FLASHDeconvAlgorithm.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $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 window_width = -1, int allowed_iso_error_for_second_best_cos = 0, PeakGroup::DecoyFlag decoyFlag = PeakGroup::DecoyFlag::target);

    void setDecoyFlag(PeakGroup::DecoyFlag flag, FLASHDeconvAlgorithm& targetFD);

  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_width_;
    DoubleList min_isotope_cosine_;

    FLASHDeconvAlgorithm* targetFD_;

    PeakGroup::DecoyFlag decoy_flag_ = PeakGroup::DecoyFlag::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_decoy;
    std::vector<double> previously_deconved_mono_masses_for_decoy;
    std::unordered_set<int> excluded_integer_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_width);

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

    void updateLogMzPeaks_();

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


    double getMassFromMassBin_(Size mass_bin, double bin_width) const;

    double getMzFromMzBin_(Size mass_bin, double bin_width) 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);

    static void removeOverlappingPeakGroups_(DeconvolvedSpectrum& dspec);

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

  };
}