PhyloLikelihoodSet.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_SETOFPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SETOFPHYLOLIKELIHOOD_H
 
 
#include "AbstractPhyloLikelihood.h"
#include "PhyloLikelihood.h"
#include "PhyloLikelihoodContainer.h"
 
namespace bpp
{
class PhyloLikelihoodSetInterface :
  public virtual PhyloLikelihoodInterface
{
public:
  virtual PhyloLikelihoodSetInterface* clone() const = 0;
 
public:
  virtual std::shared_ptr<PhyloLikelihoodContainer> getPhyloContainer() = 0;
 
  virtual std::shared_ptr<const PhyloLikelihoodContainer> getPhyloContainer() const = 0;
 
  virtual const std::vector<size_t>& getNumbersOfPhyloLikelihoods() const = 0;
 
  virtual bool addPhyloLikelihood(size_t nPhyl, const std::string& suff = "") = 0;
 
  virtual bool hasPhyloLikelihood(size_t nPhyl) = 0;
 
  virtual std::shared_ptr<const PhyloLikelihoodInterface> getPhyloLikelihood(size_t nPhyl) const = 0;
 
  virtual std::shared_ptr<PhyloLikelihoodInterface> getPhyloLikelihood(size_t nPhyl) = 0;
};
 
 
class AbstractPhyloLikelihoodSet :
  public virtual PhyloLikelihoodSetInterface,
  public virtual AbstractPhyloLikelihood,
  public virtual AbstractParametrizable
{
protected:
  std::shared_ptr<PhyloLikelihoodContainer> pPhyloCont_;
 
  std::vector<size_t> nPhylo_;
 
  mutable std::vector<std::shared_ptr<LikelihoodCalculation>> vLikCal_;
 
public:
  AbstractPhyloLikelihoodSet(
      Context& context,
      std::shared_ptr<PhyloLikelihoodContainer> pC,
      bool inCollection = true,
      const std::string& prefix = "");
 
  AbstractPhyloLikelihoodSet(
      Context& context,
      std::shared_ptr<PhyloLikelihoodContainer> pC,
      const std::vector<size_t>& nPhylo,
      bool inCollection = true,
      const std::string& prefix = "");
 
  virtual ~AbstractPhyloLikelihoodSet() {}
 
protected:
  AbstractPhyloLikelihoodSet(const AbstractPhyloLikelihoodSet& sd) :
    AbstractPhyloLikelihood(sd),
    AbstractParametrizable(sd),
    pPhyloCont_(sd.pPhyloCont_),
    nPhylo_(sd.nPhylo_),
    vLikCal_(sd.vLikCal_)
  {}
 
  AbstractPhyloLikelihoodSet& operator=(const AbstractPhyloLikelihoodSet& sd)
  {
    AbstractPhyloLikelihood::operator=(sd);
    AbstractParametrizable::operator=(sd);
    pPhyloCont_ = sd.pPhyloCont_;
    nPhylo_ = sd.nPhylo_;
    vLikCal_ = sd.vLikCal_;
    return *this;
  }
 
public:
  std::shared_ptr<PhyloLikelihoodContainer> getPhyloContainer() override
  {
    return pPhyloCont_;
  }
 
  std::shared_ptr<const PhyloLikelihoodContainer> getPhyloContainer() const override
  {
    return pPhyloCont_;
  }
 
  const std::vector<size_t>& getNumbersOfPhyloLikelihoods() const override
  {
    return nPhylo_;
  }
 
  virtual bool addPhyloLikelihood(size_t nPhyl, const std::string& suff = "") override;
 
  bool hasPhyloLikelihood(size_t nPhyl) override
  {
    return std::find(nPhylo_.begin(), nPhylo_.end(), nPhyl) != nPhylo_.end();
  }
 
  std::shared_ptr<const PhyloLikelihoodInterface> getPhyloLikelihood(size_t nPhyl) const override
  {
    return (*pPhyloCont_)[nPhyl];
  }
 
 
  std::shared_ptr<PhyloLikelihoodInterface> getPhyloLikelihood(size_t nPhyl) override
  {
    return (*pPhyloCont_)[nPhyl];
  }
 
  bool isInitialized() const override
  {
    for (auto nPhylo: nPhylo_)
    {
      if (!getPhyloLikelihood(nPhylo)->isInitialized())
        return false;
    }
    return true;
  }
 
public:
  virtual void fireParameterChanged(const ParameterList& params) override
  {
    for (auto nPhylo: nPhylo_)
    {
      getPhyloLikelihood(nPhylo)->matchParametersValues(params);
 
      // to ensure each phylolikelihood is recomputed, such as in
      // case of total aliasing
      // getAbstractPhyloLikelihood(nPhylo_[i])->update();
    }
  }
 
  ParameterList getNonDerivableParameters() const override;
 
  ParameterList getDerivableParameters() const override;
 
  ParameterList getBranchLengthParameters() const override;
 
  ParameterList getSubstitutionModelParameters() const override;
 
  ParameterList getRateDistributionParameters() const override;
 
  ParameterList getRootFrequenciesParameters() const override;
 
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SETOFPHYLOLIKELIHOOD_H