/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h is in libbpp-phyl-dev 2.1.0-1.
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// File: TreeParsimonyScore.h
// Created by: Julien Dutheil
// Created on: Thu Jul 28 17:15 2005
//
/*
Copyright or © or Copr. Bio++ Development Team, (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
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
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 _TREEPARSIMONYSCORE_H_
#define _TREEPARSIMONYSCORE_H_
#include "../TreeTemplate.h"
#include <Bpp/Clonable.h>
// From the STL:
#include <vector>
namespace bpp
{
/**
* @brief Compute a parsimony score.
*/
class TreeParsimonyScore :
public virtual Clonable
{
public:
TreeParsimonyScore() {}
virtual ~TreeParsimonyScore() {}
#if defined(NO_VIRTUAL_COV)
Clonable* clone() const = 0;
#else
TreeParsimonyScore* clone() const = 0;
#endif
public:
/**
* @brief Get the score for the current tree, i.e. the total minimum number of changes in the tree.
*
* @return The minimum total number of changes in the tree.
*/
virtual unsigned int getScore() const = 0;
/**
* @brief Get the score for a given site for the current tree, i.e. the total minimum number of changes in the tree for this site.
*
* @param site The corresponding site.
* @return The minimum total number of changes in the tree for site 'site'.
*/
virtual unsigned int getScoreForSite(size_t site) const = 0;
/**
* @brief Get the score for each site for the current tree, i.e. the total minimum number of changes in the tree for each site.
*
* @return The minimum total number of changes in the tree for each site.
*/
virtual std::vector<unsigned int> getScoreForEachSite() const = 0;
/**
* @brief Get the tree for wich scores are computed.
*
* @return The tree associated to this object.
*/
virtual const Tree& getTree() const = 0;
};
} // end of namespace bpp.
#endif // _TREEPARSIMONYSCORE_H_
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