TS98.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_TS98_H
#define BPP_PHYL_MODEL_TS98_H
 
 
#include "MarkovModulatedSubstitutionModel.h"
 
// From NumCalc:
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/Parameter.h>
 
namespace bpp
{
class TS98 :
  public MarkovModulatedSubstitutionModel
{
public:
  TS98(
      std::unique_ptr<ReversibleSubstitutionModelInterface> model,
      double s1 = 1.,
      double s2 = 1.,
      bool normalizeRateChanges = false) :
    MarkovModulatedSubstitutionModel(std::move(model), 2, normalizeRateChanges, "TS98.")
  {
    addParameter_(new Parameter("TS98.s1", s1, Parameter::R_PLUS_STAR));
    addParameter_(new Parameter("TS98.s2", s2, Parameter::R_PLUS_STAR));
    updateRatesModel_();
    updateMatrices_();
  }
 
  virtual ~TS98() {}
 
  TS98* clone() const override { return new TS98(*this); }
 
public:
  std::string getName() const override { return "TS98"; }
 
  double getRate() const override { return 1.; }
 
  void setRate(double rate) override {}
 
  void addRateParameter() override {}
 
protected:
  void updateRatesModel_() override
  {
    double s1 = getParameterValue("s1");
    double s2 = getParameterValue("s2");
    ratesFreq_[0] = s2 / (s1 + s2);
    ratesFreq_[1] = s1 / (s1 + s2);
    rates_(1, 1) = (s1 + s2) / s1;
    ratesExchangeability_(0, 1) = ratesExchangeability_(1, 0) = s1 + s2;
    ratesExchangeability_(0, 0) = -s1 * (s1 + s2) / s2;
    ratesExchangeability_(1, 1) = -s2 * (s1 + s2) / s1;
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_TS98_H