/*
	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 __LMM_H__                
#define __LMM_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 FUNC_PARAM
{

public:
	bool calc_null;
	size_t ni_test;
	size_t n_cvt;
	const gsl_vector *eval;
	const gsl_matrix *Uab;
	const gsl_vector *ab;
	size_t e_mode;
};




class LMM {

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;
	
	string file_gene;
	
	// LMM related parameters
	double l_min;
	double l_max;
	size_t n_region;
	double l_mle_null;
	double logl_mle_H0;	
	
	// 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_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<SUMSTAT> sumStat;		//Output SNPSummary Data
	
	// Main functions
	void CopyFromParam (PARAM &cPar);
	void CopyToParam (PARAM &cPar);
	void AnalyzeGene (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Utx, const gsl_matrix *W, const gsl_vector *x);
	void AnalyzePlink (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
	void AnalyzeBimbam (const gsl_matrix *U, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const gsl_matrix *W, const gsl_vector *y);
	void WriteFiles ();
	
	void CalcRLWald (const double &lambda, const FUNC_PARAM &params, double &beta, double &se, double &p_wald);
	void CalcRLScore (const double &l, const FUNC_PARAM &params, double &beta, double &se, double &p_score);	
};

void MatrixCalcLR (const gsl_matrix *U, const gsl_matrix *UtX, const gsl_vector *Uty, const gsl_vector *K_eval, const double l_min, const double l_max, const size_t n_region, vector<pair<size_t, double> > &pos_loglr);
void CalcLambda (const char func_name, FUNC_PARAM &params, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logf);
void CalcLambda (const char func_name, const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double l_min, const double l_max, const size_t n_region, double &lambda, double &logl_H0);
void CalcPve (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, const double trace_G, double &pve, double &pve_se);
void CalcLmmVgVeBeta (const gsl_vector *eval, const gsl_matrix *UtW, const gsl_vector *Uty, const double lambda, double &vg, double &ve, gsl_vector *beta, gsl_vector *se_beta);

#endif