AbstractBiblioSubstitutionModel.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_ABSTRACTBIBLIOSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_ABSTRACTBIBLIOSUBSTITUTIONMODEL_H
 
#include <Bpp/Numeric/AbstractParameterAliasable.h>
 
#include "AbstractWrappedModel.h"
#include "SubstitutionModel.h"
 
namespace bpp
{
class AbstractBiblioTransitionModel :
  public virtual AbstractTotallyWrappedTransitionModel
{
protected:
  std::map<std::string, std::string> mapParNamesFromPmodel_;
 
  ParameterList lParPmodel_;
 
public:
  AbstractBiblioTransitionModel(const std::string& prefix);
 
  AbstractBiblioTransitionModel(const AbstractBiblioTransitionModel& model);
 
  AbstractBiblioTransitionModel& operator=(const AbstractBiblioTransitionModel& model);
 
  virtual ~AbstractBiblioTransitionModel() {}
 
protected:
  virtual void updateMatrices_();
 
public:
  std::string getParNameFromPmodel(const std::string& name) const;
 
  std::string getPmodelParName(const std::string& name) const;
 
  void addRateParameter() override;
 
  void setFreqFromData(const SequenceDataInterface& data, double pseudoCount = 0) override;
 
  void setFreq(std::map<int, double>& frequ) override;
 
  /*
   * @}
   *
   */
 
  virtual void fireParameterChanged(const ParameterList& parameters) override
  {
    if (parameters.hasParameter(getNamespace() + "rate"))
    {
      model_().setRate(parameters.getParameterValue(getNamespace() + "rate"));
      if (parameters.size() != 1)
        updateMatrices_();
    }
    else
      updateMatrices_();
  }
 
  void setNamespace(const std::string& name) override;
 
  /*
   * @}
   */
};
 
class AbstractBiblioSubstitutionModel :
  public virtual AbstractBiblioTransitionModel,
  public virtual AbstractTotallyWrappedSubstitutionModel
{
public:
  AbstractBiblioSubstitutionModel(const std::string& prefix) :
    AbstractBiblioTransitionModel(prefix),
    AbstractTotallyWrappedSubstitutionModel(prefix)
  {}
 
  AbstractBiblioSubstitutionModel(const AbstractBiblioSubstitutionModel& model) :
    AbstractBiblioTransitionModel(model)
  {}
 
 
  AbstractBiblioSubstitutionModel& operator=(const AbstractBiblioSubstitutionModel& model)
  {
    AbstractBiblioTransitionModel::operator=(model);
    return *this;
  }
 
  virtual ~AbstractBiblioSubstitutionModel() {}
 
protected:
  void updateMatrices_() override
  {
    AbstractBiblioTransitionModel::updateMatrices_();
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_ABSTRACTBIBLIOSUBSTITUTIONMODEL_H