BipartitionList.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_TREE_BIPARTITIONLIST_H
#define BPP_PHYL_TREE_BIPARTITIONLIST_H
 
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/Utils/MapTools.h>
 
#include "Tree.h"
 
// From the STL:
#include <map>
#include <algorithm>
 
namespace bpp
{
class Node;
template<class N> class TreeTemplate;
 
class BipartitionList :
  public virtual Clonable
{
private:
  std::vector<int*> bitBipartitionList_;
  std::vector<std::string> elements_;
  bool sorted_;
 
public:
  BipartitionList(const Tree& tr, bool sorted = true, std::vector<int>* index = 0);
 
  BipartitionList(const std::vector<std::string>& elements, const std::vector<int*>& bipl);
 
  BipartitionList(const BipartitionList& bipl);
 
  BipartitionList& operator=(const BipartitionList& bipl);
 
  virtual ~BipartitionList();
 
  BipartitionList* clone() const { return new BipartitionList(*this); }
 
public:
  size_t getNumberOfElements() const { return elements_.size(); }
 
  const std::vector<std::string>& getElementNames() const { return elements_; }
 
  size_t getNumberOfBipartitions() const { return bitBipartitionList_.size(); }
 
  const std::vector<int*>& getBitBipartitionList() const { return bitBipartitionList_; }
 
  std::map<std::string, bool> getBipartition(size_t i) const;
 
  int* getBitBipartition(size_t i);
 
  bool haveSameElementsThan(std::map<std::string, bool>& bipart) const;
 
  void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1);
 
  void deleteBipartition(size_t i);
 
  bool isSorted() const { return sorted_; }
 
  void sortElements();
 
  bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const;
 
  bool areIdentical(size_t k1, size_t k2) const;
 
  void removeRedundantBipartitions();
 
  bool areCompatible(size_t k1, size_t k2) const;
 
  bool areAllCompatible() const;
 
  bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const;
 
  void removeTrivialBipartitions();
 
  void addTrivialBipartitions(bool checkExisting);
 
 
  void flip(size_t i);
 
  size_t getPartitionSize(size_t i) const;
 
  void sortByPartitionSize();
 
  std::unique_ptr<TreeTemplate<Node>> toTree() const;
 
  RowMatrix<int> toMatrix() const;
 
private:
  std::vector<std::string> buildBitBipartitions(const Node* nd, std::vector<int*>& bitbip, const std::vector<std::string>& elements, size_t* cpt, std::vector<int>* index) const;
};
} // end of namespace bpp.
#endif // BPP_PHYL_TREE_BIPARTITIONLIST_H