AlignedPhyloLikelihoodSet.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SETOFALIGNEDPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SETOFALIGNEDPHYLOLIKELIHOOD_H
 
 
// From bpp-seq:
#include <Bpp/Seq/Container/AlignmentData.h>
 
#include "AlignedPhyloLikelihood.h"
#include "PhyloLikelihoodSet.h"
 
namespace bpp
{
class AlignedPhyloLikelihoodSetInterface :
  public virtual PhyloLikelihoodSetInterface,
  public virtual AlignedPhyloLikelihoodInterface
{
public:
  AlignedPhyloLikelihoodSetInterface* clone() const override = 0;
 
  virtual std::shared_ptr<const AlignedPhyloLikelihoodInterface> getAlignedPhyloLikelihood(size_t nPhyl) const = 0;
 
  virtual std::shared_ptr<AlignedPhyloLikelihoodInterface> getAlignedPhyloLikelihood(size_t nPhyl) = 0;
 
  virtual const AlignedPhyloLikelihoodInterface& alignedPhyloLikelihood(size_t nPhyl) const = 0;
 
  virtual AlignedPhyloLikelihoodInterface& alignedPhyloLikelihood(size_t nPhyl) = 0;
 
  virtual DataLik getLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const = 0;
 
  virtual double getLogLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const = 0;
};
 
class AbstractAlignedPhyloLikelihoodSet :
  public virtual AlignedPhyloLikelihoodSetInterface,
  public virtual AbstractPhyloLikelihoodSet,
  public virtual AbstractAlignedPhyloLikelihood
{
public:
  AbstractAlignedPhyloLikelihoodSet(
      Context& context,
      std::shared_ptr<PhyloLikelihoodContainer> pC,
      bool inCollection = true,
      const std::string& prefix = "");
 
  AbstractAlignedPhyloLikelihoodSet(
      Context& context,
      std::shared_ptr<PhyloLikelihoodContainer> pC,
      const std::vector<size_t>& nPhylo,
      bool inCollection = true,
      const std::string& prefix = "");
 
protected:
  AbstractAlignedPhyloLikelihoodSet(const AbstractAlignedPhyloLikelihoodSet& soap) :
    AbstractPhyloLikelihood(soap),
    AbstractPhyloLikelihoodSet(soap),
    AbstractAlignedPhyloLikelihood(soap)
  {}
 
  AbstractAlignedPhyloLikelihoodSet& operator=(const AbstractAlignedPhyloLikelihoodSet& soap)
  {
    AbstractPhyloLikelihoodSet::operator=(soap);
    AbstractAlignedPhyloLikelihood::operator=(soap);
    return *this;
  }
 
public:
  virtual ~AbstractAlignedPhyloLikelihoodSet() {}
 
  bool addPhyloLikelihood(size_t nPhyl, const std::string& suff) override;
 
  std::shared_ptr<const AlignedPhyloLikelihoodInterface> getAlignedPhyloLikelihood(size_t nPhyl) const override
  {
    return std::dynamic_pointer_cast<const AlignedPhyloLikelihoodInterface>((*pPhyloCont_)[nPhyl]);
  }
 
  std::shared_ptr<AlignedPhyloLikelihoodInterface> getAlignedPhyloLikelihood(size_t nPhyl) override
  {
    return std::dynamic_pointer_cast<AlignedPhyloLikelihoodInterface>((*pPhyloCont_)[nPhyl]);
  }
 
  const AlignedPhyloLikelihoodInterface& alignedPhyloLikelihood(size_t nPhyl) const override
  {
    return dynamic_cast<const AlignedPhyloLikelihoodInterface&>(*(*pPhyloCont_)[nPhyl]);
  }
 
  AlignedPhyloLikelihoodInterface& alignedPhyloLikelihood(size_t nPhyl) override
  {
    return dynamic_cast<AlignedPhyloLikelihoodInterface&>(*(*pPhyloCont_)[nPhyl]);
  }
 
  DataLik getLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const override
  {
    return alignedPhyloLikelihood(nPhyl).getLikelihoodForASite(site);
  }
 
  double getLogLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const override
  {
    return alignedPhyloLikelihood(nPhyl).getLogLikelihoodForASite(site);
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SETOFALIGNEDPHYLOLIKELIHOOD_H