X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=e659ddeae61bb982761c08b6e7b14d83e7d1d014;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=5604ca39c1106e719779b968849b21e284f49ad5;hpb=a442f71fc61f1b8b41cedd2c2fd78a5c5323bafb;p=jalview.git diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 5604ca3..e659dde 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,43 +1,66 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.schemes; -import java.util.*; +import jalview.analysis.scoremodels.FeatureScoreModel; +import jalview.analysis.scoremodels.PIDScoreModel; +import jalview.api.analysis.ScoreModelI; -import java.awt.*; +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 scoreMatrices=new Hashtable(); - //Stores residue codes/names and colours and other things - public static final int [] aaIndex; // aaHash version 2.1.1 and below - public static final int [] nucleotideIndex; - public static final Hashtable aa3Hash = new Hashtable(); - public static final Hashtable aa2Triplet = new Hashtable(); - public static final Hashtable nucleotideName = new Hashtable(); + public static Hashtable scoreMatrices = new Hashtable(); + // Stores residue codes/names and colours and other things + public static final int[] aaIndex; // aaHash version 2.1.1 and below + + public static final int[] nucleotideIndex; + + public static final int[] purinepyrimidineIndex; + + public static final Map aa3Hash = new HashMap(); + + public static final Map aa2Triplet = new HashMap(); + + public static final Map nucleotideName = new HashMap(); + + // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET) + public static final Map modifications = new HashMap(); static { - aaIndex = new int[132]; - for(int i=0; i<132; i++) - aaIndex[i] = -1; + aaIndex = new int[255]; + for (int i = 0; i < 255; i++) + { + aaIndex[i] = 23; + } aaIndex['A'] = 0; aaIndex['R'] = 1; @@ -86,18 +109,27 @@ public class ResidueProperties aaIndex['b'] = 20; aaIndex['z'] = 21; aaIndex['x'] = 22; - aaIndex['u'] = 22; - aaIndex['-'] = 23; - aaIndex['*'] = 23; - aaIndex['.'] = 23; - aaIndex[' '] = 23; + 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[132]; - for (int i = 0; i < 132; i++) - nucleotideIndex[i] = -1; + 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; @@ -120,7 +152,6 @@ public class ResidueProperties nucleotideIndex['N'] = 9; nucleotideIndex['n'] = 9; - nucleotideName.put("A", "Adenine"); nucleotideName.put("a", "Adenine"); nucleotideName.put("G", "Guanine"); @@ -141,40 +172,88 @@ public class ResidueProperties nucleotideName.put("y", "Unknown Pyrimidine"); nucleotideName.put("N", "Unknown"); nucleotideName.put("n", "Unknown"); + nucleotideName.put("W", "Weak nucleotide (A or T)"); + nucleotideName.put("w", "Weak nucleotide (A or T)"); + nucleotideName.put("S", "Strong nucleotide (G or C)"); + nucleotideName.put("s", "Strong nucleotide (G or C)"); + nucleotideName.put("M", "Amino (A or C)"); + nucleotideName.put("m", "Amino (A or C)"); + nucleotideName.put("K", "Keto (G or T)"); + nucleotideName.put("k", "Keto (G or T)"); + nucleotideName.put("B", "Not A (G or C or T)"); + nucleotideName.put("b", "Not A (G or C or T)"); + nucleotideName.put("H", "Not G (A or C or T)"); + nucleotideName.put("h", "Not G (A or C or T)"); + nucleotideName.put("D", "Not C (A or G or T)"); + nucleotideName.put("d", "Not C (A or G or T)"); + nucleotideName.put("V", "Not T (A or G or C"); + nucleotideName.put("v", "Not T (A or G or C"); + } + static + { + purinepyrimidineIndex = new int[255]; + for (int i = 0; i < 255; i++) + { + purinepyrimidineIndex[i] = 3; // non-nucleotide symbols are all non-gap + // gaps. + } + + purinepyrimidineIndex['A'] = 0; + purinepyrimidineIndex['a'] = 0; + purinepyrimidineIndex['C'] = 1; + purinepyrimidineIndex['c'] = 1; + purinepyrimidineIndex['G'] = 0; + purinepyrimidineIndex['g'] = 0; + purinepyrimidineIndex['T'] = 1; + purinepyrimidineIndex['t'] = 1; + purinepyrimidineIndex['U'] = 1; + purinepyrimidineIndex['u'] = 1; + purinepyrimidineIndex['I'] = 2; + purinepyrimidineIndex['i'] = 2; + purinepyrimidineIndex['X'] = 2; + purinepyrimidineIndex['x'] = 2; + purinepyrimidineIndex['R'] = 0; + purinepyrimidineIndex['r'] = 0; + purinepyrimidineIndex['Y'] = 1; + purinepyrimidineIndex['y'] = 1; + purinepyrimidineIndex['N'] = 2; + purinepyrimidineIndex['n'] = 2; + } static { - aa3Hash.put("ALA", new Integer(0)); - aa3Hash.put("ARG", new Integer(1)); - aa3Hash.put("ASN", new Integer(2)); - aa3Hash.put("ASP", new Integer(3)); //D - aa3Hash.put("CYS", new Integer(4)); - aa3Hash.put("GLN", new