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ResidueProperties.java

/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, 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 <http://www.gnu.org/licenses/>.
 */
package jalview.schemes;

import java.util.*;

import java.awt.*;

00024 public class ResidueProperties
{
  public static Hashtable scoreMatrices = new Hashtable();

  // Stores residue codes/names and colours and other things
  public static final int[] aaIndex; // aaHash version 2.1.1 and below

  public static final int[] nucleotideIndex;

  public static final Hashtable aa3Hash = new Hashtable();

  public static final Hashtable aa2Triplet = new Hashtable();

  public static final Hashtable nucleotideName = new Hashtable();

  static
  {
    aaIndex = new int[255];
    for (int i = 0; i < 255; i++)
    {
      aaIndex[i] = 23;
    }

    aaIndex['A'] = 0;
    aaIndex['R'] = 1;
    aaIndex['N'] = 2;
    aaIndex['D'] = 3;
    aaIndex['C'] = 4;
    aaIndex['Q'] = 5;
    aaIndex['E'] = 6;
    aaIndex['G'] = 7;
    aaIndex['H'] = 8;
    aaIndex['I'] = 9;
    aaIndex['L'] = 10;
    aaIndex['K'] = 11;
    aaIndex['M'] = 12;
    aaIndex['F'] = 13;
    aaIndex['P'] = 14;
    aaIndex['S'] = 15;
    aaIndex['T'] = 16;
    aaIndex['W'] = 17;
    aaIndex['Y'] = 18;
    aaIndex['V'] = 19;
    aaIndex['B'] = 20;
    aaIndex['Z'] = 21;
    aaIndex['X'] = 22;
    aaIndex['U'] = 22;
    aaIndex['a'] = 0;
    aaIndex['r'] = 1;
    aaIndex['n'] = 2;
    aaIndex['d'] = 3;
    aaIndex['c'] = 4;
    aaIndex['q'] = 5;
    aaIndex['e'] = 6;
    aaIndex['g'] = 7;
    aaIndex['h'] = 8;
    aaIndex['i'] = 9;
    aaIndex['l'] = 10;
    aaIndex['k'] = 11;
    aaIndex['m'] = 12;
    aaIndex['f'] = 13;
    aaIndex['p'] = 14;
    aaIndex['s'] = 15;
    aaIndex['t'] = 16;
    aaIndex['w'] = 17;
    aaIndex['y'] = 18;
    aaIndex['v'] = 19;
    aaIndex['b'] = 20;
    aaIndex['z'] = 21;
    aaIndex['x'] = 22;
    aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also
    // extend subt. matrices
  }

  static
  {
    nucleotideIndex = new int[255];
    for (int i = 0; i < 255; i++)
    {
      nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps.
    }

    nucleotideIndex['A'] = 0;
    nucleotideIndex['a'] = 0;
    nucleotideIndex['C'] = 1;
    nucleotideIndex['c'] = 1;
    nucleotideIndex['G'] = 2;
    nucleotideIndex['g'] = 2;
    nucleotideIndex['T'] = 3;
    nucleotideIndex['t'] = 3;
    nucleotideIndex['U'] = 4;
    nucleotideIndex['u'] = 4;
    nucleotideIndex['I'] = 5;
    nucleotideIndex['i'] = 5;
    nucleotideIndex['X'] = 6;
    nucleotideIndex['x'] = 6;
    nucleotideIndex['R'] = 7;
    nucleotideIndex['r'] = 7;
    nucleotideIndex['Y'] = 8;
    nucleotideIndex['y'] = 8;
    nucleotideIndex['N'] = 9;
    nucleotideIndex['n'] = 9;

    nucleotideName.put("A", "Adenine");
    nucleotideName.put("a", "Adenine");
    nucleotideName.put("G", "Guanine");
    nucleotideName.put("g", "Guanine");
    nucleotideName.put("C", "Cytosine");
    nucleotideName.put("c", "Cytosine");
    nucleotideName.put("T", "Thymine");
    nucleotideName.put("t", "Thymine");
    nucleotideName.put("U", "Uracil");
    nucleotideName.put("u", "Uracil");
    nucleotideName.put("I", "Inosine");
    nucleotideName.put("i", "Inosine");
    nucleotideName.put("X", "Xanthine");
    nucleotideName.put("x", "Xanthine");
    nucleotideName.put("R", "Unknown Purine");
    nucleotideName.put("r", "Unknown Purine");
    nucleotideName.put("Y", "Unknown Pyrimidine");
    nucleotideName.put("y", "Unknown Pyrimidine");
    nucleotideName.put("N", "Unknown");
    nucleotideName.put("n", "Unknown");
  }

