } } return ss.toString(); } /** * Used by getRNASecStrucState * */ public static Hashtable toRNAssState; public static boolean RNAcloseParen[] = new boolean[255]; static { toRNAssState = new Hashtable(); toRNAssState.put(")", "("); toRNAssState.put("(", "("); toRNAssState.put("]", "["); toRNAssState.put("[", "["); toRNAssState.put("{", "{"); toRNAssState.put("}", "{"); toRNAssState.put(">", ">"); toRNAssState.put("<", ">"); toRNAssState.put("A", "A"); toRNAssState.put("a", "A"); toRNAssState.put("B", "B"); toRNAssState.put("b", "B"); toRNAssState.put("C", "C"); toRNAssState.put("c", "C"); toRNAssState.put("D", "D"); toRNAssState.put("d", "D"); toRNAssState.put("E", "E"); toRNAssState.put("e", "E"); toRNAssState.put("F", "F"); toRNAssState.put("f", "F"); toRNAssState.put("G", "G"); toRNAssState.put("g", "G"); toRNAssState.put("H", "H"); toRNAssState.put("h", "H"); toRNAssState.put("I", "I"); toRNAssState.put("i", "I"); toRNAssState.put("J", "J"); toRNAssState.put("j", "J"); toRNAssState.put("K", "K"); toRNAssState.put("k", "K"); toRNAssState.put("L", "L"); toRNAssState.put("l", "L"); toRNAssState.put("M", "M"); toRNAssState.put("m", "M"); toRNAssState.put("N", "N"); toRNAssState.put("n", "N"); toRNAssState.put("O", "O"); toRNAssState.put("o", "O"); toRNAssState.put("P", "P"); toRNAssState.put("p", "P"); toRNAssState.put("Q", "Q"); toRNAssState.put("q", "Q"); toRNAssState.put("R", "R"); toRNAssState.put("r", "R"); toRNAssState.put("S", "S"); toRNAssState.put("s", "S"); toRNAssState.put("T", "T"); toRNAssState.put("t", "T"); toRNAssState.put("U", "U"); toRNAssState.put("u", "U"); toRNAssState.put("V", "V"); toRNAssState.put("v", "V"); toRNAssState.put("W", "W"); toRNAssState.put("w", "W"); toRNAssState.put("X", "X"); toRNAssState.put("x", "X"); toRNAssState.put("Y", "Y"); toRNAssState.put("y", "Y"); toRNAssState.put("Z", "Z"); toRNAssState.put("z", "Z"); for (int p = 0; p < RNAcloseParen.length; p++) { RNAcloseParen[p] = false; } for (String k : toRNAssState.keySet()) { RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k) .charAt(0); } } /** * translate to RNA secondary structure representation * * @param ssstring * @return ssstring as a RNA-state secondary structure assignment. */ public static String getRNASecStrucState(String ssstring) { if (ssstring == null) { return null; } StringBuffer ss = new StringBuffer(); for (int i = 0; i < ssstring.length(); i++) { String ssc = ssstring.substring(i, i + 1); if (toRNAssState.containsKey(ssc)) { // valid ss character - so return it ss.append(ssc); // (String) toRNAssState.get(ssc)); } else { ss.append(" "); } } return ss.toString(); } public static boolean isCloseParenRNA(char dc) { return RNAcloseParen[dc]; } // main method generates perl representation of residue property hash // / cut here public static void main(String[] args) { Hashtable aa = new Hashtable(); System.out.println("my %aa = {"); // invert property hashes Enumeration prop = propHash.keys(); while (prop.hasMoreElements()) { String pname = (String) prop.nextElement(); Hashtable phash = (Hashtable) propHash.get(pname); Enumeration res = phash.keys(); while (res.hasMoreElements()) { String rname = (String) res.nextElement(); Vector aprops = (Vector) aa.get(rname); if (aprops == null) { aprops = new Vector(); aa.put(rname, aprops); } Integer hasprop = (Integer) phash.get(rname); if (hasprop.intValue() == 1) { aprops.addElement(pname); } } } Enumeration res = aa.keys(); while (res.hasMoreElements()) { String rname = (String) res.nextElement(); System.out.print("'" + rname + "' => ["); Enumeration props = ((Vector) aa.get(rname)).elements(); while (props.hasMoreElements()) { System.out.print("'" + (String) props.nextElement() + "'"); if (props.hasMoreElements()) { System.out.println(", "); } } System.out.println("]" + (res.hasMoreElements() ? "," : "")); } System.out.println("};"); } // to here /** * Returns a list of residue characters for the specified inputs * * @param nucleotide * @param includeAmbiguous * @return */ public static List getResidues(boolean nucleotide, boolean includeAmbiguous) { List result = new ArrayList(); if (nucleotide) { for (String nuc : nucleotideName.keySet()) { int val = nucleotideIndex[nuc.charAt(0)]; if ((!includeAmbiguous && val > 4) || (val >= maxNucleotideIndex)) { continue; } nuc = nuc.toUpperCase(); if (!result.contains(nuc)) { result.add(nuc); } } } else { /* * Peptide */ for (String res : aa3Hash.keySet()) { int index = aa3Hash.get(res).intValue(); if ((!includeAmbiguous && index >= 20) || index >= maxProteinIndex) { continue; } res = res.toUpperCase(); if (!result.contains(res)) { result.add(res); } } } return result; } }