GivenDataSubstitutionProcessSiteSimulator.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_SIMULATION_GIVENDATASUBSTITUTIONPROCESSSITESIMULATOR_H
#define BPP_PHYL_SIMULATION_GIVENDATASUBSTITUTIONPROCESSSITESIMULATOR_H
 
#include <Bpp/Phyl/Likelihood/DataFlow/LikelihoodCalculationSingleProcess.h>
 
#include "SimpleSubstitutionProcessSiteSimulator.h"
 
namespace bpp
{
class GivenDataSubstitutionProcessSiteSimulator :
  public SimpleSubstitutionProcessSiteSimulator
{
private:
  std::shared_ptr<LikelihoodCalculationSingleProcess> calcul_;
 
  Eigen::Index pos_;
 
  /*
   * @brief Vector of branch indexes where the data is not used, and
   * substitution probabilities are computed from the prior process.
   *
   */
 
  std::vector<uint> vPriorBranch_;
 
public:
  GivenDataSubstitutionProcessSiteSimulator(std::shared_ptr<LikelihoodCalculationSingleProcess> calcul, size_t pos, bool shrunked = false, std::vector<uint> vPrior = std::vector<uint>()) :
    SimpleSubstitutionProcessSiteSimulator(calcul->getSubstitutionProcess()),
    calcul_(calcul),
    pos_(shrunked ? Eigen::Index(pos) : Eigen::Index(calcul->getRootArrayPosition(pos))),
    vPriorBranch_(vPrior)
  {
    init();
    // Continuous rates not possible for this, since there is no a posteriori for all rates.
    continuousRates_ = false;
  }
 
  GivenDataSubstitutionProcessSiteSimulator(const GivenDataSubstitutionProcessSiteSimulator& nhss) :
    SimpleSubstitutionProcessSiteSimulator(nhss),
    calcul_(nhss.calcul_),
    pos_(nhss.pos_)
  {}
 
  GivenDataSubstitutionProcessSiteSimulator& operator=(const GivenDataSubstitutionProcessSiteSimulator& nhss)
  {
    SimpleSubstitutionProcessSiteSimulator::operator=(nhss);
    calcul_ = nhss.calcul_;
    pos_ = nhss.pos_;
 
    return *this;
  }
 
  GivenDataSubstitutionProcessSiteSimulator* clone() const override
  {
    return new GivenDataSubstitutionProcessSiteSimulator(*this);
  }
 
private:
  void init() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_SIMULATION_GIVENDATASUBSTITUTIONPROCESSSITESIMULATOR_H