  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));
    // 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));
  }

  static
  {
    aa2Triplet.put("A", "ALA");
    aa2Triplet.put("a", "ALA");
    aa2Triplet.put("R", "ARG");
    aa2Triplet.put("r", "ARG");
    aa2Triplet.put("N", "ASN");
    aa2Triplet.put("n", "ASN");
    aa2Triplet.put("D", "ASP");
    aa2Triplet.put("d", "ASP");
    aa2Triplet.put("C", "CYS");
    aa2Triplet.put("c", "CYS");
    aa2Triplet.put("Q", "GLN");
    aa2Triplet.put("q", "GLN");
    aa2Triplet.put("E", "GLU");
    aa2Triplet.put("e", "GLU");
    aa2Triplet.put("G", "GLY");
    aa2Triplet.put("g", "GLY");
    aa2Triplet.put("H", "HIS");
    aa2Triplet.put("h", "HIS");
    aa2Triplet.put("I", "ILE");
    aa2Triplet.put("i", "ILE");
    aa2Triplet.put("L", "LEU");
    aa2Triplet.put("l", "LEU");
    aa2Triplet.put("K", "LYS");
    aa2Triplet.put("k", "LYS");
    aa2Triplet.put("M", "MET");
    aa2Triplet.put("m", "MET");
    aa2Triplet.put("F", "PHE");
    aa2Triplet.put("f", "PHE");
    aa2Triplet.put("P", "PRO");
    aa2Triplet.put("p", "PRO");
    aa2Triplet.put("S", "SER");
    aa2Triplet.put("s", "SER");
    aa2Triplet.put("T", "THR");
    aa2Triplet.put("t", "THR");
    aa2Triplet.put("W", "TRP");
    aa2Triplet.put("w", "TRP");
    aa2Triplet.put("Y", "TYR");
    aa2Triplet.put("y", "TYR");
    aa2Triplet.put("V", "VAL");
    aa2Triplet.put("v", "VAL");
  }

  public static final String[] aa =
  { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F",
      "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "_", "*", ".", " " };

  public static final Color midBlue = new Color(100, 100, 255);

  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
      Color.white, // -
      Color.white, // *
      Color.white // .
  };

  public static final Color[] nucleotide =
  { new Color(100, 247, 63), // A
      new Color(255, 179, 64), // C
      new Color(235, 65, 60), // G
      new Color(60, 136, 238), // T
      new Color(60, 136, 238), // U
      Color.white, // I
      Color.white, // X
      Color.white, // R
      Color.white, // Y
      Color.white, // N
      Color.white, // Gap
  };

  // Zappo
  public static final Color[] zappo =
  { Color.pink, // A
      midBlue, // R
      Color.green, // N
      Color.red, // D
      Color.yellow, // C
      Color.green, // Q
      Color.red, // E
      Color.magenta, // G
      midBlue,// Color.red, // H
      Color.pink, // I
      Color.pink, // L
      midBlue, // K
      Color.pink, // M
      Color.orange, // F
      Color.magenta, // P
      Color.green, // S
      Color.green, // T
      Color.orange, // W
      Color.orange, // Y
      Color.pink, // V
      Color.white, // B
      Color.white, // Z
      Color.white, // X
      Color.white, // -
      Color.white, // *
      Color.white, // .
      Color.white // ' '
  };

  // Dunno where I got these numbers from
  public static final double[] hyd2 =
  { 0.62, // A
      0.29, // R
      -0.90, // N
      -0.74, // D
      1.19, // C
      0.48, // Q
      -0.40, // E
      1.38, // G
      -1.50, // H
      1.06, // I
      0.64, // L
      -0.78, // K
      0.12, // M
      -0.85, // F
      -2.53, // P
      -0.18, // S
      -0.05, // T
      1.08, // W
      0.81, // Y
      0.0, // V
      0.26, // B
      0.0, // Z
      0.0 // X
  };

  public static final double[] helix =
  { 1.42, 0.98, 0.67, 1.01, 0.70, 1.11, 1.51, 0.57, 1.00, 1.08, 1.21, 1.16,
      1.45, 1.13, 0.57, 0.77, 0.83, 1.08, 0.69, 1.06, 0.84, 1.31, 1.00, 0.0 };

  public static final double helixmin = 0.57;

  public static final double helixmax = 1.51;

