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// File: BioNJ.cpp
// Created by: Vincent Ranwez
// Created on: Tue Apr 11 14:23 2006
//
/*
Copyright or © or Copr. CNRS, (November 16, 2004, 2005, 2006)
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 _BIONJ_H_
#define _BIONJ_H_
#include "NeighborJoining.h"
namespace bpp
{
/**
* @brief The BioNJ distance method.
*
* Reference:
* Gascuel O.
* BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
* Mol Biol Evol. 1997 Jul;14(7):685-95.
*/
class BioNJ:
public NeighborJoining
{
private:
DistanceMatrix variance_;
double lambda_;
public:
BioNJ(): NeighborJoining(), variance_(0), lambda_(0) {}
BioNJ(const DistanceMatrix& matrix, bool rooted = false, bool positiveLengths = false) throw (Exception):
NeighborJoining(), //Use the default constructor, because the other one call computeTree.
variance_(matrix), lambda_(0)
{
setDistanceMatrix(matrix);
outputPositiveLengths(positiveLengths);
computeTree(rooted);
}
BioNJ* clone() const { return new BioNJ(*this); }
virtual ~BioNJ() {};
public:
virtual void setDistanceMatrix(const DistanceMatrix & matrix)
{
NeighborJoining::setDistanceMatrix(matrix);
variance_ = matrix;
}
virtual void computeTree(bool rooted) throw (Exception);
virtual double computeDistancesFromPair(const std::vector<unsigned int>& pair, const std::vector<double>& branchLengths, unsigned int pos);
};
} //end of namespace bpp.
#endif //_BIONJ_H_
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