-\r
-/* Copyright (C) 1998 Michele Clamp\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc, 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
-*/\r
-package jalview.schemes;\r
-\r
-import java.awt.Color;\r
-import java.util.*;\r
-import jalview.jbgui.*;\r
-import jalview.datamodel.*;\r
-\r
-public class ResidueProperties {\r
-\r
- //Stores residue codes/names and colours and other things\r
- public static Hashtable aaHash = new Hashtable(); // stores the number value of the aa\r
- public static Hashtable aa3Hash = new Hashtable();\r
- public static Hashtable aa2Triplet = new Hashtable();\r
-\r
- static {\r
- aaHash.put("A", new Integer(0));\r
- aaHash.put("R", new Integer(1));\r
- aaHash.put("N", new Integer(2));\r
- aaHash.put("D", new Integer(3));\r
- aaHash.put("C", new Integer(4));\r
- aaHash.put("Q", new Integer(5));\r
- aaHash.put("E", new Integer(6));\r
- aaHash.put("G", new Integer(7));\r
- aaHash.put("H", new Integer(8));\r
- aaHash.put("I", new Integer(9));\r
- aaHash.put("L", new Integer(10));\r
- aaHash.put("K", new Integer(11));\r
- aaHash.put("M", new Integer(12));\r
- aaHash.put("F", new Integer(13));\r
- aaHash.put("P", new Integer(14));\r
- aaHash.put("S", new Integer(15));\r
- aaHash.put("T", new Integer(16));\r
- aaHash.put("W", new Integer(17));\r
- aaHash.put("Y", new Integer(18));\r
- aaHash.put("V", new Integer(19));\r
- aaHash.put("B", new Integer(20));\r
- aaHash.put("Z", new Integer(21));\r
- aaHash.put("X", new Integer(22));\r
- aaHash.put("-", new Integer(23));\r
- aaHash.put("*", new Integer(23));\r
- aaHash.put(".", new Integer(23));\r
- aaHash.put(" ", new Integer(23));\r
- }\r
-\r
- // These numbers should correspond to the indices in the Color hashes\r
- public static Hashtable aaSpecialsHash = new Hashtable();\r
- static {\r
- aaSpecialsHash.put("-", new Integer(23));\r
- aaSpecialsHash.put("*", new Integer(24));\r
- aaSpecialsHash.put(".", new Integer(25));\r
- aaSpecialsHash.put(" ", new Integer(26));\r
- }\r
-\r
- static {\r
- aa3Hash.put("ALA", new Integer(0));\r
- aa3Hash.put("ARG", new Integer(1));\r
- aa3Hash.put("ASN", new Integer(2));\r
- aa3Hash.put("ASP", new Integer(3)); //D\r
- aa3Hash.put("CYS", new Integer(4));\r
- aa3Hash.put("GLN", new Integer(5)); //Q\r
- aa3Hash.put("GLU", new Integer(6)); // E\r
- aa3Hash.put("GLY", new Integer(7));\r
- aa3Hash.put("HIS", new Integer(8));\r
- aa3Hash.put("ILE", new Integer(9));\r
- aa3Hash.put("LEU", new Integer(10));\r
- aa3Hash.put("LYS", new Integer(11));\r
- aa3Hash.put("MET", new Integer(12));\r
- aa3Hash.put("PHE", new Integer(13));\r
- aa3Hash.put("PRO", new Integer(14));\r
- aa3Hash.put("SER", new Integer(15));\r
- aa3Hash.put("THR", new Integer(16));\r
- aa3Hash.put("TRP", new Integer(17));\r
- aa3Hash.put("TYR", new Integer(18));\r
- aa3Hash.put("VAL", new Integer(19));\r
- aa3Hash.put("B", new Integer(20));\r
- aa3Hash.put("Z", new Integer(21));\r
- aa3Hash.put("X", new Integer(22));\r
- aa3Hash.put("-", new Integer(23));\r
- aa3Hash.put("*", new Integer(23));\r
- aa3Hash.put(".", new Integer(23));\r
- aa3Hash.put(" ", new Integer(23));\r
- }\r
-\r
- static{\r
- aa2Triplet.put("A", "ALA");\r
- aa2Triplet.put("R", "ARG");\r
- aa2Triplet.put("N", "ASN");\r
- aa2Triplet.put("D", "ASP");\r
- aa2Triplet.put("C", "CYS");\r
- aa2Triplet.put("Q", "GLN");\r
- aa2Triplet.put("E", "GLU");\r
- aa2Triplet.put("G", "GLY");\r
- aa2Triplet.put("H", "HIS");\r
- aa2Triplet.put("I", "ILE");\r
- aa2Triplet.put("L", "LEU");\r
- aa2Triplet.put("K", "LYS");\r
- aa2Triplet.put("M", "MET");\r
- aa2Triplet.put("F", "PHE");\r
- aa2Triplet.put("P", "PRO");\r
- aa2Triplet.put("S", "SER");\r
- aa2Triplet.put("T", "THR");\r
- aa2Triplet.put("W", "TRP");\r
- aa2Triplet.put("Y", "TYR");\r
- aa2Triplet.put("V", "VAL");\r
- }\r
-\r
- public static String aa[] = {\r
- "A","R","N","D","C","Q","E","G","H","I","L","K","M","F","P","S","T","W","Y","V","B","Z","X","_","*","."," "\r
- };\r
- public static Color midBlue = new Color(100,100,255);\r
- public static Vector scaleColours = new Vector();\r
- static {\r
- scaleColours.addElement(new Color(114,0,147));\r
- scaleColours.addElement(new Color(156,0,98));\r
- scaleColours.addElement(new Color(190,0,0));\r
- scaleColours.addElement(Color.red);\r
- scaleColours.addElement(new Color(255,125,0));\r
- scaleColours.addElement(Color.orange);\r
- scaleColours.addElement(new Color(255,194,85));\r
- scaleColours.addElement(Color.yellow);\r
- scaleColours.addElement(new Color(255,255,181));\r
- scaleColours.addElement(Color.white);\r
- }\r
-\r
- public static Color[] taylor = {\r
- new Color(204,255,0), // A Greenish-yellowy-yellow\r
- new Color(0,0,255), // R Blueish-bluey-blue\r
- new Color(204,0,255), // N Blueish-reddy-blue\r
- new Color(255,0,0), // D Reddish-reddy-red\r
- new Color(255,255,0), // C Yellowish-yellowy-yellow\r
- new Color(255,0,204), // Q Reddish-bluey-red\r
- new Color(255,0,102), // E Blueish-reddy-red\r
- new Color(255,153,0), // G Yellowy-reddy-yellow\r
- new Color(0,102,255), // H Greenish-bluey-blue\r
- new Color(102,255,0), // I Greenish-yellowy-green\r
- new Color(51,255,0), // L Yellowish-greeny-green\r
- new Color(102,0,255), // K Reddish-bluey-blue\r
- new Color(0,255,0), // M Greenish-greeny-green\r
- new Color(0,255,102), // F Blueish-greeny-green\r
- new Color(255,204,0), // P Reddish-yellowy-yellow\r
- new Color(255,51,0), // S Yellowish-reddy-red\r
- new Color(255,102,0), // T Reddish-yellowy-red\r
- new Color(0,204,255), // W Blueish-greeny-green\r
- new Color(0,255,204), // Y Greenish-bluey-green\r
- new Color(153,255,0), // V Yellowish-greeny-yellow\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white // .\r
- };\r
-\r
- public static Color[] color = {\r
- Color.pink, // A\r
- midBlue, // R\r
- Color.green, // N\r
- Color.red, // D\r
- Color.yellow, // C\r
- Color.green, // Q\r
- Color.red, // E\r
- Color.magenta, // G\r
- Color.red, // H\r
- Color.pink, // I\r
- Color.pink, // L\r
- midBlue, // K\r
- Color.pink, // M\r
- Color.orange, // F\r
- Color.magenta, // P\r
- Color.green, // S\r
- Color.green, // T\r
- Color.orange, // W\r
- Color.orange, // Y\r
- Color.pink, // V\r
- Color.white, // B\r
- Color.white, // Z\r
- Color.white, // X\r
- Color.white, // -\r
- Color.white, // *\r
- Color.white, // .\r
- Color.white // ' '\r
- };\r
-\r
- // Dunno where I got these numbers from\r
- public static double[] hyd2 = {\r
- 0.62, //A\r
- 0.29, //R\r
- -0.90, //N\r
- -0.74, //D\r
- 1.19, //C\r
- 0.48, //Q\r
- -0.40, //E\r
- 1.38, //G\r
- -1.50, //H\r
- 1.06, //I\r
- 0.64, //L\r
- -0.78, //K\r
- 0.12, //M\r
- -0.85, //F\r
- -2.53, //P\r
- -0.18, //S\r
- -0.05, //T\r
- 1.08, //W\r
- 0.81, //Y\r
- 0.0, //V\r
- 0.26, //B\r
- 0.0, //Z\r
- 0.0 //X\r
- };\r
- public static double[] helix = {\r
- 1.42,\r
- 0.98,\r
- 0.67,\r
- 1.01,\r
- 0.70,\r
- 1.11,\r
- 1.51,\r
- 0.57,\r
- 1.00,\r
- 1.08,\r
- 1.21,\r
- 1.16,\r
- 1.45,\r
- 1.13,\r
- 0.57,\r
- 0.77,\r
- 0.83,\r
- 1.08,\r
- 0.69,\r
- 1.06,\r
- 0.84,\r
- 1.31,\r
- 1.00,\r
- 0.0\r
- };\r
- public static double helixmin = 0.57;\r
- public static double helixmax = 1.51;\r
-\r
- public static double[] strand = {\r
- 0.83,0.93,0.89,0.54,1.19,1.10,0.37,\r
- 0.75,0.87,1.60,1.30,0.74,1.05,1.38,0.55,\r
- 0.75,1.19,1.37,1.47,1.70,0.72,0.74,1.0,0.0};\r
-\r
- public static double strandmin = 0.37;\r
- public static double strandmax = 1.7;\r
-\r
- public static double[] turn = {\r
- 0.66,0.95,1.56,1.46,1.19,0.98,0.74,\r
- 1.56,0.95,0.47,0.59,1.01,0.60,0.60,1.52,\r
- 1.43,0.96,0.96,1.14,0.50,1.51,0.86,1.00,0,0};\r
-\r
- public static double turnmin = 0.47;\r
- public static double turnmax = 1.56;\r
-\r
- public static double[] buried = {\r
- 1.7,\r
- 0.1,\r
- 0.4,\r
- 0.4,\r
- 4.6,\r
- 0.3,\r
- 0.3,\r
- 1.8,\r
- 0.8,\r
- 3.1,\r
- 2.4,\r
- 0.05,\r
- 1.9,\r
- 2.2,\r
- 0.6,\r
- 0.8,0.7,1.6,0.5,2.9,0.4,0.3,\r
- 1.358,\r
- 0.00\r
- };\r
-\r
- public static double buriedmin = 0.05;\r
- public static double buriedmax = 4.6;\r
-\r
- // This is hydropathy index\r
- // Kyte, J., and Doolittle, R.F., J. Mol. Biol.\r
- // 1157, 105-132, 1982\r
-\r
- public static double hyd[] = {\r
- 1.8,\r
- -4.5,\r
- -3.5,\r
- -3.5,\r
- 2.5,\r
- -3.5,\r
- -3.5,\r
- -0.4,\r
- -3.2,\r
- 4.5,\r
- 3.8,\r
- -3.9,\r
- 1.9,\r
- 2.8,\r
- -1.6,\r
- -0.8,\r
- -0.7,\r
- -0.9,\r
- -1.3,\r
- 4.2,\r
- -3.5,\r
- -3.5,\r
- -0.49,\r
- 0.0\r
- };\r
-\r
- public static final double hydmax = 4.5;\r
- public static final double hydmin = -3.9;\r
-\r
- public static double getHydmax() {\r
- return hydmax;\r
- }\r
- public static double getHydmin() {\r
- return hydmin;\r
- }\r
- public static double[] getHyd() {\r
- return hyd;\r
- }\r
- //public static final double hydmax = 1.38;\r
- //public static final double hydmin = -2.53;\r
-\r
- static final int[][] BLOSUM62 = {\r
- //A R N D C Q E G H I L K M F P S T W Y V B Z X -\r
- { 4 ,-1, -2 ,-2 , 0 ,-1 ,-1 , 0 ,-2 ,-1 ,-1 ,-1 ,-1 ,-2 ,-1 , 1 , 0 ,-3 ,-2 , 0 ,-2, -1 , 0 ,-4},\r
- {-1 , 5 , 0 ,-2 ,-3 , 1 , 0 ,-2 , 0 ,-3 ,-2 , 2 ,-1 ,-3 ,-2 ,-1 ,-1 ,-3 ,-2 ,-3 ,-1 , 0 ,-1 ,-4 },\r
- {-2 , 0 , 6 , 1 ,-3 , 0 , 0 , 0 , 1 ,-3 ,-3 , 0 ,-2 ,-3 ,-2 , 1 , 0 ,-4 ,-2 ,-3 , 3 , 0 ,-1 ,-4 },\r
- {-2 ,-2 , 1 , 6 ,-3 , 0 , 2 ,-1 ,-1 ,-3 ,-4 ,-1 ,-3 ,-3 ,-1 , 0 ,-1 ,-4 ,-3 ,-3 , 4 , 1 ,-1 ,-4 },\r
- { 0 , 3 ,-3 ,-3 , 9 ,-3 ,-4 ,-3 ,-3 ,-1 ,-1 ,-3 ,-1 ,-2 ,-3 ,-1 ,-1 ,-2 ,-2 ,-1 ,-3 ,-3 ,-2 ,-4 },\r
- {-1 , 1 , 0 , 0 ,-3 , 5 , 2 ,-2 , 0 ,-3 ,-2 , 1 , 0 ,-3 ,-1 , 0 ,-1 ,-2 ,-1 ,-2 , 0 , 3 ,-1 ,-4 },\r
- {-1 , 0 , 0 , 2 ,-4 , 2 , 5 ,-2 , 0 ,-3 ,-3 , 1 ,-2 ,-3 ,-1 , 0 ,-1 ,-3 ,-2 ,-2 , 1 , 4 ,-1 ,-4 },\r
- { 0 ,-2 , 0 ,-1 ,-3 ,-2 ,-2 , 6 ,-2 ,-4 ,-4 ,-2 ,-3 ,-3 ,-2 , 0 ,-2 ,-2 ,-3 ,-3 ,-1 ,-2 ,-1 ,-4 },\r
- {-2 , 0 , 1 ,-1 ,-3 , 0 , 0 ,-2 , 8 ,-3 ,-3 ,-1 ,-2 ,-1 ,-2 ,-1 ,-2 ,-2 , 2 ,-3 , 0 , 0 ,-1 ,-4 },\r
- {-1 ,-3 ,-3 ,-3 ,-1 ,-3 ,-3 ,-4 ,-3 , 4 , 2 ,-3 , 1 , 0 ,-3 ,-2 ,-1 ,-3 ,-1 , 3 ,-3 ,-3 ,-1 ,-4 },\r
- {-1 ,-2 ,-3 ,-4 ,-1 ,-2 ,-3 ,-4 ,-3 , 2 , 4 ,-2 , 2 , 0 ,-3 ,-2 ,-1 ,-2 ,-1 , 1 ,-4 ,-3 ,-1 ,-4 },\r
- {-1 , 2 , 0 ,-1 ,-3 , 1 , 1 ,-2 ,-1 ,-3 ,-2 , 5 ,-1 ,-3 ,-1 , 0 ,-1 ,-3 ,-2 ,-2 , 0 , 1 ,-1 ,-4 },\r
- {-1 ,-1 ,-2 ,-3 ,-1 , 0 ,-2 ,-3 ,-2 , 1 , 2 ,-1 , 5 , 0 ,-2 ,-1 ,-1 ,-1 ,-1 , 1 ,-3 ,-1 ,-1 ,-4 },\r
- {-2 ,-3 ,-3 ,-3 ,-2 ,-3 ,-3 ,-3 ,-1 , 0 , 0 ,-3 , 0 , 6 ,-4 ,-2 ,-2 , 1 , 3 ,-1 ,-3 ,-3 ,-1 ,-4 },\r
