LocusInfo.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _LOCUSINFO_H_
#define _LOCUSINFO_H_
 
// From STL
#include <string>
#include <vector>
#include <memory>
 
// From local bpp-popgen
#include "AlleleInfo.h"
#include "GeneralExceptions.h"
 
#include <Bpp/Exceptions.h>
 
namespace bpp
{
class LocusInfo :
  public virtual Clonable
{
private:
  std::string name_;
  unsigned int ploidy_;
  std::vector<std::unique_ptr<AlleleInfo>> alleles_;
 
public:
  static unsigned int HAPLODIPLOID;
  static unsigned int HAPLOID;
  static unsigned int DIPLOID;
  static unsigned int UNKNOWN;
 
public:
  // Constructors and destructor
  LocusInfo(const std::string& name, const unsigned int ploidy = DIPLOID) :
    name_(name),
    ploidy_(ploidy),
    alleles_()
  {}
 
  LocusInfo(const LocusInfo& locusInfo) :
    name_(locusInfo.name_),
    ploidy_(locusInfo.ploidy_),
    alleles_(locusInfo.getNumberOfAlleles())
  {
    for (unsigned int i = 0; i < locusInfo.getNumberOfAlleles(); ++i)
    {
      alleles_[i].reset(locusInfo.getAlleleInfoByKey(i).clone());
    }
  }
 
  LocusInfo& operator=(const LocusInfo& locusInfo)
  {
    name_ = locusInfo.name_;
    ploidy_ = locusInfo.ploidy_;
    alleles_.resize(locusInfo.getNumberOfAlleles());
    for (unsigned int i = 0; i < locusInfo.getNumberOfAlleles(); ++i)
    {
      alleles_[i].reset(locusInfo.getAlleleInfoByKey(i).clone());
    }
    return *this;
  }
 
  virtual ~LocusInfo() = default;
 
  LocusInfo* clone() const override { return new LocusInfo(*this); }
 
public:
  const std::string& getName() const { return name_; }
 
  unsigned int getPloidy() const { return ploidy_; }
 
  void addAlleleInfo(const AlleleInfo& allele);
 
  const AlleleInfo& getAlleleInfoById(const std::string& id) const;
 
  const AlleleInfo& getAlleleInfoByKey(size_t key) const;
 
  unsigned int getAlleleInfoKey(const std::string& id) const;
 
  size_t getNumberOfAlleles() const { return alleles_.size(); }
 
  void clear() { alleles_.clear(); }
};
} // end of namespace bpp;
 
#endif // _LOCUSINFO_H_