MultiProcessSequencePhyloLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MULTIPROCESSSEQUENCEPHYLOLIKELIHOOD_H
#define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MULTIPROCESSSEQUENCEPHYLOLIKELIHOOD_H
 
#include <Bpp/Numeric/AbstractParametrizable.h>
 
#include "../DataFlow/LikelihoodCalculationSingleProcess.h"
#include "../MultiProcessSequenceEvolution.h"
#include "SequencePhyloLikelihood.h"
 
// From bpp-seq:
#include <Bpp/Seq/Container/AlignmentData.h>
 
using namespace std;
 
namespace bpp
{
class MultiProcessSequencePhyloLikelihood :
  public AbstractParametrizableSequencePhyloLikelihood
{
private:
  std::shared_ptr<MultiProcessSequenceEvolution> mSeqEvol_;
 
protected:
  mutable std::vector<std::shared_ptr<LikelihoodCalculationSingleProcess>> vLikCal_;
 
public:
  MultiProcessSequencePhyloLikelihood(
      std::shared_ptr<const AlignmentDataInterface> data,
      std::shared_ptr<MultiProcessSequenceEvolution> processSeqEvol,
      std::shared_ptr<CollectionNodes> collNodes,
      size_t nSeqEvol = 0,
      size_t nData = 0);
 
protected:
  MultiProcessSequencePhyloLikelihood(const MultiProcessSequencePhyloLikelihood& mpspl) :
    AbstractParametrizableSequencePhyloLikelihood(mpspl),
    mSeqEvol_(mpspl.mSeqEvol_),
    vLikCal_(mpspl.vLikCal_)
  {}
 
  MultiProcessSequencePhyloLikelihood& operator=(const MultiProcessSequencePhyloLikelihood& mpspl)
  {
    AbstractParametrizableSequencePhyloLikelihood::operator=(mpspl);
    mSeqEvol_ = mpspl.mSeqEvol_;
    vLikCal_ = mpspl.vLikCal_;
    return *this;
  }
 
public:
  virtual ~MultiProcessSequencePhyloLikelihood() {}
 
public:
  std::shared_ptr<const AlignmentDataInterface> getData() const override
  {
    return vLikCal_[0]->getData();
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const override
  {
    return vLikCal_[0]->stateMap().getAlphabet();
  }
 
public:
  std::shared_ptr<LikelihoodCalculationSingleProcess> getLikelihoodCalculationForAProcess(size_t p)
  {
    return vLikCal_[p];
  }
 
  DataLik getLikelihoodForASiteForAProcess(size_t site, size_t p) const
  {
    return vLikCal_[p]->getLikelihoodForASite(site);
  }
 
  VVdouble getLikelihoodPerSitePerProcess() const;
 
  /*
   *@brief return the posterior probabilities of subprocess on each site.
   *
   *@return 2D-vector sites x states
   */
 
  virtual VVdouble getPosteriorProbabilitiesPerSitePerProcess() const = 0;
 
  bool isInitialized() const override
  {
    for (auto& lik : vLikCal_)
    {
      if (!lik->isInitialized())
        return false;
    }
 
    return true;
  }
 
  void setData(std::shared_ptr<const AlignmentDataInterface> sites, size_t nData = 0) override;
 
  size_t getNumberOfSubstitutionProcess() const { return vLikCal_.size(); }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_MULTIPROCESSSEQUENCEPHYLOLIKELIHOOD_H