- {-1 ,-2 ,-2 ,-1 ,-3 ,-1 ,-1 ,-2 ,-2 ,-3 ,-3 ,-1 ,-2 ,-4 , 7 ,-1 ,-1 ,-4 ,-3 ,-2 ,-2 ,-1 ,-2 ,-4 },\r
- { 1 ,-1 , 1 , 0 ,-1 , 0 , 0 , 0 ,-1 ,-2 ,-2 , 0 ,-1 ,-2 ,-1 , 4 , 1 ,-3 ,-2 ,-2 , 0 , 0 , 0 ,-4 },\r
- { 0 ,-1 , 0 ,-1 ,-1 ,-1 ,-1 ,-2 ,-2 ,-1 ,-1 ,-1 ,-1 ,-2 ,-1 , 1 , 5 ,-2 ,-2 , 0 ,-1 ,-1 , 0 ,-4 },\r
- {-3 ,-3 ,-4 ,-4 ,-2 ,-2 ,-3 ,-2 ,-2 ,-3 ,-2 ,-3 ,-1 , 1 ,-4 ,-3 ,-2 ,11 , 2 ,-3 ,-4 ,-3 ,-2 ,-4 },\r
- {-2 ,-2 ,-2 ,-3 ,-2 ,-1 ,-2 ,-3 , 2 ,-1 ,-1 ,-2 ,-1 , 3 ,-3 ,-2 ,-2 , 2 , 7 ,-1 ,-3 ,-2 ,-1 ,-4 },\r
- { 0 ,-3 ,-3 ,-3 ,-1 ,-2 ,-2 ,-3 ,-3 , 3 , 1 ,-2 , 1 ,-1 ,-2 ,-2 , 0 ,-3 ,-1 , 4 ,-3 ,-2 ,-1 ,-4 },\r
- {-2 ,-1 , 3 , 4 ,-3 , 0 , 1 ,-1 , 0 ,-3 ,-4 , 0 ,-3 ,-3 ,-2 , 0 ,-1 ,-4 ,-3 ,-3 , 4 , 1 ,-1 ,-4 },\r
- {-1 , 0 , 0 , 1 ,-3 , 3 , 4 ,-2 , 0 ,-3 ,-3 , 1 ,-1 ,-3 ,-1 , 0 ,-1 ,-3 ,-2 ,-2 , 1 , 4 ,-1 ,-4 },\r
- { 0 ,-1 ,-1 ,-1 ,-2 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-1 ,-2 , 0 , 0 ,-2 ,-1 ,-1 ,-1 ,-1 ,-1 ,-4 },\r
- {-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 ,-4 , 1 },\r
- };\r
- static final int[][] PAM250 = {\r
- { 2,-2 ,0 ,0,-2 ,0 ,0 ,1,-1,-1,-2,-1,-1,-3 ,1 ,1 ,1,-6,-3 ,0 ,0 ,0 ,0,-8},\r
- { -2 ,6 ,0,-1,-4 ,1,-1,-3 ,2,-2,-3 ,3 ,0,-4 ,0 ,0,-1 ,2,-4,-2,-1 ,0,-1,-8},\r
- { 0 ,0 ,2 ,2,-4 ,1 ,1 ,0 ,2,-2,-3 ,1,-2,-3 ,0 ,1 ,0,-4,-2,-2 ,2 ,1 ,0,-8},\r
- { 0,-1 ,2 ,4,-5 ,2 ,3 ,1 ,1,-2,-4 ,0,-3,-6,-1 ,0 ,0,-7,-4,-2 ,3 ,3,-1,-8},\r
- { -2,-4,-4,-5,12,-5,-5,-3,-3,-2,-6,-5,-5,-4,-3 ,0,-2,-8 ,0,-2,-4,-5,-3,-8},\r
- { 0 ,1 ,1 ,2,-5 ,4 ,2,-1 ,3,-2,-2 ,1,-1,-5 ,0,-1,-1,-5,-4,-2 ,1 ,3,-1,-8},\r
- { 0,-1 ,1 ,3,-5 ,2 ,4 ,0 ,1,-2,-3 ,0,-2,-5,-1 ,0 ,0,-7,-4,-2 ,3 ,3,-1,-8},\r
- { 1,-3 ,0 ,1,-3,-1 ,0 ,5,-2,-3,-4,-2,-3,-5 ,0 ,1 ,0,-7,-5,-1 ,0 ,0,-1,-8},\r
- { -1 ,2 ,2 ,1,-3 ,3 ,1,-2 ,6,-2,-2 ,0,-2,-2 ,0,-1,-1,-3 ,0,-2 ,1 ,2,-1,-8},\r
- { -1,-2,-2,-2,-2,-2,-2,-3,-2 ,5 ,2,-2 ,2 ,1,-2,-1 ,0,-5,-1 ,4,-2,-2,-1,-8},\r
- { -2,-3,-3,-4,-6,-2,-3,-4,-2 ,2 ,6,-3 ,4 ,2,-3,-3,-2,-2,-1 ,2,-3,-3,-1,-8},\r
- { -1 ,3 ,1 ,0,-5 ,1 ,0,-2 ,0,-2,-3 ,5 ,0,-5,-1 ,0 ,0,-3,-4,-2 ,1 ,0,-1,-8},\r
- { -1 ,0,-2,-3,-5,-1,-2,-3,-2 ,2 ,4 ,0 ,6 ,0,-2,-2,-1,-4,-2 ,2,-2,-2,-1,-8},\r
- { -3,-4,-3,-6,-4,-5,-5,-5,-2 ,1 ,2,-5 ,0 ,9,-5,-3,-3 ,0 ,7,-1,-4,-5,-2,-8},\r
- { 1 ,0 ,0,-1,-3 ,0,-1 ,0 ,0,-2,-3,-1,-2,-5 ,6 ,1 ,0,-6,-5,-1,-1 ,0,-1,-8},\r
- { 1 ,0 ,1 ,0 ,0,-1 ,0 ,1,-1,-1,-3 ,0,-2,-3 ,1 ,2 ,1,-2,-3,-1 ,0 ,0 ,0,-8},\r
- { 1,-1 ,0 ,0,-2,-1 ,0 ,0,-1 ,0,-2 ,0,-1,-3 ,0 ,1 ,3,-5,-3 ,0 ,0,-1 ,0,-8},\r
- { -6 ,2,-4,-7,-8,-5,-7,-7,-3,-5,-2,-3,-4 ,0,-6,-2,-5,17 ,0,-6,-5,-6,-4,-8},\r
- { -3,-4,-2,-4 ,0,-4,-4,-5 ,0,-1,-1,-4,-2 ,7,-5,-3,-3 ,0,10,-2,-3,-4,-2,-8},\r
- { 0,-2,-2,-2,-2,-2,-2,-1,-2 ,4 ,2,-2 ,2,-1,-1,-1 ,0,-6,-2 ,4,-2,-2,-1,-8},\r
- { 0,-1 ,2 ,3,-4 ,1 ,3 ,0 ,1,-2,-3 ,1,-2,-4,-1 ,0 ,0,-5,-3,-2 ,3 ,2,-1,-8},\r
- { 0 ,0 ,1 ,3,-5 ,3 ,3 ,0 ,2,-2,-3 ,0,-2,-5 ,0 ,0,-1,-6,-4,-2 ,2 ,3,-1,-8},\r
- { 0,-1 ,0,-1,-3,-1,-1,-1,-1,-1,-1,-1,-1,-2,-1 ,0 ,0,-4,-2,-1,-1,-1,-1,-8},\r
- { -8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8 ,1},\r
- };\r
-\r
- public static Hashtable ssHash = new Hashtable(); // stores the number value of the aa\r
-\r
- static {\r
- ssHash.put("H", Color.magenta);\r
- ssHash.put("E", Color.yellow);\r
- ssHash.put("-", Color.white);\r
- ssHash.put(".", Color.white);\r
- ssHash.put("S", Color.cyan);\r
- ssHash.put("T", Color.blue);\r
- ssHash.put("G", Color.pink);\r
- ssHash.put("I", Color.pink);\r
- ssHash.put("B", Color.yellow);\r
- }\r
- static final int[][] DNA = {\r
- // C T A G -\r
- { 5,-4,-4,-4, 1},// C\r
- {-4, 5,-4,-4, 1},// T\r
- {-4,-4, 5,-4, 1},// A\r
- {-4,-4,-4, 5, 1},// G\r
- { 1, 1, 1, 1, 1},// -\r
- };\r
- public static Hashtable getAAHash() {\r
- return aaHash;\r
- }\r
- public static Hashtable getAA3Hash() {\r
- return aa3Hash;\r
- }\r
- public static int[][] getDNA() {\r
- return ResidueProperties.DNA;\r
- }\r
- public static int[][] getBLOSUM62() {\r
- return ResidueProperties.BLOSUM62;\r
- }\r
- public static int getPAM250(String A1, String A2) {\r
- Integer pog1 = (Integer)aaHash.get(A1);\r
- Integer pog2 = (Integer)aaHash.get(A2);\r
- int pog = ResidueProperties.PAM250[pog1.intValue()][pog2.intValue()];\r
- return pog ;\r
- }\r
- public static int getBLOSUM62(String A1, String A2) {\r
- int pog = 0;\r
- try {\r
- Integer pog1 = (Integer)aaHash.get(A1);\r
- Integer pog2 = (Integer)aaHash.get(A2);\r
- pog = ResidueProperties.BLOSUM62[pog1.intValue()][pog2.intValue()];\r
- } catch (Exception e) {\r
- //System.out.println("Unknown residue in " + A1 + " " + A2);\r
- }\r
- return pog ;\r
- }\r
-\r
- public static Color[] pidColours = {\r
- midBlue,\r
- new Color(153,153,255),\r
- // Color.lightGray,\r
- new Color(204,204,255),\r
- };\r
- public static float[] pidThresholds = {\r
- 80,\r
- 60,\r
- 40,\r
- } ;\r
- private ResidueProperties() {}\r
-\r
- public static Hashtable codonHash = new Hashtable();\r
-\r
- public static Vector Lys = new Vector();\r
- public static Vector Asn = new Vector();\r
- public static Vector Gln = new Vector();\r
- public static Vector His = new Vector();\r
- public static Vector Glu = new Vector();\r
- public static Vector Asp = new Vector();\r
- public static Vector Tyr = new Vector();\r
- public static Vector Thr = new Vector();\r
- public static Vector Pro = new Vector();\r
- public static Vector Ala = new Vector();\r
- public static Vector Ser = new Vector();\r
- public static Vector Arg = new Vector();\r
- public static Vector Gly = new Vector();\r
- public static Vector Trp = new Vector();\r
- public static Vector Cys = new Vector();\r
- public static Vector Ile = new Vector();\r
- public static Vector Met = new Vector();\r
- public static Vector Leu = new Vector();\r
- public static Vector Val = new Vector();\r
- public static Vector Phe = new Vector();\r
- public static Vector STOP = new Vector();\r
-\r
- static {\r
- codonHash.put("K",Lys);\r
- codonHash.put("N",Asn);\r
- codonHash.put("Q",Gln);\r
- codonHash.put("H",His);\r
- codonHash.put("E",Glu);\r
- codonHash.put("D",Asp);\r
- codonHash.put("Y",Tyr);\r
- codonHash.put("T",Thr);\r
- codonHash.put("P",Pro);\r
- codonHash.put("A",Ala);\r
- codonHash.put("S",Ser);\r
- codonHash.put("R",Arg);\r
- codonHash.put("G",Gly);\r
- codonHash.put("W",Trp);\r
- codonHash.put("C",Cys);\r
- codonHash.put("I",Ile);\r
- codonHash.put("M",Met);\r
- codonHash.put("L",Leu);\r
- codonHash.put("V",Val);\r
- codonHash.put("F",Phe);\r
- codonHash.put("STOP",STOP);\r
- }\r
-\r
- public static Vector getCodons(String res) {\r
- if (codonHash.containsKey(res))\r
- return (Vector)codonHash.get(res);\r
- return null;\r
- }\r
-\r
- public static String codonTranslate(String codon) {\r
- Enumeration e = codonHash.keys();\r
- while (e.hasMoreElements()) {\r
- String key = (String)e.nextElement();\r
- Vector tmp = (Vector)codonHash.get(key);\r
- if (tmp.contains(codon)) {\r
- return key;\r
- }\r
- }\r
- return null;\r
- }\r
- public static Hashtable codonHash2 = new Hashtable();\r
- static {\r
- codonHash2.put("AAA","K");\r
- codonHash2.put("AAG","K");\r
- codonHash2.put("AAC","N");\r
- codonHash2.put("AAT","N");\r
-\r
- codonHash2.put("CAA","E");\r
- codonHash2.put("CAG","E");\r
- codonHash2.put("CAC","H");\r
- codonHash2.put("CAT","H");\r
-\r
- codonHash2.put("GAA","Q");\r
- codonHash2.put("GAG","Q");\r
- codonHash2.put("GAC","D");\r
- codonHash2.put("GAT","D");\r
-\r
- codonHash2.put("TAC","Y");\r
- codonHash2.put("TAT","Y");\r
-\r
- codonHash2.put("ACA","T");\r
- codonHash2.put("AAG","T");\r
- codonHash2.put("ACC","T");\r
- codonHash2.put("ACT","T");\r
-\r
- codonHash2.put("CCA","P");\r
- codonHash2.put("CCG","P");\r
- codonHash2.put("CCC","P");\r
- codonHash2.put("CCT","P");\r
-\r
- codonHash2.put("GCA","A");\r
- codonHash2.put("GCG","A");\r
- codonHash2.put("GCC","A");\r
- codonHash2.put("GCT","A");\r
-\r
- codonHash2.put("TCA","S");\r
- codonHash2.put("TCG","S");\r
- codonHash2.put("TCC","S");\r
- codonHash2.put("TCT","S");\r
- codonHash2.put("AGC","S");\r
- codonHash2.put("AGT","S");\r
-\r
- codonHash2.put("AGA","R");\r
- codonHash2.put("AGG","R");\r
- codonHash2.put("CGA","R");\r
- codonHash2.put("CGG","R");\r
- codonHash2.put("CGC","R");\r
- codonHash2.put("CGT","R");\r
-\r
- codonHash2.put("GGA","G");\r
- codonHash2.put("GGG","G");\r
- codonHash2.put("GGC","G");\r
- codonHash2.put("GGT","G");\r
-\r
- codonHash2.put("TGA","*");\r
- codonHash2.put("TAA","*");\r
- codonHash2.put("TAG","*");\r
-\r
- codonHash2.put("TGG","W");\r
-\r
- codonHash2.put("TGC","C");\r
- codonHash2.put("TGT","C");\r
-\r
- codonHash2.put("ATA","I");\r
- codonHash2.put("ATC","I");\r
- codonHash2.put("ATT","I");\r
-\r
- codonHash2.put("ATG","M");\r
-\r
- codonHash2.put("CTA","L");\r
- codonHash2.put("CTG","L");\r
- codonHash2.put("CTC","L");\r
- codonHash2.put("CTT","L");\r
- codonHash2.put("TTA","L");\r
- codonHash2.put("TTG","L");\r
-\r
- codonHash2.put("GTA","V");\r
- codonHash2.put("GTG","V");\r
- codonHash2.put("GTC","V");\r
- codonHash2.put("GTT","V");\r
-\r
- codonHash2.put("TTC","F");\r
- codonHash2.put("TTT","F");\r
-\r
- }\r
-\r
- static {\r
- Lys.addElement("AAA");\r
- Lys.addElement("AAG");\r
- Asn.addElement("AAC");\r
- Asn.addElement("AAT");\r
-\r
- Gln.addElement("CAA");\r
- Gln.addElement("CAG");\r
- His.addElement("CAC");\r
- His.addElement("CAT");\r
-\r
- Glu.addElement("GAA");\r
- Glu.addElement("GAG");\r
- Asp.addElement("GAC");\r
- Asp.addElement("GAT");\r
-\r
- Tyr.addElement("TAC");\r
- Tyr.addElement("TAT");\r
-\r
- Thr.addElement("ACA");\r
- Thr.addElement("ACG");\r
- Thr.addElement("ACC");\r
- Thr.addElement("ACT");\r
-\r
- Pro.addElement("CCA");\r
- Pro.addElement("CCG");\r
- Pro.addElement("CCC");\r
- Pro.addElement("CCT");\r
-\r
- Ala.addElement("GCA");\r
- Ala.addElement("GCG");\r
- Ala.addElement("GCC");\r
- Ala.addElement("GCT");\r
-\r
- Ser.addElement("TCA");\r
- Ser.addElement("TCG");\r
- Ser.addElement("TCC");\r
- Ser.addElement("TCT");\r
- Ser.addElement("AGC");\r
- Ser.addElement("AGT");\r
-\r
- Arg.addElement("AGA");\r
- Arg.addElement("AGG");\r
- Arg.addElement("CGA");\r
- Arg.addElement("CGG");\r
- Arg.addElement("CGC");\r
- Arg.addElement("CGT");\r
-\r
- Gly.addElement("GGA");\r
- Gly.addElement("GGG");\r
- Gly.addElement("GGC");\r
- Gly.addElement("GGT");\r
-\r
- STOP.addElement("TGA");\r
- STOP.addElement("TAA");\r
- STOP.addElement("TAG");\r
-\r
- Trp.addElement("TGG");\r
-\r
- Cys.addElement("TGC");\r
- Cys.addElement("TGT");\r
-\r