Integer(5)); //Q - aa3Hash.put("GLU", new Integer(6)); // E - aa3Hash.put("GLY", new Integer(7)); - aa3Hash.put("HIS", new Integer(8)); - aa3Hash.put("ILE", new Integer(9)); - aa3Hash.put("LEU", new Integer(10)); - aa3Hash.put("LYS", new Integer(11)); - aa3Hash.put("MET", new Integer(12)); - aa3Hash.put("PHE", new Integer(13)); - aa3Hash.put("PRO", new Integer(14)); - aa3Hash.put("SER", new Integer(15)); - aa3Hash.put("THR", new Integer(16)); - aa3Hash.put("TRP", new Integer(17)); - aa3Hash.put("TYR", new Integer(18)); - aa3Hash.put("VAL", new Integer(19)); + 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", new Integer(20)); // "B"; - aa3Hash.put("GLX", new Integer(21)); // X - aa3Hash.put("XAA", new Integer(22));// X unknown - aa3Hash.put("-", new Integer(23)); - aa3Hash.put("*", new Integer(23)); - aa3Hash.put(".", new Integer(23)); - aa3Hash.put(" ", new Integer(23)); - aa3Hash.put("Gap", new Integer(23)); + 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 @@ -221,50 +300,49 @@ public class ResidueProperties aa2Triplet.put("v", "VAL"); } - public static final String[] aa = - { - "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", - "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " - }; - public static final Color midBlue = new Color(100, 100, 255); - public static final Vector scaleColours = new Vector(); + 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" }; - 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 midBlue = new Color(100, 100, 255); - 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 + // not currently in use + // public static final Vector scaleColours = new Vector(); + // static + // { + // scaleColours.addElement(new Color(114, 0, 147)); + // scaleColours.addElement(new Color(156, 0, 98)); + // scaleColours.addElement(new Color(190, 0, 0)); + // scaleColours.addElement(Color.red); + // scaleColours.addElement(new Color(255, 125, 0)); + // scaleColours.addElement(Color.orange); + // scaleColours.addElement(new Color(255, 194, 85)); + // scaleColours.addElement(Color.yellow); + // scaleColours.addElement(new Color(255, 255, 181)); + // scaleColours.addElement(Color.white); + // } + + public static final Color[] taylor = { new Color(204, 255, 0), + // A Greenish-yellowy-yellow + new Color(0, 0, 255), // R Blueish-bluey-blue + new Color(204, 0, 255), // N Blueish-reddy-blue + new Color(255, 0, 0), // D Reddish-reddy-red + new Color(255, 255, 0), // C Yellowish-yellowy-yellow + new Color(255, 0, 204), // Q Reddish-bluey-red + new Color(255, 0, 102), // E Blueish-reddy-red + new Color(255, 153, 0), // G Yellowy-reddy-yellow + new Color(0, 102, 255), // H Greenish-bluey-blue + new Color(102, 255, 0), // I Greenish-yellowy-green + new Color(51, 255, 0), // L Yellowish-greeny-green + new Color(102, 0, 255), // K Reddish-bluey-blue + new Color(0, 255, 0), // M Greenish-greeny-green + new Color(0, 255, 102), // F Blueish-greeny-green + new Color(255, 204, 0), // P Reddish-yellowy-yellow + new Color(255, 51, 0), // S Yellowish-reddy-red + new Color(255, 102, 0), // T Reddish-yellowy-red + new Color(0, 204, 255), // W Blueish-greeny-green + new Color(0, 255, 204), // Y Greenish-bluey-green + new Color(153, 255, 0), // V Yellowish-greeny-yellow Color.white, // B Color.white, // Z Color.white, // X @@ -272,17 +350,30 @@ public class ResidueProperties Color.white, // * Color.white // . }; - public static final Color[] nucleotide = - { - new Color(100, 247, 63), // A + + 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 + 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 }; - public static final Color[] color = - { - Color.pink, // A + + // 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 @@ -290,7 +381,7 @@ public class ResidueProperties Color.green, // Q Color.red, // E Color.magenta, // G - Color.red, // H + midBlue,// Color.red, // H Color.pink, // I Color.pink, // L midBlue, // K @@ -312,381 +403,281 @@ public class ResidueProperties }; // 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[] 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[] 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[] 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[] 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[] hyd = { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, + -3.5, -0.4, -3.2, 4.5, 3.8, -3.9, 1.9, 2.8, -1.6, -0.8, -0.7, -0.9, + -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 }; + public static final double hydmax = 4.5; - public static final double hydmin = -3.9; - //public static final double hydmax = 1.38; - //public static final double hydmin = -2.53; - private static final int[][] BLOSUM62 = - { - { - 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, - -2, 0, -2, -1, 0, -4 - }, - { - -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, - -3, -1, 0, -1, -4 - }, - { - -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, - 3, 0, -1, -4 - }, - { - -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, - -3, -3, 4, 1, -1, -4 - }, - { - 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, - -2, -1, -3, -3, -2, -4 - }, - { - -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, - -2, 0, 3, -1, -4 - }, - { - -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, - -2, 1, 4, -1, -4 - }, - { - 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, - -3, -3, -1, -2, -1, -4 - }, - { - -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, - -3, 0, 0, -1, -4 - }, - { - -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, - -1, 3, -3, -3, -1, -4 - }, - { - -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, - -1, 1, -4, -3, -1, -4 - }, - { - -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, - -2, 0, 1, -1, -4 - }, - { - -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, - -1, 1, -3, -1, -1, -4 - }, - { - -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, - -1, -3, -3, -1, -4 - }, - { - -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, - -4, -3, -2, -2, -1, -2, -4 - }, - { - 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, - -2, 0, 0, 0, -4 - }, - { - 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, - -2, 0, -1, -1, 0, -4 - }, - { - -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, - 11, 2, -3, -4, -3, -2, -4 - }, - { - -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, - 7, -1, -3, -2, -1, -4 - }, - { - 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, - -1, 4, -3, -2, -1, -4 - }, - { - -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, - -3, 4, 1, -1, -4 - }, - { - -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, - -2, 1, 4, -1, -4 - }, - { - 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, - -1, -1, -1, -1, -1, -4 - }, - { - -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, - -4, -4, -4, -4, -4, -4, 1 - }, - }; - static final int[][] PAM250 = - { - { - 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, 0, - 0, 0, 0, -8 - }, - { - -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, - -2, -1, 0, -1, -8 - }, - { - 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, - 2, 1, 0, -8 - }, - { - 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, -2, - 3, 3, -1, -8 - }, - { - -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, - -8, 0, -2, -4, -5, -3, -8 - }, - { - 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, - -2, 1, 3, -1, -8 - }, - { - 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, -2, - 3, 3, -1, -8 - }, - { - 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, - -1, 0, 0, -1, -8 - }, - { - -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, - -2, 1, 2, -1, -8 - }, - { - -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, - -1, 4, -2, -2, -1, -8 - }, - { - -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, - -1, 2, -3, -3, -1, -8 - }, - { - -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, -2, - 1, 0, -1, -8 - }, - { - -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, -2, - 2, -2, -2, -1, -8 - }, - { - -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, 7, - -1, -4, -5, -2, -8 - }, - { - 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, - -1, -1, 0, -1, -8 - }, - { - 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, -1, - 0, 0, 0, -8 - }, - { - 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, 0, - 0, -1, 0, -8 - }, - { - -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17, - 0, -6, -5, -6, -4, -8 - }, - { - -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, - 10, -2, -3, -4, -2, -8 - }, - { - 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, - -2, 4, -2, -2, -1, -8 - }, - { - 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, -2, - 3, 2, -1, -8 - }, - { - 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, -2, - 2, 3, -1, -8 - }, - { - 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, - -2, -1, -1, -1, -1, -8 - }, - { - -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, - -8, -8, -8, -8, -8, -8, 1 - }, - }; - public static final Hashtable ssHash = new Hashtable(); // stores the number value of the aa + public static final double hydmin = -3.9; - 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); - } + // 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 ssHash = new Hashtable(); + // static + // { + // ssHash.put("H", Color.magenta); + // ssHash.put("E", Color.yellow); + // ssHash.put("-", Color.white); + // ssHash.put(".", Color.white); + // ssHash.put("S", Color.cyan); + // ssHash.put("T", Color.blue); + // ssHash.put("G", Color.pink); + // ssHash.put("I", Color.pink); + // ssHash.put("B", Color.yellow); + // } + + /* + * new Color(60, 136, 238), // U Color.white, // I Color.white, // X + * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap + */ - static final int[][] DNA = - { - { - 5, -4, -4, -4, 1}, // C - { - -4, 5, -4, -4, 1}, // T - { - -4, -4, 5, -4, 1}, // A - { - -4, -4, -4, 5, 1}, // G - { - 1, 1, 1, 1, 1}, // - + // 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 Hashtable codonHash = new Hashtable(); - public static Vector Lys = new Vector(); - public static Vector Asn = new Vector(); - public static Vector Gln = new Vector(); - public static Vector His = new Vector(); - public static Vector Glu = new Vector(); - public static Vector Asp = new Vector(); - public static Vector Tyr = new Vector(); - public static Vector Thr = new Vector(); - public static Vector Pro = new Vector(); - public static Vector Ala = new Vector(); - public static Vector Ser = new Vector(); - public static Vector Arg = new Vector(); - public static Vector Gly = new Vector(); - public static Vector Trp = new Vector(); - public static Vector Cys = new Vector(); - public static Vector Ile = new Vector(); - public static Vector Met = new Vector(); - public static Vector Leu = new Vector(); - public static Vector Val = new Vector(); - public static Vector Phe = new Vector(); - public static Vector STOP = new Vector(); - static { - codonHash.put("K", Lys); - codonHash.put("N", Asn); - codonHash.put("Q", Gln); - codonHash.put("H", His); - codonHash.put("E", Glu); - codonHash.put("D", Asp); - codonHash.put("Y", Tyr); - codonHash.put("T", Thr); - codonHash.put("P", Pro); - codonHash.put("A", Ala); - codonHash.put("S", Ser); - codonHash.put("R", Arg); - codonHash.put("G", Gly); - codonHash.put("W", Trp); - codonHash.put("C", Cys); - codonHash.put("I", Ile); - codonHash.put("M", Met); - codonHash.put("L", Leu); - codonHash.put("V", Val); - codonHash.put("F", Phe); - codonHash.put("STOP", STOP); + 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 Hashtable codonHash2 = new Hashtable(); + 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 STOP = Arrays.asList("TGA", "TAA", "TAG"); + + public static String START = "ATG"; + + /** + * Nucleotide Ambiguity Codes + */ + public static final Map ambiguityCodes = new Hashtable(); + + /** + * Codon triplets with additional symbols for unambiguous codons that include + * ambiguity codes + */ + public static final Hashtable codonHash2 = new Hashtable(); + + /** + * all ambiguity codes for a given base + */ + public final static Hashtable> _ambiguityCodes = new Hashtable>(); static { + /* + * Ambiguity codes as per http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html + */ + ambiguityCodes.put("R", new String[] { "A", "G" }); + ambiguityCodes.put("Y", new String[] { "T", "C" }); + ambiguityCodes.put("W", new String[] { "A", "T" }); + ambiguityCodes.put("S", new String[] { "G", "C" }); + ambiguityCodes.put("M", new String[] { "A", "C" }); + ambiguityCodes.put("K", new String[] { "G", "T" }); + ambiguityCodes.put("H", new String[] { "A", "T", "C" }); + ambiguityCodes.put("B", new String[] { "G", "T", "C" }); + ambiguityCodes.put("V", new String[] { "G", "A", "C" }); + ambiguityCodes.put("D", new String[] { "G", "A", "T" }); + ambiguityCodes.put("N", new String[] { "G", "A", "T", "C" }); + + // Now build codon translation table codonHash2.put("AAA", "K"); codonHash2.put("AAG", "K"); codonHash2.put("AAC", "N"); codonHash2.put("AAT", "N"); - codonHash2.put("CAA", "E"); - codonHash2.put("CAG", "E"); + codonHash2.put("CAA", "Q"); + codonHash2.put("CAG", "Q"); codonHash2.put("CAC", "H"); codonHash2.put("CAT", "H"); - codonHash2.put("GAA", "Q"); - codonHash2.put("GAG", "Q"); + codonHash2.put("GAA", "E"); + codonHash2.put("GAG", "E"); codonHash2.put("GAC", "D"); codonHash2.put("GAT", "D"); @@ -694,9 +685,9 @@ public class ResidueProperties codonHash2.put("TAT", "Y"); codonHash2.put("ACA", "T"); - codonHash2.put("AAG", "T"); codonHash2.put("ACC", "T"); codonHash2.put("ACT", "T"); + codonHash2.put("ACG", "T"); codonHash2.put("CCA", "P"); codonHash2.put("CCG", "P"); @@ -756,367 +747,430 @@ public class ResidueProperties codonHash2.put("TTC", "F"); codonHash2.put("TTT", "F"); + + buildAmbiguityCodonSet(); } - static + /** + * programmatic generation of codons including ambiguity codes + */ + public static void buildAmbiguityCodonSet() { - Lys.addElement("AAA"); - Lys.addElement("AAG"); - Asn.addElement("AAC"); - Asn.addElement("AAT"); - - Gln.addElement("CAA"); - Gln.addElement("CAG"); - His.addElement("CAC"); - His.addElement("CAT"); - - Glu.addElement("GAA"); - Glu.addElement("GAG"); - Asp.addElement("GAC"); - Asp.addElement("GAT"); - - Tyr.addElement("TAC"); - Tyr.addElement("TAT"); - - Thr.addElement("ACA"); - Thr.addElement("ACG"); - Thr.addElement("ACC"); - Thr.addElement("ACT"); - - Pro.addElement("CCA"); - Pro.addElement("CCG"); - Pro.addElement("CCC"); - Pro.addElement("CCT"); - - Ala.addElement("GCA"); - Ala.addElement("GCG"); - Ala.addElement("GCC"); - Ala.addElement("GCT"); - - Ser.addElement("TCA"); - Ser.addElement("TCG"); - Ser.addElement("TCC"); - Ser.addElement("TCT"); - Ser.addElement("AGC"); - Ser.addElement("AGT"); - - Arg.addElement("AGA"); - Arg.addElement("AGG"); - Arg.addElement("CGA"); - Arg.addElement("CGG"); - Arg.addElement("CGC"); - Arg.addElement("CGT"); - - Gly.addElement("GGA"); - Gly.addElement("GGG"); - Gly.addElement("GGC"); - Gly.addElement("GGT"); - - STOP.addElement("TGA"); - STOP.addElement("TAA"); - STOP.addElement("TAG"); - - Trp.addElement("TGG"); - - Cys.addElement("TGC"); - Cys.addElement("TGT"); - - Ile.addElement("ATA"); - Ile.addElement("ATC"); - Ile.addElement("ATT"); - - Met.addElement("ATG"); - - Leu.addElement("CTA"); - Leu.addElement("CTG"); - Leu.addElement("CTC"); - Leu.addElement("CTT"); - Leu.addElement("TTA"); - Leu.addElement("TTG"); - - Val.addElement("GTA"); - Val.addElement("GTG"); - Val.addElement("GTC"); - Val.addElement("GTT"); - - Phe.addElement("TTC"); - Phe.addElement("TTT"); + if (_ambiguityCodes.size() > 0) + { + System.err + .println("Ignoring multiple calls to buildAmbiguityCodonSet"); + return; + } + // Invert the ambiguity code set + for (Map.Entry acode : ambiguityCodes.entrySet()) + { + for (String r : acode.getValue()) + { + List codesfor = _ambiguityCodes.get(r); + if (codesfor == null) + { + _ambiguityCodes.put(r, codesfor = new ArrayList()); + } + if (!codesfor.contains(acode.getKey())) + { + codesfor.add(acode.getKey()); + } + else + { + System.err + .println("Inconsistency in the IUBMB ambiguity code nomenclature table: collision for " + + acode.getKey() + " in residue " + r); + } + } + } + // and programmatically add in the ambiguity codes that yield the same amino + // acid + String[] unambcodons = codonHash2.keySet().toArray( + new String[codonHash2.size()]); + for (String codon : unambcodons) + { + String residue = codonHash2.get(codon); + String acodon[][] = new String[codon.length()][]; + for (int i = 0, iSize = codon.length(); i < iSize; i++) + { + String _ac = "" + codon.charAt(i); + List acodes = _ambiguityCodes.get(_ac); + if (acodes != null) + { + acodon[i] = acodes.toArray(new String[acodes.size()]); + } + else + { + acodon[i] = new String[] {}; + } + } + // enumerate all combinations and test for veracity of translation + int tpos[] = new int[codon.length()], cpos[] = new int[codon.length()]; + for (int i = 0; i < tpos.length; i++) + { + tpos[i] = -1; + } + tpos[acodon.length - 1] = 0; + int ipos, j; + while (tpos[0] < acodon[0].length) + { + // make all codons for this combination + char allres[][] = new char[tpos.length][]; + String _acodon = ""; + 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> propHash = new Hashtable>(); + + public static Map hydrophobic = new Hashtable(); + + public static Map polar = new Hashtable(); + + public static Map small = new Hashtable(); + + public static Map positive = new Hashtable(); + + public static Map negative = new Hashtable(); - //Stores residue codes/names and colours and other things - public static Hashtable propHash = new Hashtable(); - public static Hashtable hydrophobic = new Hashtable(); - public static Hashtable polar = new Hashtable(); - public static Hashtable small = new Hashtable(); - public static Hashtable positive = new Hashtable(); - public static Hashtable negative = new Hashtable(); - public static Hashtable charged = new Hashtable(); - public static Hashtable aromatic = new Hashtable(); - public static Hashtable aliphatic = new Hashtable(); - public static Hashtable tiny = new Hashtable(); - public static Hashtable proline = new Hashtable(); + public static Map charged = new Hashtable(); + + public static Map aromatic = new Hashtable(); + + public static Map aliphatic = new Hashtable(); + + public static Map tiny = new Hashtable(); + + public static Map proline = new Hashtable(); static { - hydrophobic.put("I", new Integer(1)); - hydrophobic.put("L", new Integer(1)); - hydrophobic.put("V", new Integer(1)); - hydrophobic.put("C", new Integer(1)); - hydrophobic.put("A", new Integer(1)); - hydrophobic.put("G", new Integer(1)); - hydrophobic.put("M", new Integer(1)); - hydrophobic.put("F", new Integer(1)); - hydrophobic.put("Y", new Integer(1)); - hydrophobic.put("W", new Integer(1)); - hydrophobic.put("H", new Integer(1)); - hydrophobic.put("K", new Integer(1)); - hydrophobic.put("X", new Integer(1)); - hydrophobic.put("-", new Integer(1)); - hydrophobic.put("*", new Integer(1)); - hydrophobic.put("R", new Integer(0)); - hydrophobic.put("E", new Integer(0)); - hydrophobic.put("Q", new Integer(0)); - hydrophobic.put("D", new Integer(0)); - hydrophobic.put("N", new Integer(0)); - hydrophobic.put("S", new Integer(0)); - hydrophobic.put("T", new Integer(0)); - hydrophobic.put("P", new Integer(0)); + 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", new Integer(1)); - polar.put("W", new Integer(1)); - polar.put("H", new Integer(1)); - polar.put("K", new Integer(1)); - polar.put("R", new Integer(1)); - polar.put("E", new Integer(1)); - polar.put("Q", new Integer(1)); - polar.put("D", new Integer(1)); - polar.put("N", new Integer(1)); - polar.put("S", new Integer(1)); - polar.put("T", new Integer(1)); - polar.put("X", new Integer(1)); - polar.put("-", new Integer(1)); - polar.put("*", new Integer(1)); - polar.put("I", new Integer(0)); - polar.put("L", new Integer(0)); - polar.put("V", new Integer(0)); - polar.put("C", new Integer(0)); - polar.put("A", new Integer(0)); - polar.put("G", new Integer(0)); - polar.put("M", new Integer(0)); - polar.put("F", new Integer(0)); - polar.put("P", new Integer(0)); + 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", new Integer(0)); - small.put("L", new Integer(0)); - small.put("V", new Integer(1)); - small.put("C", new Integer(1)); - small.put("A", new Integer(1)); - small.put("G", new Integer(1)); - small.put("M", new Integer(0)); - small.put("F", new Integer(0)); - small.put("Y", new Integer(0)); - small.put("W", new Integer(0)); - small.put("H", new Integer(0)); - small.put("K", new Integer(0)); - small.put("R", new Integer(0)); - small.put("E", new Integer(0)); - small.put("Q", new Integer(0)); - small.put("D", new Integer(1)); - small.put("N", new Integer(1)); - small.put("S", new Integer(1)); - small.put("T", new Integer(1)); - small.put("P", new Integer(1)); - small.put("-", new Integer(1)); - small.put("*", new Integer(1)); + 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", new Integer(0)); - positive.put("L", new Integer(0)); - positive.put("V", new Integer(0)); - positive.put("C", new Integer(0)); - positive.put("A", new Integer(0)); - positive.put("G", new Integer(0)); - positive.put("M", new Integer(0)); - positive.put("F", new Integer(0)); - positive.put("Y", new Integer(0)); - positive.put("W", new Integer(0)); - positive.put("H", new Integer(1)); - positive.put("K", new Integer(1)); - positive.put("R", new Integer(1)); - positive.put("E", new Integer(0)); - positive.put("Q", new Integer(0)); - positive.put("D", new Integer(0)); - positive.put("N", new Integer(0)); - positive.put("S", new Integer(0)); - positive.put("T", new Integer(0)); - positive.put("P", new Integer(0)); - positive.put("-", new Integer(1)); - positive.put("*", new Integer(1)); + 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", new Integer(0)); - negative.put("L", new Integer(0)); - negative.put("V", new Integer(0)); - negative.put("C", new Integer(0)); - negative.put("A", new Integer(0)); - negative.put("G", new Integer(0)); - negative.put("M", new Integer(0)); - negative.put("F", new Integer(0)); - negative.put("Y", new Integer(0)); - negative.put("W", new Integer(0)); - negative.put("H", new Integer(0)); - negative.put("K", new Integer(0)); - negative.put("R", new Integer(0)); - negative.put("E", new Integer(1)); - negative.put("Q", new Integer(0)); - negative.put("D", new Integer(1)); - negative.put("N", new Integer(0)); - negative.put("S", new Integer(0)); - negative.put("T", new Integer(0)); - negative.put("P", new Integer(0)); - negative.put("-", new Integer(1)); - negative.put("*", new Integer(1)); + 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", new Integer(0)); - charged.put("L", new Integer(0)); - charged.put("V", new Integer(0)); - charged.put("C", new Integer(0)); - charged.put("A", new Integer(0)); - charged.put("G", new Integer(0)); - charged.put("M", new Integer(0)); - charged.put("F", new Integer(0)); - charged.put("Y", new Integer(0)); - charged.put("W", new Integer(0)); - charged.put("H", new Integer(1)); - charged.put("K", new Integer(1)); - charged.put("R", new Integer(1)); - charged.put("E", new Integer(1)); - charged.put("Q", new Integer(0)); - charged.put("D", new Integer(1)); - charged.put("N", new Integer(1)); - charged.put("S", new Integer(0)); - charged.put("T", new Integer(0)); - charged.put("P", new Integer(0)); - charged.put("-", new Integer(1)); - charged.put("*", new Integer(1)); + 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", new Integer(0)); - aromatic.put("L", new Integer(0)); - aromatic.put("V", new Integer(0)); - aromatic.put("C", new Integer(0)); - aromatic.put("A", new Integer(0)); - aromatic.put("G", new Integer(0)); - aromatic.put("M", new Integer(0)); - aromatic.put("F", new Integer(1)); - aromatic.put("Y", new Integer(1)); - aromatic.put("W", new Integer(1)); - aromatic.put("H", new Integer(1)); - aromatic.put("K", new Integer(0)); - aromatic.put("R", new Integer(0)); - aromatic.put("E", new Integer(0)); - aromatic.put("Q", new Integer(0)); - aromatic.put("D", new Integer(0)); - aromatic.put("N", new Integer(0)); - aromatic.put("S", new Integer(0)); - aromatic.put("T", new Integer(0)); - aromatic.put("P", new Integer(0)); - aromatic.put("-", new Integer(1)); - aromatic.put("*", new Integer(1)); + 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", new Integer(1)); - aliphatic.put("L", new Integer(1)); - aliphatic.put("V", new Integer(1)); - aliphatic.put("C", new Integer(0)); - aliphatic.put("A", new Integer(0)); - aliphatic.put("G", new Integer(0)); - aliphatic.put("M", new Integer(0)); - aliphatic.put("F", new Integer(0)); - aliphatic.put("Y", new Integer(0)); - aliphatic.put("W", new Integer(0)); - aliphatic.put("H", new Integer(0)); - aliphatic.put("K", new Integer(0)); - aliphatic.put("R", new Integer(0)); - aliphatic.put("E", new Integer(0)); - aliphatic.put("Q", new Integer(0)); - aliphatic.put("D", new Integer(0)); - aliphatic.put("N", new Integer(0)); - aliphatic.put("S", new Integer(0)); - aliphatic.put("T", new Integer(0)); - aliphatic.put("P", new Integer(0)); - aliphatic.put("-", new Integer(1)); - aliphatic.put("*", new Integer(1)); + 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", new Integer(0)); - tiny.put("L", new Integer(0)); - tiny.put("V", new Integer(0)); - tiny.put("C", new Integer(0)); - tiny.put("A", new Integer(1)); - tiny.put("G", new Integer(1)); - tiny.put("M", new Integer(0)); - tiny.put("F", new Integer(0)); - tiny.put("Y", new Integer(0)); - tiny.put("W", new Integer(0)); - tiny.put("H", new Integer(0)); - tiny.put("K", new Integer(0)); - tiny.put("R", new Integer(0)); - tiny.put("E", new Integer(0)); - tiny.put("Q", new Integer(0)); - tiny.put("D", new Integer(0)); - tiny.put("N", new Integer(0)); - tiny.put("S", new Integer(1)); - tiny.put("T", new Integer(0)); - tiny.put("P", new Integer(0)); - tiny.put("-", new Integer(1)); - tiny.put("*", new Integer(1)); + 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", new Integer(0)); - proline.put("L", new Integer(0)); - proline.put("V", new Integer(0)); - proline.put("C", new Integer(0)); - proline.put("A", new Integer(0)); - proline.put("G", new Integer(0)); - proline.put("M", new Integer(0)); - proline.put("F", new Integer(0)); - proline.put("Y", new Integer(0)); - proline.put("W", new Integer(0)); - proline.put("H", new Integer(0)); - proline.put("K", new Integer(0)); - proline.put("R", new Integer(0)); - proline.put("E", new Integer(0)); - proline.put("Q", new Integer(0)); - proline.put("D", new Integer(0)); - proline.put("N", new Integer(0)); - proline.put("S", new Integer(0)); - proline.put("T", new Integer(0)); - proline.put("P", new Integer(1)); - proline.put("-", new Integer(1)); - proline.put("*", new Integer(1)); + 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 @@ -1132,6 +1186,77 @@ public class ResidueProperties 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 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() { @@ -1152,7 +1277,7 @@ public class ResidueProperties return hyd; } - public static Hashtable getAA3Hash() + public static Map getAA3Hash() { return aa3Hash; } @@ -1169,12 +1294,7 @@ public class ResidueProperties public static int getPAM250(String A1, String A2) { - int a = aaIndex[A1.charAt(0)]; - int b = aaIndex[A2.charAt(0)]; - - int pog = ResidueProperties.PAM250[a][b]; - - return pog; + return getPAM250(A1.charAt(0), A2.charAt(0)); } public static int getBLOSUM62(char c1, char c2) @@ -1187,59 +1307,1550 @@ public class ResidueProperties int b = aaIndex[c2]; pog = ResidueProperties.BLOSUM62[a][b]; - } - catch (Exception e) + } catch (Exception e) { - //System.out.println("Unknown residue in " + A1 + " " + A2); + // System.out.println("Unknown residue in " + A1 + " " + A2); } return pog; } - public static Vector getCodons(String res) + public static String codonTranslate(String lccodon) { - if (codonHash.containsKey(res)) + String cdn = codonHash2.get(lccodon.toUpperCase()); + if ("*".equals(cdn)) { - return (Vector) codonHash.get(res); + return "STOP"; } + return cdn; + } - return null; + public static int[][] getDefaultPeptideMatrix() + { + return ResidueProperties.getBLOSUM62(); } - public static String codonTranslate(String codon) + public static int[][] getDefaultDnaMatrix() { - Enumeration e = codonHash.keys(); + return ResidueProperties.getDNA(); + } - while (e.hasMoreElements()) + /** + * 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) { - String key = (String) e.nextElement(); - Vector tmp = (Vector) codonHash.get(key); + return (ScoreMatrix) val; + } + return null; + } - if (tmp.contains(codon.toUpperCase())) + /** + * get a ScoreModel based on its string name + * + * @param pwtype + * @return scoremodel of type pwtype or null + */ + public static ScoreModelI getScoreModel(String pwtype) + { + return scoreMatrices.get(pwtype); + } + + public static int getPAM250(char c, char d) + { + int a = aaIndex[c]; + int b = aaIndex[d]; + + int pog = ResidueProperties.PAM250[a][b]; + + return pog; + } + + public static Hashtable toDssp3State; + static + { + toDssp3State = new Hashtable(); + toDssp3State.put("H", "H"); + toDssp3State.put("E", "E"); + toDssp3State.put("C", " "); + toDssp3State.put(" ", " "); + toDssp3State.put("T", " "); + toDssp3State.put("B", "E"); + toDssp3State.put("G", "H"); + toDssp3State.put("I", "H"); + toDssp3State.put("X", " "); + } + + /** + * translate from other dssp secondary structure alphabets to 3-state + * + * @param ssstring + * @return ssstring as a three-state secondary structure assignment. + */ + public static String getDssp3state(String ssstring) + { + if (ssstring == null) + { + return null; + } + StringBuffer ss = new StringBuffer(); + for (int i = 0; i < ssstring.length(); i++) + { + String ssc = ssstring.substring(i, i + 1); + if (toDssp3State.containsKey(ssc)) { - return key; + 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"); - return null; } - public static int[][] getDefaultPeptideMatrix() { - return ResidueProperties.getBLOSUM62(); + public static String getCanonicalAminoAcid(String aA) + { + String canonical = modifications.get(aA); + return canonical == null ? aA : canonical; } - public static int[][] getDefaultDnaMatrix() { - return ResidueProperties.getDNA(); + + // main method generates perl representation of residue property hash + // / cut here + public static void main(String[] args) + { + Hashtable> aaProps = new Hashtable>(); + System.out.println("my %aa = {"); + // invert property hashes + for (String pname : propHash.keySet()) + { + Map phash = propHash.get(pname); + for (String rname : phash.keySet()) + { + Vector aprops = aaProps.get(rname); + if (aprops == null) + { + aprops = new Vector(); + aaProps.put(rname, aprops); + } + Integer hasprop = phash.get(rname); + if (hasprop.intValue() == 1) + { + aprops.addElement(pname); + } + } + } + Enumeration res = aaProps.keys(); + while (res.hasMoreElements()) + { + String rname = res.nextElement(); + + System.out.print("'" + rname + "' => ["); + Enumeration 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 + /** - * get a ScoreMatrix based on its string name - * @param pwtype - * @return matrix in scoreMatrices with key pwtype or null + * Returns a list of residue characters for the specified inputs + * + * @param forNucleotide + * @param includeAmbiguous + * @return */ - public static ScoreMatrix getScoreMatrix(String pwtype) { - Object val=scoreMatrices.get(pwtype); - if (val!=null) - return (ScoreMatrix) val; - return null; + public static List getResidues(boolean forNucleotide, + boolean includeAmbiguous) + { + List result = new ArrayList(); + 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); } }