// CPREV.java
//
// (c) 2000-2001 PAL Development Core Team
//
// This package may be distributed under the
// terms of the Lesser GNU General Public License (LGPL)


package pal.substmodel;

import pal.misc.*;
import pal.util.*;

import java.io.*;


/**
 * CPREV model of amino acid evolution (J.Adachi et al. 2000)
 * <i> Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA.
 * J. Adachi, P. Waddell, W. Martin and M. Hasegawa (2000) J. Mol. Evol., 50:348--358</i>
 *
 * @version $Id: CPREV.java,v 1.6 2003/11/13 04:05:39 matt Exp $
 *
 * @author Korbinian Strimmer
 * @author Alexei Drummond
 */
public class CPREV extends AminoAcidModel implements XMLConstants
{
	/**
	 * constructor
	 *
	 * @param f amino acid frequencies
	 */
	public CPREV(double[] f) {
		super(f);

	}

	// Get numerical code describing the model type
	public int getModelID()
	{
		return 6;
	}

	public void report(PrintWriter out)
	{
		out.println("Model of substitution: CPREV (Adachi et al. 2000)");
		out.println();
		printFrequencies(out);
	}

	/**
	 * get the frequencies of the original data set that
	 * formed the basis for the estimation of the rate matrix
	 *
	 * @param f array where amino acid frequencies will be stored
	 */
	public static void getOriginalFrequencies(double[] f)
	{
		f[0] = 0.076;
		f[1] = 0.062;
		f[2] = 0.041;
		f[3] = 0.037;
		f[4] = 0.009;
		f[5] = 0.038;
		f[6] = 0.049;
		f[7] = 0.084;
		f[8] = 0.025;
		f[9] = 0.081;
		f[10] = 0.101;
		f[11] = 0.050;
		f[12] = 0.022;
		f[13] = 0.051;
		f[14] = 0.043;
		f[15] = 0.062;
		f[16] = 0.054;
		f[17] = 0.018;
		f[18] = 0.031;
		f[19] = 0.066;
	}
	/**
	 * @return the frequencies of the original data set that
	 * formed the basis for the estimation of the rate matrix
	 */
	public static double[] getOriginalFrequencies() {
		double[] f = new double[20];
		getOriginalFrequencies(f);
		return f;
	}


	public String getUniqueName() {
		return CPREV;
	}

	//
	// Private stuff
	//

	// CPREV 45 model of amino acid evolution
	// Adachi, J., P.J. Waddell, W. Martin, and M. Hasegawa. 2000. JME 50:348-358
	protected void rebuildRateMatrix(double[][] rate, double[] parameters)
	{
		// Q matrix
		rate[0][1] = 105; rate[0][2] = 227;
		rate[0][3] = 175; rate[0][4] = 669;
		rate[0][5] = 157; rate[0][6] = 499;
		rate[0][7] = 665; rate[0][8] = 66;
		rate[0][9] = 145; rate[0][10] = 197;
		rate[0][11] = 236; rate[0][12] = 185;
		rate[0][13] = 68; rate[0][14] = 490;
		rate[0][15] = 2440; rate[0][16] = 1340;
		rate[0][17] = 14; rate[0][18] = 56;
		rate[0][19] = 968;

		rate[1][2] = 357; rate[1][3] = 43;
		rate[1][4] = 823; rate[1][5] = 1745;
		rate[1][6] = 152; rate[1][7] = 243;
		rate[1][8] = 715; rate[1][9] = 136;
		rate[1][10] = 203; rate[1][11] = 4482;
		rate[1][12] = 125; rate[1][13] = 53;
		rate[1][14] = 87; rate[1][15] = 385;
		rate[1][16] = 314; rate[1][17] = 230;
		rate[1][18] = 323; rate[1][19] = 92;

		rate[2][3] = 4435; rate[2][4] = 538;
		rate[2][5] = 768; rate[2][6] = 1055;
		rate[2][7] = 653; rate[2][8] = 1405;
		rate[2][9] = 168; rate[2][10] = 113;
		rate[2][11] = 2430; rate[2][12] = 61;
		rate[2][13] = 97; rate[2][14] = 173;
		rate[2][15] = 2085; rate[2][16] = 1393;
		rate[2][17] = 40; rate[2][18] = 754;
		rate[2][19] = 83;

