X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=092971d762ae5f7097cd599d6135115b5d1d09f9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=fbaab81e63deda1bd5f1bcc952aea8bc7a8bfff0;hpb=8ae2f185311811757976eeb142b4767c42a9618f;p=jalview.git diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index fbaab81..092971d 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,1249 +1,1858 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.schemes; - -import java.util.*; - -import java.awt.*; - -public class ResidueProperties -{ - //Stores residue codes/names and colours and other things - public static final Hashtable aaHash = new Hashtable(); // stores the number value of the aa - public static final Hashtable aa3Hash = new Hashtable(); - public static final Hashtable aa2Triplet = new Hashtable(); - public static final Hashtable nucleotideHash = new Hashtable(); - public static final Hashtable nucleotideName = new Hashtable(); - - static - { - aaHash.put("A", new Integer(0)); - aaHash.put("R", new Integer(1)); - aaHash.put("N", new Integer(2)); - aaHash.put("D", new Integer(3)); - aaHash.put("C", new Integer(4)); - aaHash.put("Q", new Integer(5)); - aaHash.put("E", new Integer(6)); - aaHash.put("G", new Integer(7)); - aaHash.put("H", new Integer(8)); - aaHash.put("I", new Integer(9)); - aaHash.put("L", new Integer(10)); - aaHash.put("K", new Integer(11)); - aaHash.put("M", new Integer(12)); - aaHash.put("F", new Integer(13)); - aaHash.put("P", new Integer(14)); - aaHash.put("S", new Integer(15)); - aaHash.put("T", new Integer(16)); - aaHash.put("W", new Integer(17)); - aaHash.put("Y", new Integer(18)); - aaHash.put("V", new Integer(19)); - aaHash.put("B", new Integer(20)); - aaHash.put("Z", new Integer(21)); - aaHash.put("X", new Integer(22)); - aaHash.put("U", new Integer(22)); - aaHash.put("a", new Integer(0)); - aaHash.put("r", new Integer(1)); - aaHash.put("n", new Integer(2)); - aaHash.put("d", new Integer(3)); - aaHash.put("c", new Integer(4)); - aaHash.put("q", new Integer(5)); - aaHash.put("e", new Integer(6)); - aaHash.put("g", new Integer(7)); - aaHash.put("h", new Integer(8)); - aaHash.put("i", new Integer(9)); - aaHash.put("l", new Integer(10)); - aaHash.put("k", new Integer(11)); - aaHash.put("m", new Integer(12)); - aaHash.put("f", new Integer(13)); - aaHash.put("p", new Integer(14)); - aaHash.put("s", new Integer(15)); - aaHash.put("t", new Integer(16)); - aaHash.put("w", new Integer(17)); - aaHash.put("y", new Integer(18)); - aaHash.put("v", new Integer(19)); - aaHash.put("b", new Integer(20)); - aaHash.put("z", new Integer(21)); - aaHash.put("x", new Integer(22)); - aaHash.put("u", new Integer(22)); - aaHash.put("-", new Integer(23)); - aaHash.put("*", new Integer(23)); - aaHash.put(".", new Integer(23)); - aaHash.put(" ", new Integer(23)); - } - - static - { - nucleotideHash.put("A", new Integer(0)); - nucleotideHash.put("a", new Integer(0)); - nucleotideHash.put("C", new Integer(1)); - nucleotideHash.put("c", new Integer(1)); - nucleotideHash.put("G", new Integer(2)); - nucleotideHash.put("g", new Integer(2)); - nucleotideHash.put("T", new Integer(3)); - nucleotideHash.put("t", new Integer(3)); - nucleotideHash.put("U", new Integer(4)); - nucleotideHash.put("u", new Integer(4)); - nucleotideHash.put("I", new Integer(5)); - nucleotideHash.put("i", new Integer(5)); - nucleotideHash.put("X", new Integer(6)); - nucleotideHash.put("x", new Integer(6)); - nucleotideHash.put("R", new Integer(7)); - nucleotideHash.put("r", new Integer(7)); - nucleotideHash.put("Y", new Integer(8)); - nucleotideHash.put("y", new Integer(8)); - nucleotideHash.put("N", new Integer(9)); - nucleotideHash.put("n", new Integer(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"); - } - - - 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)); - aa3Hash.put("B", new Integer(20)); - aa3Hash.put("Z", new Integer(21)); - aa3Hash.put("X", new Integer(22)); - aa3Hash.put("-", new Integer(23)); - aa3Hash.put("*", new Integer(23)); - aa3Hash.put(".", new