  public static final double[] strand =
  { 0.83, 0.93, 0.89, 0.54, 1.19, 1.10, 0.37, 0.75, 0.87, 1.60, 1.30, 0.74,
      1.05, 1.38, 0.55, 0.75, 1.19, 1.37, 1.47, 1.70, 0.72, 0.74, 1.0, 0.0 };

  public static final double strandmin = 0.37;

  public static final double strandmax = 1.7;

  public static final double[] turn =
  { 0.66, 0.95, 1.56, 1.46, 1.19, 0.98, 0.74, 1.56, 0.95, 0.47, 0.59, 1.01,
      0.60, 0.60, 1.52, 1.43, 0.96, 0.96, 1.14, 0.50, 1.51, 0.86, 1.00, 0,
      0 };

  public static final double turnmin = 0.47;

  public static final double turnmax = 1.56;

  public static final double[] buried =
  { 1.7, 0.1, 0.4, 0.4, 4.6, 0.3, 0.3, 1.8, 0.8, 3.1, 2.4, 0.05, 1.9, 2.2,
      0.6, 0.8, 0.7, 1.6, 0.5, 2.9, 0.4, 0.3, 1.358, 0.00 };

  public static final double buriedmin = 0.05;

  public static final double buriedmax = 4.6;

  // This is hydropathy index
  // Kyte, J., and Doolittle, R.F., J. Mol. Biol.
  // 1157, 105-132, 1982
  public static final double[] hyd =
  { 1.8, -4.5, -3.5, -3.5, 2.5, -3.5, -3.5, -0.4, -3.2, 4.5, 3.8, -3.9,
      1.9, 2.8, -1.6, -0.8, -0.7, -0.9, -1.3, 4.2, -3.5, -3.5, -0.49, 0.0 };

  public static final double hydmax = 4.5;

  public static final double hydmin = -3.9;

  // public static final double hydmax = 1.38;
  // public static final double hydmin = -2.53;
  private static final int[][] BLOSUM62 =
  {
      { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3,
          -2, 0, -2, -1, 0, -4 },
      { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3,
          -2, -3, -1, 0, -1, -4 },
      { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2,
          -3, 3, 0, -1, -4 },
      { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4,
          -3, -3, 4, 1, -1, -4 },
      { 0, 3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1,
          -2, -2, -1, -3, -3, -2, -4 },
      { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1,
          -2, 0, 3, -1, -4 },
      { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2,
          -2, 1, 4, -1, -4 },
      { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2,
          -3, -3, -1, -2, -1, -4 },
      { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2,
          2, -3, 0, 0, -1, -4 },
      { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3,
          -1, 3, -3, -3, -1, -4 },
      { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2,
          -1, 1, -4, -3, -1, -4 },
      { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3,
          -2, -2, 0, 1, -1, -4 },
      { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1,
          -1, 1, -3, -1, -1, -4 },
      { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1,
          3, -1, -3, -3, -1, -4 },
      { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1,
          -4, -3, -2, -2, -1, -2, -4 },
      { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2,
          -2, 0, 0, 0, -4 },
      { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2,
          -2, 0, -1, -1, 0, -4 },
      { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2,
          11, 2, -3, -4, -3, -2, -4 },
      { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2,
          2, 7, -1, -3, -2, -1, -4 },
      { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3,
          -1, 4, -3, -2, -1, -4 },
      { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4,
          -3, -3, 4, 1, -1, -4 },
      { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2,
          -2, 1, 4, -1, -4 },
      { 0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0,
          -2, -1, -1, -1, -1, -1, -4 },
      { -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4,
          -4, -4, -4, -4, -4, -4, 1 }, };

