Mapping.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_MAPPING_H
#define BPP_PHYL_MAPPING_MAPPING_H
 
#include <Bpp/Clonable.h>
#include <Bpp/Graph/AssociationTreeGraphImplObserver.h>
 
#include "../Tree/PhyloTree.h"
#include "PhyloBranchMapping.h"
 
// From the STL:
#include <vector>
#include <memory>
 
namespace bpp
{
class MappingInterface :
  public virtual Clonable
{
public:
  MappingInterface() {}
  virtual ~MappingInterface() {}
 
  MappingInterface* clone() const override = 0;
 
public:
  virtual size_t getNumberOfSites() const = 0;
 
  virtual const PhyloBranch& getBranch(unsigned int branchId) const = 0;
 
  virtual PhyloBranch& getBranch(unsigned int branchId) = 0;
 
  // virtual unsigned int getBranchIndex(const std::shared_ptr<PhyloBranch> branch) const = 0;
 
  virtual size_t getNumberOfBranches() const = 0;
 
  virtual int getSitePosition(size_t index) const = 0;
 
  virtual void setSitePosition(size_t index, int position) = 0;
};
 
 
class AbstractMapping :
  public virtual MappingInterface
{
protected:
  std::vector<int> sitesPositions_;
  size_t nbSites_;
 
public:
  AbstractMapping() : sitesPositions_(), nbSites_(0)
  {}
 
  AbstractMapping(size_t nb) : sitesPositions_(), nbSites_(nb)
  {}
 
  AbstractMapping(const AbstractMapping& absm) = default;
 
  AbstractMapping& operator=(const AbstractMapping& absm) = default;
 
  virtual ~AbstractMapping() {}
 
public:
  int getSitePosition(size_t index) const
  {
    return sitesPositions_.size() == 0 ? (int)(index + 1) : sitesPositions_[index];
  }
 
  void setSitePosition(size_t index, int position)
  {
    if (sitesPositions_.size() == 0)
      sitesPositions_.resize(nbSites_);
 
    sitesPositions_[index] = position;
  }
 
  size_t getNumberOfSites() const { return nbSites_; }
 
  virtual void setNumberOfSites(size_t numberOfSites)
  {
    nbSites_ = numberOfSites;
    sitesPositions_.clear();
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_MAPPING_H