BipartitionTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_TREE_BIPARTITIONTOOLS_H
#define BPP_PHYL_TREE_BIPARTITIONTOOLS_H
 
 
#include "BipartitionList.h"
 
// From bpp-seq:
#include <Bpp/Seq/Container/VectorSiteContainer.h>
 
namespace bpp
{
class BipartitionTools
{
public:
  static int LWORD;
 
public:
  BipartitionTools() {}
  virtual ~BipartitionTools() {}
 
public:
  static void bit1(int* list, int num);
 
  static void bit0(int* list, int num);
 
  static void bitAnd(int* listet, int* list1, int* list2, size_t len);
 
  static void bitOr(int* listou, int* list1, int* list2, size_t len);
 
  static void bitNot(int* listnon, int* list, size_t len);
 
  static bool testBit(int* list, int num);
 
  static std::unique_ptr<BipartitionList> mergeBipartitionLists(const std::vector<std::unique_ptr<BipartitionList>>& vecBipartL, bool checkElements = true);
 
  static std::unique_ptr<BipartitionList> buildBipartitionPair(const BipartitionList& bipartL1, size_t i1, const BipartitionList& bipartL2, size_t i2, bool checkElements = true);
 
  static bool areIdentical(const BipartitionList& bipart1, size_t i1, const BipartitionList& bipart2, size_t i2, bool checkElements = true);
 
  static bool areCompatible(const BipartitionList& bipart1, size_t i1, const BipartitionList& bipart2, size_t i2, bool checkElements = true);
 
  static std::unique_ptr<VectorSiteContainer> MRPEncode(
      const std::vector<std::unique_ptr<BipartitionList>>& vecBipartL);
 
  static std::unique_ptr<VectorSiteContainer> MRPEncodeMultilabel(
      const std::vector<std::unique_ptr<BipartitionList>>& vecBipartL);
};
} // end of namespace bpp.
#endif // BPP_PHYL_TREE_BIPARTITIONTOOLS_H