  static final int[][] PAM250 =
  {
      { 2, -2, 0, 0, -2, 0, 0, 1, -1, -1, -2, -1, -1, -3, 1, 1, 1, -6, -3,
          0, 0, 0, 0, -8 },
      { -2, 6, 0, -1, -4, 1, -1, -3, 2, -2, -3, 3, 0, -4, 0, 0, -1, 2, -4,
          -2, -1, 0, -1, -8 },
      { 0, 0, 2, 2, -4, 1, 1, 0, 2, -2, -3, 1, -2, -3, 0, 1, 0, -4, -2, -2,
          2, 1, 0, -8 },
      { 0, -1, 2, 4, -5, 2, 3, 1, 1, -2, -4, 0, -3, -6, -1, 0, 0, -7, -4,
          -2, 3, 3, -1, -8 },
      { -2, -4, -4, -5, 12, -5, -5, -3, -3, -2, -6, -5, -5, -4, -3, 0, -2,
          -8, 0, -2, -4, -5, -3, -8 },
      { 0, 1, 1, 2, -5, 4, 2, -1, 3, -2, -2, 1, -1, -5, 0, -1, -1, -5, -4,
          -2, 1, 3, -1, -8 },
      { 0, -1, 1, 3, -5, 2, 4, 0, 1, -2, -3, 0, -2, -5, -1, 0, 0, -7, -4,
          -2, 3, 3, -1, -8 },
      { 1, -3, 0, 1, -3, -1, 0, 5, -2, -3, -4, -2, -3, -5, 0, 1, 0, -7, -5,
          -1, 0, 0, -1, -8 },
      { -1, 2, 2, 1, -3, 3, 1, -2, 6, -2, -2, 0, -2, -2, 0, -1, -1, -3, 0,
          -2, 1, 2, -1, -8 },
      { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5, 2, -2, 2, 1, -2, -1, 0, -5,
          -1, 4, -2, -2, -1, -8 },
      { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6, -3, 4, 2, -3, -3, -2, -2,
          -1, 2, -3, -3, -1, -8 },
      { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5, 0, -5, -1, 0, 0, -3, -4,
          -2, 1, 0, -1, -8 },
      { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6, 0, -2, -2, -1, -4,
          -2, 2, -2, -2, -1, -8 },
      { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9, -5, -3, -3, 0,
          7, -1, -4, -5, -2, -8 },
      { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6, 1, 0, -6, -5,
          -1, -1, 0, -1, -8 },
      { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2, 1, -2, -3,
          -1, 0, 0, 0, -8 },
      { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3, -5, -3,
          0, 0, -1, 0, -8 },
      { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5,
          17, 0, -6, -5, -6, -4, -8 },
      { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0,
          10, -2, -3, -4, -2, -8 },
      { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6,
          -2, 4, -2, -2, -1, -8 },
      { 0, -1, 2, 3, -4, 1, 3, 0, 1, -2, -3, 1, -2, -4, -1, 0, 0, -5, -3,
          -2, 3, 2, -1, -8 },
      { 0, 0, 1, 3, -5, 3, 3, 0, 2, -2, -3, 0, -2, -5, 0, 0, -1, -6, -4,
          -2, 2, 3, -1, -8 },
      { 0, -1, 0, -1, -3, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, 0, 0, -4,
          -2, -1, -1, -1, -1, -8 },
      { -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8, -8,
          -8, -8, -8, -8, -8, -8, 1 }, };

  public static final Hashtable ssHash = new Hashtable(); // stores the number
  // value of the aa

  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 =
  {
  { 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
   */
  static
  {
    scoreMatrices.put("BLOSUM62", new ScoreMatrix("BLOSUM62", BLOSUM62, 0));
    scoreMatrices.put("PAM250", new ScoreMatrix("PAM250", PAM250, 0));
    scoreMatrices.put("DNA", new ScoreMatrix("DNA", DNA, 1));
  }

  public static final Color[] pidColours =
  { midBlue, new Color(153, 153, 255),
      // Color.lightGray,
      new Color(204, 204, 255), };

  public static final float[] pidThresholds =
  { 80, 60, 40, };

  public static Hashtable codonHash = new Hashtable();

  public static Vector Lys = new Vector();

  public static Vector Asn = new Vector();

  public static Vector Gln = new Vector();

  public static Vector His = new Vector();

  public static Vector Glu = new Vector();

  public static Vector Asp = new Vector();

  public static Vector Tyr = new Vector();

  public static Vector Thr = new Vector();

  public static Vector Pro = new Vector();

  public static Vector Ala = new Vector();

  public static Vector Ser = new Vector();

  public static Vector Arg = new Vector();

  public static Vector Gly = new Vector();

  public static Vector Trp = new Vector();

  public static Vector Cys = new Vector();

  public static Vector Ile = new Vector();

  public static Vector Met = new Vector();

  public static Vector Leu = new Vector();

  public static Vector Val = new Vector();

  public static Vector Phe = new Vector();

  public static Vector STOP = new Vector();

  static
  {
    codonHash.put("K", Lys);
    codonHash.put("N", Asn);
    codonHash.put("Q", Gln);
    codonHash.put("H", His);
    codonHash.put("E", Glu);
    codonHash.put("D", Asp);
    codonHash.put("Y", Tyr);
    codonHash.put("T", Thr);
    codonHash.put("P", Pro);
    codonHash.put("A", Ala);
    codonHash.put("S", Ser);
    codonHash.put("R", Arg);
    codonHash.put("G", Gly);
    codonHash.put("W", Trp);
    codonHash.put("C", Cys);
    codonHash.put("I", Ile);
    codonHash.put("M", Met);
    codonHash.put("L", Leu);
    codonHash.put("V", Val);
    codonHash.put("F", Phe);
    codonHash.put("STOP", STOP);
  }