Integer(23)); - aa3Hash.put(" ", 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 - }; - public static final Color[] color = - { - Color.pink, // A - midBlue, // R - Color.green, // N - Color.red, // D - Color.yellow, // C - Color.green, // Q - Color.red, // E - Color.magenta, // G - 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; - 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); - } - - static final int[][] DNA = - { - { - 5, -4, -4, -4, 1}, // C - { - -4, 5, -4, -4, 1}, // T - { - -4, -4, 5, -4, 1}, // A - { - -4, -4, -4, 5, 1}, // G - { - 1, 1, 1, 1, 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 Hashtable codonHash = new Hashtable(); - public static Vector Lys = new Vector(); - public static Vector Asn = new Vector(); - public static Vector Gln = new Vector(); - public static Vector His = new Vector(); - public static Vector Glu = new Vector(); - public static Vector Asp = new Vector(); - public static Vector Tyr = new Vector(); - public static Vector Thr = new Vector(); - public static Vector Pro = new Vector(); - public static Vector Ala = new Vector(); - public static Vector Ser = new Vector(); - public static Vector Arg = new Vector(); - public static Vector Gly = new Vector(); - public static Vector Trp = new Vector(); - public static Vector Cys = new Vector(); - public static Vector Ile = new Vector(); - public static Vector Met = new Vector(); - public static Vector Leu = new Vector(); - public static Vector Val = new Vector(); - public static Vector Phe = new Vector(); - public static Vector STOP = new Vector(); - - 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); - } - - public static Hashtable codonHash2 = new Hashtable(); - - static - { - codonHash2.put("AAA", "K"); - codonHash2.put("AAG", "K"); - codonHash2.put("AAC", "N"); - codonHash2.put("AAT", "N"); - - codonHash2.put("CAA", "E"); - codonHash2.put("CAG", "E"); - codonHash2.put("CAC", "H"); - codonHash2.put("CAT", "H"); - - codonHash2.put("GAA", "Q"); - codonHash2.put("GAG", "Q"); - codonHash2.put("GAC", "D"); - codonHash2.put("GAT", "D"); - - codonHash2.put("TAC", "Y"); - codonHash2.put("TAT", "Y"); - - codonHash2.put("ACA", "T"); - codonHash2.put("AAG", "T"); - codonHash2.put("ACC", "T"); - codonHash2.put("ACT", "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"); - } - - static - { - Lys.addElement("AAA"); - Lys.addElement("AAG"); - Asn.addElement("AAC"); - Asn.addElement("AAT"); - - Gln.addElement("CAA"); - Gln.addElement("CAG"); - His.addElement("CAC"); - His.addElement("CAT"); - - Glu.addElement("GAA"); - Glu.addElement("GAG"); - Asp.addElement("GAC"); - Asp.addElement("GAT"); - - Tyr.addElement("TAC"); - Tyr.addElement("TAT"); - - Thr.addElement("ACA"); - Thr.addElement("ACG"); - Thr.addElement("ACC"); - Thr.addElement("ACT"); - - Pro.addElement("CCA"); - Pro.addElement("CCG"); - Pro.addElement("CCC"); - Pro.addElement("CCT"); - - Ala.addElement("GCA"); - Ala.addElement("GCG"); - Ala.addElement("GCC"); - Ala.addElement("GCT"); - - Ser.addElement("TCA"); - Ser.addElement("TCG"); - Ser.addElement("TCC"); - Ser.addElement("TCT"); - Ser.addElement("AGC"); - Ser.addElement("AGT"); - - Arg.addElement("AGA"); - Arg.addElement("AGG"); - Arg.addElement("CGA"); - Arg.addElement("CGG"); - Arg.addElement("CGC"); - Arg.addElement("CGT"); - - Gly.addElement("GGA"); - Gly.addElement("GGG"); - Gly.addElement("GGC"); - Gly.addElement("GGT"); - - STOP.addElement("TGA"); - STOP.addElement("TAA"); - STOP.addElement("TAG"); - - Trp.addElement("TGG"); - - Cys.addElement("TGC"); - Cys.addElement("TGT"); - - Ile.addElement("ATA"); - Ile.addElement("ATC"); - Ile.addElement("ATT"); - - Met.addElement("ATG"); - - Leu.addElement("CTA"); - Leu.addElement("CTG"); - Leu.addElement("CTC"); - Leu.addElement("CTT"); - Leu.addElement("TTA"); - Leu.addElement("TTG"); - - Val.addElement("GTA"); - Val.addElement("GTG"); - Val.addElement("GTC"); - Val.addElement("GTT"); - - Phe.addElement("TTC"); - Phe.addElement("TTT"); - } - - public static Color[][] groupColors = - { - { - Color.red, Color.red.brighter(), Color.red.brighter().brighter()}, - { - Color.orange, Color.orange.brighter(), - Color.orange.brighter().brighter() - }, - { - Color.green, Color.green.brighter(), Color.green.brighter().brighter()}, - { - Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter()}, - { - Color.magenta, Color.magenta.brighter(), - Color.magenta.brighter().brighter() - }, - { - Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter()}, - { - Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter()}, - }; - - //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(1)); - 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); - } - - public static Hashtable chainColours = new Hashtable(); - - static - { - chainColours.put("A", Color.red); - chainColours.put("B", Color.orange); - chainColours.put("C", Color.yellow); - chainColours.put("D", Color.green); - chainColours.put("E", Color.cyan); - chainColours.put("F", Color.blue); - chainColours.put("G", Color.magenta); - chainColours.put("H", Color.pink); - } - - private ResidueProperties() - { - } - - public static double getHydmax() - { - return hydmax; - } - - public static double getHydmin() - { - return hydmin; - } - - public static double[] getHyd() - { - return hyd; - } - - public static Hashtable getAAHash() - { - return aaHash; - } - - public static Hashtable 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) - { - Integer pog1 = (Integer) aaHash.get(A1); - Integer pog2 = (Integer) aaHash.get(A2); - int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()]; - - return pog; - } - - public static int getBLOSUM62(String A1, String A2) - { - int pog = 0; - - try - { - Integer pog1 = (Integer) aaHash.get(A1); - Integer pog2 = (Integer) aaHash.get(A2); - pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()]; - } - 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 codon) - { - Enumeration e = codonHash.keys(); - - while (e.hasMoreElements()) - { - String key = (String) e.nextElement(); - Vector tmp = (Vector) codonHash.get(key); - - if (tmp.contains(codon)) - { - return key; - } - } - - return null; - } - - public static Hashtable getChainColours() - { - return chainColours; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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 jalview.analysis.scoremodels.FeatureScoreModel; +import jalview.analysis.scoremodels.PIDScoreModel; +import jalview.api.analysis.ScoreModelI; + +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; + +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(); + + // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET) + public static final Map modifications = 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 ("*".equals(cdn)) + { + 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); + } + } + + static + { + modifications.put("MSE", "MET"); // Selenomethionine + // the rest tbc; from + // http://sourceforge.net/p/jmol/mailman/message/12833570/ + // modifications.put("CSE", "CYS"); // Selenocysteine + // modifications.put("PTR", "TYR"); // Phosphotyrosine + // modifications.put("SEP", "SER"); // Phosphoserine + // modifications.put("HYP", "PRO"); // 4-hydroxyproline + // modifications.put("5HP", "GLU"); // Pyroglutamic acid; 5-hydroxyproline + // modifications.put("PCA", "GLU"); // Pyroglutamic acid + // modifications.put("LYZ", "LYS"); // 5-hydroxylysine + } + + public static String getCanonicalAminoAcid(String aa) + { + String canonical = modifications.get(aa); + return canonical == null ? aa : canonical; + } + + /** + * 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; + } + + /** + * Returns the single letter code for a three letter code, or '0' if not known + * + * @param threeLetterCode + * not case sensitive + * @return + */ + public static char getSingleCharacterCode(String threeLetterCode) + { + if (threeLetterCode == null) + { + return '0'; + } + Integer index = ResidueProperties.aa3Hash.get(threeLetterCode + .toUpperCase()); + return index == null ? '0' : aa[index].charAt(0); + } +}