AbstractTreeLikelihoodData.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_ABSTRACTTREELIKELIHOODDATA_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_ABSTRACTTREELIKELIHOODDATA_H
 
 
#include "TreeLikelihoodData.h"
 
// From the STL:
#include <vector>
#include <map>
 
namespace bpp
{
class AbstractTreeLikelihoodData :
  public TreeLikelihoodData
{
protected:
  std::vector<size_t> rootPatternLinks_;
 
  std::vector<unsigned int> rootWeights_;
 
  std::shared_ptr<const TreeTemplate<Node>> tree_;
 
  std::shared_ptr<const Alphabet> alphabet_;
 
public:
  AbstractTreeLikelihoodData(std::shared_ptr< const TreeTemplate<Node>> tree) :
    rootPatternLinks_(), rootWeights_(), tree_(tree), alphabet_(0) {}
 
  AbstractTreeLikelihoodData(const AbstractTreeLikelihoodData& atd) :
    rootPatternLinks_(atd.rootPatternLinks_),
    rootWeights_(atd.rootWeights_),
    tree_(atd.tree_),
    alphabet_(atd.alphabet_)
  {}
 
  AbstractTreeLikelihoodData& operator=(const AbstractTreeLikelihoodData& atd)
  {
    rootPatternLinks_ = atd.rootPatternLinks_;
    rootWeights_      = atd.rootWeights_;
    tree_             = atd.tree_;
    alphabet_         = atd.alphabet_;
    return *this;
  }
 
 
  virtual ~AbstractTreeLikelihoodData() {}
 
public:
  std::vector<size_t>& getRootArrayPositions() { return rootPatternLinks_; }
  const std::vector<size_t>& getRootArrayPositions() const { return rootPatternLinks_; }
  size_t getRootArrayPosition(const size_t site) const
  {
    return rootPatternLinks_[site];
  }
  unsigned int getWeight(size_t pos) const
  {
    return rootWeights_[pos];
  }
  const std::vector<unsigned int>& getWeights() const
  {
    return rootWeights_;
  }
 
  std::shared_ptr<const Alphabet> getAlphabet() const { return alphabet_; }
 
  std::shared_ptr< const TreeTemplate<Node>> getTree() const { return tree_; }
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_ABSTRACTTREELIKELIHOODDATA_H