PolymorphismMultiGContainer.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _POLYMORPHYSMMULTIGCONTAINER_H_
#define _POLYMORPHYSMMULTIGCONTAINER_H_
 
// From Utils
#include <Bpp/Clonable.h>
#include <Bpp/Exceptions.h>
#include <Bpp/Utils/MapTools.h>
#include <Bpp/Text/TextTools.h>
 
// From popgenlib
#include "MultilocusGenotype.h"
#include "GeneralExceptions.h"
 
// From STL
#include <string>
#include <vector>
#include <map>
#include <set>
 
namespace bpp
{
class PolymorphismMultiGContainer :
  public virtual Clonable
{
private:
  std::vector<std::unique_ptr<MultilocusGenotype>> multilocusGenotypes_;
  std::vector<size_t> groups_; // group id for each multilocusgenotype
  std::map<size_t, std::string> groupsNames_;
 
public:
  // Constructors and destructor
  PolymorphismMultiGContainer() :
    multilocusGenotypes_(),
    groups_(std::vector<size_t>()),
    groupsNames_(std::map<size_t, std::string>())
  {}
 
  PolymorphismMultiGContainer(const PolymorphismMultiGContainer& pmgc);
 
  virtual ~PolymorphismMultiGContainer()
  {
    clear();
  }
 
  PolymorphismMultiGContainer* clone() const override { return new PolymorphismMultiGContainer(*this); }
 
public:
  PolymorphismMultiGContainer& operator=(const PolymorphismMultiGContainer& pmgc);
 
  void addMultilocusGenotype(std::unique_ptr<MultilocusGenotype>& mg, size_t group);
 
  const MultilocusGenotype& multilocusGenotype(size_t position) const;
 
  std::unique_ptr<MultilocusGenotype> removeMultilocusGenotype(size_t position);
 
  void deleteMultilocusGenotype(size_t position);
 
  bool isAligned() const;
 
  size_t getNumberOfLoci() const;
 
  size_t getGroupId(size_t position) const;
 
  void setGroupId(size_t position, size_t groupId);
 
  std::set<size_t> getAllGroupsIds() const;
 
  std::vector<std::string> getAllGroupsNames() const;
 
  bool groupExists(size_t group) const;
 
  size_t getNumberOfGroups() const
  {
    return getAllGroupsIds().size();
  }
 
  size_t getGroupSize(size_t group) const;
 
  std::string getGroupName(size_t groupId) const;
 
  void setGroupName(size_t groupId, const std::string& name);
 
  void addGroupName(size_t groupId, const std::string& name);
 
  size_t getLocusGroupSize(size_t group, size_t locusPosition) const;
 
  size_t size() const;
 
  void clear();
};
} // end of namespace bpp;
 
#endif // _POLYMORPHYSMMULTIGCONTAINER_H_