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/*
 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 __LDR_H__                
#define __LDR_H__

#include <vector>
#include <map>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>

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


using namespace std;






class LDR {

public:	
	// IO related parameters
	int a_mode;	
	size_t d_pace;
	
	string file_bfile;
	string file_geno;
	string file_out;
	string path_out;
		
	// Summary statistics
	size_t ni_total, ns_total;	//number of total individuals and snps
	size_t ni_test, ns_test;	//number of individuals and snps used for analysis
	size_t n_cvt;				//number of covariates
	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
	gsl_rng *gsl_r; 	
	
	// Main Functions
	void CopyFromParam (PARAM &cPar);
	void CopyToParam (PARAM &cPar);
	
	void VB(const vector<vector<unsigned char> > &Xt, const gsl_matrix *W_gsl, const gsl_vector *y_gsl);
};



#endif