PeakPickerMRM.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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/KERNEL/ChromatogramPeak.h>

#include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h>
#include <OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h>
#include <OpenMS/FILTERING/SMOOTHING/GaussFilter.h>

#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>

#ifdef WITH_CRAWDAD
#include <CrawdadWrapper.h>
#endif

namespace OpenMS
{

  class OPENMS_DLLAPI PeakPickerMRM :
    public DefaultParamHandler
  {

public:

    PeakPickerMRM();

    ~PeakPickerMRM() override {}

    void pickChromatogram(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
    

    void pickChromatogram(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom, MSChromatogram& smoothed_chrom);

protected:

    void pickChromatogramCrawdad_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);

    void pickChromatogram_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);

    void integratePeaks_(const MSChromatogram& chromatogram);

    Size findClosestPeak_(const MSChromatogram& chromatogram, double target_rt, Size current_peak = 0);

    void removeOverlappingPeaks_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);


    void updateMembers_() override;

    PeakPickerMRM& operator=(const PeakPickerMRM& rhs);

    // Members
    UInt sgolay_frame_length_;
    UInt sgolay_polynomial_order_;
    double gauss_width_;
    bool use_gauss_;
    bool remove_overlapping_;

    double peak_width_;
    double signal_to_noise_;

    double sn_win_len_;
    UInt sn_bin_count_;
    bool write_sn_log_messages_;
    String method_;

    std::vector<double> integrated_intensities_;
    std::vector<int> left_width_;
    std::vector<int> right_width_;

    PeakPickerHiRes pp_;
    SavitzkyGolayFilter sgolay_;
    GaussFilter gauss_;
    SignalToNoiseEstimatorMedian<MSChromatogram > snt_;
  };
}