SimpleSubstitutionProcessSequenceSimulator.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_SIMULATION_SIMPLESUBSTITUTIONPROCESSSEQUENCESIMULATOR_H
#define BPP_PHYL_SIMULATION_SIMPLESUBSTITUTIONPROCESSSEQUENCESIMULATOR_H
 
 
#include "../Likelihood/SequenceEvolution.h"
#include "GivenDataSubstitutionProcessSiteSimulator.h"
#include "SequenceSimulator.h"
#include "SimpleSubstitutionProcessSiteSimulator.h"
#include "SiteSimulator.h"
 
namespace bpp
{
class SimpleSubstitutionProcessSequenceSimulator :
  public virtual SequenceSimulatorInterface
{
private:
  std::shared_ptr<SiteSimulatorInterface> siteSim_;
 
public:
  SimpleSubstitutionProcessSequenceSimulator(std::shared_ptr<const SubstitutionProcessInterface> process) :
    siteSim_(std::make_shared<SimpleSubstitutionProcessSiteSimulator>(process))
  {}
 
  SimpleSubstitutionProcessSequenceSimulator(
      std::shared_ptr<LikelihoodCalculationSingleProcess> calcul,
      size_t pos,
      bool shrunked = false,
      std::vector<uint> vPrior = std::vector<uint>()) :
    siteSim_(std::make_shared<GivenDataSubstitutionProcessSiteSimulator>(calcul, pos, shrunked, vPrior))
  {}
 
  SimpleSubstitutionProcessSequenceSimulator(std::shared_ptr<SiteSimulatorInterface> simul) :
    siteSim_(simul) {}
 
 
  virtual ~SimpleSubstitutionProcessSequenceSimulator() {}
 
  SimpleSubstitutionProcessSequenceSimulator(const SimpleSubstitutionProcessSequenceSimulator& nhss) :
    siteSim_(nhss.siteSim_)
  {}
 
  SimpleSubstitutionProcessSequenceSimulator* clone() const override
  {
    return new SimpleSubstitutionProcessSequenceSimulator(*this);
  }
 
public:
  std::unique_ptr<SiteContainerInterface> simulate(size_t numberOfSites) const override;
 
 
  const SiteSimulatorInterface& siteSimulator(size_t pos) const override
  {
    return *siteSim_;
  }
 
  std::vector<std::string> getSequenceNames() const override
  {
    return siteSim_->getSequenceNames();
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const override { return siteSim_->getAlphabet(); }
 
  const Alphabet& alphabet() const override { return siteSim_->alphabet(); }
  void outputInternalSequences(bool yn) override
  {
    siteSim_->outputInternalSites(yn);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_SIMULATION_SIMPLESUBSTITUTIONPROCESSSEQUENCESIMULATOR_H