SingleDataPhyloLikelihood.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_SINGLEDATAPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SINGLEDATAPHYLOLIKELIHOOD_H
 
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Container/AlignmentData.h>
 
// from bpp-core
 
#include <Bpp/Numeric/AbstractParametrizable.h>
 
#include "AlignedPhyloLikelihood.h"
 
namespace bpp
{
class SingleDataPhyloLikelihoodInterface :
  public virtual AlignedPhyloLikelihoodInterface
{
public:
  SingleDataPhyloLikelihoodInterface() {}
  virtual ~SingleDataPhyloLikelihoodInterface() {}
 
  virtual SingleDataPhyloLikelihoodInterface* clone() const = 0;
 
public:
  virtual void setData(std::shared_ptr<const AlignmentDataInterface> sites, size_t nData = 0) = 0;
 
  virtual std::shared_ptr<const AlignmentDataInterface> getData() const = 0;
 
  virtual size_t getNData() const = 0;
 
  virtual size_t getNumberOfStates() const = 0;
 
  virtual std::shared_ptr<const Alphabet> getAlphabet() const = 0;
 
};
 
 
class AbstractSingleDataPhyloLikelihood :
  public virtual SingleDataPhyloLikelihoodInterface,
  public virtual AbstractAlignedPhyloLikelihood
{
protected:
  size_t nbStates_;
 
  size_t nData_;
 
public:
  AbstractSingleDataPhyloLikelihood(Context& context, size_t nbSites, size_t nbStates, size_t nData = 0) :
    AbstractPhyloLikelihood(context),
    AbstractAlignedPhyloLikelihood(context, nbSites),
    nbStates_(nbStates),
    nData_(nData)
  {}
 
  AbstractSingleDataPhyloLikelihood(const AbstractSingleDataPhyloLikelihood& asdpl) :
    AbstractPhyloLikelihood(asdpl),
    AbstractAlignedPhyloLikelihood(asdpl),
    nbStates_(asdpl.nbStates_),
    nData_(asdpl.nData_)
  {}
 
  AbstractSingleDataPhyloLikelihood& operator=(const AbstractSingleDataPhyloLikelihood& asdpl)
  {
    AbstractAlignedPhyloLikelihood::operator=(asdpl);
    nbStates_ = asdpl.nbStates_;
    nData_ = asdpl.nData_;
    return *this;
  }
 
  virtual ~AbstractSingleDataPhyloLikelihood() {}
 
  virtual void setData(std::shared_ptr<const AlignmentDataInterface> sites, size_t nData = 0)
  {
    setNumberOfSites(sites->getNumberOfSites());
    nbStates_ = sites->alphabet().getSize();
    nData_ = nData;
  }
 
  size_t getNData() const
  {
    return nData_;
  }
 
  void setNData(size_t nData)
  {
    nData_ = nData;
  }
 
  size_t getNumberOfStates() const { return nbStates_; }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SINGLEDATAPHYLOLIKELIHOOD_H