PeakAlignment.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#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;
 
 
  };
 
}