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// File: TreeParsimonyData.h
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// Created by: Julien Dutheil
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// Created on: Tue Jan 09 17:15 2007
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// From file AbstractTreeParsimonyScore.h
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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 _TREEPARSIMONYDATA_H_
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#define _TREEPARSIMONYDATA_H_
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#include "../TreeTemplate.h"
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#include <Bpp/Clonable.h>
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* @brief TreeParsimonyScore node data structure.
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* Stores inner computation for a given node.
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* @see TreeParsimonyData
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class TreeParsimonyNodeData:
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public virtual Clonable
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TreeParsimonyNodeData() {}
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virtual ~TreeParsimonyNodeData() {}
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#ifndef NO_VIRTUAL_COV
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TreeParsimonyNodeData* clone() const = 0;
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* @brief Get the node associated to this data structure.
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* @return The node associated to this structure.
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virtual const Node* getNode() const = 0;
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* @brief Set the node associated to this data
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* @param node A pointer toward the node to be associated to this data.
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virtual void setNode(const Node* node) = 0;
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* @brief TreeParsimonyScore data structure.
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* Stores all the inner computations:
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* - subtree scores and ancestral states for each node,
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* - correspondance between sites in the dataset and array indices.
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* @see TreeParsimonyNodeData
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class TreeParsimonyData:
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public virtual Clonable
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TreeParsimonyData() {}
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virtual ~TreeParsimonyData() {}
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#ifndef NO_VIRTUAL_COV
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TreeParsimonyData* clone() const = 0;
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virtual const TreeTemplate<Node>* getTree() const = 0;
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virtual unsigned int getArrayPosition(int parentId, int sonId, unsigned int currentPosition) const = 0;
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virtual unsigned int getRootArrayPosition(const unsigned int site) const = 0;
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virtual TreeParsimonyNodeData& getNodeData(int nodeId) = 0;
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virtual const TreeParsimonyNodeData& getNodeData(int nodeId) const = 0;
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} //end of namespace bpp.
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#endif //_TREEPARSIMONYDATA_H_
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src/Bpp/Phyl/Parsimony/TreeParsimonyData.h
