YNGP_M2.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Numeric/NumConstants.h>
#include <Bpp/Numeric/Prob/SimpleDiscreteDistribution.h>
 
#include "../MixtureOfASubstitutionModel.h"
#include "YN98.h"
#include "YNGP_M2.h"
 
using namespace bpp;
using namespace std;
 
/******************************************************************************/
 
YNGP_M2::YNGP_M2(
    shared_ptr<const GeneticCode> gc,
    unique_ptr<CodonFrequencySetInterface> codonFreqs) :
  AbstractParameterAliasable("YNGP_M2."),
  AbstractWrappedModel("YNGP_M2."),
  AbstractWrappedTransitionModel("YNGP_M2."),
  AbstractTotallyWrappedTransitionModel("YNGP_M2."),
  AbstractBiblioTransitionModel("YNGP_M2."),
  YNGP_M("YNGP_M2.")
{
  // build the submodel
 
  vector<double> v1, v2;
  v1.push_back(0.5);
  v1.push_back(1);
  v1.push_back(2);
  v2.push_back(0.333333);
  v2.push_back(0.333333);
  v2.push_back(0.333334);
 
  auto psdd = make_unique<SimpleDiscreteDistribution>(v1, v2);
 
  map<string, unique_ptr<DiscreteDistributionInterface>> mpdd;
  mpdd["omega"] = std::move(psdd);
 
  auto yn98 = make_unique<YN98>(gc, std::move(codonFreqs));
 
  mixedModelPtr_.reset(new MixtureOfASubstitutionModel(gc->getSourceAlphabet(), std::move(yn98), mpdd));
  mixedSubModelPtr_ = dynamic_cast<const MixtureOfASubstitutionModel*>(&mixedModel());
 
  vector<int> supportedChars = mixedModelPtr_->getAlphabetStates();
 
  // mapping the parameters
 
  ParameterList pl = mixedModelPtr_->getParameters();
  for (size_t i = 0; i < pl.size(); ++i)
  {
    lParPmodel_.addParameter(Parameter(pl[i]));
  }
 
  vector<std::string> v = dynamic_cast<const YN98&>(mixedModelPtr_->nModel(0)).frequencySet().getParameters().getParameterNames();
 
  for (auto& vi : v)
  {
    mapParNamesFromPmodel_[vi] = vi.substr(5);
  }
 
  mapParNamesFromPmodel_["YN98.kappa"] = "kappa";
  mapParNamesFromPmodel_["YN98.omega_Simple.V1"] = "omega0";
  mapParNamesFromPmodel_["YN98.omega_Simple.theta1"] = "theta1";
  mapParNamesFromPmodel_["YN98.omega_Simple.V3"] = "omega2";
  mapParNamesFromPmodel_["YN98.omega_Simple.theta2"] = "theta2";
 
  // specific parameters
 
  string st;
  for (auto it : mapParNamesFromPmodel_)
  {
    st = mixedModelPtr_->getParameterNameWithoutNamespace(it.first);
    if (it.second.substr(0, 5) != "omega")
      addParameter_(new Parameter("YNGP_M2." + it.second, mixedModelPtr_->getParameterValue(st),
            mixedModelPtr_->parameter(st).hasConstraint() ? std::shared_ptr<ConstraintInterface>(mixedModelPtr_->parameter(st).getConstraint()->clone()) : 0));
  }
 
  addParameter_(new Parameter("YNGP_M2.omega0", 0.5, std::make_shared<IntervalConstraint>(0.002, 1, true, false)));
 
  addParameter_(new Parameter("YNGP_M2.omega2", 2, std::make_shared<IntervalConstraint>(1, 999, false, false, 0.002)));
 
  // look for synonymous codons
  for (synfrom_ = 1; synfrom_ < supportedChars.size(); ++synfrom_)
  {
    for (synto_ = 0; synto_ < synfrom_; ++synto_)
    {
      if (gc->areSynonymous(supportedChars[synfrom_], supportedChars[synto_])
          && (mixedSubModelPtr_->subNModel(0).Qij(synfrom_, synto_) != 0)
          && (mixedSubModelPtr_->subNModel(1).Qij(synfrom_, synto_) != 0))
        break;
    }
    if (synto_ < synfrom_)
      break;
  }
 
  if (synto_ == supportedChars.size())
    throw Exception("Impossible to find synonymous codons");
 
  // update Matrices
 
  computeFrequencies(false);
  updateMatrices_();
}
 
void YNGP_M2::updateMatrices_()
{
  AbstractBiblioTransitionModel::updateMatrices_();
 
  // homogeneization of the synonymous substittion rates
 
  Vdouble vd;
 
  vd.push_back(1 / mixedSubModelPtr_->subNModel(0).Qij(synfrom_, synto_));
  vd.push_back(1 / mixedSubModelPtr_->subNModel(1).Qij(synfrom_, synto_));
  vd.push_back(1 / mixedSubModelPtr_->subNModel(2).Qij(synfrom_, synto_));
 
  mixedModelPtr_->setVRates(vd);
}