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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 __LM_H__                
+#define __LM_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 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_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
+	
+	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 *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);
+	void WriteFiles ();
+};
+void MatrixCalcLmLR (const gsl_matrix *X, const gsl_vector *y, vector<pair<size_t, double> > &pos_loglr);
+#endif