ElutionPeakDetection.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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// $Maintainer: Timo Sachsenberg$
// $Authors: Erhan Kenar, Holger Franken $
// --------------------------------------------------------------------------


#pragma once

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

namespace OpenMS
{
  class OPENMS_DLLAPI ElutionPeakDetection :
    public DefaultParamHandler, public ProgressLogger
  {
public:
    ElutionPeakDetection();

    ~ElutionPeakDetection() override;

    void detectPeaks(MassTrace& mt, std::vector<MassTrace>& single_mtraces);

    void detectPeaks(std::vector<MassTrace>& mt_vec, std::vector<MassTrace>& single_mtraces);

    void filterByPeakWidth(std::vector<MassTrace>&, std::vector<MassTrace>&);

    double computeMassTraceNoise(const MassTrace&);

    double computeMassTraceSNR(const MassTrace&);

    double computeApexSNR(const MassTrace&);

    void findLocalExtrema(const MassTrace& tr, const Size& num_neighboring_peaks,
                          std::vector<Size>& chrom_maxes, std::vector<Size>& chrom_mins);

    void smoothData(MassTrace& mt, int win_size) const;

protected:
    void updateMembers_() override;

private:
    double chrom_fwhm_;
    double chrom_peak_snr_;

    double min_fwhm_;
    double max_fwhm_;

    String pw_filtering_;

    bool mt_snr_filtering_;

    void detectElutionPeaks_(MassTrace&, std::vector<MassTrace>&);
  };

} // namespace OpenMS