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// File: NNISearchable.h
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// Created by: Julien Dutheil
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// Created on: Thu Jul 28 16:32 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 _NNISEARCHABLE_H_
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#define _NNISEARCHABLE_H_
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#include "TreeTemplate.h"
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#include "TopologySearch.h"
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* @brief Interface for Nearest Neighbor Interchanges algorithms.
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* This interface defines the methods to work with NNI algorithms.
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* NNISearchable objects are supposed to work with TreeTemplate objects.
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* NNI are defined as follow:
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* -F is the focus (parent) node,
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* -A and B are the son of F
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* -X is the parent of F and so on.
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* Two NNI's are possible for branch (XF):
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* - swaping B and C, which is the same as D and A
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* - swaping A and C, which is the same as D and B
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* Because of the rooted representation, we'll consider B \f$\leftrightarrow\f$ C and A \f$\leftrightarrow\f$ C,
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* which are simpler to perform.
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* For unrooted tree, we have at the 'root' node:
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* In this case, we swap A or B with one of C or D.
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* Which one of C or D depends on the implementation, but will always be the same,
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* so that swapping A or B involve 2 distinct NNI.
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public TopologyListener,
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public virtual Clonable
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virtual ~NNISearchable() {}
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#ifndef NO_VIRTUAL_COV
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virtual NNISearchable* clone() const = 0;
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* @brief Send the score of a NNI movement, without performing it.
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* This methods sends the score variation.
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* This variation must be negative if the new point is better,
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* i.e. the object is to be used with a minimizing optimization
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* (for consistence with Optimizer objects).
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* @param nodeId The id of the node defining the NNI movement.
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* @return The score variation of the NNI.
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* @throw NodeException If the node does not define a valid NNI.
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virtual double testNNI(int nodeId) const throw (NodeException) = 0;
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* @brief Perform a NNI movement.
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* @param nodeId The id of the node defining the NNI movement.
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* @throw NodeException If the node does not define a valid NNI.
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virtual void doNNI(int nodeId) throw (NodeException) = 0;
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* @brief Get the tree associated to this NNISearchable object.
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* @return The tree associated to this instance.
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virtual const Tree& getTopology() const = 0;
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* @brief Get the current score of this NNISearchable object.
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* @return The current score of this instance.
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virtual double getTopologyValue() const throw (Exception) = 0;
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} //end of namespace bpp.
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#endif //_NNISEARCHABLE_H_
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src/Bpp/Phyl/NNISearchable.h
