AbstractAutonomousSubstitutionProcess.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_ABSTRACT_AUTONOMOUS_SUBSTITUTIONPROCESS_H
#define BPP_PHYL_LIKELIHOOD_ABSTRACT_AUTONOMOUS_SUBSTITUTIONPROCESS_H
 
#include "AbstractSubstitutionProcess.h"
#include "AutonomousSubstitutionProcess.h"
 
// From the STL:
#include <memory>
 
namespace bpp
{
class AbstractAutonomousSubstitutionProcess :
  public virtual AutonomousSubstitutionProcessInterface,
  public virtual AbstractSubstitutionProcess
{
protected:
  std::shared_ptr<ParametrizablePhyloTree> pTree_;
 
  std::shared_ptr<FrequencySetInterface> rootFrequencies_;
 
  std::shared_ptr<ModelScenario> modelScenario_;
 
protected:
  AbstractAutonomousSubstitutionProcess(
      std::shared_ptr<const PhyloTree> tree = 0,
      std::shared_ptr<FrequencySetInterface> rootFrequencies = 0,
      const std::string& prefix = "");
 
  AbstractAutonomousSubstitutionProcess(
      std::shared_ptr<ParametrizablePhyloTree> tree,
      std::shared_ptr<FrequencySetInterface> rootFrequencies = 0,
      const std::string& prefix = "");
 
  AbstractAutonomousSubstitutionProcess(const AbstractAutonomousSubstitutionProcess& asp);
 
  AbstractAutonomousSubstitutionProcess& operator=(const AbstractAutonomousSubstitutionProcess& asp);
 
public:
  void setPhyloTree(const PhyloTree& phyloTree);
 
  const ParametrizablePhyloTree& parametrizablePhyloTree() const
  {
    return *pTree_;
  }
 
  std::shared_ptr<const ParametrizablePhyloTree> getParametrizablePhyloTree() const
  {
    return pTree_;
  }
 
  bool hasRootFrequencySet() const
  {
    return rootFrequencies_ != 0;
  }
 
  const FrequencySetInterface& rootFrequencySet() const
  {
    return *rootFrequencies_;
  }
 
  std::shared_ptr<const FrequencySetInterface> getRootFrequencySet() const
  {
    return rootFrequencies_;
  }
 
  FrequencySetInterface& rootFrequencySet()
  {
    return *rootFrequencies_;
  }
 
  std::shared_ptr<FrequencySetInterface> getRootFrequencySet()
  {
    return rootFrequencies_;
  }
 
  void setRootFrequencySet(std::shared_ptr<FrequencySetInterface> rootfrequency)
  {
    if (rootFrequencies_)
      getParameters_().deleteParameters(rootFrequencies_->getParameters().getParameterNames(), false);
    rootFrequencies_ = rootfrequency;
    if (rootFrequencies_)
      addParameters_(rootFrequencies_->getParameters());
  }
 
  ParameterList getRootFrequenciesParameters(bool independent) const
  {
    if (!hasRootFrequencySet())
      return ParameterList();
    else
      return rootFrequencies_->getParameters();
  }
 
 
  void fireParameterChanged(const ParameterList& pl);
 
  std::shared_ptr<const ModelScenario> getModelScenario() const
  {
    return modelScenario_;
  }
 
  virtual void setModelScenario(std::shared_ptr<ModelScenario> modelScenario) = 0;
};
} // end namespace bpp
 
#endif // BPP_PHYL_LIKELIHOOD_ABSTRACT_AUTONOMOUS_SUBSTITUTIONPROCESS