AlignedPhyloLikelihoodMixture.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "AlignedPhyloLikelihoodMixture.h"
 
using namespace bpp;
using namespace std;
 
AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(
    Context& context,
    std::shared_ptr<PhyloLikelihoodContainer> pC,
    const std::vector<size_t>& nPhylo,
    bool inCollection) :
  AbstractPhyloLikelihood(context),
  AbstractParametrizable(""),
  AbstractPhyloLikelihoodSet(context, pC, nPhylo, inCollection),
  AbstractAlignedPhyloLikelihood(context, 0),
  AbstractAlignedPhyloLikelihoodSet(context, pC, nPhylo, inCollection, ""),
  likCal_(make_shared<AlignedLikelihoodCalculation>(context))
{
  Simplex simplex(getNumbersOfPhyloLikelihoods().size(), 1, false, "Mixture.");
 
  // parameters of the simplex
  const auto& param = simplex.getParameters();
  ParameterList paramList;
 
  for (size_t i = 0; i < param.size(); ++i)
  {
    paramList.shareParameter(ConfiguredParameter::create(this->context(), param[i]));
  }
 
  shareParameters_(paramList);
 
  // make Simplex DF & Frequencies from it
 
  simplex_ = ConfiguredParametrizable::createConfigured<Simplex, ConfiguredSimplex>(this->context(), simplex, paramList, "");
 
  // for derivates
  auto deltaNode = NumericMutable<double>::create(this->context(), 0.001);
  auto config = NumericalDerivativeType::ThreePoints;
 
  simplex_->config.delta = deltaNode;
  simplex_->config.type = config;
 
  auto fsf = ConfiguredParametrizable::createRowVector<ConfiguredSimplex, FrequenciesFromSimplex, Eigen::RowVectorXd>(this->context(), {simplex_}, RowVectorDimension (Eigen::Index(simplex.dimension())));
 
  // get RowVectorXd for each single Calculation
  std::vector<std::shared_ptr<Node_DF>> vSL;
 
  for (auto np : nPhylo)
  {
    vSL.push_back(alignedPhyloLikelihood(np).alignedLikelihoodCalculation().getSiteLikelihoods(false));
  }
 
  // put probabilities of the simplex
 
  vSL.push_back(fsf);
 
  auto sL = CWiseMean<RowLik, ReductionOf<RowLik>, Eigen::RowVectorXd>::create(this->context(), std::move(vSL), RowVectorDimension (Eigen::Index(nbSites_)));
 
  likCal_->setSiteLikelihoods(sL);
 
  auto su = SumOfLogarithms<RowLik>::create (this->context(), {sL}, RowVectorDimension (Eigen::Index (nbSites_)));
 
  likCal_->setLikelihoodNode(su);
}
 
Vdouble AlignedPhyloLikelihoodMixture::getPhyloProbabilities() const
{
  return accessValueConstCast<const Simplex*>(*simplex_)->getFrequencies();
}
 
double AlignedPhyloLikelihoodMixture::getPhyloProb(size_t index) const
{
  return accessValueConstCast<const Simplex*>(*simplex_)->prob(index);
}
 
/******************************************************************************/
 
void AlignedPhyloLikelihoodMixture::fireParameterChanged(const ParameterList& parameters)
{
  // simplex_->matchParametersValues(parameters);
  // SetOfAbstractPhyloLikelihood::fireParameterChanged(parameters);
}
 
void AlignedPhyloLikelihoodMixture::setPhyloProb(const Simplex& si)
{
  simplex_->matchParametersValues(si.getParameters());
  //  matchParametersValues(simplex_.getParameters());
}