FLASHDeconvAlgorithm.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: 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<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