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// File: SimpleIndexDistance.h
// Created by: Julien Dutheil
// Created on: Tue Apr 21 2005
//
/*
Copyright or © or Copr. Bio++ Development Team, (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 _SIMPLEINDEXDISTANCE_H_
#define _SIMPLEINDEXDISTANCE_H_
// from the STL:
#include <string>
#include "AlphabetIndex1.h"
#include "AlphabetIndex2.h"
#include "../Alphabet/ProteicAlphabet.h"
#include "../Alphabet/AlphabetExceptions.h"
#include <Bpp/Exceptions.h>
#include <Bpp/Numeric/Matrix/Matrix.h>
namespace bpp
{
/**
* @brief Simple dissimilarity distance.
*
* Take a one-dimensional index end return the difference between the
* indexes of two states.
*/
class SimpleIndexDistance :
public virtual AlphabetIndex2
{
private:
std::auto_ptr<AlphabetIndex1> index_;
bool sym_;
public:
SimpleIndexDistance(AlphabetIndex1* index) :
index_(index),
sym_(false)
{}
SimpleIndexDistance(const SimpleIndexDistance& sid) :
index_(dynamic_cast<AlphabetIndex1*>(sid.index_->clone())),
sym_(sid.sym_)
{}
SimpleIndexDistance& operator=(const SimpleIndexDistance& sid)
{
index_.reset(dynamic_cast<AlphabetIndex1*>(sid.index_->clone()));
sym_ = sid.sym_;
return *this;
}
virtual ~SimpleIndexDistance() {}
public:
double getIndex(int state1, int state2) const throw (BadIntException)
{
double d = index_->getIndex(state2) - index_->getIndex(state1);
return sym_ ? NumTools::abs<double>(d) : d;
}
double getIndex(const std::string& state1, const std::string& state2) const throw (BadCharException)
{
double d = index_->getIndex(state2) - index_->getIndex(state1);
return sym_ ? NumTools::abs<double>(d) : d;
}
const Alphabet* getAlphabet() const { return index_->getAlphabet(); }
Clonable* clone() const { return new SimpleIndexDistance(*this); }
Matrix<double>* getIndexMatrix() const
{
size_t n = index_->getAlphabet()->getSize(); //We should change to "supported ints" there...
RowMatrix<double>* m = new RowMatrix<double>(n, n);
for (int i = 0; i < static_cast<int>(n); i++)
{
for (int j = 0; j < static_cast<int>(n); j++)
{
(*m)(i, j) = getIndex(i, j);
}
}
return m;
}
public:
void setSymmetric(bool yn) { sym_ = yn; }
bool isSymmetric() const { return sym_; }
/**
* @return The AlphabetIndex1 object associated to this object.
*/
const AlphabetIndex1& getAlphabetIndex1() const { return *index_; }
/**
* @return The AlphabetIndex1 object associated to this object.
*/
AlphabetIndex1& getAlphabetIndex1() { return *index_; }
};
} // end of namespace bpp.
#endif // _SIMPLEINDEXDISTANCE_H_
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