PeakPickerMRM.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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_;
  };
}