#ifndef __FAMILY_H_
#define __FAMILY_H_

#include <stdlib.h>
#include <vector>
#include <utility>
#include <map>
#include <string>
#include <iostream>
#include <fstream>
#include <sstream>
#include <math.h>
#include <ctype.h>
#include <string.h>

#include "matrix.h"
#include "genotype.h"

using namespace std;


class Family{

 public:

  int fam_id;
  vector<int *> fam_member;  // dimension is N * 5
  int N;
  int Affected;
  int UnAffected;
  int Unknown;
  int N_typed;

  map<pair<int, int>, double> kinship_coeff;
  map<pair<int, int>, double> IBD2_coeff;
  map<pair<int, int>, double> IBD1_coeff;
  map<pair<int, int>, double> IBD0_coeff;
  
  int *typed;
  double *weight;  // complete-data weight
  double *test_weight;  // dimension is N
  double *test_trio_weight1;
  double *test_trio_weight2;
  double *test_trio_weight3;
  
  map<int, int> member_map;  // key: ind_id   value: order starting from 0

  int **gcode;  // genotype data of family member, dimension is N*nmark
  int nmark;
  int *cat;
  int *mis_cat;
  int *trio_cat;
  int *mis_trio_cat;
  int *mis_par_order;  // 0-same order; 1-reverse order
  

  Family(vector<int *> & fam_member, int fam_id);
  void set();
  void set_gcode(int *input_code, int loc);
  void set_gcode(int nmark);
  void fill_typed();
  void fill_info_gcode(vector<Genotype *> & geno_list);
  void print();
  void set_cat(int m, int loc){
    cat[loc] = m;
  }
  void set_mis_cat(int m, int loc){
    mis_cat[loc] = m;
  }
  void set_trio_cat(int m, int loc){
    trio_cat[loc] = m;
  }
  void set_mis_trio_cat(int m, int loc){
    mis_trio_cat[loc] = m;
  }
  void set_mis_par_order(int m, int loc){
    mis_par_order[loc] = m;
  }

  void compute_weight();
  void compute_test_weight(double mean);
  void compute_test_trio_weight(double mean);
  void delete_gcode();

  ~Family();
};

#endif