MarginalAncestralStateReconstruction.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _LEGACY_MARGINAL_ANCESTRAL_STATES_RECONSTRUCTION_H_
#define _LEGACY_MARGINAL_ANCESTRAL_STATES_RECONSTRUCTION_H_
 
#include "../AncestralStateReconstruction.h"
#include "DRTreeLikelihood.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Container/AlignedSequenceContainer.h>
#include <Bpp/Seq/Sequence.h>
 
// From the STL:
#include <vector>
 
namespace bpp
{
class LegacyMarginalAncestralStateReconstruction :
  public virtual LegacyAncestralStateReconstruction
{
private:
  std::shared_ptr<const DRTreeLikelihoodInterface> likelihood_;
  TreeTemplate<Node> tree_;
  std::shared_ptr<const Alphabet> alphabet_;
  size_t nbSites_;
  size_t nbDistinctSites_;
  size_t nbClasses_;
  size_t nbStates_;
  std::vector<size_t> rootPatternLinks_;
  std::vector<double> r_;
  std::vector<double> l_;
 
public:
  LegacyMarginalAncestralStateReconstruction(std::shared_ptr<const DRTreeLikelihoodInterface> drl) :
    likelihood_      (drl),
    tree_            (drl->tree()),
    alphabet_        (drl->getAlphabet()),
    nbSites_         (drl->likelihoodData().getNumberOfSites()),
    nbDistinctSites_ (drl->likelihoodData().getNumberOfDistinctSites()),
    nbClasses_       (drl->likelihoodData().getNumberOfClasses()),
    nbStates_        (drl->likelihoodData().getNumberOfStates()),
    rootPatternLinks_(drl->likelihoodData().getRootArrayPositions()),
    r_               (drl->rateDistribution().getProbabilities()),
    l_               (drl->likelihoodData().getRootRateSiteLikelihoodArray())
  {}
 
  LegacyMarginalAncestralStateReconstruction(const LegacyMarginalAncestralStateReconstruction& masr) = default;
 
  LegacyMarginalAncestralStateReconstruction& operator=(const LegacyMarginalAncestralStateReconstruction& masr) = default;
 
  LegacyMarginalAncestralStateReconstruction* clone() const { return new LegacyMarginalAncestralStateReconstruction(*this); }
 
  virtual ~LegacyMarginalAncestralStateReconstruction() {}
 
public:
  std::vector<size_t> getAncestralStatesForNode(int nodeId, VVdouble& probs, bool sample) const;
 
  std::vector<size_t> getAncestralStatesForNode(int nodeId) const override
  {
    VVdouble probs(nbSites_);
    return getAncestralStatesForNode(nodeId, probs, false);
  }
 
  std::map<int, std::vector<size_t>> getAllAncestralStates() const override;
 
  std::unique_ptr<Sequence> getAncestralSequenceForNode(int nodeId, VVdouble* probs, bool sample) const;
 
  std::unique_ptr<Sequence> getAncestralSequenceForNode(int nodeId) const override
  {
    return getAncestralSequenceForNode(nodeId, 0, false);
  }
 
  std::unique_ptr<SiteContainerInterface> getAncestralSequences() const override
  {
    return getAncestralSequences(false);
  }
 
  std::unique_ptr<SiteContainerInterface> getAncestralSequences(bool sample) const;
 
private:
  void recursiveMarginalAncestralStates(
      const Node* node,
      std::map<int, std::vector<size_t>>& ancestors,
      AlignedSequenceContainer& data) const;
};
} // end of namespace bpp.
 
#endif // _LEGACY_MARGINAL_ANCESTRAL_STATES_RECONSTRUCTION_H_