OneJumpSubstitutionCount.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_ONEJUMPSUBSTITUTIONCOUNT_H
#define BPP_PHYL_MAPPING_ONEJUMPSUBSTITUTIONCOUNT_H
 
 
#include "../Model/SubstitutionModel.h"
#include "SubstitutionCount.h"
 
namespace bpp
{
class OneJumpSubstitutionCount :
  public AbstractSubstitutionCount
{
private:
  std::shared_ptr<const SubstitutionModelInterface> model_;
  mutable RowMatrix<double> tmp_;
 
public:
  OneJumpSubstitutionCount(std::shared_ptr<const SubstitutionModelInterface> model) :
    AbstractSubstitutionCount(std::make_shared<const TotalSubstitutionRegister>(model->getStateMap())),
    model_(model), tmp_() {}
 
  OneJumpSubstitutionCount(std::shared_ptr<const StateMapInterface> statemap) :
    AbstractSubstitutionCount(std::make_shared<const TotalSubstitutionRegister>(statemap)),
    model_(nullptr), tmp_() {}
 
  OneJumpSubstitutionCount(const OneJumpSubstitutionCount& ojsc) :
    AbstractSubstitutionCount(ojsc),
    model_(ojsc.model_), tmp_(ojsc.tmp_) {}
 
  OneJumpSubstitutionCount& operator=(const OneJumpSubstitutionCount& ojsc)
  {
    AbstractSubstitutionCount::operator=(ojsc);
    model_    = ojsc.model_;
    tmp_      = ojsc.tmp_;
    return *this;
  }
 
  virtual ~OneJumpSubstitutionCount() {}
 
  virtual OneJumpSubstitutionCount* clone() const override { return new OneJumpSubstitutionCount(*this); }
 
public:
  double getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type = 1) const override
  {
    if (!model_)
      throw Exception("OneJumpSubstitutionCount::getNumberOfSubstitutions: model not defined.");
 
    if (finalState != initialState) return 1.;
    else return 1. - model_->Pij_t(initialState, finalState, length);
  }
 
  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 { model_ = model; }
 
  /*
   *@param reg pointer to a SubstitutionRegister
   *
   */
  void setSubstitutionRegister(std::shared_ptr<const SubstitutionRegisterInterface> reg) override
  {
    throw Exception("OneJumpSubstitutionCount::setSubstitutionRegister. This SubstitutionsCount only works with a TotalSubstitutionRegister.");
  }
 
private:
  void substitutionRegisterHasChanged() override {}
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_ONEJUMPSUBSTITUTIONCOUNT_H