/*
 Genome-wide Efficient Mixed Model Association (GEMMA)
 Copyright (C) 2011-2017 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 __LM_H__
#define __LM_H__

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

using namespace std;

class LM {

public:
	// IO-related parameters.
	int a_mode;	// Analysis mode: 50+1/2/3/4 for Frequentist tests.
	size_t d_pace;	// Display pace.

	string file_bfile;
	string file_geno;
	string file_oxford;
	string file_out;
	string path_out;

	string file_gene;

	// Summary statistics.
	size_t ni_total, ni_test;  // Number of individuals.
	size_t ns_total, ns_test;  // Number of SNPs.
	size_t ng_total, ng_test;  // Number of genes.
	size_t n_cvt;
	double time_opt;	   // Time spent.

        // Indicator for individuals (phenotypes): 0 missing, 1
        // available for analysis.
	vector<int> indicator_idv;

        // Sequence indicator for SNPs: 0 ignored because of (a) maf,
        // (b) miss, (c) non-poly; 1 available for analysis.
	vector<int> indicator_snp;

	vector<SNPINFO> snpInfo;  // Record SNP information.

	// Not included in PARAM.
	vector<SUMSTAT> sumStat;  // Output SNPSummary Data.

	// Main functions.
	void CopyFromParam (PARAM &cPar);
	void CopyToParam (PARAM &cPar);
	void AnalyzeGene (const gsl_matrix *W, const gsl_vector *x);
	void AnalyzePlink (const gsl_matrix *W, const gsl_vector *y);
	void AnalyzeBimbam (const gsl_matrix *W, const gsl_vector *y);
	// WJA added.
	void Analyzebgen (const gsl_matrix *W, const gsl_vector *y);

	void WriteFiles ();
};

void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y,
		     vector<pair<size_t, double> > &pos_loglr);

#endif