DiploidIndividual.hpp

// Copyright 2021 Arnaud Becheler    <abechele@umich.edu> Florence Jornod <florence@jornod.com>
 
/*********************************************************************** * 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 2 of the License, or    * (at your option) any later version. *
 *                                                                      *
 ************************************************************************/
 
#ifndef __DIPLOID_INDIVIDUAL_H_INCLUDED__
#define __DIPLOID_INDIVIDUAL_H_INCLUDED__
 
#include <map>
#include <set>
#include <string>
 
namespace quetzal::format
{
namespace genetics
{
 
template <typename Allele> class DiploidIndividual
{
  public:
    using allele_type = Allele;
    using locus_ID_type = std::string;
 
    DiploidIndividual() = default;
 
    DiploidIndividual(std::pair<allele_type, allele_type> const &locus, locus_ID_type const &name)
    {
        m_loci[name] = locus;
    }
 
    DiploidIndividual(locus_ID_type const &name, std::pair<allele_type, allele_type> const &locus)
    {
        m_loci[name] = locus;
    }
    DiploidIndividual(locus_ID_type const &name, allele_type allele_1, allele_type allele_2)
    {
        m_loci[name] = std::make_pair(allele_1, allele_2);
    }
    DiploidIndividual(allele_type allele_1, allele_type allele_2, locus_ID_type const &name)
    {
        m_loci[name] = std::make_pair(allele_1, allele_2);
    }
 
    DiploidIndividual<Allele> &add(locus_ID_type const &name, allele_type a1, allele_type a2)
    {
        m_loci[name] = std::make_pair(a1, a2);
        return *this;
    }
 
    DiploidIndividual<Allele> &add(std::pair<allele_type, allele_type> const &locus, locus_ID_type const &name)
    {
        m_loci[name] = locus;
        return *this;
    }
 
    DiploidIndividual<Allele> &add(locus_ID_type const &name, std::pair<allele_type, allele_type> const &locus)
    {
        m_loci[name] = locus;
        return *this;
    }
 
    unsigned int nGenotypedLoci() const
    {
        return m_loci.size();
    }
 
    std::pair<allele_type, allele_type> const &alleles(locus_ID_type const &locus) const
    {
        return m_loci.at(locus);
    }
 
    std::set<locus_ID_type> loci() const
    {
        std::set<locus_ID_type> loci;
        for (auto const &it : m_loci)
        {
            loci.insert(it.first);
        }
        return loci;
    }
 
  private:
    std::map<locus_ID_type, std::pair<allele_type, allele_type>> m_loci;
};
 
} // namespace genetics
} // namespace quetzal::format
 
#endif