- Ile.addElement("ATA");\r
- Ile.addElement("ATC");\r
- Ile.addElement("ATT");\r
-\r
- Met.addElement("ATG");\r
-\r
- Leu.addElement("CTA");\r
- Leu.addElement("CTG");\r
- Leu.addElement("CTC");\r
- Leu.addElement("CTT");\r
- Leu.addElement("TTA");\r
- Leu.addElement("TTG");\r
-\r
- Val.addElement("GTA");\r
- Val.addElement("GTG");\r
- Val.addElement("GTC");\r
- Val.addElement("GTT");\r
-\r
- Phe.addElement("TTC");\r
- Phe.addElement("TTT");\r
- }\r
-\r
- public static Color[][] groupColors = {\r
- {Color.red,Color.red.brighter(),Color.red.brighter().brighter()},\r
- {Color.orange,Color.orange.brighter(),Color.orange.brighter().brighter()},\r
- {Color.green,Color.green.brighter(),Color.green.brighter().brighter()},\r
- {Color.blue,Color.blue.brighter(),Color.blue.brighter().brighter()},\r
- {Color.magenta,Color.magenta.brighter(),Color.magenta.brighter().brighter()},\r
- {Color.cyan,Color.cyan.brighter(),Color.cyan.brighter().brighter()},\r
- {Color.pink,Color.pink.brighter(),Color.pink.brighter().brighter()},\r
-\r
- };\r
-\r
-\r
-\r
- //Stores residue codes/names and colours and other things\r
- public static Hashtable propHash = new Hashtable();\r
- public static Hashtable hydrophobic = new Hashtable();\r
- public static Hashtable polar = new Hashtable();\r
- public static Hashtable small = new Hashtable();\r
- public static Hashtable positive = new Hashtable();\r
- public static Hashtable negative = new Hashtable();\r
- public static Hashtable charged = new Hashtable();\r
- public static Hashtable aromatic = new Hashtable();\r
- public static Hashtable aliphatic = new Hashtable();\r
- public static Hashtable tiny = new Hashtable();\r
- public static Hashtable proline = new Hashtable();\r
-\r
- static {\r
- hydrophobic.put("I",new Integer(1));\r
- hydrophobic.put("L",new Integer(1));\r
- hydrophobic.put("V",new Integer(1));\r
- hydrophobic.put("C",new Integer(1));\r
- hydrophobic.put("A",new Integer(1));\r
- hydrophobic.put("G",new Integer(1));\r
- hydrophobic.put("M",new Integer(1));\r
- hydrophobic.put("F",new Integer(1));\r
- hydrophobic.put("Y",new Integer(1));\r
- hydrophobic.put("W",new Integer(1));\r
- hydrophobic.put("H",new Integer(1));\r
- hydrophobic.put("K",new Integer(1));\r
- hydrophobic.put("X",new Integer(1));\r
- hydrophobic.put("-",new Integer(1));\r
- hydrophobic.put("*",new Integer(1));\r
- hydrophobic.put("R",new Integer(0));\r
- hydrophobic.put("E",new Integer(0));\r
- hydrophobic.put("Q",new Integer(0));\r
- hydrophobic.put("D",new Integer(0));\r
- hydrophobic.put("N",new Integer(0));\r
- hydrophobic.put("S",new Integer(0));\r
- hydrophobic.put("T",new Integer(0));\r
- hydrophobic.put("P",new Integer(0));\r
- }\r
- static {\r
- polar.put("Y",new Integer(1));\r
- polar.put("W",new Integer(1));\r
- polar.put("H",new Integer(1));\r
- polar.put("K",new Integer(1));\r
- polar.put("R",new Integer(1));\r
- polar.put("E",new Integer(1));\r
- polar.put("Q",new Integer(1));\r
- polar.put("D",new Integer(1));\r
- polar.put("N",new Integer(1));\r
- polar.put("S",new Integer(1));\r
- polar.put("T",new Integer(1));\r
- polar.put("X",new Integer(1));\r
- polar.put("-",new Integer(1));\r
- polar.put("*",new Integer(1));\r
- polar.put("I",new Integer(0));\r
- polar.put("L",new Integer(0));\r
- polar.put("V",new Integer(0));\r
- polar.put("C",new Integer(0));\r
- polar.put("A",new Integer(0));\r
- polar.put("G",new Integer(0));\r
- polar.put("M",new Integer(0));\r
- polar.put("F",new Integer(0));\r
- polar.put("P",new Integer(0));\r
-\r
- }\r
- static {\r
- small.put("I",new Integer(0));\r
- small.put("L",new Integer(0));\r
- small.put("V",new Integer(1));\r
- small.put("C",new Integer(1));\r
- small.put("A",new Integer(1));\r
- small.put("G",new Integer(1));\r
- small.put("M",new Integer(0));\r
- small.put("F",new Integer(0));\r
- small.put("Y",new Integer(0));\r
- small.put("W",new Integer(0));\r
- small.put("H",new Integer(0));\r
- small.put("K",new Integer(0));\r
- small.put("R",new Integer(0));\r
- small.put("E",new Integer(0));\r
- small.put("Q",new Integer(0));\r
- small.put("D",new Integer(1));\r
- small.put("N",new Integer(1));\r
- small.put("S",new Integer(1));\r
- small.put("T",new Integer(1));\r
- small.put("P",new Integer(1));\r
- small.put("-",new Integer(1));\r
- small.put("*",new Integer(1));\r
- }\r
- static {\r
- positive.put("I",new Integer(0));\r
- positive.put("L",new Integer(0));\r
- positive.put("V",new Integer(0));\r
- positive.put("C",new Integer(0));\r
- positive.put("A",new Integer(0));\r
- positive.put("G",new Integer(0));\r
- positive.put("M",new Integer(0));\r
- positive.put("F",new Integer(0));\r
- positive.put("Y",new Integer(0));\r
- positive.put("W",new Integer(0));\r
- positive.put("H",new Integer(1));\r
- positive.put("K",new Integer(1));\r
- positive.put("R",new Integer(1));\r
- positive.put("E",new Integer(0));\r
- positive.put("Q",new Integer(0));\r
- positive.put("D",new Integer(0));\r
- positive.put("N",new Integer(0));\r
- positive.put("S",new Integer(0));\r
- positive.put("T",new Integer(0));\r
- positive.put("P",new Integer(0));\r
- positive.put("-",new Integer(1));\r
- positive.put("*",new Integer(1));\r
- }\r
- static {\r
- negative.put("I",new Integer(0));\r
- negative.put("L",new Integer(0));\r
- negative.put("V",new Integer(0));\r
- negative.put("C",new Integer(0));\r
- negative.put("A",new Integer(0));\r
- negative.put("G",new Integer(0));\r
- negative.put("M",new Integer(0));\r
- negative.put("F",new Integer(0));\r
- negative.put("Y",new Integer(0));\r
- negative.put("W",new Integer(0));\r
- negative.put("H",new Integer(0));\r
- negative.put("K",new Integer(0));\r
- negative.put("R",new Integer(0));\r
- negative.put("E",new Integer(1));\r
- negative.put("Q",new Integer(0));\r
- negative.put("D",new Integer(1));\r
- negative.put("N",new Integer(0));\r
- negative.put("S",new Integer(0));\r
- negative.put("T",new Integer(0));\r
- negative.put("P",new Integer(0));\r
- negative.put("-",new Integer(1));\r
- negative.put("*",new Integer(1));\r
- }\r
- static {\r
- charged.put("I",new Integer(0));\r
- charged.put("L",new Integer(0));\r
- charged.put("V",new Integer(0));\r
- charged.put("C",new Integer(0));\r
- charged.put("A",new Integer(0));\r
- charged.put("G",new Integer(0));\r
- charged.put("M",new Integer(0));\r
- charged.put("F",new Integer(0));\r
- charged.put("Y",new Integer(0));\r
- charged.put("W",new Integer(0));\r
- charged.put("H",new Integer(1));\r
- charged.put("K",new Integer(1));\r
- charged.put("R",new Integer(1));\r
- charged.put("E",new Integer(1));\r
- charged.put("Q",new Integer(0));\r
- charged.put("D",new Integer(1));\r
- charged.put("N",new Integer(1));\r
- charged.put("S",new Integer(0));\r
- charged.put("T",new Integer(0));\r
- charged.put("P",new Integer(0));\r
- charged.put("-",new Integer(1));\r
- charged.put("*",new Integer(1));\r
- }\r
- static {\r
- aromatic.put("I",new Integer(0));\r
- aromatic.put("L",new Integer(0));\r
- aromatic.put("V",new Integer(0));\r
- aromatic.put("C",new Integer(0));\r
- aromatic.put("A",new Integer(0));\r
- aromatic.put("G",new Integer(0));\r
- aromatic.put("M",new Integer(0));\r
- aromatic.put("F",new Integer(1));\r
- aromatic.put("Y",new Integer(1));\r
- aromatic.put("W",new Integer(1));\r
- aromatic.put("H",new Integer(1));\r
- aromatic.put("K",new Integer(0));\r
- aromatic.put("R",new Integer(0));\r
- aromatic.put("E",new Integer(0));\r
- aromatic.put("Q",new Integer(0));\r
- aromatic.put("D",new Integer(0));\r
- aromatic.put("N",new Integer(0));\r
- aromatic.put("S",new Integer(0));\r
- aromatic.put("T",new Integer(0));\r
- aromatic.put("P",new Integer(0));\r
- aromatic.put("-",new Integer(1));\r
- aromatic.put("*",new Integer(1));\r
- }\r
- static {\r
- aliphatic.put("I",new Integer(1));\r
- aliphatic.put("L",new Integer(1));\r
- aliphatic.put("V",new Integer(1));\r
- aliphatic.put("C",new Integer(0));\r
- aliphatic.put("A",new Integer(0));\r
- aliphatic.put("G",new Integer(0));\r
- aliphatic.put("M",new Integer(0));\r
- aliphatic.put("F",new Integer(0));\r
- aliphatic.put("Y",new Integer(0));\r
- aliphatic.put("W",new Integer(0));\r
- aliphatic.put("H",new Integer(0));\r
- aliphatic.put("K",new Integer(0));\r
- aliphatic.put("R",new Integer(0));\r
- aliphatic.put("E",new Integer(0));\r
- aliphatic.put("Q",new Integer(0));\r
- aliphatic.put("D",new Integer(0));\r
- aliphatic.put("N",new Integer(0));\r
- aliphatic.put("S",new Integer(0));\r
- aliphatic.put("T",new Integer(0));\r
- aliphatic.put("P",new Integer(0));\r
- aliphatic.put("-",new Integer(1));\r
- aliphatic.put("*",new Integer(1));\r
- }\r
-\r
- static {\r
- tiny.put("I",new Integer(0));\r
- tiny.put("L",new Integer(0));\r
- tiny.put("V",new Integer(0));\r
- tiny.put("C",new Integer(0));\r
- tiny.put("A",new Integer(1));\r
- tiny.put("G",new Integer(1));\r
- tiny.put("M",new Integer(0));\r
- tiny.put("F",new Integer(0));\r
- tiny.put("Y",new Integer(0));\r
- tiny.put("W",new Integer(0));\r
- tiny.put("H",new Integer(0));\r
- tiny.put("K",new Integer(0));\r
- tiny.put("R",new Integer(0));\r
- tiny.put("E",new Integer(0));\r
- tiny.put("Q",new Integer(0));\r
- tiny.put("D",new Integer(0));\r
- tiny.put("N",new Integer(0));\r
- tiny.put("S",new Integer(1));\r
- tiny.put("T",new Integer(0));\r
- tiny.put("P",new Integer(0));\r
- tiny.put("-",new Integer(1));\r
- tiny.put("*",new Integer(1));\r
- }\r
-\r
- static {\r
- proline.put("I",new Integer(0));\r
- proline.put("L",new Integer(0));\r
- proline.put("V",new Integer(0));\r
- proline.put("C",new Integer(0));\r
- proline.put("A",new Integer(0));\r
- proline.put("G",new Integer(0));\r
- proline.put("M",new Integer(0));\r
- proline.put("F",new Integer(0));\r
- proline.put("Y",new Integer(0));\r
- proline.put("W",new Integer(0));\r
- proline.put("H",new Integer(0));\r
- proline.put("K",new Integer(0));\r
- proline.put("R",new Integer(0));\r
- proline.put("E",new Integer(0));\r
- proline.put("Q",new Integer(0));\r
- proline.put("D",new Integer(0));\r
- proline.put("N",new Integer(0));\r
- proline.put("S",new Integer(0));\r
- proline.put("T",new Integer(0));\r
- proline.put("P",new Integer(1));\r
- proline.put("-",new Integer(1));\r
- proline.put("*",new Integer(1));\r
- }\r
-\r
-\r
- static {\r
- propHash.put("hydrophobic",hydrophobic);\r
- propHash.put("small",small);\r
