ModelScenario.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_MODELSCENARIO_H
#define BPP_PHYL_LIKELIHOOD_MODELSCENARIO_H
 
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "ModelPath.h"
 
namespace bpp
{
class ModelScenario
{
private:
  std::vector< std::shared_ptr<ModelPath>> vModelPaths_;
 
public:
  ModelScenario() :
    vModelPaths_() {}
 
  virtual ~ModelScenario(){}
 
  ModelScenario(std::vector<std::shared_ptr<ModelPath>> vModelPaths) :
    vModelPaths_(vModelPaths)
  {}
 
  ModelScenario(const ModelScenario& set) :
    vModelPaths_(set.vModelPaths_)
  {}
 
  ModelScenario& operator=(const ModelScenario& set)
  {
    vModelPaths_ = set.vModelPaths_;
    return *this;
  }
 
  //  ModelScenario* clone() const { return new ModelScenario(*this); }
 
  void clear()
  {
    vModelPaths_.clear();
  }
 
  /*
   *@brief adds the copy of an ModelPath to the end of the
   * ModelPaths list.
   */
  void addModelPath(std::shared_ptr<ModelPath> hn)
  {
    vModelPaths_.push_back(hn);
  }
 
  /*
   *@brief change from a MixedTransitionModel to a
   * MixedTransitionModel in all ModelPath.
   *
   */
 
  void changeModel(std::shared_ptr<MixedTransitionModelInterface> m1,
      std::shared_ptr<MixedTransitionModelInterface> m2);
 
  /*
   *@brief If necessary, adds a new ModelPath such that all submodels
   *       of the declared mixture models are at least in an
   *       ModelPath.
   *
   * Returns true iff a new path has been built.
   *
   */
 
  bool complete();
 
  /*
   *@brief adds a submodel number to the nMth mixed model of the
   *  nHth ModelPath of the list (default nH=0). Checks if all the
   *  numbers are valid.
   *
   *@param nM number of the mixed model
   *@param vnS number of the submodel
   *@param nH number of the concerned ModelPath (default the last element of
   *     the list)
   */
 
  //  void addToModelPath(size_t nM, const Vint& vnS, int nH = -1);
 
  size_t getNumberOfModelPaths() const { return vModelPaths_.size(); }
 
  std::shared_ptr<ModelPath> getModelPath(size_t i) { return vModelPaths_[i]; }
 
  std::shared_ptr<const ModelPath> getModelPath(size_t i) const { return vModelPaths_[i]; }
 
  std::vector<std::shared_ptr<MixedTransitionModelInterface>> getModels() const;
 
  bool hasExclusivePaths() const;
 
  void computeModelPathsProbabilities();
 
  std::string toString() const;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_MODELSCENARIO_H