G2001.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_G2001_H
#define BPP_PHYL_MODEL_G2001_H
 
#include <Bpp/Numeric/Parameter.h>
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
 
#include "MarkovModulatedSubstitutionModel.h"
 
namespace bpp
{
class G2001 :
  public MarkovModulatedSubstitutionModel
{
private:
  std::unique_ptr<DiscreteDistributionInterface> rDist_;
 
  std::string nestedRatePrefix_;
 
public:
  G2001(
      std::unique_ptr<ReversibleSubstitutionModelInterface> model,
      std::unique_ptr<DiscreteDistributionInterface> rDist,
      double nu = 1.,
      bool normalizeRateChanges = false) :
    MarkovModulatedSubstitutionModel(std::move(model), static_cast<unsigned int>(rDist->getNumberOfCategories()), normalizeRateChanges, "G01."),
    rDist_(std::move(rDist)),
    nestedRatePrefix_("rdist_" + rDist->getNamespace())
  {
    ratesFreq_ = std::vector<double>(nbRates_, 1. / static_cast<double>(nbRates_));
    rDist_->setNamespace(getNamespace() + nestedRatePrefix_);
    addParameters_(rDist_->getIndependentParameters());
    addParameter_(new Parameter("G01.nu", nu, Parameter::R_PLUS));
    updateRatesModel_();
    updateMatrices_();
  }
 
  G2001(const G2001& model) :
    MarkovModulatedSubstitutionModel(model),
    rDist_(model.rDist_->clone()),
    nestedRatePrefix_(model.nestedRatePrefix_)
  {}
 
  G2001& operator=(const G2001& model)
  {
    MarkovModulatedSubstitutionModel::operator=(model);
    rDist_.reset(model.rDist_->clone());
    nestedRatePrefix_ = model.nestedRatePrefix_;
    return *this;
  }
 
  virtual ~G2001() { }
 
  G2001* clone() const override { return new G2001(*this); }
 
public:
  std::string getName() const override { return "G01"; }
 
  void fireParameterChanged(const ParameterList& parameters) override
  {
    rDist_->matchParametersValues(parameters);
    MarkovModulatedSubstitutionModel::fireParameterChanged(parameters);
  }
 
  const DiscreteDistributionInterface& rateDistribution() const { return *rDist_; }
 
  void setNamespace(const std::string& prefix) override
  {
    MarkovModulatedSubstitutionModel::setNamespace(prefix);
    // We also need to update the namespace of the nested distribution:
    rDist_->setNamespace(prefix + nestedRatePrefix_);
  }
 
 
  double getRate() const override {  return 1.; }
 
  void setRate(double rate) override {}
 
  void addRateParameter() override {}
 
protected:
  void updateRatesModel_() override
  {
    double nu = getParameterValue("nu");
    for (size_t i = 0; i < nbRates_; ++i)
    {
      rates_(i, i) = rDist_->getCategory(i);
      for (size_t j = 0; j < nbRates_; ++j)
      {
        if (i == j)
        {
          ratesExchangeability_(i, j) = -static_cast<double>(nbRates_) * nu;
        }
        else
        {
          ratesExchangeability_(i, j) = static_cast<double>(nbRates_) * nu / static_cast<double>(nbRates_ - 1);
        }
      }
    }
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_G2001_H