- propHash.put("positive",positive);\r
- propHash.put("negative",negative);\r
- propHash.put("charged",charged);\r
- propHash.put("aromatic",aromatic);\r
- propHash.put("aliphatic",aliphatic);\r
- propHash.put("tiny",tiny);\r
- propHash.put("proline",proline);\r
- propHash.put("polar",polar);\r
- }\r
-\r
- public static Hashtable chainColours = new Hashtable();\r
- static {\r
- chainColours.put("A",Color.red);\r
- chainColours.put("B",Color.orange);\r
- chainColours.put("C",Color.yellow);\r
- chainColours.put("D",Color.green);\r
- chainColours.put("E",Color.cyan);\r
- chainColours.put("F",Color.blue);\r
- chainColours.put("G",Color.magenta);\r
- chainColours.put("H",Color.pink);\r
- }\r
- public static Hashtable getChainColours() {\r
- return chainColours;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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.Arrays;
+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<String, ScoreModelI> scoreMatrices = new Hashtable<String, ScoreModelI>();
+
+ // 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<String, Integer> aa3Hash = new HashMap<String, Integer>();
+
+ public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
+
+ public static final Map<String, String> nucleotideName = new HashMap<String, String>();
+
+ // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
+ public static final Map<String, String> modifications = new HashMap<String, String>();
+
+ 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", Integer.valueOf(0));
+ aa3Hash.put("ARG", Integer.valueOf(1));
+ aa3Hash.put("ASN", Integer.valueOf(2));
+ aa3Hash.put("ASP", Integer.valueOf(3)); // D
+ aa3Hash.put("CYS", Integer.valueOf(4));
+ aa3Hash.put("GLN", Integer.valueOf(5)); // Q
+ aa3Hash.put("GLU", Integer.valueOf(6)); // E
+ aa3Hash.put("GLY", Integer.valueOf(7));
+ aa3Hash.put("HIS", Integer.valueOf(8));
+ aa3Hash.put("ILE", Integer.valueOf(9));
+ aa3Hash.put("LEU", Integer.valueOf(10));
+ aa3Hash.put("LYS", Integer.valueOf(11));
+ aa3Hash.put("MET", Integer.valueOf(12));
+ aa3Hash.put("PHE", Integer.valueOf(13));
+ aa3Hash.put("PRO", Integer.valueOf(14));
+ aa3Hash.put("SER", Integer.valueOf(15));
+ aa3Hash.put("THR", Integer.valueOf(16));
+ aa3Hash.put("TRP", Integer.valueOf(17));
+ aa3Hash.put("TYR", Integer.valueOf(18));
+ aa3Hash.put("VAL", Integer.valueOf(19));
+ // IUB Nomenclature for ambiguous peptides
+ aa3Hash.put("ASX", Integer.valueOf(20)); // "B";
+ aa3Hash.put("GLX", Integer.valueOf(21)); // Z
+ aa3Hash.put("XAA", Integer.valueOf(22)); // X unknown
+ aa3Hash.put("-", Integer.valueOf(23));
+ aa3Hash.put("*", Integer.valueOf(23));
+ aa3Hash.put(".", Integer.valueOf(23));
+ aa3Hash.put(" ", Integer.valueOf(23));
+ aa3Hash.put("Gap", Integer.valueOf(23));
+ aa3Hash.put("UR3", Integer.valueOf(24));
+ }
+
+ 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", "_", "*", ".", " ", "U" };
+
+ public static final Color midBlue = new Color(100, 100, 255);
+
+ // not currently in use
+ // public static final Vector<Color> scaleColours = new Vector<Color>();
+ // 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 }, };
+
+ // not currently used
+ // public static final Map<String, Color> ssHash = new Hashtable<String,
+ // Color>();
+ // 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 List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
+
+ public static String START = "ATG";
+
+ /**
+ * Nucleotide Ambiguity Codes
+ */
+ public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+
+ /**
+ * Codon triplets with additional symbols for unambiguous codons that include
+ * ambiguity codes
+ */
+ public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+
+ /**
+ * all ambiguity codes for a given base
+ */
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
+
+ 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<String, String[]> acode : ambiguityCodes.entrySet())
+ {
+ for (String r : acode.getValue())
+ {
+ List<String> codesfor = _ambiguityCodes.get(r);
+ if (codesfor == null)
+ {
+ _ambiguityCodes.put(r, codesfor = new ArrayList<String>());
+ }
+ 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<String> 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 = "";
+ 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--;
+ }
+ }
+ }
+ }
+
+ // Stores residue codes/names and colours and other things
+ public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
+
+ public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> polar = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> small = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> positive = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> negative = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> charged = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
+
+ public static Map<String, Integer> proline = new Hashtable<String, Integer>();
+
+ static
+ {
+ hydrophobic.put("I", Integer.valueOf(1));
+ hydrophobic.put("L", Integer.valueOf(1));
+ hydrophobic.put("V", Integer.valueOf(1));
+ hydrophobic.put("C", Integer.valueOf(1));
+ hydrophobic.put("A", Integer.valueOf(1));
+ hydrophobic.put("G", Integer.valueOf(1));
+ hydrophobic.put("M", Integer.valueOf(1));
+ hydrophobic.put("F", Integer.valueOf(1));
+ hydrophobic.put("Y", Integer.valueOf(1));
+ hydrophobic.put("W", Integer.valueOf(1));
+ hydrophobic.put("H", Integer.valueOf(1));
+ hydrophobic.put("K", Integer.valueOf(1));
+ hydrophobic.put("X", Integer.valueOf(1));
+ hydrophobic.put("-", Integer.valueOf(1));
+ hydrophobic.put("*", Integer.valueOf(1));
+ hydrophobic.put("R", Integer.valueOf(0));
+ hydrophobic.put("E", Integer.valueOf(0));
+ hydrophobic.put("Q", Integer.valueOf(0));
+ hydrophobic.put("D", Integer.valueOf(0));
+ hydrophobic.put("N", Integer.valueOf(0));
+ hydrophobic.put("S", Integer.valueOf(0));
+ hydrophobic.put("T", Integer.valueOf(0));
+ hydrophobic.put("P", Integer.valueOf(0));
+ }
+
+ static
+ {
+ polar.put("Y", Integer.valueOf(1));
+ polar.put("W", Integer.valueOf(1));
+ polar.put("H", Integer.valueOf(1));
+ polar.put("K", Integer.valueOf(1));
+ polar.put("R", Integer.valueOf(1));
+ polar.put("E", Integer.valueOf(1));
+ polar.put("Q", Integer.valueOf(1));
+ polar.put("D", Integer.valueOf(1));
+ polar.put("N", Integer.valueOf(1));
+ polar.put("S", Integer.valueOf(1));
+ polar.put("T", Integer.valueOf(1));
+ polar.put("X", Integer.valueOf(1));
+ polar.put("-", Integer.valueOf(1));
+ polar.put("*", Integer.valueOf(1));
+ polar.put("I", Integer.valueOf(0));
+ polar.put("L", Integer.valueOf(0));
+ polar.put("V", Integer.valueOf(0));
+ polar.put("C", Integer.valueOf(0));
+ polar.put("A", Integer.valueOf(0));
+ polar.put("G", Integer.valueOf(0));
+ polar.put("M", Integer.valueOf(0));
+ polar.put("F", Integer.valueOf(0));
+ polar.put("P", Integer.valueOf(0));
+ }
+
+ static
+ {
+ small.put("I", Integer.valueOf(0));
+ small.put("L", Integer.valueOf(0));
+ small.put("V", Integer.valueOf(1));
+ small.put("C", Integer.valueOf(1));
+ small.put("A", Integer.valueOf(1));
+ small.put("G", Integer.valueOf(1));
+ small.put("M", Integer.valueOf(0));
+ small.put("F", Integer.valueOf(0));
+ small.put("Y", Integer.valueOf(0));
+ small.put("W", Integer.valueOf(0));
+ small.put("H", Integer.valueOf(0));
+ small.put("K", Integer.valueOf(0));
+ small.put("R", Integer.valueOf(0));
+ small.put("E", Integer.valueOf(0));
+ small.put("Q", Integer.valueOf(0));
+ small.put("D", Integer.valueOf(1));
+ small.put("N", Integer.valueOf(1));
+ small.put("S", Integer.valueOf(1));
+ small.put("T", Integer.valueOf(1));
+ small.put("P", Integer.valueOf(1));
+ small.put("-", Integer.valueOf(1));
+ small.put("*", Integer.valueOf(1));
+ }
+
+ static
+ {
+ positive.put("I", Integer.valueOf(0));
+ positive.put("L", Integer.valueOf(0));
+ positive.put("V", Integer.valueOf(0));
+ positive.put("C", Integer.valueOf(0));
+ positive.put("A", Integer.valueOf(0));
+ positive.put("G", Integer.valueOf(0));
+ positive.put("M", Integer.valueOf(0));
+ positive.put("F", Integer.valueOf(0));
+ positive.put("Y", Integer.valueOf(0));
+ positive.put("W", Integer.valueOf(0));
+ positive.put("H", Integer.valueOf(1));
+ positive.put("K", Integer.valueOf(1));
+ positive.put("R", Integer.valueOf(1));
+ positive.put("E", Integer.valueOf(0));
+ positive.put("Q", Integer.valueOf(0));
+ positive.put("D", Integer.valueOf(0));
+ positive.put("N", Integer.valueOf(0));
+ positive.put("S", Integer.valueOf(0));
+ positive.put("T", Integer.valueOf(0));
+ positive.put("P", Integer.valueOf(0));
+ positive.put("-", Integer.valueOf(1));
+ positive.put("*", Integer.valueOf(1));
+ }
+
+ static
+ {
+ negative.put("I", Integer.valueOf(0));
+ negative.put("L", Integer.valueOf(0));
+ negative.put("V", Integer.valueOf(0));
+ negative.put("C", Integer.valueOf(0));
+ negative.put("A", Integer.valueOf(0));
+ negative.put("G", Integer.valueOf(0));
+ negative.put("M", Integer.valueOf(0));
+ negative.put("F", Integer.valueOf(0));
+ negative.put("Y", Integer.valueOf(0));
+ negative.put("W", Integer.valueOf(0));
+ negative.put("H", Integer.valueOf(0));
+ negative.put("K", Integer.valueOf(0));
+ negative.put("R", Integer.valueOf(0));
+ negative.put("E", Integer.valueOf(1));
+ negative.put("Q", Integer.valueOf(0));
+ negative.put("D", Integer.valueOf(1));
+ negative.put("N", Integer.valueOf(0));
+ negative.put("S", Integer.valueOf(0));
+ negative.put("T", Integer.valueOf(0));
+ negative.put("P", Integer.valueOf(0));
+ negative.put("-", Integer.valueOf(1));
+ negative.put("*", Integer.valueOf(1));
+ }
+
+ static
+ {
+ charged.put("I", Integer.valueOf(0));
+ charged.put("L", Integer.valueOf(0));
+ charged.put("V", Integer.valueOf(0));
+ charged.put("C", Integer.valueOf(0));
+ charged.put("A", Integer.valueOf(0));
+ charged.put("G", Integer.valueOf(0));
+ charged.put("M", Integer.valueOf(0));
+ charged.put("F", Integer.valueOf(0));
+ charged.put("Y", Integer.valueOf(0));
+ charged.put("W", Integer.valueOf(0));
+ charged.put("H", Integer.valueOf(1));
+ charged.put("K", Integer.valueOf(1));
+ charged.put("R", Integer.valueOf(1));
+ charged.put("E", Integer.valueOf(1));
+ charged.put("Q", Integer.valueOf(0));
+ charged.put("D", Integer.valueOf(1));
+ charged.put("N", Integer.valueOf(0)); // Asparagine is polar but not
+ // charged.
+ // Alternative would be charged and
+ // negative (in basic form)?
