BipartitionList.h

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//
// File: BipartitionList.h
// Created by: Nicolas Galtier and Julien Dutheil
// Created on: Tue Apr 13 15:09 2007
//

/*
Copyright or © or Copr. CNRS, (November 16, 2004)

This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.

This software is governed by the CeCILL  license under French law and
abiding by the rules of distribution of free software.  You can  use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited
liability.

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and,  more generally, to use and operate it in the
same conditions as regards security.

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/

#ifndef _BIPARTITIONLIST_H_
#define _BIPARTITIONLIST_H_

#include "Tree.h"

#include <Bpp/Utils/MapTools.h>
#include <Bpp/Numeric/Matrix/Matrix.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();

#ifndef NO_VIRTUAL_COV
    BipartitionList*
#else
    Clonable*
#endif
    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 throw (Exception);

    int* getBitBipartition(size_t i) throw (Exception);

    bool haveSameElementsThan(std::map<std::string, bool>& bipart) const;

    void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);

    void deleteBipartition(size_t i) throw(Exception);

    bool isSorted() const { return sorted_; }

    void sortElements();

    bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);

    bool areIdentical(size_t k1, size_t k2) const throw(Exception);

    void removeRedundantBipartitions();

    bool areCompatible(size_t k1, size_t k2) const throw(Exception);

    bool areAllCompatible() const;

    bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);

    void removeTrivialBipartitions();

    void addTrivialBipartitions(bool checkExisting);


    void flip(size_t i) throw(Exception);

    size_t getPartitionSize(size_t i) const throw(Exception);

    void sortByPartitionSize();

    TreeTemplate<Node>* toTree() const throw(Exception);

    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 //_BIPARTITIONLIST_H_