MixtureSequenceEvolution.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_MIXTURESEQUENCEEVOLUTION_H
#define BPP_PHYL_LIKELIHOOD_MIXTURESEQUENCEEVOLUTION_H
 
#include <Bpp/Numeric/Prob/Simplex.h>
 
#include "MultiProcessSequenceEvolution.h"
 
namespace bpp
{
class MixtureSequenceEvolution :
  public MultiProcessSequenceEvolution
{
private:
  Simplex simplex_;
 
public:
  MixtureSequenceEvolution(
      std::shared_ptr<SubstitutionProcessCollection> processColl,
      std::vector<size_t>& nProc);
 
  MixtureSequenceEvolution(const MixtureSequenceEvolution& mlc) :
    MultiProcessSequenceEvolution(mlc),
    simplex_(mlc.simplex_) {}
 
  MixtureSequenceEvolution& operator=(const MixtureSequenceEvolution& mlc)
  {
    MultiProcessSequenceEvolution::operator=(mlc);
    simplex_ = mlc.simplex_;
    return *this;
  }
 
  virtual ~MixtureSequenceEvolution() {}
 
  MixtureSequenceEvolution* clone() const override { return new MixtureSequenceEvolution(*this); }
 
public:
  void setNamespace(const std::string& nameSpace) override;
 
  void fireParameterChanged(const ParameterList& parameters) override;
 
  ParameterList getNonDerivableParameters() const override;
 
  const std::vector<double>& getSubProcessProbabilities() const
  {
    return simplex_.getFrequencies();
  }
 
  Simplex& simplex()
  {
    return simplex_;
  }
 
  double getSubProcessProb(size_t i) const
  {
    return simplex_.prob(i);
  }
 
  void setSubProcessProb(const Simplex& si);
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_MIXTURESEQUENCEEVOLUTION_H