PeakPickerHiRes.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Author: Erhan Kenar $
// $Maintainer: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/PROCESSING/NOISEESTIMATION/SignalToNoiseEstimatorMedianSettings.h>
 
#define DEBUG_PEAK_PICKING
#undef DEBUG_PEAK_PICKING
//#undef DEBUG_DECONV
namespace OpenMS
{
  class MSChromatogram;
  class Mobilogram;
  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 Mobilogram& input, Mobilogram& 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 pick(const Mobilogram& input, Mobilogram& 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_;
 
    SignalToNoiseEstimatorMedianSettings sn_settings_;
 
    // 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_;
 
    bool allow_missing_flank_;
 
    // docu in base class
    void updateMembers_() override;
 
  }; // end PeakPickerHiRes
 
} // namespace OpenMS