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// File: MiyataAAChemicalDistance.h
// Created by: jdutheil <Julien.Dutheil@univ-montp2.fr>
// Created on: Mon Feb 21 17:42 2005
//
/*
Copyright or © or Copr. CNRS, (November 17, 2004)
Julien.Dutheil@univ-montp2.fr
This software is a computer program whose purpose is to provide classes
for sequences 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 _MIYATAAACHEMICALDISTANCE_H_
#define _MIYATAAACHEMICALDISTANCE_H_
// from the STL:
#include <string>
#include "AlphabetIndex2.h"
#include "../Alphabet/ProteicAlphabet.h"
#include "../Alphabet/AlphabetExceptions.h"
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Matrix/Matrix.h>
namespace bpp
{
/**
* @brief Miyata et al. (1979) Amino-Acid chemical distance.
*
* Two kinds of matrix can be built:
* - a symmetric one, with \f$I_{i,j} = I_{i,j}\f$,
* - or a non-symmetric one, with \f$I_{i,j} = -I_{i,j}\f$.
*
* Reference:
* Miyata, T., Miyazawa, S. and Yasunaga, T.
* Two types of amino acid substitutions in protein evolution
* J. Mol. Evol. 12, 219-236 (1979)
*
* Data from AAIndex2 database, Accession Number MIYT790101.
*/
class MiyataAAChemicalDistance:
public AlphabetIndex2<double>
{
private:
LinearMatrix<double> distanceMatrix_;
const ProteicAlphabet* alpha_;
bool sym_;
public:
MiyataAAChemicalDistance();
MiyataAAChemicalDistance(const MiyataAAChemicalDistance& md):
distanceMatrix_(md.distanceMatrix_),
alpha_(md.alpha_),
sym_(md.sym_)
{}
MiyataAAChemicalDistance& operator=(const MiyataAAChemicalDistance& md)
{
distanceMatrix_ = md.distanceMatrix_;
alpha_ = md.alpha_;
sym_ = md.sym_;
return *this;
}
virtual ~MiyataAAChemicalDistance() {}
MiyataAAChemicalDistance* clone() const { return new MiyataAAChemicalDistance(); }
public:
/**
* @name Methods from the AlphabetIndex2 interface.
*
* @{
*/
double getIndex(int state1, int state2) const throw (BadIntException);
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException);
const Alphabet* getAlphabet() const { return alpha_; };
Matrix<double>* getIndexMatrix() const;
/** @} */
public:
void setSymmetric(bool yn) { sym_ = yn; }
bool isSymmetric() const { return sym_; }
};
} //end of namespace bpp.
#endif //_MIYATAAACHEMICALDISTANCE_H_
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