X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=4c8394ff147a72f91e7b18f8fbbd0eda7b927a5c;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=e55ce18b3bbd6a14dcdcd364fb27251e2c820470;hpb=95ab75b20edeba686d7ec4aefedd8b9cd93186ad;p=jalview.git diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index e55ce18..4c8394f 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,20 +1,19 @@ /* - * 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 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.schemes; @@ -25,11 +24,18 @@ import java.awt.*; public class ResidueProperties { public static Hashtable scoreMatrices = new Hashtable(); - //Stores residue codes/names and colours and other things + + // 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 Hashtable aa3Hash = new Hashtable(); + public static final Hashtable aa2Triplet = new Hashtable(); + public static final Hashtable nucleotideName = new Hashtable(); static @@ -87,7 +93,8 @@ 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 } static @@ -95,7 +102,7 @@ public class ResidueProperties 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; @@ -139,6 +146,54 @@ 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 @@ -146,9 +201,9 @@ public class ResidueProperties 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("ASP", new Integer(3)); // D aa3Hash.put("CYS", new Integer(4)); - aa3Hash.put("GLN", new Integer(5)); //Q + 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)); @@ -219,11 +274,11 @@ public class ResidueProperties } 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", "_", "*", ".", " " - }; + { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", + "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " }; + public static final Color midBlue = new Color(100, 100, 255); + public static final Vector scaleColours = new Vector(); static @@ -241,27 +296,26 @@ public class ResidueProperties } 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 + { 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 +323,32 @@ public class ResidueProperties Color.white, // * Color.white // . }; + public static final Color[] nucleotide = - { - new Color(100, 247, 63), // A + { 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 + { Color.pink, // A midBlue, // R Color.green, // N Color.red, // D @@ -311,272 +379,181 @@ 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 + { 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 - }; + { 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 - }; + { 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 - }; + { 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 - }; + { 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 - }; + { 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; + // 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 - }, - }; + { + { 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 + { + { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3, + 0, 0, 0, 0, -8 }, + { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4, + -2, -1, 0, -1, -8 }, + { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2, + 2, 1, 0, -8 }, + { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4, + -2, 3, 3, -1, -8 }, + { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2, + -8, 0, -2, -4, -5, -3, -8 }, + { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4, + -2, 1, 3, -1, -8 }, + { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4, + -2, 3, 3, -1, -8 }, + { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5, + -1, 0, 0, -1, -8 }, + { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0, + -2, 1, 2, -1, -8 }, + { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5, + -1, 4, -2, -2, -1, -8 }, + { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2, + -1, 2, -3, -3, -1, -8 }, + { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4, + -2, 1, 0, -1, -8 }, + { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4, + -2, 2, -2, -2, -1, -8 }, + { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0, + 7, -1, -4, -5, -2, -8 }, + { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5, + -1, -1, 0, -1, -8 }, + { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3, + -1, 0, 0, 0, -8 }, + { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3, + 0, 0, -1, 0, -8 }, + { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, + 17, 0, -6, -5, -6, -4, -8 }, + { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, + 10, -2, -3, -4, -2, -8 }, + { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, + -2, 4, -2, -2, -1, -8 }, + { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3, + -2, 3, 2, -1, -8 }, + { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4, + -2, 2, 3, -1, -8 }, + { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4, + -2, -1, -1, -1, -1, -8 }, + { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, + -8, -8, -8, -8, -8, -8, 1 }, }; + + public static final Hashtable ssHash = new Hashtable(); // stores the number + // value of the aa static { @@ -591,18 +568,23 @@ public class ResidueProperties 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}, // - + { + { 10, -8, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // C + { -8, 10, -8, -8, 1, 0, 0, 0, 0, 0, 1 }, // T + { -8, -8, 10, -8, 1, 0, 0, 0, 0, 0, 1 }, // A + { -8, -8, -8, 10, 1, 0, 0, 0, 0, 0, 1 }, // G + { 1, 1, 1, 1, 10, 0, 0, 0, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 10, 0, 0, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 10, 0, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 0, 10, 0, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 0, 0, 10, 0, 1 }, // - + { 1, 1, 1, 1, 1, 0, 0, 0, 0, 10, 1 }, // - + { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }, // - }; /** * register matrices in list @@ -615,35 +597,55 @@ public class ResidueProperties } public static final Color[] pidColours = - { - midBlue, new Color(153, 153, 255), - // Color.lightGray, - new Color(204, 204, 255), - }; + { midBlue, new Color(153, 153, 255), + // Color.lightGray, + new Color(204, 204, 255), }; + public static final float[] pidThresholds = - { - 80, 60, 40, }; + { 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 @@ -843,17 +845,27 @@ public class ResidueProperties Phe.addElement("TTT"); } - //Stores residue codes/names and colours and other things + // Stores residue codes/names and colours and other things public static Hashtable propHash = new Hashtable(); + public static Hashtable hydrophobic = new Hashtable(); + public static Hashtable polar = new Hashtable(); + public static Hashtable small = new Hashtable(); + public static Hashtable positive = new Hashtable(); + public static Hashtable negative = new Hashtable(); + public static Hashtable charged = new Hashtable(); + public static Hashtable aromatic = new Hashtable(); + public static Hashtable aliphatic = new Hashtable(); + public static Hashtable tiny = new Hashtable(); + public static Hashtable proline = new Hashtable(); static @@ -1006,7 +1018,9 @@ public class ResidueProperties 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("N", new Integer(0)); // Asparagine is polar but not charged. + // Alternative would be charged and + // negative (in basic form)? charged.put("S", new Integer(0)); charged.put("T", new Integer(0)); charged.put("P", new Integer(0)); @@ -1181,10 +1195,9 @@ 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; @@ -1200,8 +1213,14 @@ public class ResidueProperties return null; } - public static String codonTranslate(String codon) + public static String codonTranslate(String lccodon) { + String codon = lccodon.toUpperCase(); + // all base ambiguity codes yield an 'X' amino acid residue + if (codon.indexOf('X') > -1 || codon.indexOf('N') > -1) + { + return "X"; + } Enumeration e = codonHash.keys(); while (e.hasMoreElements()) @@ -1209,7 +1228,7 @@ public class ResidueProperties String key = (String) e.nextElement(); Vector tmp = (Vector) codonHash.get(key); - if (tmp.contains(codon.toUpperCase())) + if (tmp.contains(codon)) { return key; } @@ -1230,6 +1249,7 @@ public class ResidueProperties /** * get a ScoreMatrix based on its string name + * * @param pwtype * @return matrix in scoreMatrices with key pwtype or null */ @@ -1254,7 +1274,8 @@ public class ResidueProperties } public static Hashtable toDssp3State; - static { + static + { toDssp3State = new Hashtable(); toDssp3State.put("H", "H"); toDssp3State.put("E", "E"); @@ -1266,28 +1287,122 @@ 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 ["); + Enumeration props = ((Vector) aa.get(rname)).elements(); + while (props.hasMoreElements()) + { + System.out.print("'" + (String) props.nextElement() + "'"); + if (props.hasMoreElements()) + { + System.out.println(", "); + } + } + System.out.println("]" + (res.hasMoreElements() ? "," : "")); + } + System.out.println("};"); + } + // to here }