/usr/include/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h is in libbpp-seq-dev 2.1.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 | //
// File: AAIndex2Entry.h
// Created by: Julien Dutheil
// Created on: Fri Jan 19 17:07 2007
//
/*
Copyright or © or Copr. CNRS, (November 17, 2004)
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 _AAINDEX2ENTRY_H_
#define _AAINDEX2ENTRY_H_
#include "AlphabetIndex2.h"
#include "../Alphabet/ProteicAlphabet.h"
#include <Bpp/Numeric/Matrix/Matrix.h>
namespace bpp
{
/**
* @brief Create a AlphabetIndex2 object from an AAIndex2 entry.
*/
class AAIndex2Entry :
public virtual AlphabetIndex2
{
private:
LinearMatrix<double> property_;
const ProteicAlphabet* alpha_;
public:
/**
* @brief Create a new AAIndex2Entry from an input stream.
*
* @param input The input stream to use.
* @param sym Tell if the matrix is symmetric.
* This option as an effect only if the matrix is specified as a triangle in the entry.
* If sym==true, the oher triangle will be built by symmetry.
* If sym==false, the other triangle will be set to (-) the given triangle.
* @throw IOException if the stream content does not follow the AAIndex2 database entry format.
*/
AAIndex2Entry(std::istream& input, bool sym = true) throw (IOException);
AAIndex2Entry(const AAIndex2Entry& index) :
property_(index.property_),
alpha_(index.alpha_)
{}
AAIndex2Entry& operator=(const AAIndex2Entry& index)
{
property_ = index.property_;
alpha_ = index.alpha_;
return *this;
}
virtual ~AAIndex2Entry() {}
public:
const Alphabet* getAlphabet() const { return alpha_; }
AAIndex2Entry* clone() const { return new AAIndex2Entry(*this); }
double getIndex(int state1, int state2) const throw (BadIntException)
{
if (state1 < 0 || state1 > 19) throw BadIntException(state1, "AAIndex2Entry::getIndex(). Invalid state1.", alpha_);
if (state2 < 0 || state2 > 19) throw BadIntException(state2, "AAIndex2Entry::getIndex(). Invalid state2.", alpha_);
return property_(state1, state2);
}
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
{
return property_(alpha_->charToInt(state1), alpha_->charToInt(state2));
}
LinearMatrix<double>* getIndexMatrix() const { return new LinearMatrix<double>(property_); }
};
} // end of namespace bpp.
#endif // _AAINDEX2ENTRY_H_
|