SiteSimulator.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_SIMULATION_SITESIMULATOR_H
#define BPP_PHYL_SIMULATION_SITESIMULATOR_H
 
// From bpp-core
#include <Bpp/Clonable.h>
 
// From bpp-seq:
#include <Bpp/Seq/Site.h>
 
namespace bpp
{
class SiteSimulatorInterface :
  public virtual Clonable
{
public:
  SiteSimulatorInterface() {}
  virtual ~SiteSimulatorInterface() {}
 
  SiteSimulatorInterface* clone() const override = 0;
 
public:
  virtual std::unique_ptr<Site> simulateSite() const = 0;
 
  virtual std::unique_ptr<Site> simulateSite(size_t rateClass) const = 0;
 
  virtual std::unique_ptr<Site> simulateSite(double rate) const = 0;
 
  virtual std::unique_ptr<Site> simulateSite(size_t ancestralStateIndex, double rate) const = 0;
 
  virtual std::vector<std::string> getSequenceNames() const = 0;
 
  virtual std::shared_ptr<const Alphabet> getAlphabet() const = 0;
 
  virtual const Alphabet& alphabet() const = 0;
 
  virtual void outputInternalSites(bool yn) = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_SIMULATION_SITESIMULATOR_H