SequenceEvolution.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_SEQUENCEEVOLUTION_H
#define BPP_PHYL_LIKELIHOOD_SEQUENCEEVOLUTION_H
 
 
#include "SubstitutionProcess.h"
 
// From bpp-core:
#include <Bpp/Numeric/ParameterAliasable.h>
#include <Bpp/Numeric/AbstractParameterAliasable.h>
 
// From bpp-seq:
 
#include <Bpp/Seq/Container/AlignmentData.h>
 
// From the STL:
#include <memory>
 
namespace bpp
{
class SequenceEvolution :
  public virtual ParameterAliasable
{
public:
  virtual SequenceEvolution* clone() const override = 0;
 
public:
  virtual bool isCompatibleWith(const AlignmentDataInterface& data) const = 0;
 
  virtual const std::vector<size_t>& getSubstitutionProcessNumbers() const = 0;
 
  virtual const SubstitutionProcessInterface& substitutionProcess(size_t number) const = 0;
 
  virtual std::shared_ptr<const SubstitutionProcessInterface> getSubstitutionProcess(size_t number) const = 0;
 
  const StateMapInterface& stateMap() const
  {
    return substitutionProcess(getSubstitutionProcessNumbers()[0]).stateMap();
  }
 
  std::shared_ptr<const StateMapInterface> getStateMap() const
  {
    return substitutionProcess(getSubstitutionProcessNumbers()[0]).getStateMap();
  }
 
  virtual ParameterList getBranchLengthParameters(bool independent) const = 0;
 
  virtual ParameterList getSubstitutionModelParameters(bool independent) const = 0;
 
  virtual ParameterList getSubstitutionProcessParameters(bool independent) const = 0;
 
  virtual ParameterList getRateDistributionParameters(bool independent) const = 0;
 
  virtual ParameterList getRootFrequenciesParameters(bool independent) const = 0;
 
 
  virtual ParameterList getNonDerivableParameters() const = 0;
};
} // end namespace bpp
#endif // BPP_PHYL_LIKELIHOOD_SEQUENCEEVOLUTION_H