X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=092971d762ae5f7097cd599d6135115b5d1d09f9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=77938dddc67929e28bd1cd78a69b115289a08d14;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 77938dd..092971d 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -1,41 +1,57 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * - * 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 file is part of Jalview. * - * 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 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 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.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(); + 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 int[] purinepyrimidineIndex; + + public static final Map aa3Hash = new HashMap(); + + public static final Map aa2Triplet = new HashMap(); - public static final Hashtable aa2Triplet = new Hashtable(); + public static final Map nucleotideName = new HashMap(); - public static final Hashtable nucleotideName = new Hashtable(); + // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET) + public static final Map modifications = new HashMap(); static { @@ -93,15 +109,25 @@ public class ResidueProperties aaIndex['z'] = 21; aaIndex['x'] = 22; aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also - // extend subt. matrices + // 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; @@ -145,6 +171,54 @@ 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 @@ -224,9 +298,9 @@ 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 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); @@ -246,8 +320,8 @@ public class ResidueProperties scaleColours.addElement(Color.white); } - public static final Color[] taylor = - { new Color(204, 255, 0), // A Greenish-yellowy-yellow + 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 @@ -275,17 +349,29 @@ public class ResidueProperties 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 @@ -315,8 +401,7 @@ public class ResidueProperties }; // Dunno where I got these numbers from - public static final double[] hyd2 = - { 0.62, // A + public static final double[] hyd2 = { 0.62, // A 0.29, // R -0.90, // N -0.74, // D @@ -341,34 +426,33 @@ public class ResidueProperties 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[] 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; @@ -377,9 +461,9 @@ public class ResidueProperties // 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; @@ -387,8 +471,7 @@ public class ResidueProperties // public static final double hydmax = 1.38; // public static final double hydmin = -2.53; - private static final int[][] BLOSUM62 = - { + 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, @@ -438,8 +521,7 @@ public class ResidueProperties { -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 = - { + 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, @@ -490,7 +572,7 @@ public class ResidueProperties -8, -8, -8, -8, -8, -8, 1 }, }; public static final Hashtable ssHash = new Hashtable(); // stores the number - // value of the aa + // value of the aa static { @@ -505,13 +587,27 @@ public class ResidueProperties ssHash.put("B", Color.yellow); } - 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 }, // - + /* + * new Color(60, 136, 238), // U Color.white, // I Color.white, // X + * Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap + */ + + // JBPNote: patch matrix for T/U equivalence when working with DNA or RNA. + // Will equate sequences if working with mixed nucleotide sets. + // treats T and U identically. R and Y weak equivalence with AG and CTU. + // N matches any other base weakly + // + static final int[][] DNA = { { 10, -8, -8, -8, -8, 1, 1, 1, -8, 1, 1 }, // A + { -8, 10, -8, -8, -8, 1, 1, -8, 1, 1, 1 }, // C + { -8, -8, 