SpectrumAlignmentScore.h

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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 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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//
#ifndef OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENTSCORE_H
#define OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENTSCORE_H

#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>

#include <boost/math/special_functions/erf.hpp>
#include <cmath>

namespace OpenMS
{

  class OPENMS_DLLAPI SpectrumAlignmentScore :
    public PeakSpectrumCompareFunctor
  {
public:

    // @name Constructors and Destructors
    // @{
    SpectrumAlignmentScore();

    SpectrumAlignmentScore(const SpectrumAlignmentScore & source);

    virtual ~SpectrumAlignmentScore();
    // @}

    // @name Operators
    // @{
    SpectrumAlignmentScore & operator=(const SpectrumAlignmentScore & source);

    double operator()(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const;

    double operator()(const PeakSpectrum & spec) const;
    // @}

    // @name Accessors
    // @{
    static PeakSpectrumCompareFunctor * create() { return new SpectrumAlignmentScore(); }

    static const String getProductName()
    {
      return "SpectrumAlignmentScore";
    }

    // @}

protected:

    double getFactor_(double mz_tolerance, double mz_difference, bool is_gaussian = false) const;
  };

}
#endif //OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENTSCORE_H