LaplaceSubstitutionCount.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_LAPLACESUBSTITUTIONCOUNT_H
#define BPP_PHYL_MAPPING_LAPLACESUBSTITUTIONCOUNT_H
 
 
#include "../Model/SubstitutionModel.h"
#include "SubstitutionCount.h"
 
namespace bpp
{
class LaplaceSubstitutionCount :
  public AbstractSubstitutionCount
{
private:
  std::shared_ptr<const SubstitutionModelInterface> model_;
  size_t cutOff_;
  mutable double currentLength_;
  mutable RowMatrix<double> m_;
 
public:
  LaplaceSubstitutionCount(
      std::shared_ptr<const SubstitutionModelInterface> model,
      size_t cutOff) :
    AbstractSubstitutionCount(std::make_shared<TotalSubstitutionRegister>(model->getStateMap())),
    model_        (model),
    cutOff_       (cutOff),
    currentLength_(0),
    m_            (model->getNumberOfStates(), model->getNumberOfStates())
  {}
 
  LaplaceSubstitutionCount(std::shared_ptr<const StateMapInterface> stateMap, size_t cutOff) :
    AbstractSubstitutionCount(std::make_shared<TotalSubstitutionRegister>(stateMap)),
    model_        (0),
    cutOff_       (cutOff),
    currentLength_(0),
    m_            (stateMap->getNumberOfModelStates(), stateMap->getNumberOfModelStates())
  {}
 
  LaplaceSubstitutionCount(const LaplaceSubstitutionCount& asc) :
    AbstractSubstitutionCount(asc),
    model_        (asc.model_),
    cutOff_       (asc.cutOff_),
    currentLength_(asc.currentLength_),
    m_            (asc.m_)
  {}
 
  LaplaceSubstitutionCount& operator=(const LaplaceSubstitutionCount& asc)
  {
    AbstractSubstitutionCount::operator=(asc);
    model_         = asc.model_;
    cutOff_        = asc.cutOff_;
    currentLength_ = asc.currentLength_;
    m_             = asc.m_;
    return *this;
  }
 
  virtual ~LaplaceSubstitutionCount() {}
 
  LaplaceSubstitutionCount* clone() const override { return new LaplaceSubstitutionCount(*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
  {
    std::vector<double> v(0);
    v[0] = getNumberOfSubstitutions(initialState, finalState, length, 0);
    return v;
  }
 
  void setSubstitutionModel(std::shared_ptr<const SubstitutionModelInterface> model) override;
 
  /*
   *@param reg pointer to a SubstitutionRegister
   *
   */
  void setSubstitutionRegister(std::shared_ptr<const SubstitutionRegisterInterface> reg) override
  {
    throw Exception("LaplaceSubstitutionCount::setSubstitutionRegister. This SubstitutionsCount only works with a TotalSubstitutionRegister.");
  }
 
protected:
  void computeCounts(double length) const;
  void substitutionRegisterHasChanged() override {}
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_LAPLACESUBSTITUTIONCOUNT_H