PeakPickerHiRes.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 2002-2022.
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// $Author: Erhan Kenar $
// $Maintainer: Timo Sachsenberg $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/MSExperiment.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

#define DEBUG_PEAK_PICKING
#undef DEBUG_PEAK_PICKING
//#undef DEBUG_DECONV
namespace OpenMS
{
  class MSChromatogram;
  class OnDiscMSExperiment;

  class OPENMS_DLLAPI PeakPickerHiRes :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    PeakPickerHiRes();

    ~PeakPickerHiRes() override;

    struct PeakBoundary
    {
        double mz_min;
        double mz_max;
    };

    void pick(const MSSpectrum& input, MSSpectrum& output) const;

    void pick(const MSChromatogram& input, MSChromatogram& output) const;

    void pick(const MSSpectrum& input, MSSpectrum& output, std::vector<PeakBoundary>& boundaries, bool check_spacings = true) const;

    void pick(const MSChromatogram& input, MSChromatogram& output, std::vector<PeakBoundary>& boundaries, bool check_spacings = false) const;

    void pickExperiment(const PeakMap& input, PeakMap& output, const bool check_spectrum_type = true) const;

    void pickExperiment(const PeakMap& input,
                        PeakMap& output,
                        std::vector<std::vector<PeakBoundary> >& boundaries_spec,
                        std::vector<std::vector<PeakBoundary> >& boundaries_chrom,
                        const bool check_spectrum_type = true) const;

    void pickExperiment(/* const */ OnDiscMSExperiment& input, PeakMap& output, const bool check_spectrum_type = true) const;

protected:

    template <typename ContainerType>
    void pick_(const ContainerType& input, ContainerType& output, std::vector<PeakBoundary>& boundaries, bool check_spacings = true, int im_index = -1) const;

    // signal-to-noise parameter
    double signal_to_noise_;

    // maximal spacing difference defining a large gap
    double spacing_difference_gap_;
    
    // maximal spacing difference defining a missing data point
    double spacing_difference_;

    // maximum number of missing points
    unsigned missing_;

    // MS levels to which peak picking is applied
    std::vector<Int> ms_levels_;

    bool report_FWHM_;

    bool report_FWHM_as_ppm_;

    // docu in base class
    void updateMembers_() override;

  }; // end PeakPickerHiRes

} // namespace OpenMS