+ charged.put("S", Integer.valueOf(0));
+ charged.put("T", Integer.valueOf(0));
+ charged.put("P", Integer.valueOf(0));
+ charged.put("-", Integer.valueOf(1));
+ charged.put("*", Integer.valueOf(1));
+ }
+
+ static
+ {
+ aromatic.put("I", Integer.valueOf(0));
+ aromatic.put("L", Integer.valueOf(0));
+ aromatic.put("V", Integer.valueOf(0));
+ aromatic.put("C", Integer.valueOf(0));
+ aromatic.put("A", Integer.valueOf(0));
+ aromatic.put("G", Integer.valueOf(0));
+ aromatic.put("M", Integer.valueOf(0));
+ aromatic.put("F", Integer.valueOf(1));
+ aromatic.put("Y", Integer.valueOf(1));
+ aromatic.put("W", Integer.valueOf(1));
+ aromatic.put("H", Integer.valueOf(1));
+ aromatic.put("K", Integer.valueOf(0));
+ aromatic.put("R", Integer.valueOf(0));
+ aromatic.put("E", Integer.valueOf(0));
+ aromatic.put("Q", Integer.valueOf(0));
+ aromatic.put("D", Integer.valueOf(0));
+ aromatic.put("N", Integer.valueOf(0));
+ aromatic.put("S", Integer.valueOf(0));
+ aromatic.put("T", Integer.valueOf(0));
+ aromatic.put("P", Integer.valueOf(0));
+ aromatic.put("-", Integer.valueOf(1));
+ aromatic.put("*", Integer.valueOf(1));
+ }
+
+ static
+ {
+ aliphatic.put("I", Integer.valueOf(1));
+ aliphatic.put("L", Integer.valueOf(1));
+ aliphatic.put("V", Integer.valueOf(1));
+ aliphatic.put("C", Integer.valueOf(0));
+ aliphatic.put("A", Integer.valueOf(0));
+ aliphatic.put("G", Integer.valueOf(0));
+ aliphatic.put("M", Integer.valueOf(0));
+ aliphatic.put("F", Integer.valueOf(0));
+ aliphatic.put("Y", Integer.valueOf(0));
+ aliphatic.put("W", Integer.valueOf(0));
+ aliphatic.put("H", Integer.valueOf(0));
+ aliphatic.put("K", Integer.valueOf(0));
+ aliphatic.put("R", Integer.valueOf(0));
+ aliphatic.put("E", Integer.valueOf(0));
+ aliphatic.put("Q", Integer.valueOf(0));
+ aliphatic.put("D", Integer.valueOf(0));
+ aliphatic.put("N", Integer.valueOf(0));
+ aliphatic.put("S", Integer.valueOf(0));
+ aliphatic.put("T", Integer.valueOf(0));
+ aliphatic.put("P", Integer.valueOf(0));
+ aliphatic.put("-", Integer.valueOf(1));
+ aliphatic.put("*", Integer.valueOf(1));
+ }
+
+ static
+ {
+ tiny.put("I", Integer.valueOf(0));
+ tiny.put("L", Integer.valueOf(0));
+ tiny.put("V", Integer.valueOf(0));
+ tiny.put("C", Integer.valueOf(0));
+ tiny.put("A", Integer.valueOf(1));
+ tiny.put("G", Integer.valueOf(1));
+ tiny.put("M", Integer.valueOf(0));
+ tiny.put("F", Integer.valueOf(0));
+ tiny.put("Y", Integer.valueOf(0));
+ tiny.put("W", Integer.valueOf(0));
+ tiny.put("H", Integer.valueOf(0));
+ tiny.put("K", Integer.valueOf(0));
+ tiny.put("R", Integer.valueOf(0));
+ tiny.put("E", Integer.valueOf(0));
+ tiny.put("Q", Integer.valueOf(0));
+ tiny.put("D", Integer.valueOf(0));
+ tiny.put("N", Integer.valueOf(0));
+ tiny.put("S", Integer.valueOf(1));
+ tiny.put("T", Integer.valueOf(0));
+ tiny.put("P", Integer.valueOf(0));
+ tiny.put("-", Integer.valueOf(1));
+ tiny.put("*", Integer.valueOf(1));
+ }
+
+ static
+ {
+ proline.put("I", Integer.valueOf(0));
+ proline.put("L", Integer.valueOf(0));
+ proline.put("V", Integer.valueOf(0));
+ proline.put("C", Integer.valueOf(0));
+ proline.put("A", Integer.valueOf(0));
+ proline.put("G", Integer.valueOf(0));
+ proline.put("M", Integer.valueOf(0));
+ proline.put("F", Integer.valueOf(0));
+ proline.put("Y", Integer.valueOf(0));
+ proline.put("W", Integer.valueOf(0));
+ proline.put("H", Integer.valueOf(0));
+ proline.put("K", Integer.valueOf(0));
+ proline.put("R", Integer.valueOf(0));
+ proline.put("E", Integer.valueOf(0));
+ proline.put("Q", Integer.valueOf(0));
+ proline.put("D", Integer.valueOf(0));
+ proline.put("N", Integer.valueOf(0));
+ proline.put("S", Integer.valueOf(0));
+ proline.put("T", Integer.valueOf(0));
+ proline.put("P", Integer.valueOf(1));
+ proline.put("-", Integer.valueOf(1));
+ proline.put("*", Integer.valueOf(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 (String ph : propHash.keySet())
+ {
+ Map<String, Integer> pph = 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<String, Integer> 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 String codonTranslate(String lccodon)
+ {
+ String cdn = codonHash2.get(lccodon.toUpperCase());
+ if ("*".equals(cdn))
+ {
+ return "STOP";
+ }
+ return cdn;
+ }
+
+ 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<String, String> toDssp3State;
+ static
+ {
+ toDssp3State = new Hashtable<String, String>();
+ 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(toDssp3State.get(ssc));
+ }
+ else
+ {
+ ss.append(" ");
+ }
+ }
+ return ss.toString();
+ }
+
+ 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
+
+ // Additional protein alphabets used in the SCOP database and PDB files
+ // source:
+ // https://github.com/biopython/biopython/blob/master/Bio/Data/SCOPData.py
+ modifications.put("00C", "CYS");
+ modifications.put("01W", "XAA");
+ modifications.put("02K", "ALA");
+ modifications.put("03Y", "CYS");
+ modifications.put("07O", "CYS");
+ modifications.put("08P", "CYS");
+ modifications.put("0A0", "ASP");
+ modifications.put("0A1", "TYR");
+ modifications.put("0A2", "LYS");
+ modifications.put("0A8", "CYS");
+ modifications.put("0AA", "VAL");
+ modifications.put("0AB", "VAL");
+ modifications.put("0AC", "GLY");
+ modifications.put("0AD", "GLY");
+ modifications.put("0AF", "TRP");
+ modifications.put("0AG", "LEU");
+ modifications.put("0AH", "SER");
+ modifications.put("0AK", "ASP");
+ modifications.put("0AM", "ALA");
+ modifications.put("0AP", "CYS");
+ modifications.put("0AU", "UR3");
+ modifications.put("0AV", "ALA");
+ modifications.put("0AZ", "PRO");
+ modifications.put("0BN", "PHE");
+ modifications.put("0C ", "CYS");
+ modifications.put("0CS", "ALA");
+ modifications.put("0DC", "CYS");
+ modifications.put("0DG", "GLY");
+ modifications.put("0DT", "THR");
+ modifications.put("0FL", "ALA");
+ modifications.put("0G ", "GLY");
+ modifications.put("0NC", "ALA");
+ modifications.put("0SP", "ALA");
+ modifications.put("0U ", "UR3");
+ modifications.put("0YG", "YG");
+ modifications.put("10C", "CYS");
+ modifications.put("125", "UR3");
+ modifications.put("126", "UR3");
+ modifications.put("127", "UR3");
+ modifications.put("128", "ASN");
+ modifications.put("12A", "ALA");
+ modifications.put("143", "CYS");
+ modifications.put("175", "ASG");
+ modifications.put("193", "XAA");
+ modifications.put("1AP", "ALA");
+ modifications.put("1MA", "ALA");
+ modifications.put("1MG", "GLY");
+ modifications.put("1PA", "PHE");
+ modifications.put("1PI", "ALA");
+ modifications.put("1PR", "ASN");
+ modifications.put("1SC", "CYS");
+ modifications.put("1TQ", "TRP");
+ modifications.put("1TY", "TYR");
+ modifications.put("1X6", "SER");
+ modifications.put("200", "PHE");
+ modifications.put("23F", "PHE");
+ modifications.put("23S", "XAA");
+ modifications.put("26B", "THR");
+ modifications.put("2AD", "XAA");
+ modifications.put("2AG", "ALA");
+ modifications.put("2AO", "XAA");
+ modifications.put("2AR", "ALA");
+ modifications.put("2AS", "XAA");
+ modifications.put("2AT", "THR");
+ modifications.put("2AU", "UR3");
+ modifications.put("2BD", "ILE");
+ modifications.put("2BT", "THR");
+ modifications.put("2BU", "ALA");
+ modifications.put("2CO", "CYS");
+ modifications.put("2DA", "ALA");
+ modifications.put("2DF", "ASN");
+ modifications.put("2DM", "ASN");
+ modifications.put("2DO", "XAA");
+ modifications.put("2DT", "THR");
+ modifications.put("2EG", "GLY");
+ modifications.put("2FE", "ASN");
+ modifications.put("2FI", "ASN");
+ modifications.put("2FM", "MET");
+ modifications.put("2GT", "THR");
+ modifications.put("2HF", "HIS");
+ modifications.put("2LU", "LEU");
+ modifications.put("2MA", "ALA");
+ modifications.put("2MG", "GLY");
+ modifications.put("2ML", "LEU");
+ modifications.put("2MR", "ARG");
+ modifications.put("2MT", "PRO");
+ modifications.put("2MU", "UR3");
+ modifications.put("2NT", "THR");
+ modifications.put("2OM", "UR3");
+ modifications.put("2OT", "THR");
+ modifications.put("2PI", "XAA");
+ modifications.put("2PR", "GLY");
+ modifications.put("2SA", "ASN");
+ modifications.put("2SI", "XAA");
+ modifications.put("2ST", "THR");
+ modifications.put("2TL", "THR");
+ modifications.put("2TY", "TYR");
+ modifications.put("2VA", "VAL");
+ modifications.put("2XA", "CYS");
+ modifications.put("32S", "XAA");
+ modifications.put("32T", "XAA");
+ modifications.put("3AH", "HIS");
+ modifications.put("3AR", "XAA");
+ modifications.put("3CF", "PHE");
+ modifications.put("3DA", "ALA");
+ modifications.put("3DR", "ASN");
+ modifications.put("3GA", "ALA");
+ modifications.put("3MD", "ASP");
+ modifications.put("3ME", "UR3");
+ modifications.put("3NF", "TYR");
+ modifications.put("3QN", "LYS");
+ modifications.put("3TY", "XAA");
+ modifications.put("3XH", "GLY");
+ modifications.put("4AC", "ASN");
+ modifications.put("4BF", "TYR");
+ modifications.put("4CF", "PHE");
+ modifications.put("4CY", "MET");
+ modifications.put("4DP", "TRP");
+ modifications.put("4F3", "GYG");
+ modifications.put("4FB", "PRO");
+ modifications.put("4FW", "TRP");
+ modifications.put("4HT", "TRP");
+ modifications.put("4IN", "TRP");
+ modifications.put("4MF", "ASN");
+ modifications.put("4MM", "XAA");
+ modifications.put("4OC", "CYS");
+ modifications.put("4PC", "CYS");
+ modifications.put("4PD", "CYS");
+ modifications.put("4PE", "CYS");
+ modifications.put("4PH", "PHE");
+ modifications.put("4SC", "CYS");
+ modifications.put("4SU", "UR3");
+ modifications.put("4TA", "ASN");
+ modifications.put("4U7", "ALA");
+ modifications.put("56A", "HIS");
+ modifications.put("5AA", "ALA");
+ modifications.put("5AB", "ALA");
+ modifications.put("5AT", "THR");
+ modifications.put("5BU", "UR3");
+ modifications.put("5CG", "GLY");
+ modifications.put("5CM", "CYS");
+ modifications.put("5CS", "CYS");
+ modifications.put("5FA", "ALA");
+ modifications.put("5FC", "CYS");
+ modifications.put("5FU", "UR3");
+ modifications.put("5HP", "GLU");
+ modifications.put("5HT", "THR");
+ modifications.put("5HU", "UR3");
+ modifications.put("5IC", "CYS");
+ modifications.put("5IT", "THR");
+ modifications.put("5IU", "UR3");
+ modifications.put("5MC", "CYS");
+ modifications.put("5MD", "ASN");
+ modifications.put("5MU", "UR3");
+ modifications.put("5NC", "CYS");
+ modifications.put("5PC", "CYS");
+ modifications.put("5PY", "THR");
+ modifications.put("5SE", "UR3");
+ modifications.put("5ZA", "TWG");
+ modifications.put("64T", "THR");
+ modifications.put("6CL", "LYS");
+ modifications.put("6CT", "THR");
+ modifications.put("6CW", "TRP");
+ modifications.put("6HA", "ALA");
+ modifications.put("6HC", "CYS");
+ modifications.put("6HG", "GLY");
+ modifications.put("6HN", "LYS");
+ modifications.put("6HT", "THR");
+ modifications.put("6IA", "ALA");
+ modifications.put("6MA", "ALA");
+ modifications.put("6MC", "ALA");
+ modifications.put("6MI", "ASN");
+ modifications.put("6MT", "ALA");
+ modifications.put("6MZ", "ASN");
+ modifications.put("6OG", "GLY");
+ modifications.put("70U", "UR3");
+ modifications.put("7DA", "ALA");
+ modifications.put("7GU", "GLY");
+ modifications.put("7JA", "ILE");
+ modifications.put("7MG", "GLY");
+ modifications.put("8AN", "ALA");
+ modifications.put("8FG", "GLY");
+ modifications.put("8MG", "GLY");
+ modifications.put("8OG", "GLY");
+ modifications.put("9NE", "GLU");
+ modifications.put("9NF", "PHE");
+ modifications.put("9NR", "ARG");
+ modifications.put("9NV", "VAL");
+ modifications.put("A ", "ALA");
+ modifications.put("A1P", "ASN");
+ modifications.put("A23", "ALA");
+ modifications.put("A2L", "ALA");
+ modifications.put("A2M", "ALA");
+ modifications.put("A34", "ALA");
+ modifications.put("A35", "ALA");
+ modifications.put("A38", "ALA");
+ modifications.put("A39", "ALA");
+ modifications.put("A3A", "ALA");
+ modifications.put("A3P", "ALA");
+ modifications.put("A40", "ALA");
+ modifications.put("A43", "ALA");
+ modifications.put("A44", "ALA");
+ modifications.put("A47", "ALA");
+ modifications.put("A5L", "ALA");
+ modifications.put("A5M", "CYS");
+ modifications.put("A5N", "ASN");
+ modifications.put("A5O", "ALA");
+ modifications.put("A66", "XAA");
+ modifications.put("AA3", "ALA");
+ modifications.put("AA4", "ALA");
+ modifications.put("AAR", "ARG");
+ modifications.put("AB7", "XAA");
+ modifications.put("ABA", "ALA");
+ modifications.put("ABR", "ALA");
+ modifications.put("ABS", "ALA");
+ modifications.put("ABT", "ASN");
+ modifications.put("ACB", "ASP");
+ modifications.put("ACL", "ARG");
+ modifications.put("AD2", "ALA");
+ modifications.put("ADD", "XAA");
+ modifications.put("ADX", "ASN");
+ modifications.put("AEA", "XAA");
+ modifications.put("AEI", "ASP");
+ modifications.put("AET", "ALA");
+ modifications.put("AFA", "ASN");
+ modifications.put("AFF", "ASN");
+ modifications.put("AFG", "GLY");
+ modifications.put("AGM", "ARG");
+ modifications.put("AGT", "CYS");
+ modifications.put("AHB", "ASN");
+ modifications.put("AHH", "XAA");
+ modifications.put("AHO", "ALA");
+ modifications.put("AHP", "ALA");
+ modifications.put("AHS", "XAA");
