TreeLikelihoodData.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_TREELIKELIHOODDATA_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_TREELIKELIHOODDATA_H
 
 
#include "../../Tree/Node.h"
#include "../../Tree/TreeTemplate.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Container/AlignmentData.h>
 
namespace bpp
{
class TreeLikelihoodNodeData :
  public virtual Clonable
{
public:
  TreeLikelihoodNodeData() {}
  virtual ~TreeLikelihoodNodeData() {}
 
  TreeLikelihoodNodeData* clone() const = 0;
 
public:
  virtual const Node* getNode() const = 0;
 
  virtual void setNode(const Node* node) = 0;
};
 
class TreeLikelihoodData :
  public virtual Clonable
{
public:
  TreeLikelihoodData() {}
  virtual ~TreeLikelihoodData() {}
 
  TreeLikelihoodData* clone() const = 0;
 
public:
  virtual std::shared_ptr<const Alphabet> getAlphabet() const = 0;
  virtual std::shared_ptr< const TreeTemplate<Node>> getTree() const = 0;
  virtual size_t getArrayPosition(int parentId, int sonId, size_t currentPosition) const = 0;
  virtual size_t getRootArrayPosition(size_t site) const = 0;
  virtual TreeLikelihoodNodeData& getNodeData(int nodeId) = 0;
  virtual const TreeLikelihoodNodeData& getNodeData(int nodeId) const = 0;
 
  virtual size_t getNumberOfDistinctSites() const = 0;
 
  virtual size_t getNumberOfSites() const = 0;
 
  virtual size_t getNumberOfStates() const = 0;
 
  virtual unsigned int getWeight(size_t pos) const = 0;
 
  virtual const std::vector<unsigned int>& getWeights() const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_TREELIKELIHOODDATA_H