  public static Hashtable codonHash2 = new Hashtable();

  static
  {
    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("CAC", "H");
    codonHash2.put("CAT", "H");

    codonHash2.put("GAA", "Q");
    codonHash2.put("GAG", "Q");
    codonHash2.put("GAC", "D");
    codonHash2.put("GAT", "D");

    codonHash2.put("TAC", "Y");
    codonHash2.put("TAT", "Y");

    codonHash2.put("ACA", "T");
    codonHash2.put("AAG", "T");
    codonHash2.put("ACC", "T");
    codonHash2.put("ACT", "T");

    codonHash2.put("CCA", "P");
    codonHash2.put("CCG", "P");
    codonHash2.put("CCC", "P");
    codonHash2.put("CCT", "P");

    codonHash2.put("GCA", "A");
    codonHash2.put("GCG", "A");
    codonHash2.put("GCC", "A");
    codonHash2.put("GCT", "A");

    codonHash2.put("TCA", "S");
    codonHash2.put("TCG", "S");
    codonHash2.put("TCC", "S");
    codonHash2.put("TCT", "S");
    codonHash2.put("AGC", "S");
    codonHash2.put("AGT", "S");

    codonHash2.put("AGA", "R");
    codonHash2.put("AGG", "R");
    codonHash2.put("CGA", "R");
    codonHash2.put("CGG", "R");
    codonHash2.put("CGC", "R");
    codonHash2.put("CGT", "R");

    codonHash2.put("GGA", "G");
    codonHash2.put("GGG", "G");
    codonHash2.put("GGC", "G");
    codonHash2.put("GGT", "G");

    codonHash2.put("TGA", "*");
    codonHash2.put("TAA", "*");
    codonHash2.put("TAG", "*");

    codonHash2.put("TGG", "W");

    codonHash2.put("TGC", "C");
    codonHash2.put("TGT", "C");

    codonHash2.put("ATA", "I");
    codonHash2.put("ATC", "I");
    codonHash2.put("ATT", "I");

    codonHash2.put("ATG", "M");

    codonHash2.put("CTA", "L");
    codonHash2.put("CTG", "L");
    codonHash2.put("CTC", "L");
    codonHash2.put("CTT", "L");
    codonHash2.put("TTA", "L");
    codonHash2.put("TTG", "L");

    codonHash2.put("GTA", "V");
    codonHash2.put("GTG", "V");
    codonHash2.put("GTC", "V");
    codonHash2.put("GTT", "V");

    codonHash2.put("TTC", "F");
    codonHash2.put("TTT", "F");
  }

  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");
  }

  // 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
  {
    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));
  }

  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));
  }

  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));
  }

  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));
  }

  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));
  }

  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(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));
    charged.put("-", new Integer(1));
    charged.put("*", new Integer(1));
  }

  static
  {
    aromatic.put("I", new Integer(0));
    aromatic.put("L", new Integer(0));
    aromatic.put("V", new Integer(0));
    aromatic.put("C", new Integer(0));
    aromatic.put("A", new Integer(0));
    aromatic.put("G", new Integer(0));
    aromatic.put("M", new Integer(0));
    aromatic.put("F", new Integer(1));
    aromatic.put("Y", new Integer(1));
    aromatic.put("W", new Integer(1));
    aromatic.put("H", new Integer(1));
    aromatic.put("K", new Integer(0));
    aromatic.put("R", new Integer(0));
    aromatic.put("E", new Integer(0));
    aromatic.put("Q", new Integer(0));
    aromatic.put("D", new Integer(0));
    aromatic.put("N", new Integer(0));
    aromatic.put("S", new Integer(0));
    aromatic.put("T", new Integer(0));
    aromatic.put("P", new Integer(0));
    aromatic.put("-", new Integer(1));
    aromatic.put("*", new Integer(1));
  }

