FLASHDeconvAlgorithm.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: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/Matrix.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <boost/dynamic_bitset.hpp>
#include <iostream>

namespace OpenMS
{
  class OPENMS_DLLAPI FLASHDeconvAlgorithm : public DefaultParamHandler
  {
  public:
    typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine;
    typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak;

    FLASHDeconvAlgorithm();

    FLASHDeconvAlgorithm(const FLASHDeconvAlgorithm&) = default;

    FLASHDeconvAlgorithm(FLASHDeconvAlgorithm&& other) = default;

    FLASHDeconvAlgorithm& operator=(const FLASHDeconvAlgorithm& fd) = default;

    FLASHDeconvAlgorithm& operator=(FLASHDeconvAlgorithm&& fd) = default;

    ~FLASHDeconvAlgorithm() = default;

    void performSpectrumDeconvolution(const MSSpectrum& spec, const std::vector<DeconvolvedSpectrum>& survey_scans, int scan_number,
                                      const std::map<int, std::vector<std::vector<float>>>& precursor_map_for_FLASHIda);

    DeconvolvedSpectrum& getDeconvolvedSpectrum();

    const PrecalculatedAveragine& getAveragine();

    void setAveragine(const PrecalculatedAveragine& avg);

    void setTargetMasses(const std::vector<double>& masses, bool exclude = false);

    void calculateAveragine(bool use_RNA_averagine);

    static int getNominalMass(double mass);

    static float getCosine(const std::vector<float>& a, int a_start, int a_end, const IsotopeDistribution& b, int b_size, int offset, int min_iso_size);


    static float getIsotopeCosineAndDetermineIsotopeIndex(double mono_mass, const std::vector<float>& per_isotope_intensities, int& offset, const PrecalculatedAveragine& avg, int iso_int_shift = 0, int window_width = -1,
                                                          int allowed_iso_error_for_second_best_cos = 0, PeakGroup::TargetDummyType target_dummy_type = PeakGroup::TargetDummyType::target);

    static void addMZsToExcludsionList(const DeconvolvedSpectrum& dspec, std::unordered_set<double>& excluded_mzs);

    void setTargetDummyType(PeakGroup::TargetDummyType target_dummy_type, DeconvolvedSpectrum& target_dspec_for_dummy_calcualtion);

  protected:
    void updateMembers_() override;

  private:

    const static int min_iso_size_ = 2;

    int allowed_iso_error_ = 1;

    double min_rt_, max_rt_;
    double min_mz_, max_mz_;
    int min_abs_charge_, max_abs_charge_;
    bool is_positive_;
    double min_mass_, max_mass_;
    int current_max_charge_;
    double current_max_mass_;
    double current_min_mass_;
    double intensity_threshold_;
    const static int min_support_peak_count_ = 2;
    DoubleList tolerance_;
    DoubleList bin_mul_factors_;
    DoubleList min_isotope_cosine_;

    DeconvolvedSpectrum* target_dspec_for_dummy_calcualtion_;

    PeakGroup::TargetDummyType target_dummy_type_ = PeakGroup::TargetDummyType::target;

    FLASHDeconvHelperStructs::PrecalculatedAveragine avg_;

    boost::dynamic_bitset<> target_mass_bins_;
    std::vector<double> target_mono_masses_;

    std::vector<double> excluded_masses_;

    boost::dynamic_bitset<> previously_deconved_mass_bins_for_dummy_;
    std::vector<double> previously_deconved_mono_masses_for_dummy_;
    std::unordered_set<double> excluded_peak_mzs_;

    std::vector<LogMzPeak> log_mz_peaks_;
    DeconvolvedSpectrum deconvolved_spectrum_;
    boost::dynamic_bitset<> mass_bins_;
    boost::dynamic_bitset<> mz_bins_;
    // std::vector<int> mz_bin_peak_index_;

    std::vector<double> filter_;
    Matrix<double> harmonic_filter_matrix_;

    double iso_da_distance_;

    std::vector<int> bin_offsets_;
    Matrix<int> harmonic_bin_offset_matrix_;

    double mass_bin_min_value_;
    double mz_bin_min_value_;

    uint ms_level_;

    double isolation_window_size_;

    static double getBinValue_(Size bin, double min_value, double bin_mul_factor);

    static Size getBinNumber_(double value, double min_value, double bin_mul_factor);

    void updateLogMzPeaks_();

    void updateMzBins_(Size bin_number, std::vector<float>& mz_bin_intensities);


    double getMassFromMassBin_(Size mass_bin, double bin_mul_factor) const;

    double getMzFromMzBin_(Size mass_bin, double bin_mul_factor) const;

    void generatePeakGroupsFromSpectrum_();

    Matrix<int> updateMassBins_(const std::vector<float>& mz_intensities);

    Matrix<int> filterMassBins_(const std::vector<float>& mass_intensities);

    void updateCandidateMassBins_(std::vector<float>& mass_intensities, const std::vector<float>& mz_intensities);

    void getCandidatePeakGroups_(const Matrix<int>& per_mass_abs_charge_ranges);

    void setFilters_();

    void scoreAndFilterPeakGroups_();

    void removeChargeErrorPeakGroups_(DeconvolvedSpectrum& dspec) const;

    void removeOverlappingPeakGroups_(DeconvolvedSpectrum& dspec, double tol);

    bool registerPrecursor_(const std::vector<DeconvolvedSpectrum>& survey_scans, const std::map<int, std::vector<std::vector<float>>>& precursor_map_for_real_time_acquisition);
  };
} // namespace OpenMS