// TwoStateModel.java
//
// (c) 1999-2001 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.datatype.*;
import pal.util.*;

import java.io.*;


/**
 * implements the most general reversible rate matrix for two-state data
 *
 * @version $Id: TwoStateModel.java,v 1.7 2003/11/13 04:05:39 matt Exp $
 *
 * @author Korbinian Strimmer
 * @author Alexei Drummond
 */
public class TwoStateModel extends AbstractRateMatrix implements RateMatrix, XMLConstants
{
	/**
	 * constructor
	 *
	 * @param f frequencies
	 *
	 * @return rate matrix
	 */
	public TwoStateModel(double[] f)
	{
		// Dimension = 2
		super(2);

		setDataType(new TwoStates());
		setFrequencies(f);
	}

	/**
	 * get numerical code describing the model type
	 *
	 * @return 0 (there is only one model)
	 */
	public int getModelID()
	{
		return 0;
	}

	/**
	 * create object using an instance method
	 *
	 * @param freq model frequencies
	 *
	 * @return rate matrix
	 */
	public static TwoStateModel getInstance(double[] freq)
	{
 		return new TwoStateModel(freq);
 	}

 	// interface Report

	public void report(PrintWriter out)
	{
		out.println("Model of substitution: Proportional Model (F81)");
		out.println();
		out.println("Frequencies of the two states:");
		printFrequencies(out);
	}

	// interface Parameterized

	public int getNumParameters()
	{
		return 0;
	}


	public void setParameterSE(double paramSE, int n)
	{
		return;
	}

	public double getLowerLimit(int n)
	{
		return 0.0;
	}

	public double getUpperLimit(int n)
	{
		return 0.0;
	}

	public double getDefaultValue(int n)
	{
		return 0.0;
	}

	public String getParameterName(int i) {
		return UNKNOWN;
	}

	public String getUniqueName() {
		return TWO_STATE;
	}
	protected final void rebuildRateMatrix(double[][] rate, double[] parameters) {
	  rate[0][1] = 1;
		rate[0][0] = 0;
		rate[1][1] = 0;
		rate[1][0] = 0;

	}
}