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/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES//Matrix.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <iostream>
#include <boost/dynamic_bitset.hpp>
 
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;
 
    void performSpectrumDeconvolution(const MSSpectrum& spec,
                                      const std::vector<DeconvolvedSpectrum>& survey_scans,
                                      const int scan_number,
                                      const bool write_detail,
                                      const std::map<int, std::vector<std::vector<double>>>& precursor_map_for_FLASHIda);
 
    DeconvolvedSpectrum& getDeconvolvedSpectrum();
    DeconvolvedSpectrum& getDecoyDeconvolvedSpectrum();
 
    const PrecalculatedAveragine& getAveragine();
 
    void setAveragine(const PrecalculatedAveragine& avg);
 
    void setTargetMasses(const std::vector<double>& masses);
 
    void calculateAveragine(const bool use_RNA_averagine);
 
    void addExcludedMonoMass(const double m);
 
    void clearExcludedMonoMasses();
 
    static int getNominalMass(const double mass);
 
    static float getCosine(const std::vector<float>& a,
                             int a_start,
                             int a_end,
                             const IsotopeDistribution& b,
                             int b_size,
                             int offset);
 
    static float getIsotopeCosineAndDetermineIsotopeIndex(const double mono_mass,
                                                           const std::vector<float>& per_isotope_intensities,
                                                           int& offset,
                                                           int& second_best_iso_offset,
                                                           const PrecalculatedAveragine& avg,
                                                           int window_width = -1, int allowed_iso_error = 1);
 
    void setDecoyFlag(int flag);
 
  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_;
    bool write_detail_ = false;
    double min_mass_, max_mass_;
    int current_min_charge_;
    int current_max_charge_;
    double current_max_mass_;
    double current_min_mass_;
    double intensity_threshold_;
    const IntList min_support_peak_count_ = {3,3,3,3,3,3,3,3};
    DoubleList tolerance_;
    DoubleList bin_width_;
    DoubleList min_isotope_cosine_;
    //IntList max_mass_count_;
 
    int decoy_run_flag_ = 0;
 
    static const int charge_decoy_ = 1;
    static const int noise_decoy_ = 2;
    static const int isotope_decoy_ = 3;
 
    FLASHDeconvHelperStructs::PrecalculatedAveragine avg_;
    std::vector<std::vector<Size>> prev_mass_bins_ms1_;
    std::vector<std::map<int, std::vector<Size>>> prev_mass_bins_ms2_;
    std::vector<double> prev_rts_ms1_;
    std::vector<double> prev_rts_ms2_;
 
    boost::dynamic_bitset<> target_mass_bins_;
    std::vector<double> target_masses_;
 
    boost::dynamic_bitset<> excluded_mass_bins_;
    std::vector<double> excluded_masses_;
 
    const std::vector<int> harmonic_charges_{2, 3, 5, 7};
    std::vector<LogMzPeak> log_mz_peaks_;
    DeconvolvedSpectrum deconvolved_spectrum_;
    DeconvolvedSpectrum decoy_deconvolved_spectrum_;
    boost::dynamic_bitset<> mass_bins_;
    boost::dynamic_bitset<> mz_bins_;
    boost::dynamic_bitset<> mz_bins_for_edge_effect_;
 
    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_;
 
    int ms_level_;
 
    const int low_charge_ = 6; //10 inclusive
 
    double isolation_window_size_;
 
    const int max_peak_count_ = 30000;//30000
 
    static double getBinValue_(const Size bin, const double min_value, const double bin_width);
 
    static Size getBinNumber_(const double value, const double min_value, const double bin_width);
 
    void updateLogMzPeaks_(const MSSpectrum *spec);
 
    void updateMzBins_(const Size bin_number, std::vector<float>& mz_bin_intensities);
 
    void unionPrevMassBins_();
 
 
    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 removeHarmonicsPeakGroups_(DeconvolvedSpectrum& dpec);
 
    void removeOverlappingPeakGroups_(DeconvolvedSpectrum& dpec, const double tol, const int iso_length = 1);
 
    void filterPeakGroupsByIsotopeCosine_(const int current_max_mass_count);
 
    bool registerPrecursor(const std::vector<DeconvolvedSpectrum>& survey_scans,
                                  const std::map<int, std::vector<std::vector<double>>>& precursor_map_for_real_time_acquisition);
 
  };
}