/*
	Genome-wide Efficient Mixed Model Association (GEMMA)
    Copyright (C) 2011  Xiang Zhou

    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 3 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, see <http://www.gnu.org/licenses/>.
*/

#ifndef __VC_H__                
#define __VC_H__

#include "gsl/gsl_vector.h"
#include "gsl/gsl_matrix.h"


#ifdef FORCE_FLOAT
#include "param_float.h"
#include "io_float.h"
#else
#include "param.h"
#include "io.h"
#endif

using namespace std;



class VC_PARAM
{

public:	
	const gsl_matrix *K;
	const gsl_matrix *W;
	const gsl_vector *y;
	gsl_matrix *P;
	gsl_vector *Py;
	gsl_matrix *KPy_mat;
	gsl_matrix *PKPy_mat;
	gsl_matrix *Hessian;
};




class VC {

public:
	// IO related parameters
	string file_out;
	string path_out;

	vector<double> v_sigma2;
	vector<double> v_se_sigma2;
	vector<double> v_pve;
	vector<double> v_se_pve;
	vector<double> v_traceG;
	vector<double> v_beta;
	vector<double> v_se_beta;

	double time_UtX;
	double time_opt;
	
	// Main functions
	void CopyFromParam (PARAM &cPar);
	void CopyToParam (PARAM &cPar);
	void CalcVChe (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
	void CalcVCreml (const gsl_matrix *K, const gsl_matrix *W, const gsl_vector *y);
};

#endif