GivenDataSubstitutionProcessSequenceSimulator.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_SIMULATION_GIVENDATASUBSTITUTIONPROCESSSEQUENCESIMULATOR_H
#define BPP_PHYL_SIMULATION_GIVENDATASUBSTITUTIONPROCESSSEQUENCESIMULATOR_H
 
 
#include "GivenDataSubstitutionProcessSiteSimulator.h"
#include "SequenceSimulator.h"
 
namespace bpp
{
class GivenDataSubstitutionProcessSequenceSimulator :
  public virtual SequenceSimulatorInterface
{
private:
  std::shared_ptr<LikelihoodCalculationSingleProcess> calcul_;
 
  /*
   * @brief Vector of site specific site simulators on SHRUNKED data
   *
   * More efficient implementation is possible (all in ona).
   *
   */
 
  std::vector<std::shared_ptr<GivenDataSubstitutionProcessSiteSimulator>> vSiteSim_;
 
  /*
   * @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:
  GivenDataSubstitutionProcessSequenceSimulator(std::shared_ptr<LikelihoodCalculationSingleProcess> calcul, std::vector<uint> vPrior = std::vector<uint>()) :
    calcul_(calcul), vSiteSim_(), vPriorBranch_(vPrior)
  {
    for (size_t i = 0; i < calcul_->getNumberOfDistinctSites(); i++)
    {
      vSiteSim_.push_back(std::make_shared<GivenDataSubstitutionProcessSiteSimulator>(calcul_, i, true, vPriorBranch_));
    }
  }
 
  virtual ~GivenDataSubstitutionProcessSequenceSimulator()
  {}
 
  GivenDataSubstitutionProcessSequenceSimulator(const GivenDataSubstitutionProcessSequenceSimulator& nhss) :
    calcul_(nhss.calcul_), vSiteSim_(nhss.vSiteSim_)
  {}
 
  GivenDataSubstitutionProcessSequenceSimulator* clone() const override
  {
    return new GivenDataSubstitutionProcessSequenceSimulator(*this);
  }
 
public:
  std::unique_ptr<SiteContainerInterface> simulate() const
  {
    return simulate(calcul_->getNumberOfSites());
  }
 
  std::unique_ptr<SiteContainerInterface> simulate(size_t numberOfSites) const override;
 
  const SiteSimulatorInterface& siteSimulator(size_t pos) const override
  {
    
    return *vSiteSim_[calcul_->getRootArrayPosition(pos)];
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const override
  {
    return vSiteSim_[0]->getAlphabet();
  }
 
  const Alphabet& alphabet() const override
  {
    return vSiteSim_[0]->alphabet();
  }
 
  std::vector<std::string> getSequenceNames() const override
  {
    return vSiteSim_[0]->getSequenceNames();
  }
 
  size_t getNumberOfSites() const
  {
    return calcul_->getNumberOfSites();
  }
 
  void outputInternalSequences(bool yn) override
  {
    for (auto& siteSim : vSiteSim_)
    {
      siteSim->outputInternalSites(yn);
    }
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_SIMULATION_GIVENDATASUBSTITUTIONPROCESSSEQUENCESIMULATOR_H