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// File: DRTreeParsimonyScore.h
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// Created by: Julien Dutheil
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// Created on: Thu Jul 28 18:31 2005
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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 _DRTREEPARSIMONYSCORE_H_
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#define _DRTREEPARSIMONYSCORE_H_
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#include "AbstractTreeParsimonyScore.h"
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#include "DRTreeParsimonyData.h"
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#include "../NNISearchable.h"
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#include "../TreeTools.h"
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* @brief Double recursive implementation of interface TreeParsimonyScore.
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* Uses a DRTreeParsimonyData object for data storage.
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class DRTreeParsimonyScore :
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public AbstractTreeParsimonyScore,
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public virtual NNISearchable
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DRTreeParsimonyData *parsimonyData_;
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unsigned int nbDistinctSites_;
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const SiteContainer& data,
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DRTreeParsimonyScore(const DRTreeParsimonyScore& tp);
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DRTreeParsimonyScore& operator=(const DRTreeParsimonyScore& tp);
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virtual ~DRTreeParsimonyScore();
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#ifndef NO_VIRTUAL_COV
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clone() const { return new DRTreeParsimonyScore(* this); }
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* @brief Compute all scores.
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* Call the computeScoresPreorder and computeScoresPostorder methods, and then initialize rootBitsets_ and rootScores_.
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virtual void computeScores();
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* @brief Compute scores (preorder algorithm).
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virtual void computeScoresPreorder(const Node *);
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* @brief Compute scores (postorder algorithm).
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virtual void computeScoresPostorder(const Node *);
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unsigned int getScore() const;
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unsigned int getScoreForSite(unsigned int site) const;
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* @brief Compute bitsets and scores for each site for a node, in postorder.
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* @param pData The node data to use.
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* @param rBitsets The bitset array where to store the resulting bitsets.
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* @param rScores The score array where to write the resulting scores.
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static void computeScoresPostorderForNode(
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const DRTreeParsimonyNodeData& pData,
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std::vector<Bitset>& rBitsets,
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std::vector<unsigned int>& rScores);
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* @brief Compute bitsets and scores for each site for a node, in preorder.
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* @param pData The node data to use.
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* @param source The node where we are coming from.
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* @param rBitsets The bitset array where to store the resulting bitsets.
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* @param rScores The score array where to write the resulting scores.
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static void computeScoresPreorderForNode(
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const DRTreeParsimonyNodeData& pData,
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std::vector<Bitset>& rBitsets,
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std::vector<unsigned int>& rScores);
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* @brief Compute bitsets and scores for each site for a node, in all directions.
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* @param pData The node data to use.
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* @param rBitsets The bitset array where to store the resulting bitsets.
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* @param rScores The score array where to write the resulting scores.
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static void computeScoresForNode(
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const DRTreeParsimonyNodeData& pData, std::vector<Bitset>& rBitsets,
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std::vector<unsigned int>& rScores);
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* @brief Compute bitsets and scores from an array of arrays.
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* This method is the more general score computation.
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* Depending on what is passed as input, it may computes scroes fo a subtree
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* @param iBitsets The vector of bitset arrays to use.
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* @param iScores The vector of score arrays to use.
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* @param oBitsets The bitset array where to store the resulting bitsets.
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* @param oScores The score array where to write the resulting scores.
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static void computeScoresFromArrays(
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const std::vector<const std::vector<Bitset>*>& iBitsets,
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const std::vector<const std::vector<unsigned int>*>& iScores,
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std::vector<Bitset>& oBitsets,
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std::vector<unsigned int>& oScores);
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* @name Thee NNISearchable interface.
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double getTopologyValue() const throw (Exception) { return getScore(); }
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double testNNI(int nodeId) const throw (NodeException);
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void doNNI(int nodeId) throw (NodeException);
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//Tree& getTopology() { return getTree(); } do we realy need this one?
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const Tree& getTopology() const { return getTree(); }
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void topologyChangeTested(const TopologyChangeEvent & event)
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parsimonyData_->reInit();
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void topologyChangeSuccessful(const TopologyChangeEvent & event) {}
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} //end of namespace bpp.
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#endif //_DRTREEPARSIMONYSCORE_H_
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src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h
