X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=67211cd5434f6a32dc8bb93f4610c7a74a855256;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=0a2c43e8d5ef4a6e77e4fc839e72c422a97415a7;hpb=f133411520d32ce26f766f8157c8d10139920140;p=jalview.git diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 0a2c43e..67211cd 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,1012 +1,1310 @@ - -/* Copyright (C) 1998 Michele Clamp -* -* 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, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. -*/ -package jalview.schemes; - -import java.awt.Color; -import java.util.*; -import jalview.jbgui.*; -import jalview.datamodel.*; - -public class ResidueProperties { - - //Stores residue codes/names and colours and other things - public static Hashtable aaHash = new Hashtable(); // stores the number value of the aa - public static Hashtable aa3Hash = new Hashtable(); - public static Hashtable aa2Triplet = new Hashtable(); - public static Hashtable nucleotideHash = 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("-", 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("C", new Integer(1)); - nucleotideHash.put("G", new Integer(2)); - nucleotideHash.put("T", new Integer(3)); - nucleotideHash.put("U", new Integer(4)); - } - - // These numbers should correspond to the indices in the Color hashes - public static Hashtable aaSpecialsHash = new Hashtable(); - static { - aaSpecialsHash.put("-", new Integer(23)); - aaSpecialsHash.put("*", new Integer(24)); - aaSpecialsHash.put(".", new Integer(25)); - aaSpecialsHash.put(" ", new Integer(26)); - } - - 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("R", "ARG"); - aa2Triplet.put("N", "ASN"); - aa2Triplet.put("D", "ASP"); - aa2Triplet.put("C", "CYS"); - aa2Triplet.put("Q", "GLN"); - aa2Triplet.put("E", "GLU"); - aa2Triplet.put("G", "GLY"); - aa2Triplet.put("H", "HIS"); - aa2Triplet.put("I", "ILE"); - aa2Triplet.put("L", "LEU"); - aa2Triplet.put("K", "LYS"); - aa2Triplet.put("M", "MET"); - aa2Triplet.put("F", "PHE"); - aa2Triplet.put("P", "PRO"); - aa2Triplet.put("S", "SER"); - aa2Triplet.put("T", "THR"); - aa2Triplet.put("W", "TRP"); - aa2Triplet.put("Y", "TYR"); - aa2Triplet.put("V", "VAL"); - } - - public static 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 Color midBlue = new Color(100,100,255); - public static 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 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 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 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 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 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 double helixmin = 0.57; - public static double helixmax = 1.51; - - public static 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 double strandmin = 0.37; - public static double strandmax = 1.7; - - public static 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 double turnmin = 0.47; - public static double turnmax = 1.56; - - public static 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 double buriedmin = 0.05; - public static double buriedmax = 4.6; - - // This is hydropathy index - // Kyte, J., and Doolittle, R.F., J. Mol. Biol. - // 1157, 105-132, 1982 - - public static 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 double getHydmax() { - return hydmax; - } - public static double getHydmin() { - return hydmin; - } - public static double[] getHyd() { - return hyd; - } - //public static final double hydmax = 1.38; - //public static final double hydmin = -2.53; - - static final int[][] BLOSUM62 = { - //A R N D C Q E G H I L K M F P S T W Y V B Z X - - { 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 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 = { - // C T A G - - { 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 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 Color[] pidColours = { - midBlue, - new Color(153,153,255), - // Color.lightGray, - new Color(204,204,255), - }; - public static float[] pidThresholds = { - 80, - 60, - 40, - } ; - private ResidueProperties() {} - - 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 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 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); - } - public static Hashtable getChainColours() { - return chainColours; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . + */ +package jalview.schemes; + +import java.util.*; + +import java.awt.*; + +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 Hashtable aa3Hash = new Hashtable(); + + public static final Hashtable aa2Triplet = new Hashtable(); + + public static final Hashtable nucleotideName = new Hashtable(); + + 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 + } + + 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"); + } + + 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 + Color.white, // X + Color.white, // R + Color.white, // Y + Color.white, // N + 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 + */ + static final int[][] DNA = + { + { 10, -8, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // C + { -8, 10, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // T + { -8, -8, 10, -8, 1, 0, 0, 0, 0, 0, 1 }, // A + { -8, -8, -8, 10, 1, 0, 0, 0, 0, 0, 1 }, // G + { 1, 1, 1, 1, 10, 0, 0, 0, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 10, 0, 0, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 10, 0, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 0, 10, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 0, 0, 10, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 0, 0, 0, 10, 1 }, // - + { 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 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"); + } + + // 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); + } + + private ResidueProperties() + { + } + + public static double getHydmax() + { + return hydmax; + } + + public static double getHydmin() + { + return hydmin; + } + + public static double[] getHyd() + { + return hyd; + } + + 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) + { + 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) + { + 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"; + } + 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 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) + { + return (ScoreMatrix) val; + } + return null; + } + + 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(); + } + + // 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 +}