  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));
  }

  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));
  }

  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));
  }

  static
  {
    propHash.put("hydrophobic", hydrophobic);
    propHash.put("small", small);
    propHash.put("positive", positive);
    propHash.put("negative", negative);
    propHash.put("charged", charged);
    propHash.put("aromatic", aromatic);
    propHash.put("aliphatic", aliphatic);
    propHash.put("tiny", tiny);
    propHash.put("proline", proline);
    propHash.put("polar", polar);
  }

  private ResidueProperties()
  {
  }

  public static double getHydmax()
  {
    return hydmax;
  }

  public static double getHydmin()
  {
    return hydmin;
  }

  public static double[] getHyd()
  {
    return hyd;
  }

  public static Hashtable getAA3Hash()
  {
    return aa3Hash;
  }

  public static int[][] getDNA()
  {
    return ResidueProperties.DNA;
  }

  public static int[][] getBLOSUM62()
  {
    return ResidueProperties.BLOSUM62;
  }

  public static int getPAM250(String A1, String A2)
  {
    return getPAM250(A1.charAt(0), A2.charAt(0));
  }

  public static int getBLOSUM62(char c1, char c2)
  {
    int pog = 0;

    try
    {
      int a = aaIndex[c1];
      int b = aaIndex[c2];

      pog = ResidueProperties.BLOSUM62[a][b];
    } catch (Exception e)
    {
      // System.out.println("Unknown residue in " + A1 + " " + A2);
    }

    return pog;
  }

  public static Vector getCodons(String res)
  {
    if (codonHash.containsKey(res))
    {
      return (Vector) codonHash.get(res);
    }

    return null;
  }

  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())
    {
      String key = (String) e.nextElement();
      Vector tmp = (Vector) codonHash.get(key);

      if (tmp.contains(codon))
      {
        return key;
      }
    }

    return null;
  }

  public static int[][] getDefaultPeptideMatrix()
  {
    return ResidueProperties.getBLOSUM62();
  }

  public static int[][] getDefaultDnaMatrix()
  {
    return ResidueProperties.getDNA();
  }

  /**
   * get a ScoreMatrix based on its string name
   * 
   * @param pwtype
   * @return matrix in scoreMatrices with key pwtype or null
   */
01198   public static ScoreMatrix getScoreMatrix(String pwtype)
  {
    Object val = scoreMatrices.get(pwtype);
    if (val != null)
    {
      return (ScoreMatrix) val;
    }
    return null;
  }

  public static int getPAM250(char c, char d)
  {
    int a = aaIndex[c];
    int b = aaIndex[d];

    int pog = ResidueProperties.PAM250[a][b];

    return pog;
  }

  public static Hashtable toDssp3State;
  static
  {
    toDssp3State = new Hashtable();
    toDssp3State.put("H", "H");
    toDssp3State.put("E", "E");
    toDssp3State.put("C", " ");
    toDssp3State.put(" ", " ");
    toDssp3State.put("T", " ");
    toDssp3State.put("B", "E");
    toDssp3State.put("G", "H");
    toDssp3State.put("I", "H");
    toDssp3State.put("X", " ");
  }

  /**
   * translate from other dssp secondary structure alphabets to 3-state
   * 
   * @param ssstring
   * @return ssstring as a three-state secondary structure assignment.
   */
01239   public static String getDssp3state(String ssstring)
  {
    if (ssstring == null)
    {
      return null;
    }
    StringBuffer ss = new StringBuffer();
    for (int i = 0; i < ssstring.length(); i++)
    {
      String ssc = ssstring.substring(i, i + 1);
      if (toDssp3State.containsKey(ssc))
      {
        ss.append((String) toDssp3State.get(ssc));
      }
      else
      {
        ss.append(" ");
      }
    }
    return ss.toString();
  }

  // main method generates perl representation of residue property hash
  // / cut here
  public static void main(String[] args)
  {
    Hashtable aa = new Hashtable();
    System.out.println("my %aa = {");
    // invert property hashes
    Enumeration prop = propHash.keys();
    while (prop.hasMoreElements())
    {
      String pname = (String) prop.nextElement();
      Hashtable phash = (Hashtable) propHash.get(pname);
      Enumeration res = phash.keys();
      while (res.hasMoreElements())
      {
        String rname = (String) res.nextElement();
        Vector aprops = (Vector) aa.get(rname);
        if (aprops == null)
        {
          aprops = new Vector();
          aa.put(rname, aprops);
        }
        Integer hasprop = (Integer) phash.get(rname);
        if (hasprop.intValue() == 1)
        {
          aprops.addElement(pname);
        }
      }
    }
    Enumeration res = aa.keys();
    while (res.hasMoreElements())
    {
      String rname = (String) res.nextElement();

      System.out.print("'" + rname + "' => [");
      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
}

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