/usr/include/OpenMS/COMPARISON/CLUSTERING/EuclideanSimilarity.h is in libopenms-dev 1.11.1-3.
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// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_COMPARISON_CLUSTERING_EUCLIDEANSIMILARITY_H
#define OPENMS_COMPARISON_CLUSTERING_EUCLIDEANSIMILARITY_H
#include <cmath>
#include <OpenMS/CONCEPT/Exception.h>
namespace OpenMS
{
/**
@brief CompareFunctor for 2Dpoints
each 2D point as a pair of Real holds a Real coordinate for each Dimension
@ingroup DummyComparison
*/
class OPENMS_DLLAPI EuclideanSimilarity
{
private:
Real scale_;
public:
/// default constructor
EuclideanSimilarity();
/// copy constructor
EuclideanSimilarity(const EuclideanSimilarity & source);
/// destructor
virtual ~EuclideanSimilarity();
/// assignment operator
EuclideanSimilarity & operator=(const EuclideanSimilarity & source);
/**
@brief calculates similarity between two points in euclidean space
@param a a pair of Real, giving the x and the y coordinates of the first point
@param b a pair of Real, giving the x and the y coordinates of the second point
calculates similarity from the euclidean distance between given 2D points, scaled in [0,1] @see setScale
*/
Real operator()(const std::pair<Real, Real> & a, const std::pair<Real, Real> & b) const;
/**
@brief calculates self similarity, will yield 0
@param c a pair of Real, giving the x and the y coordinates
*/
Real operator()(const std::pair<Real, Real> & c) const;
/**
@brief clusters the indices according to their respective element distances
@param x Real value to scale the result
@throw Exception::DivisionByZero if scaling is unapplicable because it is 0
sets the scale so that similarities can be correctly calculated from distances. Should be set so that the greatest distance in a chosen set will be scales to 1 (i.e. @p x = greatest possible distance in the set)
*/
void setScale(Real x);
};
}
#endif //OPENMS_COMPARISON_CLUSTERING_EUCLIDEANSIMILARITY_H
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