+ modifications.put("AHT", "XAA");
+ modifications.put("AIB", "ALA");
+ modifications.put("AKL", "ASP");
+ modifications.put("AKZ", "ASP");
+ modifications.put("ALA", "ALA");
+ modifications.put("ALC", "ALA");
+ modifications.put("ALM", "ALA");
+ modifications.put("ALN", "ALA");
+ modifications.put("ALO", "THR");
+ modifications.put("ALQ", "XAA");
+ modifications.put("ALS", "ALA");
+ modifications.put("ALT", "ALA");
+ modifications.put("ALV", "ALA");
+ modifications.put("ALY", "LYS");
+ modifications.put("AN8", "ALA");
+ modifications.put("AP7", "ALA");
+ modifications.put("APE", "XAA");
+ modifications.put("APH", "ALA");
+ modifications.put("API", "LYS");
+ modifications.put("APK", "LYS");
+ modifications.put("APM", "XAA");
+ modifications.put("APP", "XAA");
+ modifications.put("AR2", "ARG");
+ modifications.put("AR4", "GLU");
+ modifications.put("AR7", "ARG");
+ modifications.put("ARG", "ARG");
+ modifications.put("ARM", "ARG");
+ modifications.put("ARO", "ARG");
+ modifications.put("ARV", "XAA");
+ modifications.put("AS ", "ALA");
+ modifications.put("AS2", "ASP");
+ modifications.put("AS9", "XAA");
+ modifications.put("ASA", "ASP");
+ modifications.put("ASB", "ASP");
+ modifications.put("ASI", "ASP");
+ modifications.put("ASK", "ASP");
+ modifications.put("ASL", "ASP");
+ modifications.put("ASM", "XAA");
+ modifications.put("ASN", "ASN");
+ modifications.put("ASP", "ASP");
+ modifications.put("ASQ", "ASP");
+ modifications.put("ASU", "ASN");
+ modifications.put("ASX", "ASX");
+ modifications.put("ATD", "THR");
+ modifications.put("ATL", "THR");
+ modifications.put("ATM", "THR");
+ modifications.put("AVC", "ALA");
+ modifications.put("AVN", "XAA");
+ modifications.put("AYA", "ALA");
+ modifications.put("AYG", "AYG");
+ modifications.put("AZK", "LYS");
+ modifications.put("AZS", "SER");
+ modifications.put("AZY", "TYR");
+ modifications.put("B1F", "PHE");
+ modifications.put("B1P", "ASN");
+ modifications.put("B2A", "ALA");
+ modifications.put("B2F", "PHE");
+ modifications.put("B2I", "ILE");
+ modifications.put("B2V", "VAL");
+ modifications.put("B3A", "ALA");
+ modifications.put("B3D", "ASP");
+ modifications.put("B3E", "GLU");
+ modifications.put("B3K", "LYS");
+ modifications.put("B3L", "XAA");
+ modifications.put("B3M", "XAA");
+ modifications.put("B3Q", "XAA");
+ modifications.put("B3S", "SER");
+ modifications.put("B3T", "XAA");
+ modifications.put("B3U", "HIS");
+ modifications.put("B3X", "ASN");
+ modifications.put("B3Y", "TYR");
+ modifications.put("BB6", "CYS");
+ modifications.put("BB7", "CYS");
+ modifications.put("BB8", "PHE");
+ modifications.put("BB9", "CYS");
+ modifications.put("BBC", "CYS");
+ modifications.put("BCS", "CYS");
+ modifications.put("BE2", "XAA");
+ modifications.put("BFD", "ASP");
+ modifications.put("BG1", "SER");
+ modifications.put("BGM", "GLY");
+ modifications.put("BH2", "ASP");
+ modifications.put("BHD", "ASP");
+ modifications.put("BIF", "PHE");
+ modifications.put("BIL", "XAA");
+ modifications.put("BIU", "ILE");
+ modifications.put("BJH", "XAA");
+ modifications.put("BLE", "LEU");
+ modifications.put("BLY", "LYS");
+ modifications.put("BMP", "ASN");
+ modifications.put("BMT", "THR");
+ modifications.put("BNN", "PHE");
+ modifications.put("BNO", "XAA");
+ modifications.put("BOE", "THR");
+ modifications.put("BOR", "ARG");
+ modifications.put("BPE", "CYS");
+ modifications.put("BRU", "UR3");
+ modifications.put("BSE", "SER");
+ modifications.put("BT5", "ASN");
+ modifications.put("BTA", "LEU");
+ modifications.put("BTC", "CYS");
+ modifications.put("BTR", "TRP");
+ modifications.put("BUC", "CYS");
+ modifications.put("BUG", "VAL");
+ modifications.put("BVP", "UR3");
+ modifications.put("BZG", "ASN");
+ modifications.put("C ", "CYS");
+ modifications.put("C12", "TYG");
+ modifications.put("C1X", "LYS");
+ modifications.put("C25", "CYS");
+ modifications.put("C2L", "CYS");
+ modifications.put("C2S", "CYS");
+ modifications.put("C31", "CYS");
+ modifications.put("C32", "CYS");
+ modifications.put("C34", "CYS");
+ modifications.put("C36", "CYS");
+ modifications.put("C37", "CYS");
+ modifications.put("C38", "CYS");
+ modifications.put("C3Y", "CYS");
+ modifications.put("C42", "CYS");
+ modifications.put("C43", "CYS");
+ modifications.put("C45", "CYS");
+ modifications.put("C46", "CYS");
+ modifications.put("C49", "CYS");
+ modifications.put("C4R", "CYS");
+ modifications.put("C4S", "CYS");
+ modifications.put("C5C", "CYS");
+ modifications.put("C66", "XAA");
+ modifications.put("C6C", "CYS");
+ modifications.put("C99", "TFG");
+ modifications.put("CAF", "CYS");
+ modifications.put("CAL", "XAA");
+ modifications.put("CAR", "CYS");
+ modifications.put("CAS", "CYS");
+ modifications.put("CAV", "XAA");
+ modifications.put("CAY", "CYS");
+ modifications.put("CB2", "CYS");
+ modifications.put("CBR", "CYS");
+ modifications.put("CBV", "CYS");
+ modifications.put("CCC", "CYS");
+ modifications.put("CCL", "LYS");
+ modifications.put("CCS", "CYS");
+ modifications.put("CCY", "CYG");
+ modifications.put("CDE", "XAA");
+ modifications.put("CDV", "XAA");
+ modifications.put("CDW", "CYS");
+ modifications.put("CEA", "CYS");
+ modifications.put("CFL", "CYS");
+ modifications.put("CFY", "FCYG"); // check
+ modifications.put("CG1", "GLY");
+ modifications.put("CGA", "GLU");
+ modifications.put("CGU", "GLU");
+ modifications.put("CH ", "CYS");
+ modifications.put("CH6", "MYG");
+ modifications.put("CH7", "KYG");
+ modifications.put("CHF", "XAA");
+ modifications.put("CHG", "XAA");
+ modifications.put("CHP", "GLY");
+ modifications.put("CHS", "XAA");
+ modifications.put("CIR", "ARG");
+ modifications.put("CJO", "GYG");
+ modifications.put("CLE", "LEU");
+ modifications.put("CLG", "LYS");
+ modifications.put("CLH", "LYS");
+ modifications.put("CLV", "AFG");
+ modifications.put("CM0", "ASN");
+ modifications.put("CME", "CYS");
+ modifications.put("CMH", "CYS");
+ modifications.put("CML", "CYS");
+ modifications.put("CMR", "CYS");
+ modifications.put("CMT", "CYS");
+ modifications.put("CNU", "UR3");
+ modifications.put("CP1", "CYS");
+ modifications.put("CPC", "XAA");
+ modifications.put("CPI", "XAA");
+ modifications.put("CQR", "GYG");
+ modifications.put("CR0", "TLG");
+ modifications.put("CR2", "GYG");
+ modifications.put("CR5", "GLY");
+ modifications.put("CR7", "KYG");
+ modifications.put("CR8", "HYG");
+ modifications.put("CRF", "TWG");
+ modifications.put("CRG", "THG");
+ modifications.put("CRK", "MYG");
+ modifications.put("CRO", "GYG");
+ modifications.put("CRQ", "QYG");
+ modifications.put("CRU", "EYG");
+ modifications.put("CRW", "ASG");
+ modifications.put("CRX", "ASG");
+ modifications.put("CS0", "CYS");
+ modifications.put("CS1", "CYS");
+ modifications.put("CS3", "CYS");
+ modifications.put("CS4", "CYS");
+ modifications.put("CS8", "ASN");
+ modifications.put("CSA", "CYS");
+ modifications.put("CSB", "CYS");
+ modifications.put("CSD", "CYS");
+ modifications.put("CSE", "CYS");
+ modifications.put("CSF", "CYS");
+ modifications.put("CSH", "SHG");
+ modifications.put("CSI", "GLY");
+ modifications.put("CSJ", "CYS");
+ modifications.put("CSL", "CYS");
+ modifications.put("CSO", "CYS");
+ modifications.put("CSP", "CYS");
+ modifications.put("CSR", "CYS");
+ modifications.put("CSS", "CYS");
+ modifications.put("CSU", "CYS");
+ modifications.put("CSW", "CYS");
+ modifications.put("CSX", "CYS");
+ modifications.put("CSY", "SYG");
+ modifications.put("CSZ", "CYS");
+ modifications.put("CTE", "TRP");
+ modifications.put("CTG", "THR");
+ modifications.put("CTH", "THR");
+ modifications.put("CUC", "XAA");
+ modifications.put("CWR", "SER");
+ modifications.put("CXM", "MET");
+ modifications.put("CY0", "CYS");
+ modifications.put("CY1", "CYS");
+ modifications.put("CY3", "CYS");
+ modifications.put("CY4", "CYS");
+ modifications.put("CYA", "CYS");
+ modifications.put("CYD", "CYS");
+ modifications.put("CYF", "CYS");
+ modifications.put("CYG", "CYS");
+ modifications.put("CYJ", "XAA");
+ modifications.put("CYM", "CYS");
+ modifications.put("CYQ", "CYS");
+ modifications.put("CYR", "CYS");
+ modifications.put("CYS", "CYS");
+ modifications.put("CZ2", "CYS");
+ modifications.put("CZO", "GYG");
+ modifications.put("CZZ", "CYS");
+ modifications.put("D11", "THR");
+ modifications.put("D1P", "ASN");
+ modifications.put("D3 ", "ASN");
+ modifications.put("D33", "ASN");
+ modifications.put("D3P", "GLY");
+ modifications.put("D3T", "THR");
+ modifications.put("D4M", "THR");
+ modifications.put("D4P", "XAA");
+ modifications.put("DA ", "ALA");
+ modifications.put("DA2", "XAA");
+ modifications.put("DAB", "ALA");
+ modifications.put("DAH", "PHE");
+ modifications.put("DAL", "ALA");
+ modifications.put("DAR", "ARG");
+ modifications.put("DAS", "ASP");
+ modifications.put("DBB", "THR");
+ modifications.put("DBM", "ASN");
+ modifications.put("DBS", "SER");
+ modifications.put("DBU", "THR");
+ modifications.put("DBY", "TYR");
+ modifications.put("DBZ", "ALA");
+ modifications.put("DC ", "CYS");
+ modifications.put("DC2", "CYS");
+ modifications.put("DCG", "GLY");
+ modifications.put("DCI", "XAA");
+ modifications.put("DCL", "XAA");
+ modifications.put("DCT", "CYS");
+ modifications.put("DCY", "CYS");
+ modifications.put("DDE", "HIS");
+ modifications.put("DDG", "GLY");
+ modifications.put("DDN", "UR3");
+ modifications.put("DDX", "ASN");
+ modifications.put("DFC", "CYS");
+ modifications.put("DFG", "GLY");
+ modifications.put("DFI", "XAA");
+ modifications.put("DFO", "XAA");
+ modifications.put("DFT", "ASN");
+ modifications.put("DG ", "GLY");
+ modifications.put("DGH", "GLY");
+ modifications.put("DGI", "GLY");
+ modifications.put("DGL", "GLU");
+ modifications.put("DGN", "GLN");
+ modifications.put("DHA", "SER");
+ modifications.put("DHI", "HIS");
+ modifications.put("DHL", "XAA");
+ modifications.put("DHN", "VAL");
+ modifications.put("DHP", "XAA");
+ modifications.put("DHU", "UR3");
+ modifications.put("DHV", "VAL");
+ modifications.put("DI ", "ILE");
+ modifications.put("DIL", "ILE");
+ modifications.put("DIR", "ARG");
+ modifications.put("DIV", "VAL");
+ modifications.put("DLE", "LEU");
+ modifications.put("DLS", "LYS");
+ modifications.put("DLY", "LYS");
+ modifications.put("DM0", "LYS");
+ modifications.put("DMH", "ASN");
+ modifications.put("DMK", "ASP");
+ modifications.put("DMT", "XAA");
+ modifications.put("DN ", "ASN");
+ modifications.put("DNE", "LEU");
+ modifications.put("DNG", "LEU");
+ modifications.put("DNL", "LYS");
+ modifications.put("DNM", "LEU");
+ modifications.put("DNP", "ALA");
+ modifications.put("DNR", "CYS");
+ modifications.put("DNS", "LYS");
+ modifications.put("DOA", "XAA");
+ modifications.put("DOC", "CYS");
+ modifications.put("DOH", "ASP");
+ modifications.put("DON", "LEU");
+ modifications.put("DPB", "THR");
+ modifications.put("DPH", "PHE");
+ modifications.put("DPL", "PRO");
+ modifications.put("DPP", "ALA");
+ modifications.put("DPQ", "TYR");
+ modifications.put("DPR", "PRO");
+ modifications.put("DPY", "ASN");
+ modifications.put("DRM", "UR3");
+ modifications.put("DRP", "ASN");
+ modifications.put("DRT", "THR");
+ modifications.put("DRZ", "ASN");
+ modifications.put("DSE", "SER");
+ modifications.put("DSG", "ASN");
+ modifications.put("DSN", "SER");
+ modifications.put("DSP", "ASP");
+ modifications.put("DT ", "THR");
+ modifications.put("DTH", "THR");
+ modifications.put("DTR", "TRP");
+ modifications.put("DTY", "TYR");
+ modifications.put("DU ", "UR3");
+ modifications.put("DVA", "VAL");
+ modifications.put("DXD", "ASN");
+ modifications.put("DXN", "ASN");
+ modifications.put("DYG", "DYG");
+ modifications.put("DYS", "CYS");
+ modifications.put("DZM", "ALA");
+ modifications.put("E ", "ALA");
+ modifications.put("E1X", "ALA");
+ modifications.put("ECC", "GLN");
+ modifications.put("EDA", "ALA");
+ modifications.put("EFC", "CYS");
+ modifications.put("EHP", "PHE");
+ modifications.put("EIT", "THR");
+ modifications.put("ENP", "ASN");
+ modifications.put("ESB", "TYR");
+ modifications.put("ESC", "MET");
+ modifications.put("EXB", "XAA");
+ modifications.put("EXY", "LEU");
+ modifications.put("EY5", "ASN");
+ modifications.put("EYS", "XAA");
+ modifications.put("F2F", "PHE");
+ modifications.put("FA2", "ALA");
+ modifications.put("FA5", "ASN");
+ modifications.put("FAG", "ASN");
+ modifications.put("FAI", "ASN");
+ modifications.put("FB5", "ALA");
+ modifications.put("FB6", "ALA");
+ modifications.put("FCL", "PHE");
+ modifications.put("FFD", "ASN");
+ modifications.put("FGA", "GLU");
+ modifications.put("FGL", "GLY");
+ modifications.put("FGP", "SER");
+ modifications.put("FHL", "XAA");
+ modifications.put("FHO", "LYS");
+ modifications.put("FHU", "UR3");
+ modifications.put("FLA", "ALA");
+ modifications.put("FLE", "LEU");
+ modifications.put("FLT", "TYR");
+ modifications.put("FME", "MET");
+ modifications.put("FMG", "GLY");
+ modifications.put("FMU", "ASN");
+ modifications.put("FOE", "CYS");
+ modifications.put("FOX", "GLY");
