AbstractTreeParsimonyData.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_PARSIMONY_ABSTRACTTREEPARSIMONYDATA_H
#define BPP_PHYL_PARSIMONY_ABSTRACTTREEPARSIMONYDATA_H
 
 
#include "TreeParsimonyData.h"
 
namespace bpp
{
class AbstractTreeParsimonyData :
  public virtual TreeParsimonyDataInterface
{
protected:
  std::vector<size_t> rootPatternLinks_;
  std::vector<unsigned int> rootWeights_;
  std::shared_ptr<const TreeTemplate<Node>> tree_;
 
public:
  AbstractTreeParsimonyData(std::shared_ptr<const TreeTemplate<Node>> tree) :
    rootPatternLinks_(),
    rootWeights_(),
    tree_(tree)
  {}
 
  AbstractTreeParsimonyData(const AbstractTreeParsimonyData& atpd) :
    rootPatternLinks_(atpd.rootPatternLinks_),
    rootWeights_(atpd.rootWeights_),
    tree_(atpd.tree_)
  {}
 
  AbstractTreeParsimonyData& operator=(const AbstractTreeParsimonyData& atpd)
  {
    rootPatternLinks_ = atpd.rootPatternLinks_;
    rootWeights_      = atpd.rootWeights_;
    tree_             = atpd.tree_;
    return *this;
  }
 
 
  virtual ~AbstractTreeParsimonyData() {}
 
public:
  size_t getRootArrayPosition(size_t site) const override
  {
    return rootPatternLinks_[site];
  }
 
  unsigned int getWeight(size_t pos) const
  {
    return rootWeights_[pos];
  }
 
  const TreeTemplate<Node>& tree() const override { return *tree_; }
 
  std::shared_ptr<const TreeTemplate<Node>> getTree() const override { return tree_; }
 
protected:
  void setTree(std::shared_ptr<const TreeTemplate<Node>> tree) { tree_ = tree; }
};
} // end of namespace bpp.
#endif // BPP_PHYL_PARSIMONY_ABSTRACTTREEPARSIMONYDATA_H