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// File: BipartitionList.h
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// Created by: Nicolas Galtier and Julien Dutheil
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// Created on: Tue Apr 13 15:09 2007
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Copyright or © or Copr. CNRS, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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This software is governed by the CeCILL license under French law and
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abiding by the rules of distribution of free software. You can use,
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modify and/ or redistribute the software under the terms of the CeCILL
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license as circulated by CEA, CNRS and INRIA at the following URL
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"http://www.cecill.info".
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As a counterpart to the access to the source code and rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors have only limited
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In this respect, the user's attention is drawn to the risks associated
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with loading, using, modifying and/or developing or reproducing the
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software by the user in light of its specific status of free software,
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that may mean that it is complicated to manipulate, and that also
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therefore means that it is reserved for developers and experienced
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professionals having in-depth computer knowledge. Users are therefore
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encouraged to load and test the software's suitability as regards their
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requirements in conditions enabling the security of their systems and/or
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data to be ensured and, more generally, to use and operate it in the
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same conditions as regards security.
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The fact that you are presently reading this means that you have had
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knowledge of the CeCILL license and that you accept its terms.
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#ifndef _BIPARTITIONLIST_H_
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#define _BIPARTITIONLIST_H_
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#include <Bpp/Utils/MapTools.h>
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#include <Bpp/Numeric/Matrix/Matrix.h>
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template<class N> class TreeTemplate;
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* @brief This class deals with the bipartitions defined by trees
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* Any branch of a tree defines a bipartition, i.e. two non-overlapping subsets of leaves
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* whose union is the whole set of leaves. A tree topology can therefore be represented by
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* the list of bipartitions its branches define - the so-called matrix representation.
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* Coding trees this way is useful for comparing topologies, calculating topological distances,
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* producing consensus trees or super-trees, calculating bootstrap support.
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* A BipartitionList includes a set of element names (typically leaf names) and a vector of arrays of bits
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* (int*, not bitsets, are used to allow for dynamic memory allocation). Each array of bit codes for one bipartition.
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* Each bit in an array of bit corresponds to one element, so the order of element names matter.
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* Bits set to zero versus bits set to one define the two partitions of elements.
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* A BipartitionList is called sorted if its elements (leaf names) are in alphabetic order (recommended).
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* BipartitionList objects are typically created from a tree, in which case elements are leaf names.
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* Note that BipartitionList is an unrooted object: a rooted or unrooted versions of the same tree will
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* yield the same BipartitionList in which the root location is ignored. Bipartitions can be accessed as
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* arrays of bits (e.g. getBitBipartition), or as map<string, bool>, in which keys are leaf names and
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* true/false values define the two partitions (e.g. getBipartition, addBipartition).
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* @see BipartitionTools
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class BipartitionList:
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public virtual Clonable
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std::vector<int*> bitBipartitionList_;
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std::vector<std::string> elements_;
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* @brief The main contructor
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* @param tr The tree to be coded as bipartitions
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* @param sorted Tells whether leave names should be alphabetically sorted (recommended)
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* @param index An output optional vector to keep trace of the nodes id underlying each bipartition.
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BipartitionList(const Tree& tr, bool sorted = true, std::vector<int>* index = 0);
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* @brief An alternative constructor in which elements and bipartitions are passed directly
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* @param elements Leaf names
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* @param bipl The list of bit-encoded bipartitions
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BipartitionList(const std::vector<std::string>& elements, const std::vector<int*>& bipl);
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* @brief Copy-constructor
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BipartitionList(const BipartitionList& bipl);
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* @brief Assignment operator
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BipartitionList& operator=(const BipartitionList& bipl);
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virtual ~BipartitionList();
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#ifndef NO_VIRTUAL_COV
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clone() const { return new BipartitionList(*this); }
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unsigned int getNumberOfElements() const { return elements_.size(); }
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const std::vector<std::string>& getElementNames() const { return elements_; }
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unsigned int getNumberOfBipartitions() const { return bitBipartitionList_.size(); }
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const std::vector<int*> & getBitBipartitionList() const { return bitBipartitionList_; }
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std::map<std::string, bool> getBipartition(unsigned int i) const throw (Exception);
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int* getBitBipartition(unsigned int i) throw (Exception);
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bool haveSameElementsThan(std::map<std::string, bool>& bipart) const;
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void addBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) throw(Exception);
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void deleteBipartition(unsigned int i) throw(Exception);
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bool isSorted() const { return sorted_; }
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bool containsBipartition(std::map<std::string, bool>& bipart, bool checkElements = 1) const throw(Exception);
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bool areIdentical(unsigned int k1, unsigned int k2) const throw(Exception);
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void removeRedundantBipartitions();
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* @brief Tells whether 2 bipartitions from the list are compatible
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* Let A=A1|A2 and B=B1|B2 be two bipartitions (such that A1 U A2 = B1 U B2 = set of leaves)
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* A and B are said compatible if (A1 contains B1 and B2 contains A2) or (A1 contains B2
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* and B1 contains A2) or (B1 contains A1 and A2 contains B2) or (B2 contains A1 and A2
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* contains B1). Only compatible bipartitions can belong to the same tree.
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bool areCompatible(unsigned int k1, unsigned int k2) const throw(Exception);
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* @brief Tells whether all bipartitions in the list are compatible with each other
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bool areAllCompatible() const;
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* @brief Tells whether all bipartitions in the list are compatible with a given bipartition
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* @param bipart A map representing a bipartition.
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* @param checkElements Check the correspondance of element sets or not.
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bool areAllCompatibleWith(std::map<std::string, bool>& bipart, bool checkElements = true) const throw (Exception);
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* @brief Removes bipartitions corresponding to external branches (1 vs n-1)
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void removeTrivialBipartitions();
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* @brief Adds bipartitions corresponding to external branches if missing
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void addTrivialBipartitions(bool checkExisting);
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* @brief Replaces ones by zeros and zeros by ones in the ith bipartition
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void flip(unsigned int i) throw(Exception);
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* @brief Returns the size of the smallest of the two partitions (e.g. 1 for external branches)
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unsigned int getPartitionSize(unsigned int i) const throw(Exception);
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* @brief Sort bipartitions by partition size
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void sortByPartitionSize();
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* @brief Translate into a tree
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TreeTemplate<Node>* toTree() const throw(Exception);
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* @brief Create a matrix representation of the bifurcations.
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* Each row corresponds to an element, each column to a bipartition.
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* NB: using RowMatrix<bool> leads to unexplained compilation error...
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* @return A boolean matrix.
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RowMatrix<int> toMatrix() const;
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std::vector<std::string> buildBitBipartitions(const Node* nd, std::vector<int*>& bitbip, const std::vector<std::string> & elements, unsigned int* cpt, std::vector<int>* index) const;
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} //end of namespace bpp.
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#endif //_BIPARTITIONLIST_H_
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src/Bpp/Phyl/BipartitionList.h
