jobo_individual.h

#ifndef JOBO_INDIVIDUAL_H
#define JOBO_INDIVIDUAL_H

#include <random>
#include "jobo_genotype.h"

namespace jobo {

class individual
{
public:
  individual(
    const std::string& genotype = ""
  );

  int get_n_loci() const noexcept { return static_cast<int>(m_genotype.size()); }
  const std::string& get_genotype() const noexcept {return m_genotype;}
  double get_fitness(){return m_fitness;}

private:
  genotype m_genotype;
  double m_fitness;
};

/// Create a genotype of length 'n_loci', creating a genotype like
/// 'abcdef...' to have the correct length
std::string create_initial_genotype(const int n_loci);

/// Creates a kid from random recombination of parents' genotype
/// Will throw if genotypes are of different lengths
individual create_offspring(
  const individual& mother,
  const individual& father,
  std::mt19937& rng_engine
);

/// Creates individual that has completer the mutation step,
/// none locus, one locus or multiple loci can be mutated
individual create_mutation(
  const jobo::individual& before_mutation,
  const double mutation_rate,
  std::mt19937& rng_engine
);

/// Randomly combines genotypes mother and father
/// Will throw if genotypes are of different lengths
genotype recombine(
  const genotype& p,
  const genotype& q,
  std::mt19937& rng_engine
);

/// Looks at each locus in the genotype of individual if mutation occurs,
/// If mutation occurs, mutation is build in that certain locus/loci
genotype mutation_check_all_loci(
  const genotype& r,
  const double mutation_rate,
  std::mt19937& rng_engine
);

bool is_viable_species(const genotype w);
double calc_fitness(const individual& i);

std::ostream& operator<<(std::ostream& os, const individual& i) noexcept;

bool operator==(const individual& lhs, const individual& rhs) noexcept;
bool operator!=(const individual& lhs, const individual& rhs) noexcept;

} //~namespace jobo

#endif // JOBO_INDIVIDUAL_H