DecompositionSubstitutionCount.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_DECOMPOSITIONSUBSTITUTIONCOUNT_H
#define BPP_PHYL_MAPPING_DECOMPOSITIONSUBSTITUTIONCOUNT_H
 
#include <Bpp/Numeric/Matrix/Matrix.h>
 
#include "DecompositionMethods.h"
#include "SubstitutionDistance.h"
#include "WeightedSubstitutionCount.h"
 
namespace bpp
{
class DecompositionSubstitutionCount :
  public AbstractSubstitutionCount,
  public AbstractWeightedSubstitutionCount,
  public AbstractSubstitutionDistance,
  public DecompositionMethods
{
private:
  mutable std::vector< RowMatrix<double>> counts_;
  mutable double currentLength_;
 
public:
  DecompositionSubstitutionCount(
      std::shared_ptr<const SubstitutionModelInterface> model,
      std::shared_ptr<const SubstitutionRegisterInterface> reg,
      std::shared_ptr<const AlphabetIndex2> weights = nullptr,
      std::shared_ptr<const AlphabetIndex2> distances = nullptr);
 
  DecompositionSubstitutionCount(
      std::shared_ptr<const SubstitutionRegisterInterface> reg,
      std::shared_ptr<const AlphabetIndex2> weights = nullptr,
      std::shared_ptr<const AlphabetIndex2> distances = nullptr);
 
  DecompositionSubstitutionCount(const DecompositionSubstitutionCount& dsc) :
    AbstractSubstitutionCount(dsc),
    AbstractWeightedSubstitutionCount(dsc),
    AbstractSubstitutionDistance(dsc),
    DecompositionMethods(dsc),
    counts_(dsc.counts_),
    currentLength_(dsc.currentLength_)
  {}
 
  DecompositionSubstitutionCount& operator=(const DecompositionSubstitutionCount& dsc)
  {
    AbstractSubstitutionCount::operator=(dsc);
    AbstractWeightedSubstitutionCount::operator=(dsc);
    AbstractSubstitutionDistance::operator=(dsc);
    DecompositionMethods::operator=(dsc);
    counts_         = dsc.counts_;
    currentLength_  = dsc.currentLength_;
    return *this;
  }
 
  virtual ~DecompositionSubstitutionCount() {}
 
  DecompositionSubstitutionCount* clone() const override { return new DecompositionSubstitutionCount(*this); }
 
public:
  double getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type = 1) const override;
 
  std::unique_ptr< Matrix<double>> getAllNumbersOfSubstitutions(double length, size_t type = 1) const override;
 
  void storeAllNumbersOfSubstitutions(double length, size_t type, Eigen::MatrixXd& mat) const override;
 
  std::vector<double> getNumberOfSubstitutionsPerType(size_t initialState, size_t finalState, double length) const override;
 
  void setSubstitutionModel(std::shared_ptr<const SubstitutionModelInterface> model) override;
 
protected:
  void initCounts_();
 
  void computeCounts_(double length) const;
 
  void substitutionRegisterHasChanged() override;
 
  void weightsHaveChanged() override;
 
  void distancesHaveChanged() override;
 
private:
  void fillBMatrices_();
 
  void setDistanceBMatrices_();
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_DECOMPOSITIONSUBSTITUTIONCOUNT_H