JCprot.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_PROTEIN_JCPROT_H
#define BPP_PHYL_MODEL_PROTEIN_JCPROT_H
 
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
 
#include "../AbstractSubstitutionModel.h"
#include "../FrequencySet/ProteinFrequencySet.h"
#include "ProteinSubstitutionModel.h"
 
namespace bpp
{
class JCprot :
  public AbstractReversibleProteinSubstitutionModel
{
private:
  mutable double exp_;
  mutable RowMatrix<double> p_;
  std::unique_ptr<ProteinFrequencySetInterface> freqSet_;
  bool withFreq_;
 
public:
  JCprot(std::shared_ptr<const ProteicAlphabet> alpha);
 
  JCprot(
      std::shared_ptr<const ProteicAlphabet> alpha,
      std::unique_ptr<ProteinFrequencySetInterface> freqSet,
      bool initFreqs = false);
 
  JCprot(const JCprot& model) :
    AbstractParameterAliasable(model),
    AbstractReversibleProteinSubstitutionModel(model),
    exp_(model.exp_),
    p_(model.p_),
    freqSet_(model.freqSet_->clone()),
    withFreq_(model.withFreq_)
  {}
 
  JCprot& operator=(const JCprot& model)
  {
    AbstractParameterAliasable::operator=(model);
    AbstractReversibleProteinSubstitutionModel::operator=(model);
    exp_ = model.exp_;
    p_   = model.p_;
    freqSet_.reset(model.freqSet_->clone());
    withFreq_ = model.withFreq_;
    return *this;
  }
 
  virtual ~JCprot() {}
 
  JCprot* clone() const override { return new JCprot(*this); }
 
public:
  double Pij_t    (size_t i, size_t j, double d) const override;
  double dPij_dt  (size_t i, size_t j, double d) const override;
  double d2Pij_dt2(size_t i, size_t j, double d) const override;
  const Matrix<double>& getPij_t    (double d) const override;
  const Matrix<double>& getdPij_dt  (double d) const override;
  const Matrix<double>& getd2Pij_dt2(double d) const override;
 
  std::string getName() const override
  {
    return withFreq_ ? "JC69+F" : "JC69";
  }
 
  void fireParameterChanged(const ParameterList& parameters) override
  {
    freqSet_->matchParametersValues(parameters);
    freq_ = freqSet_->getFrequencies();
    AbstractReversibleSubstitutionModel::fireParameterChanged(parameters);
  }
 
  void setFrequencySet(const ProteinFrequencySetInterface& freqSet)
  {
    freqSet_.reset(freqSet.clone());
    resetParameters_();
    addParameters_(freqSet_->getParameters());
  }
 
  const FrequencySetInterface& frequencySet() const override
  {
    if (freqSet_)
      return *freqSet_;
    throw NullPointerException("JCprot::frequencySet(). No associated FrequencySet.");
  }
 
  void setNamespace(const std::string& prefix) override
  {
    AbstractParameterAliasable::setNamespace(prefix);
    freqSet_->setNamespace(prefix + freqSet_->getName() + ".");
  }
 
  void setFreqFromData(const SequenceDataInterface& data, double pseudoCount = 0) override;
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_PROTEIN_JCPROT_H