+ modifications.put("FP9", "PRO");
+ modifications.put("FPA", "PHE");
+ modifications.put("FRD", "XAA");
+ modifications.put("FT6", "TRP");
+ modifications.put("FTR", "TRP");
+ modifications.put("FTY", "TYR");
+ modifications.put("FVA", "VAL");
+ modifications.put("FZN", "LYS");
+ modifications.put("G ", "GLY");
+ modifications.put("G25", "GLY");
+ modifications.put("G2L", "GLY");
+ modifications.put("G2S", "GLY");
+ modifications.put("G31", "GLY");
+ modifications.put("G32", "GLY");
+ modifications.put("G33", "GLY");
+ modifications.put("G36", "GLY");
+ modifications.put("G38", "GLY");
+ modifications.put("G42", "GLY");
+ modifications.put("G46", "GLY");
+ modifications.put("G47", "GLY");
+ modifications.put("G48", "GLY");
+ modifications.put("G49", "GLY");
+ modifications.put("G4P", "ASN");
+ modifications.put("G7M", "GLY");
+ modifications.put("GAO", "GLY");
+ modifications.put("GAU", "GLU");
+ modifications.put("GCK", "CYS");
+ modifications.put("GCM", "XAA");
+ modifications.put("GDP", "GLY");
+ modifications.put("GDR", "GLY");
+ modifications.put("GFL", "GLY");
+ modifications.put("GGL", "GLU");
+ modifications.put("GH3", "GLY");
+ modifications.put("GHG", "GLN");
+ modifications.put("GHP", "GLY");
+ modifications.put("GL3", "GLY");
+ modifications.put("GLH", "GLN");
+ modifications.put("GLJ", "GLU");
+ modifications.put("GLK", "GLU");
+ modifications.put("GLM", "XAA");
+ modifications.put("GLN", "GLN");
+ modifications.put("GLQ", "GLU");
+ modifications.put("GLU", "GLU");
+ modifications.put("GLX", "GLX");
+ modifications.put("GLY", "GLY");
+ modifications.put("GLZ", "GLY");
+ modifications.put("GMA", "GLU");
+ modifications.put("GMS", "GLY");
+ modifications.put("GMU", "UR3");
+ modifications.put("GN7", "GLY");
+ modifications.put("GND", "XAA");
+ modifications.put("GNE", "ASN");
+ modifications.put("GOM", "GLY");
+ modifications.put("GPL", "LYS");
+ modifications.put("GS ", "GLY");
+ modifications.put("GSC", "GLY");
+ modifications.put("GSR", "GLY");
+ modifications.put("GSS", "GLY");
+ modifications.put("GSU", "GLU");
+ modifications.put("GT9", "CYS");
+ modifications.put("GTP", "GLY");
+ modifications.put("GVL", "XAA");
+ modifications.put("GYC", "CYG");
+ modifications.put("GYS", "SYG");
+ modifications.put("H2U", "UR3");
+ modifications.put("H5M", "PRO");
+ modifications.put("HAC", "ALA");
+ modifications.put("HAR", "ARG");
+ modifications.put("HBN", "HIS");
+ modifications.put("HCS", "XAA");
+ modifications.put("HDP", "UR3");
+ modifications.put("HEU", "UR3");
+ modifications.put("HFA", "XAA");
+ modifications.put("HGL", "XAA");
+ modifications.put("HHI", "HIS");
+ modifications.put("HHK", "AK"); // check
+ modifications.put("HIA", "HIS");
+ modifications.put("HIC", "HIS");
+ modifications.put("HIP", "HIS");
+ modifications.put("HIQ", "HIS");
+ modifications.put("HIS", "HIS");
+ modifications.put("HL2", "LEU");
+ modifications.put("HLU", "LEU");
+ modifications.put("HMR", "ARG");
+ modifications.put("HOL", "ASN");
+ modifications.put("HPC", "PHE");
+ modifications.put("HPE", "PHE");
+ modifications.put("HPH", "PHE");
+ modifications.put("HPQ", "PHE");
+ modifications.put("HQA", "ALA");
+ modifications.put("HRG", "ARG");
+ modifications.put("HRP", "TRP");
+ modifications.put("HS8", "HIS");
+ modifications.put("HS9", "HIS");
+ modifications.put("HSE", "SER");
+ modifications.put("HSL", "SER");
+ modifications.put("HSO", "HIS");
+ modifications.put("HTI", "CYS");
+ modifications.put("HTN", "ASN");
+ modifications.put("HTR", "TRP");
+ modifications.put("HV5", "ALA");
+ modifications.put("HVA", "VAL");
+ modifications.put("HY3", "PRO");
+ modifications.put("HYP", "PRO");
+ modifications.put("HZP", "PRO");
+ modifications.put("I ", "ILE");
+ modifications.put("I2M", "ILE");
+ modifications.put("I58", "LYS");
+ modifications.put("I5C", "CYS");
+ modifications.put("IAM", "ALA");
+ modifications.put("IAR", "ARG");
+ modifications.put("IAS", "ASP");
+ modifications.put("IC ", "CYS");
+ modifications.put("IEL", "LYS");
+ modifications.put("IEY", "HYG");
+ modifications.put("IG ", "GLY");
+ modifications.put("IGL", "GLY");
+ modifications.put("IGU", "GLY");
+ modifications.put("IIC", "SHG");
+ modifications.put("IIL", "ILE");
+ modifications.put("ILE", "ILE");
+ modifications.put("ILG", "GLU");
+ modifications.put("ILX", "ILE");
+ modifications.put("IMC", "CYS");
+ modifications.put("IML", "ILE");
+ modifications.put("IOY", "PHE");
+ modifications.put("IPG", "GLY");
+ modifications.put("IPN", "ASN");
+ modifications.put("IRN", "ASN");
+ modifications.put("IT1", "LYS");
+ modifications.put("IU ", "UR3");
+ modifications.put("IYR", "TYR");
+ modifications.put("IYT", "THR");
+ modifications.put("IZO", "MET");
+ modifications.put("JJJ", "CYS");
+ modifications.put("JJK", "CYS");
+ modifications.put("JJL", "CYS");
+ modifications.put("JW5", "ASN");
+ modifications.put("K1R", "CYS");
+ modifications.put("KAG", "GLY");
+ modifications.put("KCX", "LYS");
+ modifications.put("KGC", "LYS");
+ modifications.put("KNB", "ALA");
+ modifications.put("KOR", "MET");
+ modifications.put("KPI", "LYS");
+ modifications.put("KST", "LYS");
+ modifications.put("KYQ", "LYS");
+ modifications.put("L2A", "XAA");
+ modifications.put("LA2", "LYS");
+ modifications.put("LAA", "ASP");
+ modifications.put("LAL", "ALA");
+ modifications.put("LBY", "LYS");
+ modifications.put("LC ", "CYS");
+ modifications.put("LCA", "ALA");
+ modifications.put("LCC", "ASN");
+ modifications.put("LCG", "GLY");
+ modifications.put("LCH", "ASN");
+ modifications.put("LCK", "LYS");
+ modifications.put("LCX", "LYS");
+ modifications.put("LDH", "LYS");
+ modifications.put("LED", "LEU");
+ modifications.put("LEF", "LEU");
+ modifications.put("LEH", "LEU");
+ modifications.put("LEI", "VAL");
+ modifications.put("LEM", "LEU");
+ modifications.put("LEN", "LEU");
+ modifications.put("LET", "XAA");
+ modifications.put("LEU", "LEU");
+ modifications.put("LEX", "LEU");
+ modifications.put("LG ", "GLY");
+ modifications.put("LGP", "GLY");
+ modifications.put("LHC", "XAA");
+ modifications.put("LHU", "UR3");
+ modifications.put("LKC", "ASN");
+ modifications.put("LLP", "LYS");
+ modifications.put("LLY", "LYS");
+ modifications.put("LME", "GLU");
+ modifications.put("LMF", "LYS");
+ modifications.put("LMQ", "GLN");
+ modifications.put("LMS", "ASN");
+ modifications.put("LP6", "LYS");
+ modifications.put("LPD", "PRO");
+ modifications.put("LPG", "GLY");
+ modifications.put("LPL", "XAA");
+ modifications.put("LPS", "SER");
+ modifications.put("LSO", "XAA");
+ modifications.put("LTA", "XAA");
+ modifications.put("LTR", "TRP");
+ modifications.put("LVG", "GLY");
+ modifications.put("LVN", "VAL");
+ modifications.put("LYF", "LYS");
+ modifications.put("LYK", "LYS");
+ modifications.put("LYM", "LYS");
+ modifications.put("LYN", "LYS");
+ modifications.put("LYR", "LYS");
+ modifications.put("LYS", "LYS");
+ modifications.put("LYX", "LYS");
+ modifications.put("LYZ", "LYS");
+ modifications.put("M0H", "CYS");
+ modifications.put("M1G", "GLY");
+ modifications.put("M2G", "GLY");
+ modifications.put("M2L", "LYS");
+ modifications.put("M2S", "MET");
+ modifications.put("M30", "GLY");
+ modifications.put("M3L", "LYS");
+ modifications.put("M5M", "CYS");
+ modifications.put("MA ", "ALA");
+ modifications.put("MA6", "ALA");
+ modifications.put("MA7", "ALA");
+ modifications.put("MAA", "ALA");
+ modifications.put("MAD", "ALA");
+ modifications.put("MAI", "ARG");
+ modifications.put("MBQ", "TYR");
+ modifications.put("MBZ", "ASN");
+ modifications.put("MC1", "SER");
+ modifications.put("MCG", "XAA");
+ modifications.put("MCL", "LYS");
+ modifications.put("MCS", "CYS");
+ modifications.put("MCY", "CYS");
+ modifications.put("MD3", "CYS");
+ modifications.put("MD6", "GLY");
+ modifications.put("MDH", "XAA");
+ modifications.put("MDO", "ASG");
+ modifications.put("MDR", "ASN");
+ modifications.put("MEA", "PHE");
+ modifications.put("MED", "MET");
+ modifications.put("MEG", "GLU");
+ modifications.put("MEN", "ASN");
+ modifications.put("MEP", "UR3");
+ modifications.put("MEQ", "GLN");
+ modifications.put("MET", "MET");
+ modifications.put("MEU", "GLY");
+ modifications.put("MF3", "XAA");
+ modifications.put("MFC", "GYG");
+ modifications.put("MG1", "GLY");
+ modifications.put("MGG", "ARG");
+ modifications.put("MGN", "GLN");
+ modifications.put("MGQ", "ALA");
+ modifications.put("MGV", "GLY");
+ modifications.put("MGY", "GLY");
+ modifications.put("MHL", "LEU");
+ modifications.put("MHO", "MET");
+ modifications.put("MHS", "HIS");
+ modifications.put("MIA", "ALA");
+ modifications.put("MIS", "SER");
+ modifications.put("MK8", "LEU");
+ modifications.put("ML3", "LYS");
+ modifications.put("MLE", "LEU");
+ modifications.put("MLL", "LEU");
+ modifications.put("MLY", "LYS");
+ modifications.put("MLZ", "LYS");
+ modifications.put("MME", "MET");
+ modifications.put("MMO", "ARG");
+ modifications.put("MMT", "THR");
+ modifications.put("MND", "ASN");
+ modifications.put("MNL", "LEU");
+ modifications.put("MNU", "UR3");
+ modifications.put("MNV", "VAL");
+ modifications.put("MOD", "XAA");
+ modifications.put("MP8", "PRO");
+ modifications.put("MPH", "XAA");
+ modifications.put("MPJ", "XAA");
+ modifications.put("MPQ", "GLY");
+ modifications.put("MRG", "GLY");
+ modifications.put("MSA", "GLY");
+ modifications.put("MSE", "MET");
+ modifications.put("MSL", "MET");
+ modifications.put("MSO", "MET");
+ modifications.put("MSP", "XAA");
+ modifications.put("MT2", "MET");
+ modifications.put("MTR", "THR");
+ modifications.put("MTU", "ALA");
+ modifications.put("MTY", "TYR");
+ modifications.put("MVA", "VAL");
+ modifications.put("N ", "ASN");
+ modifications.put("N10", "SER");
+ modifications.put("N2C", "XAA");
+ modifications.put("N5I", "ASN");
+ modifications.put("N5M", "CYS");
+ modifications.put("N6G", "GLY");
+ modifications.put("N7P", "PRO");
+ modifications.put("NA8", "ALA");
+ modifications.put("NAL", "ALA");
+ modifications.put("NAM", "ALA");
+ modifications.put("NB8", "ASN");
+ modifications.put("NBQ", "TYR");
+ modifications.put("NC1", "SER");
+ modifications.put("NCB", "ALA");
+ modifications.put("NCX", "ASN");
+ modifications.put("NCY", "XAA");
+ modifications.put("NDF", "PHE");
+ modifications.put("NDN", "UR3");
+ modifications.put("NEM", "HIS");
+ modifications.put("NEP", "HIS");
+ modifications.put("NF2", "ASN");
+ modifications.put("NFA", "PHE");
+ modifications.put("NHL", "GLU");
+ modifications.put("NIT", "XAA");
+ modifications.put("NIY", "TYR");
+ modifications.put("NLE", "LEU");
+ modifications.put("NLN", "LEU");
+ modifications.put("NLO", "LEU");
+ modifications.put("NLP", "LEU");
+ modifications.put("NLQ", "GLN");
+ modifications.put("NMC", "GLY");
+ modifications.put("NMM", "ARG");
+ modifications.put("NMS", "THR");
+ modifications.put("NMT", "THR");
+ modifications.put("NNH", "ARG");
+ modifications.put("NP3", "ASN");
+ modifications.put("NPH", "CYS");
+ modifications.put("NPI", "ALA");
+ modifications.put("NRP", "LYG");
+ modifications.put("NRQ", "MYG");
+ modifications.put("NSK", "XAA");
+ modifications.put("NTY", "TYR");
+ modifications.put("NVA", "VAL");
+ modifications.put("NYC", "TWG");
+ modifications.put("NYG", "NYG");
+ modifications.put("NYM", "ASN");
+ modifications.put("NYS", "CYS");
+ modifications.put("NZH", "HIS");
+ modifications.put("O12", "XAA");
+ modifications.put("O2C", "ASN");
+ modifications.put("O2G", "GLY");
+ modifications.put("OAD", "ASN");
+ modifications.put("OAS", "SER");
+ modifications.put("OBF", "XAA");
+ modifications.put("OBS", "XAA");
+ modifications.put("OCS", "CYS");
+ modifications.put("OCY", "CYS");
+ modifications.put("ODP", "ASN");
+ modifications.put("OHI", "HIS");
+ modifications.put("OHS", "ASP");
+ modifications.put("OIC", "XAA");
+ modifications.put("OIP", "ILE");
+ modifications.put("OLE", "XAA");
+ modifications.put("OLT", "THR");
+ modifications.put("OLZ", "SER");
+ modifications.put("OMC", "CYS");
+ modifications.put("OMG", "GLY");
+ modifications.put("OMT", "MET");
+ modifications.put("OMU", "UR3");
+ modifications.put("ONE", "UR3");
+ modifications.put("ONH", "ALA");
+ modifications.put("ONL", "XAA");
+ modifications.put("OPR", "ARG");
+ modifications.put("ORN", "ALA");
+ modifications.put("ORQ", "ARG");
+ modifications.put("OSE", "SER");
+ modifications.put("OTB", "XAA");
+ modifications.put("OTH", "THR");
+ modifications.put("OTY", "TYR");
+ modifications.put("OXX", "ASP");
+ modifications.put("P ", "GLY");
+ modifications.put("P1L", "CYS");
+ modifications.put("P1P", "ASN");
+ modifications.put("P2T", "THR");
+ modifications.put("P2U", "UR3");
+ modifications.put("P2Y", "PRO");
+ modifications.put("P5P", "ALA");
+ modifications.put("PAQ", "TYR");
+ modifications.put("PAS", "ASP");
+ modifications.put("PAT", "TRP");
+ modifications.put("PAU", "ALA");
+ modifications.put("PBB", "CYS");
+ modifications.put("PBF", "PHE");
+ modifications.put("PBT", "ASN");
+ modifications.put("PCA", "GLU");