10, -8, -8, 1, 1, 1, -8, 1, 1 }, // G + { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // T + { -8, -8, -8, 10, 10, 1, 1, -8, 1, 1, 1 }, // U + { 1, 1, 1, 1, 1, 10, 0, 0, 0, 1, 1 }, // I + { 1, 1, 1, 1, 1, 0, 10, 0, 0, 1, 1 }, // X + { 1, -8, 1, -8, -8, 0, 0, 10, -8, 1, 1 }, // R + { -8, 1, -8, 1, 1, 0, 0, -8, 10, 1, 1 }, // Y + { 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1 }, // N + { 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }, // - }; /** * register matrices in list @@ -521,59 +617,61 @@ public class ResidueProperties 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, + 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 final float[] pidThresholds = { 80, 60, 40, }; + + public static Map> codonHash = new HashMap>(); - public static Hashtable codonHash = new Hashtable(); + private static List Lys = new ArrayList(); - public static Vector Lys = new Vector(); + private static List Asn = new ArrayList(); - public static Vector Asn = new Vector(); + private static List Gln = new ArrayList(); - public static Vector Gln = new Vector(); + private static List His = new ArrayList(); - public static Vector His = new Vector(); + private static List Glu = new ArrayList(); - public static Vector Glu = new Vector(); + private static List Asp = new ArrayList(); - public static Vector Asp = new Vector(); + private static List Tyr = new ArrayList(); - public static Vector Tyr = new Vector(); + private static List Thr = new ArrayList(); - public static Vector Thr = new Vector(); + private static List Pro = new ArrayList(); - public static Vector Pro = new Vector(); + private static List Ala = new ArrayList(); - public static Vector Ala = new Vector(); + private static List Ser = new ArrayList(); - public static Vector Ser = new Vector(); + private static List Arg = new ArrayList(); - public static Vector Arg = new Vector(); + private static List Gly = new ArrayList(); - public static Vector Gly = new Vector(); + private static List Trp = new ArrayList(); - public static Vector Trp = new Vector(); + private static List Cys = new ArrayList(); - public static Vector Cys = new Vector(); + private static List Ile = new ArrayList(); - public static Vector Ile = new Vector(); + private static List Met = new ArrayList(); - public static Vector Met = new Vector(); + private static List Leu = new ArrayList(); - public static Vector Leu = new Vector(); + private static List Val = new ArrayList(); - public static Vector Val = new Vector(); + private static List Phe = new ArrayList(); - public static Vector Phe = new Vector(); + public static List STOP = new ArrayList(); - public static Vector STOP = new Vector(); + public static String START = "ATG"; static { @@ -600,22 +698,52 @@ public class ResidueProperties codonHash.put("STOP", STOP); } - public static Hashtable codonHash2 = new Hashtable(); + /** + * 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"); @@ -623,9 +751,9 @@ 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"); @@ -685,91 +813,229 @@ public class ResidueProperties codonHash2.put("TTC", "F"); codonHash2.put("TTT", "F"); + + buildAmbiguityCodonSet(); + } + + /** + * programmatic generation of codons including ambiguity codes + */ + public static void buildAmbiguityCodonSet() + { + if (_ambiguityCodes.size() > 0) + { + System.err + .println("Ignoring multiple calls to buildAmbiguityCodonSet"); + return; + } + // Invert the ambiguity code set + for (Map.Entry 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 = ""; + char _anuc; + 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--; + } + } + } + } static { - Lys.addElement("AAA"); - Lys.addElement("AAG"); - Asn.addElement("AAC"); - Asn.addElement("AAT"); - - Gln.addElement("CAA"); - Gln.addElement("CAG"); - His.addElement("CAC"); - His.addElement("CAT"); - - Glu.addElement("GAA"); - Glu.addElement("GAG"); - Asp.addElement("GAC"); - Asp.addElement("GAT"); - - Tyr.addElement("TAC"); - Tyr.addElement("TAT"); - - Thr.addElement("ACA"); - Thr.addElement("ACG"); - Thr.addElement("ACC"); - Thr.addElement("ACT"); - - Pro.addElement("CCA"); - Pro.addElement("CCG"); - Pro.addElement("CCC"); - Pro.addElement("CCT"); - - Ala.addElement("GCA"); - Ala.addElement("GCG"); - Ala.addElement("GCC"); - Ala.addElement("GCT"); - - Ser.addElement("TCA"); - Ser.addElement("TCG"); - Ser.addElement("TCC"); - Ser.addElement("TCT"); - Ser.addElement("AGC"); - Ser.addElement("AGT"); - - Arg.addElement("AGA"); - Arg.addElement("AGG"); - Arg.addElement("CGA"); - Arg.addElement("CGG"); - Arg.addElement("CGC"); - Arg.addElement("CGT"); - - Gly.addElement("GGA"); - Gly.addElement("GGG"); - Gly.addElement("GGC"); - Gly.addElement("GGT"); - - STOP.addElement("TGA"); - STOP.addElement("TAA"); - STOP.addElement("TAG"); - - Trp.addElement("TGG"); - - Cys.addElement("TGC"); - Cys.addElement("TGT"); - - Ile.addElement("ATA"); - Ile.addElement("ATC"); - Ile.addElement("ATT"); - - Met.addElement("ATG"); - - Leu.addElement("CTA"); - Leu.addElement("CTG"); - Leu.addElement("CTC"); - Leu.addElement("CTT"); - Leu.addElement("TTA"); - Leu.addElement("TTG"); - - Val.addElement("GTA"); - Val.addElement("GTG"); - Val.addElement("GTC"); - Val.addElement("GTT"); - - Phe.addElement("TTC"); - Phe.addElement("TTT"); + Lys.add("AAA"); + Lys.add("AAG"); + Asn.add("AAC"); + Asn.add("AAT"); + + Gln.add("CAA"); + Gln.add("CAG"); + His.add("CAC"); + His.add("CAT"); + + Glu.add("GAA"); + Glu.add("GAG"); + Asp.add("GAC"); + Asp.add("GAT"); + + Tyr.add("TAC"); + Tyr.add("TAT"); + + Thr.add("ACA"); + Thr.add("ACG"); + Thr.add("ACC"); + Thr.add("ACT"); + + Pro.add("CCA"); + Pro.add("CCG"); + Pro.add("CCC"); + Pro.add("CCT"); + + Ala.add("GCA"); + Ala.add("GCG"); + Ala.add("GCC"); + Ala.add("GCT"); + + Ser.add("TCA"); + Ser.add("TCG"); + Ser.add("TCC"); + Ser.add("TCT"); + Ser.add("AGC"); + Ser.add("AGT"); + + Arg.add("AGA"); + Arg.add("AGG"); + Arg.add("CGA"); + Arg.add("CGG"); + Arg.add("CGC"); + Arg.add("CGT"); + + Gly.add("GGA"); + Gly.add("GGG"); + Gly.add("GGC"); + Gly.add("GGT"); + + STOP.add("TGA"); + STOP.add("TAA"); + STOP.add("TAG"); + + Trp.add("TGG"); + + Cys.add("TGC"); + Cys.add("TGT"); + + Ile.add("ATA"); + Ile.add("ATC"); + Ile.add("ATT"); + + Met.add("ATG"); + + Leu.add("CTA"); + Leu.add("CTG"); + Leu.add("CTC"); + Leu.add("CTT"); + Leu.add("TTA"); + Leu.add("TTG"); + + Val.add("GTA"); + Val.add("GTG"); + Val.add("GTC"); + Val.add("GTT"); + + Phe.add("TTC"); + Phe.add("TTT"); } // Stores residue codes/names and colours and other things @@ -945,7 +1211,9 @@ 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)); @@ -1070,6 +1338,79 @@ 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 (Enumeration en = propHash.keys(); en.hasMoreElements();) + { + String ph = en.nextElement(); + Map pph = (Map) 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() { @@ -1090,7 +1431,7 @@ public class ResidueProperties return hyd; } - public static Hashtable getAA3Hash() + public static Map getAA3Hash() { return aa3Hash; } @@ -1138,16 +1479,31 @@ public class ResidueProperties return null; } - public static String codonTranslate(String codon) + public static String codonTranslate(String lccodon) { - Enumeration e = codonHash.keys(); - - while (e.hasMoreElements()) + if (false) + { + return _codonTranslate(lccodon); + } + String cdn = codonHash2.get(lccodon.toUpperCase()); + if ("*".equals(cdn)) { - String key = (String) e.nextElement(); - Vector tmp = (Vector) codonHash.get(key); + return "STOP"; + } + return cdn; + } - if (tmp.contains(codon.toUpperCase())) + 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"; + } + for (String key : codonHash.keySet()) + { + if (codonHash.get(key).contains(codon)) { return key; } @@ -1175,13 +1531,24 @@ public class ResidueProperties 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]; @@ -1235,6 +1602,141 @@ public class ResidueProperties return ss.toString(); } + /** + * Used by getRNASecStrucState + * + */ + public static Hashtable toRNAssState; + + public static boolean RNAcloseParen[] = new boolean[255]; + static + { + toRNAssState = new Hashtable(); + toRNAssState.put(")", "("); + toRNAssState.put("(", "("); + toRNAssState.put("]", "["); + toRNAssState.put("[", "["); + toRNAssState.put("{", "{"); + toRNAssState.put("}", "{"); + toRNAssState.put(">", ">"); + toRNAssState.put("<", ">"); + toRNAssState.put("A", "A"); + toRNAssState.put("a", "A"); + toRNAssState.put("B", "B"); + toRNAssState.put("b", "B"); + toRNAssState.put("C", "C"); + toRNAssState.put("c", "C"); + toRNAssState.put("D", "D"); + toRNAssState.put("d", "D"); + toRNAssState.put("E", "E"); + toRNAssState.put("e", "E"); + toRNAssState.put("F", "F"); + toRNAssState.put("f", "F"); + toRNAssState.put("G", "G"); + toRNAssState.put("g", "G"); + toRNAssState.put("H", "H"); + toRNAssState.put("h", "H"); + toRNAssState.put("I", "I"); + toRNAssState.put("i", "I"); + toRNAssState.put("J", "J"); + toRNAssState.put("j", "J"); + toRNAssState.put("K", "K"); + toRNAssState.put("k", "K"); + toRNAssState.put("L", "L"); + toRNAssState.put("l", "L"); + toRNAssState.put("M", "M"); + toRNAssState.put("m", "M"); + toRNAssState.put("N", "N"); + toRNAssState.put("n", "N"); + toRNAssState.put("O", "O"); + toRNAssState.put("o", "O"); + toRNAssState.put("P", "P"); + toRNAssState.put("p", "P"); + toRNAssState.put("Q", "Q"); + toRNAssState.put("q", "Q"); + toRNAssState.put("R", "R"); + toRNAssState.put("r", "R"); + toRNAssState.put("S", "S"); + toRNAssState.put("s", "S"); + toRNAssState.put("T", "T"); + toRNAssState.put("t", "T"); + toRNAssState.put("U", "U"); + toRNAssState.put("u", "U"); + toRNAssState.put("V", "V"); + toRNAssState.put("v", "V"); + toRNAssState.put("W", "W"); + toRNAssState.put("w", "W"); + toRNAssState.put("X", "X"); + toRNAssState.put("x", "X"); + toRNAssState.put("Y", "Y"); + toRNAssState.put("y", "Y"); + toRNAssState.put("Z", "Z"); + toRNAssState.put("z", "Z"); + for (int p = 0; p < RNAcloseParen.length; p++) + { + RNAcloseParen[p] = false; + } + for (String k : toRNAssState.keySet()) + { + RNAcloseParen[k.charAt(0)] = k.charAt(0) != toRNAssState.get(k) + .charAt(0); + } + } + + 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 + } + + public static String getCanonicalAminoAcid(String aa) + { + String canonical = modifications.get(aa); + return canonical == null ? aa : canonical; + } + + /** + * translate to RNA secondary structure representation + * + * @param ssstring + * @return ssstring as a RNA-state secondary structure assignment. + */ + public static String getRNASecStrucState(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 (toRNAssState.containsKey(ssc)) + { + // valid ss character - so return it + ss.append(ssc); // (String) toRNAssState.get(ssc)); + } + else + { + ss.append(" "); + } + } + return ss.toString(); + } + + public static boolean isCloseParenRNA(char dc) + { + return RNAcloseParen[dc]; + } + // main method generates perl representation of residue property hash // / cut here public static void main(String[] args) @@ -1283,5 +1785,74 @@ public class ResidueProperties } System.out.println("};"); } + // to here + + /** + * Returns a list of residue characters for the specified inputs + * + * @param nucleotide + * @param includeAmbiguous + * @return + */ + public static List getResidues(boolean nucleotide, + boolean includeAmbiguous) + { + List result = new ArrayList(); + if (nucleotide) + { + 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); + } }