libbpp-phyl-dev 2.1.0-1 / usr / include / Bpp / Phyl / BipartitionList.h

//
// 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
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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;

/**
 * @brief This class deals with the bipartitions defined by trees
 *
 * Any branch of a tree defines a bipartition, i.e. two non-overlapping subsets of leaves
 * whose union is the whole set of leaves. A tree topology can therefore be represented by
 * the list of bipartitions its branches define - the so-called matrix representation.
 * Coding trees this way is useful for comparing topologies, calculating topological distances,
 * producing consensus trees or super-trees, calculating bootstrap support.
 *
 * A BipartitionList includes a set of element names (typically leaf names) and a vector of arrays of bits
 * (int*, not bitsets, are used to allow for dynamic memory allocation). Each array of bit codes for one bipartition.
 * Each bit in an array of bit corresponds to one element, so the order of element names matter.
 * Bits set to zero versus bits set to one define the two partitions of elements.
 * A BipartitionList is called sorted if its elements (leaf names) are in alphabetic order (recommended).
 *
 * BipartitionList objects are typically created from a tree, in which case elements are leaf names.
 * Note that BipartitionList is an unrooted object: a rooted or unrooted versions of the same tree will
 * yield the same BipartitionList in which the root location is ignored. Bipartitions can be accessed as
 * arrays of bits (e.g. getBitBipartition), or as map<string, bool>, in which keys are leaf names and
 * true/false values define the two partitions (e.g. getBipartition, addBipartition).
 *
 * @see Tree
 * @see BipartitionTools
 * @see TreeTools
 */
class BipartitionList:
  public virtual Clonable
{
  private:

    std::vector<int*> bitBipartitionList_;
    std::vector<std::string> elements_;
    bool sorted_;

  public:

    /**
     * @brief The main contructor
     *
     * @param tr The tree to be coded as bipartitions
     * @param sorted Tells whether leave names should be alphabetically sorted (recommended)
     * @param index An output optional vector to keep trace of the nodes id underlying each bipartition.
     */
    BipartitionList(const Tree& tr, bool sorted = true, std::vector<int>* index = 0);

    /**
     * @brief An alternative constructor in which elements and bipartitions are passed directly
     *
     * @param elements Leaf names
     * @param bipl The list of bit-encoded bipartitions
     */
    BipartitionList(const std::vector<std::string>& elements, const std::vector<int*>& bipl);

    /**
     * @brief Copy-constructor
     */
    BipartitionList(const BipartitionList& bipl);

    /**
     * @brief Assignment operator
     */
    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();

    /**
     * @brief Tells whether 2 bipartitions from the list are compatible
     *
     * Let A=A1|A2 and B=B1|B2 be two bipartitions (such that A1 U A2 = B1 U B2 = set of leaves)
     * A and B are said compatible if (A1 contains B1 and B2 contains A2) or (A1 contains B2
     * and B1 contains A2) or (B1 contains A1 and A2 contains B2) or (B2 contains A1 and A2
     * contains B1). Only compatible bipartitions can belong to the same tree.
     */
    bool areCompatible(size_t k1, size_t k2) const throw(Exception);

    /**
     * @brief Tells whether all bipartitions in the list are compatible with each other
     */
    bool areAllCompatible() const;

    /**
     * @brief Tells whether all bipartitions in the list are compatible with a given bipartition
     *
     * @param bipart A map representing a bipartition.
     * @param checkElements Check the correspondance of element sets or not.
     */
    bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);

    /**
     * @brief Removes bipartitions corresponding to external branches (1 vs n-1)
     */
    void removeTrivialBipartitions();

    /**
     * @brief Adds bipartitions corresponding to external branches if missing
     */
    void addTrivialBipartitions(bool checkExisting);


    /**
     * @brief Replaces ones by zeros and zeros by ones in the ith bipartition
     */
    void flip(size_t i) throw(Exception);

    /**
     * @brief Returns the size of the smallest of the two partitions (e.g. 1 for external branches)
     */
    size_t getPartitionSize(size_t i) const throw(Exception);

    /**
     * @brief Sort bipartitions by partition size
     */
    void sortByPartitionSize();

    /**
     * @brief Translate into a tree
     */
    TreeTemplate<Node>* toTree() const throw(Exception);

    /**
     * @brief Create a matrix representation of the bifurcations.
     *
     * Each row corresponds to an element, each column to a bipartition.
     *
     * NB: using RowMatrix<bool> leads to unexplained compilation error...
     *
     * @return A boolean matrix.
     */
    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_