SubstitutionDistance.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_SUBSTITUTIONDISTANCE_H
#define BPP_PHYL_MAPPING_SUBSTITUTIONDISTANCE_H
 
 
#include "SubstitutionCount.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex2.h>
 
namespace bpp
{
class SubstitutionDistance :
  public virtual SubstitutionCountInterface
{
public:
  virtual void setDistances(std::shared_ptr<const AlphabetIndex2> index) = 0;
  virtual bool hasDistances() const = 0;
  virtual std::shared_ptr<const AlphabetIndex2> getDistances() const = 0;
};
 
class AbstractSubstitutionDistance :
  public virtual SubstitutionDistance
{
protected:
  std::shared_ptr<const AlphabetIndex2> distances_;
 
public:
  AbstractSubstitutionDistance(std::shared_ptr<const AlphabetIndex2> distances) :
    distances_(distances)
  {}
 
  AbstractSubstitutionDistance(const AbstractSubstitutionDistance& index) :
    distances_(index.distances_)
  {}
 
  AbstractSubstitutionDistance& operator=(const AbstractSubstitutionDistance& index)
  {
    distances_ = index.distances_;
 
    return *this;
  }
 
  virtual ~AbstractSubstitutionDistance()
  {}
 
public:
  void setDistances(std::shared_ptr<const AlphabetIndex2> distances);
  bool hasDistances() const { return distances_.get() != 0; }
  std::shared_ptr<const AlphabetIndex2> getDistances() const { return distances_; }
 
protected:
  virtual void distancesHaveChanged() = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_SUBSTITUTIONDISTANCE_H