PeakPickerMRM.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: 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 {}
 
  enum FLOATINDICES { IDX_FWHM = 0, IDX_ABUNDANCE = 1, IDX_LEFTBORDER = 2, IDX_RIGHTBORDER = 3, SIZE_OF_FLOATINDICES };
 
    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_;
  };
}