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// OpenMS -- Open-Source Mass Spectrometry
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// 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:
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// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
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// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_COMPARISON_SPECTRA_BINNEDSUMAGREEINGINTENSITIES_H
#define OPENMS_COMPARISON_SPECTRA_BINNEDSUMAGREEINGINTENSITIES_H
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrumCompareFunctor.h>
#include <cmath>
#include <cfloat>
namespace OpenMS
{
/**
@brief Compare functor scoring the sum of agreeing intensities for similarity measurement
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process
Witold E Wolski , Maciej Lalowski* , Peter Martus* , Ralf Herwig* , Patrick Giavalisco , Johan Gobom , Albert Sickmann , Hans Lehrach and Knut Reinert*
BMC Bioinformatics 2005, 6:285 doi:10.1186/1471-2105-6-285
@htmlinclude OpenMS_BinnedSumAgreeingIntensities.parameters
@see BinnedSpectrumCompareFunctor @see BinnedSpectrum
@ingroup SpectraComparison
*/
class OPENMS_DLLAPI BinnedSumAgreeingIntensities :
public BinnedSpectrumCompareFunctor
{
public:
/// default constructor
BinnedSumAgreeingIntensities();
/// copy constructor
BinnedSumAgreeingIntensities(const BinnedSumAgreeingIntensities & source);
/// destructor
virtual ~BinnedSumAgreeingIntensities();
/// assignment operator
BinnedSumAgreeingIntensities & operator=(const BinnedSumAgreeingIntensities & source);
/** function call operator, calculates the similarity of the given arguments
@param spec1 First spectrum given as a binned representation
@param spec2 Second spectrum given as a binned representation
@throw IncompatibleBinning is thrown if the binning of the two input spectra are not the same
*/
double operator()(const BinnedSpectrum & spec1, const BinnedSpectrum & spec2) const;
/// function call operator, calculates self similarity
double operator()(const BinnedSpectrum & spec) const;
///
static BinnedSpectrumCompareFunctor * create() { return new BinnedSumAgreeingIntensities(); }
/// get the identifier for this DefaultParamHandler
static const String getProductName()
{
return "BinnedSumAgreeingIntensities";
}
};
}
#endif //OPENMS_COMPARISON_SPECTRA_BINNEDSUMAGREEINGINTENSITIES_H
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