YNGP_M9.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Numeric/Prob/BetaDiscreteDistribution.h>
#include <Bpp/Numeric/Prob/GammaDiscreteDistribution.h>
#include <Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.h>
#include <Bpp/Text/TextTools.h>
 
#include "../MixtureOfASubstitutionModel.h"
#include "YN98.h"
#include "YNGP_M9.h"
 
using namespace bpp;
using namespace std;
 
/******************************************************************************/
 
YNGP_M9::YNGP_M9(
    std::shared_ptr<const GeneticCode> gc,
    std::unique_ptr<CodonFrequencySetInterface> codonFreqs,
    unsigned int nbBeta,
    unsigned int nbGamma) :
  AbstractParameterAliasable("YNGP_M9."),
  AbstractWrappedModel("YNGP_M9."),
  AbstractWrappedTransitionModel("YNGP_M9."),
  AbstractTotallyWrappedTransitionModel("YNGP_M9."),
  AbstractBiblioTransitionModel("YNGP_M9."),
  YNGP_M("YNGP_M9."),
  nBeta_(nbBeta),
  nGamma_(nbGamma)
{
  if (nbBeta <= 0)
    throw Exception("Bad number of classes for beta distribution of model YNGP_M9: " + TextTools::toString(nbBeta));
  if (nbGamma <= 0)
    throw Exception("Bad number of classes for gamma distribution of model YNGP_M9: " + TextTools::toString(nbGamma));
 
  // build the submodel
 
  auto pbdd = make_unique<BetaDiscreteDistribution>(nbBeta, 2, 2);
  auto pgdd = make_unique<GammaDiscreteDistribution>(nbGamma, 1, 1);
 
  vector<unique_ptr<DiscreteDistributionInterface>> v_distr;
  v_distr.push_back(std::move(pbdd));
  v_distr.push_back(std::move(pgdd));
  vector<double> prob;
  prob.push_back(0.5);
  prob.push_back(0.5);
 
  auto pmodd = make_unique<MixtureOfDiscreteDistributions>(v_distr, prob);
 
  map<string, unique_ptr<DiscreteDistributionInterface>> mpdd;
  mpdd["omega"] = std::move(pmodd);
 
  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_Mixture.theta1"] = "p0";
  mapParNamesFromPmodel_["YN98.omega_Mixture.1_Beta.alpha"] = "p";
  mapParNamesFromPmodel_["YN98.omega_Mixture.1_Beta.beta"] = "q";
  mapParNamesFromPmodel_["YN98.omega_Mixture.2_Gamma.alpha"] = "alpha";
  mapParNamesFromPmodel_["YN98.omega_Mixture.2_Gamma.beta"] = "beta";
 
  // specific parameters
 
  string st;
  for (auto& it : mapParNamesFromPmodel_)
  {
    st = mixedModelPtr_->getParameterNameWithoutNamespace(it.first);
    addParameter_(new Parameter("YNGP_M9." + it.second, mixedModelPtr_->getParameterValue(st),
          mixedModelPtr_->parameter(st).hasConstraint() ? shared_ptr<ConstraintInterface>(mixedModelPtr_->parameter(st).getConstraint()->clone()) : 0));
  }
 
  // 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_ == gc->getSourceAlphabet()->getSize())
    throw Exception("Impossible to find synonymous codons");
 
  // update Matrices
  computeFrequencies(false);
  updateMatrices_();
}
 
void YNGP_M9::updateMatrices_()
{
  AbstractBiblioTransitionModel::updateMatrices_();
 
  // homogeneization of the synonymous substittion rates
 
  Vdouble vd;
 
  for (unsigned int i = 0; i < mixedModelPtr_->getNumberOfModels(); ++i)
  {
    vd.push_back(1 / mixedSubModelPtr_->subNModel(i).Qij(synfrom_, synto_));
  }
 
  mixedModelPtr_->setVRates(vd);
}