AutoCorrelationSequenceEvolution.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_AUTOCORRELATIONSEQUENCEEVOLUTION_H
#define BPP_PHYL_LIKELIHOOD_AUTOCORRELATIONSEQUENCEEVOLUTION_H
 
 
#include "HmmProcessAlphabet.h"
#include "MultiProcessSequenceEvolution.h"
 
// From Numeric
#include <Bpp/Numeric/Hmm/AutoCorrelationTransitionMatrix.h>
 
#include <memory>
 
namespace bpp
{
class AutoCorrelationSequenceEvolution :
  public MultiProcessSequenceEvolution
{
private:
  std::shared_ptr<HmmProcessAlphabet> hmmAlph_;
  std::shared_ptr<AutoCorrelationTransitionMatrix> autoCorrTransMat_;
 
public:
  AutoCorrelationSequenceEvolution(
      std::shared_ptr<SubstitutionProcessCollection> processColl,
      std::vector<size_t>& nProc);
 
  AutoCorrelationSequenceEvolution(const AutoCorrelationSequenceEvolution& mlc) :
    MultiProcessSequenceEvolution(mlc),
    hmmAlph_(mlc.hmmAlph_->clone()),
    autoCorrTransMat_(mlc.autoCorrTransMat_->clone()){}
 
  AutoCorrelationSequenceEvolution& operator=(const AutoCorrelationSequenceEvolution& mlc)
  {
    MultiProcessSequenceEvolution::operator=(mlc);
 
    hmmAlph_ = std::shared_ptr<HmmProcessAlphabet>(new HmmProcessAlphabet(*mlc.hmmAlph_.get()));
    autoCorrTransMat_ = std::shared_ptr<AutoCorrelationTransitionMatrix>(new AutoCorrelationTransitionMatrix(*mlc.autoCorrTransMat_.get()));
 
    return *this;
  }
 
  virtual ~AutoCorrelationSequenceEvolution() {}
 
  AutoCorrelationSequenceEvolution* clone() const { return new AutoCorrelationSequenceEvolution(*this); }
 
public:
  void setNamespace(const std::string& nameSpace);
 
  void fireParameterChanged(const ParameterList& parameters);
 
  const AutoCorrelationTransitionMatrix& hmmTransitionMatrix() const
  {
    return *autoCorrTransMat_.get();
  }
 
  AutoCorrelationTransitionMatrix& hmmTransitionMatrix()
  {
    return *autoCorrTransMat_.get();
  }
 
  std::shared_ptr<AutoCorrelationTransitionMatrix> getHmmTransitionMatrix()
  {
    return autoCorrTransMat_;
  }
 
  std::shared_ptr<const AutoCorrelationTransitionMatrix> getHmmTransitionMatrix() const
  {
    return autoCorrTransMat_;
  }
 
  HmmProcessAlphabet& hmmProcessAlphabet()
  {
    return *hmmAlph_.get();
  }
 
  const HmmProcessAlphabet& hmmProcessAlphabet() const
  {
    return *hmmAlph_.get();
  }
 
  std::shared_ptr<HmmProcessAlphabet> getHmmProcessAlphabet()
  {
    return hmmAlph_;
  }
 
  std::shared_ptr<const HmmProcessAlphabet> getHmmProcessAlphabet() const
  {
    return hmmAlph_;
  }
 
  ParameterList getNonDerivableParameters() const;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_AUTOCORRELATIONSEQUENCEEVOLUTION_H