AlignedPhyloLikelihoodProduct.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "AlignedPhyloLikelihoodProduct.h"
 
using namespace bpp;
using namespace std;
 
AlignedPhyloLikelihoodProduct::AlignedPhyloLikelihoodProduct(
    Context& context,
    std::shared_ptr<PhyloLikelihoodContainer> pC,
    bool inCollection) :
  AbstractPhyloLikelihood(context),
  AbstractParametrizable(""),
  AbstractPhyloLikelihoodSet(context, pC, {}, inCollection),
  AbstractAlignedPhyloLikelihood(context, 0),
  AbstractAlignedPhyloLikelihoodSet(context, pC, inCollection)
{
  auto nPhylo = pC->getNumbersOfPhyloLikelihoods();
 
  // 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));
  }
 
  auto sL = CWiseMul<RowLik, ReductionOf<RowLik>>::create(this->context(), std::move(vSL), RowVectorDimension (nbSites_));
 
  likCal_->setSiteLikelihoods(sL);
 
  auto su = SumOfLogarithms<RowLik>::create (this->context(), {sL}, RowVectorDimension (Eigen::Index (nbSites_)));
 
  likCal_->setLikelihoodNode(su);
}
 
AlignedPhyloLikelihoodProduct::AlignedPhyloLikelihoodProduct(
    Context& context,
    std::shared_ptr<PhyloLikelihoodContainer> pC,
    const std::vector<size_t>& nPhylo,
    bool inCollection) :
  AbstractPhyloLikelihood(context),
  AbstractParametrizable(""),
  AbstractPhyloLikelihoodSet(context, pC, {}, inCollection),
  AbstractAlignedPhyloLikelihood(context, 0),
  AbstractAlignedPhyloLikelihoodSet(context, pC, nPhylo, inCollection),
  likCal_(make_shared<AlignedLikelihoodCalculation>(context))
{
  // 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));
  }
 
  auto sL = CWiseMul<RowLik, ReductionOf<RowLik>>::create(this->context(), std::move(vSL), RowVectorDimension (nbSites_));
 
  likCal_->setSiteLikelihoods(sL);
 
  auto su = SumOfLogarithms<Eigen::RowVectorXd>::create (this->context(), {sL}, RowVectorDimension (nbSites_));
 
  likCal_->setLikelihoodNode(su);
}