ElutionPeakDetection.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
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $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) const;
 
    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