OneProcessSequenceEvolution.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_ONEPROCESSSEQUENCEEVOLUTION_H
#define BPP_PHYL_LIKELIHOOD_ONEPROCESSSEQUENCEEVOLUTION_H
 
 
// From bpp-core:
#include <Bpp/Numeric/ParameterAliasable.h>
 
// From the STL:
#include <memory>
 
#include "SequenceEvolution.h"
#include "SubstitutionProcess.h"
 
namespace bpp
{
class OneProcessSequenceEvolution :
  public virtual SequenceEvolution,
  public AbstractParameterAliasable
{
protected:
  std::shared_ptr<SubstitutionProcessInterface> subsProc_;
 
  size_t nProc_;
 
  std::vector<size_t> vProc_;
 
public:
  OneProcessSequenceEvolution(std::shared_ptr<SubstitutionProcessInterface> process, size_t nProc = 0);
 
  OneProcessSequenceEvolution(const OneProcessSequenceEvolution& evol);
 
  OneProcessSequenceEvolution& operator=(const OneProcessSequenceEvolution& evol);
 
  OneProcessSequenceEvolution* clone() const override
  {
    return new OneProcessSequenceEvolution(*this);
  }
 
  bool isCompatibleWith(const AlignmentDataInterface& data) const override
  {
    return subsProc_->isCompatibleWith(data);
  }
 
  const size_t getSubstitutionProcessNumber() const
  {
    return nProc_;
  }
 
  const SubstitutionProcessInterface& substitutionProcess() const
  {
    return *subsProc_;
  }
 
  std::shared_ptr<const SubstitutionProcessInterface> getSubstitutionProcess() const
  {
    return subsProc_;
  }
 
  SubstitutionProcessInterface& substitutionProcess()
  {
    return *subsProc_;
  }
 
  std::shared_ptr<SubstitutionProcessInterface> getSubstitutionProcess()
  {
    return subsProc_;
  }
 
  const std::vector<size_t>& getSubstitutionProcessNumbers() const override
  {
    return vProc_;
  }
 
  const SubstitutionProcessInterface& substitutionProcess(size_t number) const override
  {
    return *subsProc_;
  }
 
  std::shared_ptr<const SubstitutionProcessInterface> getSubstitutionProcess(size_t number) const override
  {
    return subsProc_;
  }
 
  std::shared_ptr<const ParametrizablePhyloTree> tree() const
  {
    return subsProc_->getParametrizablePhyloTree();
  }
 
  void fireParameterChanged(const ParameterList& pl) override
  {
    // Updates substitution process:
    subsProc_->matchParametersValues(pl);
  }
 
 
  ParameterList getBranchLengthParameters(bool independent) const override
  {
    return subsProc_->getBranchLengthParameters(independent);
  }
 
  ParameterList getRootFrequenciesParameters(bool independent) const override
  {
    return subsProc_->getRootFrequenciesParameters(independent);
  }
 
  ParameterList getRateDistributionParameters(bool independent) const override
  {
    return subsProc_->getRateDistributionParameters(independent);
  }
 
  ParameterList getSubstitutionModelParameters(bool independent) const override
  {
    return subsProc_->getSubstitutionModelParameters(independent);
  }
 
  ParameterList getSubstitutionProcessParameters(bool independent) const override
  {
    if (independent)
      return subsProc_->getIndependentParameters();
    else
      return subsProc_->getParameters();
  }
 
  const ParameterList& getParameters() const override
  {
    return subsProc_->getParameters();
  }
 
  const ParameterList& getIndependentParameters() const override
  {
    return subsProc_->getIndependentParameters();
  }
 
  ParameterList getNonDerivableParameters() const override
  {
    return subsProc_->getNonDerivableParameters();
  }
};
} // end namespace bpp
#endif // BPP_PHYL_LIKELIHOOD_ONEPROCESSSEQUENCEEVOLUTION_H