		rate[3][4] = 10; rate[3][5] = 400;
		rate[3][6] = 3691; rate[3][7] = 431;
		rate[3][8] = 331; rate[3][9] = 10;
		rate[3][10] = 10; rate[3][11] = 412;
		rate[3][12] = 47; rate[3][13] = 22;
		rate[3][14] = 170; rate[3][15] = 590;
		rate[3][16] = 266; rate[3][17] = 18;
		rate[3][18] = 281; rate[3][19] = 75;

		rate[4][5] = 10; rate[4][6] = 10;
		rate[4][7] = 303; rate[4][8] = 441;
		rate[4][9] = 280; rate[4][10] = 396;
		rate[4][11] = 48; rate[4][12] = 159;
		rate[4][13] = 726; rate[4][14] = 285;
		rate[4][15] = 2331; rate[4][16] = 576;
		rate[4][17] = 435; rate[4][18] = 1466;
		rate[4][19] = 592;

		rate[5][6] = 3122; rate[5][7] = 133;
		rate[5][8] = 1269; rate[5][9] = 92;
		rate[5][10] = 286; rate[5][11] = 3313;
		rate[5][12] = 202; rate[5][13] = 10;
		rate[5][14] = 323; rate[5][15] = 396;
		rate[5][16] = 241; rate[5][17] = 53;
		rate[5][18] = 391; rate[5][19] = 54;

		rate[6][7] = 379; rate[6][8] = 162;
		rate[6][9] = 148; rate[6][10] = 82;
		rate[6][11] = 2629; rate[6][12] = 113;
		rate[6][13] = 145; rate[6][14] = 185;
		rate[6][15] = 568; rate[6][16] = 369;
		rate[6][17] = 63; rate[6][18] = 142;
		rate[6][19] = 200;

		rate[7][8] = 19; rate[7][9] = 40;
		rate[7][10] = 20; rate[7][11] = 263;
		rate[7][12] = 21; rate[7][13] = 25;
		rate[7][14] = 28; rate[7][15] = 691;
		rate[7][16] = 92; rate[7][17] = 82;
		rate[7][18] = 10; rate[7][19] = 91;

		rate[8][9] = 29; rate[8][10] = 66;
		rate[8][11] = 305; rate[8][12] = 10;
		rate[8][13] = 127; rate[8][14] = 152;
		rate[8][15] = 303; rate[8][16] = 32;
		rate[8][17] = 69; rate[8][18] = 1971;
		rate[8][19] = 25;

		rate[9][10] = 1745; rate[9][11] = 345;
		rate[9][12] = 1772; rate[9][13] = 454;
		rate[9][14] = 117; rate[9][15] = 216;
		rate[9][16] = 1040; rate[9][17] = 42;
		rate[9][18] = 89; rate[9][19] = 4797;

		rate[10][11] = 218; rate[10][12] = 1351;
		rate[10][13] = 1268; rate[10][14] = 219;
		rate[10][15] = 516; rate[10][16] = 156;
		rate[10][17] = 159; rate[10][18] = 189;
		rate[10][19] = 865;

		rate[11][12] = 193; rate[11][13] = 72;
		rate[11][14] = 302; rate[11][15] = 868;
		rate[11][16] = 918; rate[11][17] = 10;
		rate[11][18] = 247; rate[11][19] = 249;

		rate[12][13] = 327; rate[12][14] = 100;
		rate[12][15] = 93; rate[12][16] = 645;
		rate[12][17] = 86; rate[12][18] = 215;
		rate[12][19] = 475;

		rate[13][14] = 43; rate[13][15] = 487;
		rate[13][16] = 148; rate[13][17] = 468;
		rate[13][18] = 2370; rate[13][19] = 317;

		rate[14][15] = 1202; rate[14][16] = 260;
		rate[14][17] = 49; rate[14][18] = 97;
		rate[14][19] = 122;

		rate[15][16] = 2151; rate[15][17] = 73;
		rate[15][18] = 522; rate[15][19] = 167;

		rate[16][17] = 29; rate[16][18] = 71;
		rate[16][19] = 760;

		rate[17][18] = 346; rate[17][19] = 10;

		rate[18][19] = 119;
	}
}