SpectrumAlignmentScore.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// 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.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//
#pragma once

#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);

    ~SpectrumAlignmentScore() override;
    // @}

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

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

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

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

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

    // @}

  };

}