SubstitutionProcessSequenceSimulator.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_SIMULATION_SUBSTITUTIONPROCESSSEQUENCESIMULATOR_H
#define BPP_PHYL_SIMULATION_SUBSTITUTIONPROCESSSEQUENCESIMULATOR_H
 
#include <Bpp/Phyl/Likelihood/SequenceEvolution.h>
 
#include "SequenceSimulator.h"
#include "SiteSimulator.h"
 
namespace bpp
{
class SubstitutionProcessSequenceSimulator :
  public virtual SequenceSimulatorInterface
{
protected:
  std::map<size_t, std::shared_ptr<SiteSimulatorInterface>> mProcess_;
 
  mutable std::vector<size_t> vMap_;
 
  std::vector<std::string> seqNames_;
 
  std::map<size_t, std::vector<size_t>> mvPosNames_;
 
public:
  SubstitutionProcessSequenceSimulator(const SequenceEvolution& evol);
 
  SubstitutionProcessSequenceSimulator(const SubstitutionProcessSequenceSimulator&);
 
  SubstitutionProcessSequenceSimulator& operator=(const SubstitutionProcessSequenceSimulator&);
 
  SubstitutionProcessSequenceSimulator* clone() const override { return new SubstitutionProcessSequenceSimulator(*this); }
 
  virtual ~SubstitutionProcessSequenceSimulator() {}
 
  const SiteSimulatorInterface& siteSimulator(size_t pos) const override
  {
    if (pos > vMap_.size())
      throw BadIntegerException("Out of range position for SubstitutionProcessSequenceSimulator", (int)pos);
    return *mProcess_.at(vMap_[pos]);
  }
 
  std::vector<std::string> getSequenceNames() const override
  {
    return seqNames_;
  }
 
  void outputInternalSequences(bool yn) override;
 
  void setMap(std::vector<size_t> vMap);
 
  size_t getNumberOfSites() const
  {
    return vMap_.size();
  }
 
  std::unique_ptr<SiteContainerInterface> simulate(size_t numberOfSites) const override;
 
  std::unique_ptr<SiteContainerInterface> simulate(const std::vector<double>& rates) const;
 
  std::unique_ptr<SiteContainerInterface> simulate(const std::vector<size_t>& states) const;
 
  std::unique_ptr<SiteContainerInterface> simulate(const std::vector<double>& rates, const std::vector<size_t>& states) const;
 
  std::shared_ptr<const Alphabet> getAlphabet() const override;
 
  const Alphabet& alphabet() const override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_SIMULATION_SUBSTITUTIONPROCESSSEQUENCESIMULATOR_H