AnalyzedLoci.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _ANALYZEDLOCI_H_
#define _ANALYZEDLOCI_H_
 
// From STL
#include <vector>
#include <string>
 
#include <Bpp/Exceptions.h>
 
// From local
#include "../LocusInfo.h"
#include "../GeneralExceptions.h"
 
namespace bpp
{
class AnalyzedLoci :
  public virtual Clonable
{
private:
  std::vector<std::unique_ptr<LocusInfo>> loci_;
 
public:
  // Constructors and Destructor
  AnalyzedLoci(size_t numberOfLoci) : loci_(numberOfLoci) {}
 
  AnalyzedLoci(const AnalyzedLoci& analyzedLoci) :
    loci_(analyzedLoci.loci_.size())
  {
    size_t i = 0;
    for (const auto& locus : analyzedLoci.loci_)
    {
      loci_[i++].reset(locus->clone());
    }
  }
 
  AnalyzedLoci& operator=(const AnalyzedLoci& analyzedLoci)
  {
    loci_.resize(analyzedLoci.loci_.size());
    size_t i = 0;
    for (const auto& locus : analyzedLoci.loci_)
    {
      loci_[i++].reset(locus->clone());
    }
    return *this;
  }
 
  virtual ~AnalyzedLoci() = default;
 
  AnalyzedLoci* clone() const { return new AnalyzedLoci(*this); }
 
public:
  // Other methods
  void setLocusInfo(size_t locusPosition, const LocusInfo& locus);
 
  size_t getLocusInfoPosition(const std::string& locusName) const;
 
  const LocusInfo& getLocusInfoByName(const std::string& locusName) const;
 
  const LocusInfo& getLocusInfoAtPosition(size_t locusPosition) const;
 
  void addAlleleInfoByLocusName(const std::string& locusName,
      const AlleleInfo& allele);
 
  void addAlleleInfoByLocusPosition(size_t locusosition,
      const AlleleInfo& allele);
 
  size_t getNumberOfLoci() const { return loci_.size(); }
 
  std::vector<size_t> getNumberOfAlleles() const;
 
  unsigned int getPloidyByLocusName(const std::string& locusName) const;
 
  unsigned int getPloidyByLocusPosition(size_t locusPosition) const;
};
} // end of namespace bpp;
 
#endif // _ANALYZEDLOCI_H_