SpectralDeconvolution.h

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// Copyright (c) 2002-present, OpenMS Inc. -- 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/FLASHHelperClasses.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 <memory>
#include <optional>
#include <utility>
#include <iostream>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SpectralDeconvolution : public DefaultParamHandler
  {
  public:
    typedef FLASHHelperClasses::PrecalculatedAveragine PrecalculatedAveragine;
    typedef FLASHHelperClasses::LogMzPeak LogMzPeak;
 
    SpectralDeconvolution();
 
    SpectralDeconvolution(const SpectralDeconvolution&) = default;
 
    SpectralDeconvolution(SpectralDeconvolution&& other) = default;
 
    SpectralDeconvolution& operator=(const SpectralDeconvolution& fd) = default;
 
    SpectralDeconvolution& operator=(SpectralDeconvolution&& fd) = default;
 
    ~SpectralDeconvolution() = default;
 
    void performSpectrumDeconvolution(const MSSpectrum& spec, int scan_number, const PeakGroup& precursor_peak_group);
 
    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);
 
    void setToleranceEstimation()
    {
      max_mass_dalton_tolerance_ = 100;
    }
 
    static int getNominalMass(double mass);
 
    static float getCosine(const std::vector<float>& a, int a_start, int a_end, const IsotopeDistribution& b, int offset, int min_iso_len);
 
 
    static float getIsotopeCosineAndIsoOffset(double mono_mass, const std::vector<float>& per_isotope_intensities, int& offset,
                                              const PrecalculatedAveragine& avg, int iso_int_shift,
                                              int window_width, const std::vector<double>& excluded_masses);
 
    void setTargetDecoyType(PeakGroup::TargetDecoyType target_decoy_type, const DeconvolvedSpectrum& target_dspec_for_decoy_calcualtion);
 
    const static int min_iso_size = 2;
 
  protected:
    void updateMembers_() override;
 
    using MassRanges = std::vector<std::pair<double, double>>;
 
    struct CandidateSelectionContext
    {
      const PrecalculatedAveragine& averagine; 
      double tolerance; 
      double isotope_distance; 
      double max_mass; 
      int min_charge; 
      int max_charge; 
      bool positive; 
    };
 
    virtual std::optional<MassRanges> selectCandidateMassRanges_(const CandidateSelectionContext& context,
      const DeconvolvedSpectrum* evidence, const std::vector<Size>& valid) const;
 
  private:
 
    int allowed_iso_error_ = -1;
 
    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 noise_iso_delta_ =  .9444;
    const static int min_support_peak_count_ = 2;
    DoubleList tolerance_;
    DoubleList bin_mul_factors_;
    DoubleList min_isotope_cosine_;
    DoubleList min_snr_;
    double min_qscore_ = .2;
 
    const DeconvolvedSpectrum* target_dspec_for_decoy_calculation_;
 
    PeakGroup::TargetDecoyType target_decoy_type_ = PeakGroup::TargetDecoyType::target;
 
    FLASHHelperClasses::PrecalculatedAveragine avg_;
 
    struct OPENMS_DLLAPI Bitsets
    {
      struct Impl;
      std::unique_ptr<Impl> impl;
      Bitsets();
      Bitsets(const Bitsets& other);
      Bitsets(Bitsets&& other) noexcept;
      Bitsets& operator=(const Bitsets& other);
      Bitsets& operator=(Bitsets&& other) noexcept;
      ~Bitsets();
    };
    Bitsets bitsets_;
 
    void restrictCandidateMassBins_(std::vector<std::pair<double, double>> intervals);
 
    std::vector<Size> scorePeakGroups_();
 
    std::vector<double> target_mono_masses_;
 
    std::vector<double> excluded_masses_;
 
    std::vector<double> excluded_peak_masses_for_decoy_runs_;
    std::vector<double> excluded_masses_for_decoy_runs_;
 
    std::vector<LogMzPeak> log_mz_peaks_;
    DeconvolvedSpectrum deconvolved_spectrum_;
    std::vector<double> universal_pattern_;
    Matrix<double> harmonic_pattern_matrix_;
 
    std::vector<int> binned_universal_pattern_;
    Matrix<int> binned_harmonic_patterns;
 
    double mass_bin_min_value_;
    double mz_bin_min_value_;
 
    uint ms_level_;
 
    double iso_da_distance_;
 
    int target_precursor_charge_ = 0;
    double target_precursor_mz_ = 0;
 
    double max_mass_dalton_tolerance_ = .16;
 
    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 binLogMzPeaks_(Size bin_number, std::vector<float>& binned_log_mz_peak_intensities);
 
    double getMassFromMassBin_(Size mass_bin, double bin_mul_factor) const;
 
    double getMzFromMzBin_(Size mass_bin, double bin_mul_factor) const;
 
    void generatePeakGroupsFromSpectrum_();
 
    static void removeOverlappingPeakGroups_(DeconvolvedSpectrum& dspec, double tol, PeakGroup::TargetDecoyType target_decoy_type = PeakGroup::TargetDecoyType::target);
 
    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 PeakGroup::TargetDecoyType& target_decoy_type) const;
 
    void removeExcludedMasses_(DeconvolvedSpectrum& dspec, std::vector<double> excluded_masses, double tol) const;
 
    void setTargetPrecursorCharge_();
 
    void prepareSignalDecoyExclusions_();
 
    void prepareNoiseDecoySpectrum_(const MSSpectrum& spec);
 
    void registerPrecursorForMSn_(const PeakGroup& precursor_peak_group);
 
    bool isPeakGroupInExcludedMassForDecoyRuns_(const PeakGroup& peak_group, double tol, int offset = 0) const;
  };
  } // namespace OpenMS