PhyloLikelihoodFormula.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_FORMULAOFPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_FORMULAOFPHYLOLIKELIHOOD_H
 
#include <Bpp/Numeric/Function/Operators/ComputationTree.h>
 
#include "PhyloLikelihoodSet.h"
 
namespace bpp
{
class PhyloLikelihoodFormula :
  public AbstractPhyloLikelihoodSet
{
private:
  std::unique_ptr<ComputationTree> compTree_;
 
  std::shared_ptr<LikelihoodCalculation> likCal_;
 
public:
  PhyloLikelihoodFormula(Context& context, std::shared_ptr<PhyloLikelihoodContainer> pC, const std::string& formula, bool inCollection = true);
 
  virtual ~PhyloLikelihoodFormula() {}
 
protected:
  PhyloLikelihoodFormula(const PhyloLikelihoodFormula& sd) :
    AbstractPhyloLikelihood(sd),
    AbstractParametrizable(sd),
    AbstractPhyloLikelihoodSet(sd),
    compTree_(sd.compTree_->clone()),
    likCal_(sd.likCal_)
  {}
 
  PhyloLikelihoodFormula& operator=(const PhyloLikelihoodFormula& sd)
  {
    AbstractPhyloLikelihoodSet::operator=(sd);
    compTree_.reset(sd.compTree_->clone());
    likCal_ = sd.likCal_;
    return *this;
  }
 
 
  PhyloLikelihoodFormula* clone() const
  {
    return new PhyloLikelihoodFormula(*this);
  }
 
public:
  void readFormula(const std::string& formula, bool inCollection = true);
 
  std::string output() const;
 
  LikelihoodCalculation& likelihoodCalculation() const
  {
    return *likCal_;
  }
 
  std::shared_ptr<LikelihoodCalculation> getLikelihoodCalculation() const
  {
    return likCal_;
  }
 
private:
  ValueRef<DataLik> makeLikelihoods()
  {
    return makeLikelihoodsFromOperator(compTree_->getRoot());
  }
 
  ValueRef<DataLik> makeLikelihoodsFromOperator(std::shared_ptr<Operator> op);
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_FORMULAOFPHYLOLIKELIHOOD_H