PeakAlignment.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 2002-2018.
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// $Maintainer: Mathias Walzer $
// $Authors: $
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//
#pragma once

#include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
#include <vector>

namespace OpenMS
{

  class OPENMS_DLLAPI PeakAlignment :
    public PeakSpectrumCompareFunctor
  {
public:

    PeakAlignment();

    PeakAlignment(const PeakAlignment & source);

    ~PeakAlignment() override;

    PeakAlignment & operator=(const PeakAlignment & source);

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

    double operator()(const PeakSpectrum & spec) const override;

    static PeakSpectrumCompareFunctor * create() { return new PeakAlignment(); }

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

    std::vector<std::pair<Size, Size> > getAlignmentTraceback(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const;

private:

    double peakPairScore_(double & pos1, double & intens1, double & pos2, double & intens2, const double & sigma) const;


  };

}