MultilocusGenotype.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _MULTILOCUSGENOTYPE_H_
#define _MULTILOCUSGENOTYPE_H_
 
// From STL
#include <vector>
#include <string>
#include <memory>
 
#include <Bpp/Exceptions.h>
 
// From Pop
#include "MonolocusGenotype.h"
#include "MonolocusGenotypeTools.h"
#include "BiAlleleMonolocusGenotype.h"
#include "MonoAlleleMonolocusGenotype.h"
#include "LocusInfo.h"
 
namespace bpp
{
class MultilocusGenotype :
  public virtual Clonable
{
private:
  std::vector<std::unique_ptr<MonolocusGenotypeInterface>> loci_;
 
public:
  MultilocusGenotype(size_t lociNumber);
 
  MultilocusGenotype(const MultilocusGenotype& genotype);
 
  virtual ~MultilocusGenotype();
 
  MultilocusGenotype* clone() const override { return new MultilocusGenotype(*this); }
 
public:
  void setMonolocusGenotype(
      size_t locusPosition,
      const MonolocusGenotypeInterface& monogen);
 
  void setMonolocusGenotypeByAlleleKey(
      size_t locusPosition,
      const std::vector<size_t>& alleleKeys);
 
  void setMonolocusGenotypeByAlleleId(
      size_t locusPosition,
      const std::vector<std::string>& alleleId,
      const LocusInfo& locusInfo);
 
  void setMonolocusGenotypeAsMissing(size_t locusPosition);
 
  bool isMonolocusGenotypeMissing(size_t locusPosition) const;
 
  const MonolocusGenotypeInterface& monolocusGenotype(size_t locusPosition) const;
 
  size_t size() const;
 
  size_t countNonMissingLoci() const;
 
  size_t countHomozygousLoci() const;
 
  size_t countHeterozygousLoci() const;
};
} // end of namespace bpp;
 
#endif // _MULTILOCUSGENOTYPE_H_