SubstitutionProcess.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_SUBSTITUTIONPROCESS_H
#define BPP_PHYL_LIKELIHOOD_SUBSTITUTIONPROCESS_H
 
 
#include "../Model/SubstitutionModel.h"
#include "ModelScenario.h"
#include "ParametrizablePhyloTree.h"
 
// From bpp-core:
#include <Bpp/Numeric/ParameterAliasable.h>
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
 
#include <Bpp/Seq/Container/AlignmentData.h>
 
// From the STL:
#include <memory>
 
namespace bpp
{
class SubstitutionProcessInterface :
  public virtual ParameterAliasable
{
public:
  virtual SubstitutionProcessInterface* clone() const = 0;
 
public:
  virtual const StateMapInterface& stateMap() const = 0;
 
  virtual std::shared_ptr<const StateMapInterface> getStateMap() const = 0;
 
  virtual bool isCompatibleWith(const AlignmentDataInterface& data) const = 0;
 
  virtual const ParametrizablePhyloTree& parametrizablePhyloTree() const = 0;
 
  virtual std::shared_ptr<const ParametrizablePhyloTree> getParametrizablePhyloTree() const = 0;
 
  virtual size_t getNumberOfClasses() const = 0;
 
  virtual size_t getNumberOfStates() const = 0;
 
  virtual size_t getNumberOfModels() const = 0;
 
  virtual std::vector<size_t> getModelNumbers() const = 0;
 
  virtual const BranchModelInterface& model(size_t i) const = 0;
 
  virtual std::shared_ptr<const BranchModelInterface> getModel(size_t i) const = 0;
 
  virtual const BranchModelInterface& model(
      unsigned int nodeId,
      size_t classIndex) const = 0;
 
  virtual std::shared_ptr<const BranchModelInterface> getModel(
      unsigned int nodeId,
      size_t classIndex) const = 0;
 
  virtual std::shared_ptr<const ModelScenario> getModelScenario() const = 0;
 
  virtual const std::vector<unsigned int> getNodesWithModel(size_t i) const = 0;
 
  virtual size_t getModelNumberForNode(unsigned int nodeId) const = 0;
 
  virtual std::shared_ptr<const BranchModelInterface> getModelForNode(unsigned int nodeId) const = 0;
 
  virtual const DiscreteDistributionInterface& rateDistribution() const = 0;
 
  virtual DiscreteDistributionInterface& rateDistribution() = 0;
 
  virtual std::shared_ptr<const DiscreteDistributionInterface> getRateDistribution() const = 0;
 
  virtual std::shared_ptr<DiscreteDistributionInterface> getRateDistribution() = 0;
 
 
  virtual ParameterList getSubstitutionModelParameters(bool independent) const = 0;
 
  virtual ParameterList getRateDistributionParameters(bool independent) const = 0;
 
  virtual ParameterList getRootFrequenciesParameters(bool independent) const = 0;
 
  virtual ParameterList getBranchLengthParameters(bool independent) const = 0;
 
  virtual ParameterList getNonDerivableParameters() const = 0;
 
  virtual const std::vector<double>& getRootFrequencies() const = 0;
 
  virtual bool hasRootFrequencySet() const = 0;
 
  virtual const FrequencySetInterface& rootFrequencySet() const = 0;
 
  virtual std::shared_ptr<const FrequencySetInterface> getRootFrequencySet() const = 0;
 
  virtual FrequencySetInterface& rootFrequencySet() = 0;
 
  virtual std::shared_ptr<FrequencySetInterface> getRootFrequencySet() = 0;
 
  virtual double getProbabilityForModel(size_t classIndex) const = 0;
 
  virtual Vdouble getClassProbabilities() const = 0;
 
  virtual double getRateForModel(size_t classIndex) const = 0;
 
  // virtual bool transitionProbabilitiesHaveChanged() const = 0; Not sure we need that anymore...
};
} // end namespace bpp
#endif // BPP_PHYL_LIKELIHOOD_SUBSTITUTIONPROCESS_H