/*
    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 __PRDT_H__
#define __PRDT_H__

#include "gsl/gsl_matrix.h"
#include "gsl/gsl_vector.h"
#include "param.h"
#include <map>
#include <string.h>
#include <vector>

using namespace std;

class PRDT {

public:
  // IO-related parameters.
  size_t a_mode;
  size_t d_pace;

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

  vector<vector<int>> indicator_pheno;
  vector<int> indicator_cvt;
  vector<int> indicator_idv;
  vector<SNPINFO> snpInfo;
  map<string, double> mapRS2est;

  size_t n_ph;
  size_t np_obs, np_miss;
  size_t ns_total;
  size_t ns_test;

  double time_eigen;

  // Main functions.
  void CopyFromParam(PARAM &cPar);
  void CopyToParam(PARAM &cPar);
  void WriteFiles(gsl_vector *y_prdt);
  void WriteFiles(gsl_matrix *Y_full);
  void AddBV(gsl_matrix *G, const gsl_vector *u_hat, gsl_vector *y_prdt);
  void AnalyzeBimbam(gsl_vector *y_prdt);
  void AnalyzePlink(gsl_vector *y_prdt);
  void MvnormPrdt(const gsl_matrix *Y_hat, const gsl_matrix *H,
                  gsl_matrix *Y_full);
};

#endif