+ modifications.put("PCC", "PRO");
+ modifications.put("PCE", "XAA");
+ modifications.put("PCS", "PHE");
+ modifications.put("PDL", "XAA");
+ modifications.put("PDU", "UR3");
+ modifications.put("PEC", "CYS");
+ modifications.put("PF5", "PHE");
+ modifications.put("PFF", "PHE");
+ modifications.put("PFX", "XAA");
+ modifications.put("PG1", "SER");
+ modifications.put("PG7", "GLY");
+ modifications.put("PG9", "GLY");
+ modifications.put("PGL", "XAA");
+ modifications.put("PGN", "GLY");
+ modifications.put("PGP", "GLY");
+ modifications.put("PGY", "GLY");
+ modifications.put("PHA", "PHE");
+ modifications.put("PHD", "ASP");
+ modifications.put("PHE", "PHE");
+ modifications.put("PHI", "PHE");
+ modifications.put("PHL", "PHE");
+ modifications.put("PHM", "PHE");
+ modifications.put("PIA", "AYG");
+ modifications.put("PIV", "XAA");
+ modifications.put("PLE", "LEU");
+ modifications.put("PM3", "PHE");
+ modifications.put("PMT", "CYS");
+ modifications.put("POM", "PRO");
+ modifications.put("PPN", "PHE");
+ modifications.put("PPU", "ALA");
+ modifications.put("PPW", "GLY");
+ modifications.put("PQ1", "ASN");
+ modifications.put("PR3", "CYS");
+ modifications.put("PR5", "ALA");
+ modifications.put("PR9", "PRO");
+ modifications.put("PRN", "ALA");
+ modifications.put("PRO", "PRO");
+ modifications.put("PRS", "PRO");
+ modifications.put("PSA", "PHE");
+ modifications.put("PSH", "HIS");
+ modifications.put("PST", "THR");
+ modifications.put("PSU", "UR3");
+ modifications.put("PSW", "CYS");
+ modifications.put("PTA", "XAA");
+ modifications.put("PTH", "TYR");
+ modifications.put("PTM", "TYR");
+ modifications.put("PTR", "TYR");
+ modifications.put("PU ", "ALA");
+ modifications.put("PUY", "ASN");
+ modifications.put("PVH", "HIS");
+ modifications.put("PVL", "XAA");
+ modifications.put("PYA", "ALA");
+ modifications.put("PYO", "UR3");
+ modifications.put("PYX", "CYS");
+ modifications.put("PYY", "ASN");
+ modifications.put("QLG", "QLG");
+ modifications.put("QMM", "GLN");
+ modifications.put("QPA", "CYS");
+ modifications.put("QPH", "PHE");
+ modifications.put("QUO", "GLY");
+ modifications.put("R ", "ALA");
+ modifications.put("R1A", "CYS");
+ modifications.put("R4K", "TRP");
+ modifications.put("RC7", "HYG");
+ modifications.put("RE0", "TRP");
+ modifications.put("RE3", "TRP");
+ modifications.put("RIA", "ALA");
+ modifications.put("RMP", "ALA");
+ modifications.put("RON", "XAA");
+ modifications.put("RT ", "THR");
+ modifications.put("RTP", "ASN");
+ modifications.put("S1H", "SER");
+ modifications.put("S2C", "CYS");
+ modifications.put("S2D", "ALA");
+ modifications.put("S2M", "THR");
+ modifications.put("S2P", "ALA");
+ modifications.put("S4A", "ALA");
+ modifications.put("S4C", "CYS");
+ modifications.put("S4G", "GLY");
+ modifications.put("S4U", "UR3");
+ modifications.put("S6G", "GLY");
+ modifications.put("SAC", "SER");
+ modifications.put("SAH", "CYS");
+ modifications.put("SAR", "GLY");
+ modifications.put("SBL", "SER");
+ modifications.put("SC ", "CYS");
+ modifications.put("SCH", "CYS");
+ modifications.put("SCS", "CYS");
+ modifications.put("SCY", "CYS");
+ modifications.put("SD2", "XAA");
+ modifications.put("SDG", "GLY");
+ modifications.put("SDP", "SER");
+ modifications.put("SEB", "SER");
+ modifications.put("SEC", "ALA");
+ modifications.put("SEG", "ALA");
+ modifications.put("SEL", "SER");
+ modifications.put("SEM", "SER");
+ modifications.put("SEN", "SER");
+ modifications.put("SEP", "SER");
+ modifications.put("SER", "SER");
+ modifications.put("SET", "SER");
+ modifications.put("SGB", "SER");
+ modifications.put("SHC", "CYS");
+ modifications.put("SHP", "GLY");
+ modifications.put("SHR", "LYS");
+ modifications.put("SIB", "CYS");
+ modifications.put("SIC", "DC"); // check
+ modifications.put("SLA", "PRO");
+ modifications.put("SLR", "PRO");
+ modifications.put("SLZ", "LYS");
+ modifications.put("SMC", "CYS");
+ modifications.put("SME", "MET");
+ modifications.put("SMF", "PHE");
+ modifications.put("SMP", "ALA");
+ modifications.put("SMT", "THR");
+ modifications.put("SNC", "CYS");
+ modifications.put("SNN", "ASN");
+ modifications.put("SOC", "CYS");
+ modifications.put("SOS", "ASN");
+ modifications.put("SOY", "SER");
+ modifications.put("SPT", "THR");
+ modifications.put("SRA", "ALA");
+ modifications.put("SSU", "UR3");
+ modifications.put("STY", "TYR");
+ modifications.put("SUB", "XAA");
+ modifications.put("SUI", "DG");
+ modifications.put("SUN", "SER");
+ modifications.put("SUR", "UR3");
+ modifications.put("SVA", "SER");
+ modifications.put("SVV", "SER");
+ modifications.put("SVW", "SER");
+ modifications.put("SVX", "SER");
+ modifications.put("SVY", "SER");
+ modifications.put("SVZ", "XAA");
+ modifications.put("SWG", "SWG");
+ modifications.put("SYS", "CYS");
+ modifications.put("T ", "THR");
+ modifications.put("T11", "PHE");
+ modifications.put("T23", "THR");
+ modifications.put("T2S", "THR");
+ modifications.put("T2T", "ASN");
+ modifications.put("T31", "UR3");
+ modifications.put("T32", "THR");
+ modifications.put("T36", "THR");
+ modifications.put("T37", "THR");
+ modifications.put("T38", "THR");
+ modifications.put("T39", "THR");
+ modifications.put("T3P", "THR");
+ modifications.put("T41", "THR");
+ modifications.put("T48", "THR");
+ modifications.put("T49", "THR");
+ modifications.put("T4S", "THR");
+ modifications.put("T5O", "UR3");
+ modifications.put("T5S", "THR");
+ modifications.put("T66", "XAA");
+ modifications.put("T6A", "ALA");
+ modifications.put("TA3", "THR");
+ modifications.put("TA4", "XAA");
+ modifications.put("TAF", "THR");
+ modifications.put("TAL", "ASN");
+ modifications.put("TAV", "ASP");
+ modifications.put("TBG", "VAL");
+ modifications.put("TBM", "THR");
+ modifications.put("TC1", "CYS");
+ modifications.put("TCP", "THR");
+ modifications.put("TCQ", "TYR");
+ modifications.put("TCR", "TRP");
+ modifications.put("TCY", "ALA");
+ modifications.put("TDD", "LEU");
+ modifications.put("TDY", "THR");
+ modifications.put("TFE", "THR");
+ modifications.put("TFO", "ALA");
+ modifications.put("TFQ", "PHE");
+ modifications.put("TFT", "THR");
+ modifications.put("TGP", "GLY");
+ modifications.put("TH6", "THR");
+ modifications.put("THC", "THR");
+ modifications.put("THO", "XAA");
+ modifications.put("THR", "THR");
+ modifications.put("THX", "ASN");
+ modifications.put("THZ", "ARG");
+ modifications.put("TIH", "ALA");
+ modifications.put("TLB", "ASN");
+ modifications.put("TLC", "THR");
+ modifications.put("TLN", "UR3");
+ modifications.put("TMB", "THR");
+ modifications.put("TMD", "THR");
+ modifications.put("TNB", "CYS");
+ modifications.put("TNR", "SER");
+ modifications.put("TOX", "TRP");
+ modifications.put("TP1", "THR");
+ modifications.put("TPC", "CYS");
+ modifications.put("TPG", "GLY");
+ modifications.put("TPH", "XAA");
+ modifications.put("TPL", "TRP");
+ modifications.put("TPO", "THR");
+ modifications.put("TPQ", "TYR");
+ modifications.put("TQI", "TRP");
+ modifications.put("TQQ", "TRP");
+ modifications.put("TRF", "TRP");
+ modifications.put("TRG", "LYS");
+ modifications.put("TRN", "TRP");
+ modifications.put("TRO", "TRP");
+ modifications.put("TRP", "TRP");
+ modifications.put("TRQ", "TRP");
+ modifications.put("TRW", "TRP");
+ modifications.put("TRX", "TRP");
+ modifications.put("TS ", "ASN");
+ modifications.put("TST", "XAA");
+ modifications.put("TT ", "ASN");
+ modifications.put("TTD", "THR");
+ modifications.put("TTI", "UR3");
+ modifications.put("TTM", "THR");
+ modifications.put("TTQ", "TRP");
+ modifications.put("TTS", "TYR");
+ modifications.put("TY1", "TYR");
+ modifications.put("TY2", "TYR");
+ modifications.put("TY3", "TYR");
+ modifications.put("TY5", "TYR");
+ modifications.put("TYB", "TYR");
+ modifications.put("TYI", "TYR");
+ modifications.put("TYJ", "TYR");
+ modifications.put("TYN", "TYR");
+ modifications.put("TYO", "TYR");
+ modifications.put("TYQ", "TYR");
+ modifications.put("TYR", "TYR");
+ modifications.put("TYS", "TYR");
+ modifications.put("TYT", "TYR");
+ modifications.put("TYU", "ASN");
+ modifications.put("TYW", "TYR");
+ modifications.put("TYX", "XAA");
+ modifications.put("TYY", "TYR");
+ modifications.put("TZB", "XAA");
+ modifications.put("TZO", "XAA");
+ modifications.put("U ", "UR3");
+ modifications.put("U25", "UR3");
+ modifications.put("U2L", "UR3");
+ modifications.put("U2N", "UR3");
+ modifications.put("U2P", "UR3");
+ modifications.put("U31", "UR3");
+ modifications.put("U33", "UR3");
+ modifications.put("U34", "UR3");
+ modifications.put("U36", "UR3");
+ modifications.put("U37", "UR3");
+ modifications.put("U8U", "UR3");
+ modifications.put("UAR", "UR3");
+ modifications.put("UCL", "UR3");
+ modifications.put("UD5", "UR3");
+ modifications.put("UDP", "ASN");
+ modifications.put("UFP", "ASN");
+ modifications.put("UFR", "UR3");
+ modifications.put("UFT", "UR3");
+ modifications.put("UMA", "ALA");
+ modifications.put("UMP", "UR3");
+ modifications.put("UMS", "UR3");
+ modifications.put("UN1", "XAA");
+ modifications.put("UN2", "XAA");
+ modifications.put("UNK", "XAA");
+ modifications.put("UR3", "UR3");
+ modifications.put("URD", "UR3");
+ modifications.put("US1", "UR3");
+ modifications.put("US2", "UR3");
+ modifications.put("US3", "THR");
+ modifications.put("US5", "UR3");
+ modifications.put("USM", "UR3");
+ modifications.put("VAD", "VAL");
+ modifications.put("VAF", "VAL");
+ modifications.put("VAL", "VAL");
+ modifications.put("VB1", "LYS");
+ modifications.put("VDL", "XAA");
+ modifications.put("VLL", "XAA");
+ modifications.put("VLM", "XAA");
+ modifications.put("VMS", "XAA");
+ modifications.put("VOL", "XAA");
+ modifications.put("WCR", "GYG");
+ modifications.put("X ", "GLY");
+ modifications.put("X2W", "GLU");
+ modifications.put("X4A", "ASN");
+ modifications.put("X9Q", "AFG");
+ modifications.put("XAD", "ALA");
+ modifications.put("XAE", "ASN");
+ modifications.put("XAL", "ALA");
+ modifications.put("XAR", "ASN");
+ modifications.put("XCL", "CYS");
+ modifications.put("XCN", "CYS");
+ modifications.put("XCP", "XAA");
+ modifications.put("XCR", "CYS");
+ modifications.put("XCS", "ASN");
+ modifications.put("XCT", "CYS");
+ modifications.put("XCY", "CYS");
+ modifications.put("XGA", "ASN");
+ modifications.put("XGL", "GLY");
+ modifications.put("XGR", "GLY");
+ modifications.put("XGU", "GLY");
+ modifications.put("XPR", "PRO");
+ modifications.put("XSN", "ASN");
+ modifications.put("XTH", "THR");
+ modifications.put("XTL", "THR");
+ modifications.put("XTR", "THR");
+ modifications.put("XTS", "GLY");
+ modifications.put("XTY", "ASN");
+ modifications.put("XUA", "ALA");
+ modifications.put("XUG", "GLY");
+ modifications.put("XX1", "LYS");
+ modifications.put("XXY", "THG");
+ modifications.put("XYG", "DYG");
+ modifications.put("Y ", "ALA");
+ modifications.put("YCM", "CYS");
+ modifications.put("YG ", "GLY");
+ modifications.put("YOF", "TYR");
+ modifications.put("YRR", "ASN");
+ modifications.put("YYG", "GLY");
+ modifications.put("Z ", "CYS");
+ modifications.put("Z01", "ALA");
+ modifications.put("ZAD", "ALA");
+ modifications.put("ZAL", "ALA");
+ modifications.put("ZBC", "CYS");
+ modifications.put("ZBU", "UR3");
+ modifications.put("ZCL", "PHE");
+ modifications.put("ZCY", "CYS");
+ modifications.put("ZDU", "UR3");
+ modifications.put("ZFB", "XAA");
+ modifications.put("ZGU", "GLY");
+ modifications.put("ZHP", "ASN");
+ modifications.put("ZTH", "THR");
+ modifications.put("ZU0", "THR");
+ modifications.put("ZZJ", "ALA");
+
+ }
+
+ public static String getCanonicalAminoAcid(String aA)
+ {
+ String canonical = modifications.get(aA);
+ return canonical == null ? aA : canonical;
+ }
+
+ // main method generates perl representation of residue property hash
+ // / cut here
+ public static void main(String[] args)
+ {
+ Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
+ System.out.println("my %aa = {");
+ // invert property hashes
+ for (String pname : propHash.keySet())
+ {
+ Map<String, Integer> phash = propHash.get(pname);
+ for (String rname : phash.keySet())
+ {
+ Vector<String> aprops = aaProps.get(rname);
+ if (aprops == null)
+ {
+ aprops = new Vector<String>();
+ aaProps.put(rname, aprops);
+ }
+ Integer hasprop = phash.get(rname);
+ if (hasprop.intValue() == 1)
+ {
+ aprops.addElement(pname);
+ }
+ }
+ }
+ Enumeration<String> res = aaProps.keys();
+ while (res.hasMoreElements())
+ {
+ String rname = res.nextElement();
+
+ System.out.print("'" + rname + "' => [");
+ Enumeration<String> props = aaProps.get(rname).elements();
+ while (props.hasMoreElements())
+ {
+ System.out.print("'" + 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 forNucleotide
+ * @param includeAmbiguous
+ * @return
+ */
+ public static List<String> getResidues(boolean forNucleotide,
+ boolean includeAmbiguous)
+ {
+ List<String> result = new ArrayList<String>();
+ if (forNucleotide)
+ {
+ 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);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff