X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=94fdf71d4c256643cc5a28b08a2bd4be1b6578cb;hb=53efd00e5fe4b886ede8ec0a6eaa36bc7c8a781e;hp=e55ce18b3bbd6a14dcdcd364fb27251e2c820470;hpb=95ab75b20edeba686d7ec4aefedd8b9cd93186ad;p=jalview.git diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index e55ce18..94fdf71 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,36 +1,58 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * 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 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 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 { @@ -87,15 +109,26 @@ public class ResidueProperties aaIndex['b'] = 20; aaIndex['z'] = 21; aaIndex['x'] = 22; - aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also extend subt. matrices + aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also + // extend subt. matrices } + /** + * maximum (gap) index for matrices involving protein alphabet + */ + public final static int maxProteinIndex = 23; + + /** + * maximum (gap) index for matrices involving nucleotide alphabet + */ + public final static int maxNucleotideIndex = 10; + static { nucleotideIndex = new int[255]; for (int i = 0; i < 255; i++) { - nucleotideIndex[i] = -1; + nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps. } nucleotideIndex['A'] = 0; @@ -139,39 +172,92 @@ 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 { - 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)); + 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; + } + + private static final Integer ONE = Integer.valueOf(1); + + private static final Integer ZERO = Integer.valueOf(0); + + static + { + aa3Hash.put("ALA", ZERO); + aa3Hash.put("ARG", ONE); + 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 @@ -218,50 +304,49 @@ 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 @@ -269,18 +354,30 @@ 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 + }; + + // 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 + public static final Color[] zappo = { Color.pink, // A midBlue, // R Color.green, // N Color.red, // D @@ -310,299 +407,213 @@ 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 @@ -614,79 +625,63 @@ public class ResidueProperties 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(); + public static final Color[] pidColours = { midBlue, + new Color(153, 153, 255), + // Color.lightGray, + new Color(204, 204, 255), }; - static - { - codonHash.put("K", Lys); - codonHash.put("N", Asn); - codonHash.put("Q", Gln); - codonHash.put("H", His); - codonHash.put("E", Glu); - codonHash.put("D", Asp); - codonHash.put("Y", Tyr); - codonHash.put("T", Thr); - codonHash.put("P", Pro); - codonHash.put("A", Ala); - codonHash.put("S", Ser); - codonHash.put("R", Arg); - codonHash.put("G", Gly); - codonHash.put("W", Trp); - codonHash.put("C", Cys); - codonHash.put("I", Ile); - codonHash.put("M", Met); - codonHash.put("L", Leu); - codonHash.put("V", Val); - codonHash.put("F", Phe); - codonHash.put("STOP", STOP); - } + public static 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(); - public static 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 +689,9 @@ 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"); @@ -756,366 +751,430 @@ 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 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(); + // 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(); + + 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", ONE); + hydrophobic.put("L", ONE); + hydrophobic.put("V", ONE); + hydrophobic.put("C", ONE); + hydrophobic.put("A", ONE); + hydrophobic.put("G", ONE); + hydrophobic.put("M", ONE); + hydrophobic.put("F", ONE); + hydrophobic.put("Y", ONE); + hydrophobic.put("W", ONE); + hydrophobic.put("H", ONE); + hydrophobic.put("K", ONE); + hydrophobic.put("X", ONE); + hydrophobic.put("-", ONE); + hydrophobic.put("*", ONE); + hydrophobic.put("R", ZERO); + hydrophobic.put("E", ZERO); + hydrophobic.put("Q", ZERO); + hydrophobic.put("D", ZERO); + hydrophobic.put("N", ZERO); + hydrophobic.put("S", ZERO); + hydrophobic.put("T", ONE); + hydrophobic.put("P", ZERO); } 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", ONE); + polar.put("W", ONE); + polar.put("H", ONE); + polar.put("K", ONE); + polar.put("R", ONE); + polar.put("E", ONE); + polar.put("Q", ONE); + polar.put("D", ONE); + polar.put("N", ONE); + polar.put("S", ONE); + polar.put("T", ONE); + polar.put("X", ONE); + polar.put("-", ONE); + polar.put("*", ONE); + polar.put("I", ZERO); + polar.put("L", ZERO); + polar.put("V", ZERO); + polar.put("C", ZERO); + polar.put("A", ZERO); + polar.put("G", ZERO); + polar.put("M", ZERO); + polar.put("F", ZERO); + polar.put("P", ZERO); } 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", ZERO); + small.put("L", ZERO); + small.put("V", ONE); + small.put("C", ONE); + small.put("A", ONE); + small.put("G", ONE); + small.put("M", ZERO); + small.put("F", ZERO); + small.put("Y", ZERO); + small.put("W", ZERO); + small.put("H", ZERO); + small.put("K", ZERO); + small.put("R", ZERO); + small.put("E", ZERO); + small.put("Q", ZERO); + small.put("D", ONE); + small.put("N", ONE); + small.put("S", ONE); + small.put("T", ONE); + small.put("P", ONE); + small.put("-", ONE); + small.put("*", ONE); } 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", ZERO); + positive.put("L", ZERO); + positive.put("V", ZERO); + positive.put("C", ZERO); + positive.put("A", ZERO); + positive.put("G", ZERO); + positive.put("M", ZERO); + positive.put("F", ZERO); + positive.put("Y", ZERO); + positive.put("W", ZERO); + positive.put("H", ONE); + positive.put("K", ONE); + positive.put("R", ONE); + positive.put("E", ZERO); + positive.put("Q", ZERO); + positive.put("D", ZERO); + positive.put("N", ZERO); + positive.put("S", ZERO); + positive.put("T", ZERO); + positive.put("P", ZERO); + positive.put("-", ONE); + positive.put("*", ONE); } 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", ZERO); + negative.put("L", ZERO); + negative.put("V", ZERO); + negative.put("C", ZERO); + negative.put("A", ZERO); + negative.put("G", ZERO); + negative.put("M", ZERO); + negative.put("F", ZERO); + negative.put("Y", ZERO); + negative.put("W", ZERO); + negative.put("H", ZERO); + negative.put("K", ZERO); + negative.put("R", ZERO); + negative.put("E", ONE); + negative.put("Q", ZERO); + negative.put("D", ONE); + negative.put("N", ZERO); + negative.put("S", ZERO); + negative.put("T", ZERO); + negative.put("P", ZERO); + negative.put("-", ONE); + negative.put("*", ONE); } 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", ZERO); + charged.put("L", ZERO); + charged.put("V", ZERO); + charged.put("C", ZERO); + charged.put("A", ZERO); + charged.put("G", ZERO); + charged.put("M", ZERO); + charged.put("F", ZERO); + charged.put("Y", ZERO); + charged.put("W", ZERO); + charged.put("H", ONE); + charged.put("K", ONE); + charged.put("R", ONE); + charged.put("E", ONE); + charged.put("Q", ZERO); + charged.put("D", ONE); + charged.put("N", ZERO); // Asparagine is polar but not + // charged. + // Alternative would be charged and + // negative (in basic form)? + charged.put("S", ZERO); + charged.put("T", ZERO); + charged.put("P", ZERO); + charged.put("-", ONE); + charged.put("*", ONE); } 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", ZERO); + aromatic.put("L", ZERO); + aromatic.put("V", ZERO); + aromatic.put("C", ZERO); + aromatic.put("A", ZERO); + aromatic.put("G", ZERO); + aromatic.put("M", ZERO); + aromatic.put("F", ONE); + aromatic.put("Y", ONE); + aromatic.put("W", ONE); + aromatic.put("H", ONE); + aromatic.put("K", ZERO); + aromatic.put("R", ZERO); + aromatic.put("E", ZERO); + aromatic.put("Q", ZERO); + aromatic.put("D", ZERO); + aromatic.put("N", ZERO); + aromatic.put("S", ZERO); + aromatic.put("T", ZERO); + aromatic.put("P", ZERO); + aromatic.put("-", ONE); + aromatic.put("*", ONE); } 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", ONE); + aliphatic.put("L", ONE); + aliphatic.put("V", ONE); + aliphatic.put("C", ZERO); + aliphatic.put("A", ZERO); + aliphatic.put("G", ZERO); + aliphatic.put("M", ZERO); + aliphatic.put("F", ZERO); + aliphatic.put("Y", ZERO); + aliphatic.put("W", ZERO); + aliphatic.put("H", ZERO); + aliphatic.put("K", ZERO); + aliphatic.put("R", ZERO); + aliphatic.put("E", ZERO); + aliphatic.put("Q", ZERO); + aliphatic.put("D", ZERO); + aliphatic.put("N", ZERO); + aliphatic.put("S", ZERO); + aliphatic.put("T", ZERO); + aliphatic.put("P", ZERO); + aliphatic.put("-", ONE); + aliphatic.put("*", ONE); } 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", ZERO); + tiny.put("L", ZERO); + tiny.put("V", ZERO); + tiny.put("C", ZERO); + tiny.put("A", ONE); + tiny.put("G", ONE); + tiny.put("M", ZERO); + tiny.put("F", ZERO); + tiny.put("Y", ZERO); + tiny.put("W", ZERO); + tiny.put("H", ZERO); + tiny.put("K", ZERO); + tiny.put("R", ZERO); + tiny.put("E", ZERO); + tiny.put("Q", ZERO); + tiny.put("D", ZERO); + tiny.put("N", ZERO); + tiny.put("S", ONE); + tiny.put("T", ZERO); + tiny.put("P", ZERO); + tiny.put("-", ONE); + tiny.put("*", ONE); } 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", ZERO); + proline.put("L", ZERO); + proline.put("V", ZERO); + proline.put("C", ZERO); + proline.put("A", ZERO); + proline.put("G", ZERO); + proline.put("M", ZERO); + proline.put("F", ZERO); + proline.put("Y", ZERO); + proline.put("W", ZERO); + proline.put("H", ZERO); + proline.put("K", ZERO); + proline.put("R", ZERO); + proline.put("E", ZERO); + proline.put("Q", ZERO); + proline.put("D", ZERO); + proline.put("N", ZERO); + proline.put("S", ZERO); + proline.put("T", ZERO); + proline.put("P", ONE); + proline.put("-", ONE); + proline.put("*", ONE); } static @@ -1131,6 +1190,77 @@ 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() { @@ -1151,7 +1281,7 @@ public class ResidueProperties return hyd; } - public static Hashtable getAA3Hash() + public static Map getAA3Hash() { return aa3Hash; } @@ -1181,41 +1311,22 @@ 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) - { - if (codonHash.containsKey(res)) - { - return (Vector) codonHash.get(res); - } - - return null; - } - - public static String codonTranslate(String codon) + public static String codonTranslate(String lccodon) { - Enumeration e = codonHash.keys(); - - while (e.hasMoreElements()) + String cdn = codonHash2.get(lccodon.toUpperCase()); + if ("*".equals(cdn)) { - String key = (String) e.nextElement(); - Vector tmp = (Vector) codonHash.get(key); - - if (tmp.contains(codon.toUpperCase())) - { - return key; - } + return "STOP"; } - - return null; + return cdn; } public static int[][] getDefaultPeptideMatrix() @@ -1230,19 +1341,31 @@ public class ResidueProperties /** * 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) + if (val != null && val instanceof ScoreMatrix) { return (ScoreMatrix) val; } return null; } + /** + * get a ScoreModel based on its string name + * + * @param pwtype + * @return scoremodel of type pwtype or null + */ + public static ScoreModelI getScoreModel(String pwtype) + { + return scoreMatrices.get(pwtype); + } + public static int getPAM250(char c, char d) { int a = aaIndex[c]; @@ -1253,9 +1376,10 @@ public class ResidueProperties return pog; } - public static Hashtable toDssp3State; - static { - toDssp3State = new Hashtable(); + public static Hashtable toDssp3State; + static + { + toDssp3State = new Hashtable(); toDssp3State.put("H", "H"); toDssp3State.put("E", "E"); toDssp3State.put("C", " "); @@ -1266,28 +1390,1471 @@ public class ResidueProperties 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) + if (ssstring == null) { return null; } StringBuffer ss = new StringBuffer(); - for (int i=0; i> 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 + + /** + * Returns a list of residue characters for the specified inputs + * + * @param forNucleotide + * @param includeAmbiguous + * @return + */ + 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); + } }