/*
 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 __MVLMM_H__                
#define __MVLMM_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 MVLMM {
	
public:
	// IO related parameters
	int a_mode;				//analysis mode, 1/2/3/4 for Frequentist tests
	size_t d_pace;		//display pace
	
	string file_bfile;
	string file_geno;
	string file_out;
	string path_out;
	
	// MVLMM related parameters
	double l_min;
	double l_max;
	size_t n_region;
	double logl_remle_H0, logl_mle_H0;
	vector<double> Vg_remle_null, Ve_remle_null, Vg_mle_null, Ve_mle_null;
	vector<double> VVg_remle_null, VVe_remle_null, VVg_mle_null, VVe_mle_null;
	vector<double> beta_remle_null, se_beta_remle_null, beta_mle_null, se_beta_mle_null;
	double p_nr;
	size_t em_iter, nr_iter;
	double em_prec, nr_prec;
	size_t crt;
		
	// Summary statistics
	size_t ni_total, ni_test;	//number of individuals
	size_t ns_total, ns_test;	//number of snps
	size_t n_cvt;
	size_t n_ph;
	double time_UtX;		//time spent on optimization iterations
	double time_opt;		//time spent on optimization iterations
	
	vector<int> indicator_idv;				//indicator for individuals (phenotypes), 0 missing, 1 available for analysis
	vector<int> indicator_snp;				//sequence indicator for SNPs: 0 ignored because of (a) maf, (b) miss, (c) non-poly; 1 available for analysis
	
	vector<SNPINFO> snpInfo;		//record SNP information
	
	// Not included in PARAM
	vector<MPHSUMSTAT> sumStat;		//Output SNPSummary Data
	
	// Main functions
	void CopyFromParam (PARAM &cPar);
	void CopyToParam (PARAM &cPar);
	void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
	void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY);
	void WriteFiles ();
	
};

void CalcMvLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_matrix *UtY, const size_t em_iter, const size_t nr_iter, const double em_prec, const double nr_prec, const double l_min, const double l_max, const size_t n_region, gsl_matrix *V_g, gsl_matrix *V_e, gsl_matrix *B, gsl_matrix *se_B);

#endif