#ifndef __GENOTYPETRIO_H_
#define __GENOTYPETRIO_H_

#include <stdlib.h>
#include <vector>
#include <utility>
#include <map>
#include "genotype.h"
#include "function.h"

using namespace std;


class inheritance
{
 public:

  pair<int, int> hp_par1;
  pair<int, int> hp_par2;
  pair<int, int> hp_offspring;
};


class Genotypetrio  // record all possible haplotype that is compatible with the observed genotype
{
 private:

  int count;
  int size;  // number of SNPs in the genotype/haplotype

  vector<inheritance> inh_vec;  // record trio haplotype pairs
  vector<inheritance> inh_vec_complete;  // also expand the untyped parent

  vector<double> hap_num;  // store Z-\mu, demension a
  

 public:

  int typed_o;
  int typed_par1;
  int typed_par2;

  int info;  // if inh_vec.size()=0, info=0, otherwise info=1

  Genotype * offspring;
  Genotype * par1;
  Genotype * par2;
  int phase;
 
  /* Constructor */
  Genotypetrio(Genotype * offspring, Genotype * par1, Genotype * par2, int typed_o, int typed_par1, int typed_par2, int size);
  Genotypetrio(Genotype * offspring, int typed_o, int typed_par1, int typed_par2, int size);

  const vector<inheritance> & get_inh_vec()
  {
    return inh_vec;
  }
  const vector<inheritance> & get_inh_vec_complete()
  {
    return inh_vec_complete;
  }
  int get_size()
  {
    return size;
  }

  int get_num()
  {
    return count;
  }
  void increase_num()
  {
    count++;
  }
  void record_trio_hap_structure();  // fill in inh_vec and inh_vec_complete

  // function for IQL_b
  void expected_hap_num(map<int, double> & hap_freq_table, double *freq, map<pair<int, int>, double> & geno_freq_table, map<pair<int, int>, int> & hap_pair_map, int **count, const vector<int> & sites);
  const vector<double> & get_hap_num()
  {
    return hap_num;
  }

  void display(const pair<int, int> & hap);
  void show_content();  // print inh_vec
  void show_gstat();  // print trio genotype with its count
  void push_vec(const vector<pair<int, int> > & hap_vec, int f0, int f1, int m0, int m1, int a, int b);
  void push_vec_complete(const vector<pair<int, int> > & hap_vec, int f0, int f1, int m0, int m1, int a, int b);
  void determin_phase();

  ~Genotypetrio();  // delete


 private:

  void push_vec(int f0, int f1, int m0, int m1, int a, int b);
  void push_vec_complete(int f0, int f1, int m0, int m1, int a, int b);
};

int is_in(const vector<pair<int, int> > & hap_vec, int o1, int o2);

#endif