PeakGroup.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/FLASHDeconvHelperStructs.h>
#include <OpenMS/DATASTRUCTURES/Matrix.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI PeakGroup
  {
    typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak;
    typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine;
 
  public:
    enum TargetDecoyType
    {
      target = 0,
      charge_decoy,
      noise_decoy,
      isotope_decoy,
      non_specific
    };
 
 
    PeakGroup() = default;
 
    explicit PeakGroup(int min_abs_charge, int max_abs_charge, bool is_positive);
 
    ~PeakGroup() = default;
 
    PeakGroup(const PeakGroup&) = default;
 
    PeakGroup(PeakGroup&& other) = default;
 
    bool operator<(const PeakGroup& a) const;
 
    bool operator>(const PeakGroup& a) const;
 
    bool operator==(const PeakGroup& a) const;
 
    PeakGroup& operator=(const PeakGroup& t) = default;
 
    void updateMonoMassAndIsotopeIntensities();
 
    int updateQscore(std::vector<LogMzPeak>& noisy_peaks, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg, double min_cos, bool is_low_charge, bool is_profile = false, int allowed_iso_error = 1);
 
    std::vector<LogMzPeak> recruitAllPeaksInSpectrum(const MSSpectrum& spec, double tol, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg, double mono_mass);
 
    bool isSignalMZ(double mz, double tol) const;
 
    void setScanNumber(int scan_number);
 
    void setChargeIsotopeCosine(int abs_charge, float cos);
 
    void setAbsChargeRange(int min_abs_charge, int max_abs_charge);
 
    void setIsotopeCosine(float cos);
 
    void setRepAbsCharge(int max_snr_abs_charge);
 
    void setMonoisotopicMass(double mono_mass);
 
    void setQscore(double qscore);
 
    void setChargeScore(float charge_score);
 
    void setAvgPPMError(float error);
 
    void setSNR(float snr);
 
    void setChargeSNR(int abs_charge, float c_snr);
 
    void setTargeted();
 
    int getScanNumber() const;
 
    double getMonoMass() const;
 
    float getIntensity() const;
 
    float getChargeSNR(int abs_charge) const;
 
    float getChargeIsotopeCosine(int abs_charge) const;
 
    float getChargeIntensity(int abs_charge) const;
 
    std::tuple<double, double> getRepMzRange() const;
 
    std::tuple<double, double> getMzRange(int abs_charge) const;
 
    std::tuple<int, int> getAbsChargeRange() const;
 
    const std::vector<float>& getIsotopeIntensities() const;
 
    float getIsotopeCosine() const;
 
    int getRepAbsCharge() const;
 
    double getQscore() const;
 
    double getQscore2D() const;
 
    float getSNR() const;
 
    float getChargeScore() const;
 
    float getAvgPPMError() const;
 
    float getAvgDaError() const;
 
    bool isPositive() const;
 
    bool isTargeted() const;
 
    PeakGroup::TargetDecoyType getTargetDecoyType() const;
 
    void setTargetDecoyType(PeakGroup::TargetDecoyType index);
 
    float getQvalue(PeakGroup::TargetDecoyType target_decoy_type = PeakGroup::TargetDecoyType::target) const;
 
    void setQvalue(double q, PeakGroup::TargetDecoyType target_decoy_type);
 
    void setIsotopeDaDistance(double d);
 
    double getIsotopeDaDistance() const;
 
    int getMinNegativeIsotopeIndex() const;
 
    void setIndex(uint i);
 
    void setQscore2D(double fqscore);
 
    void setFeatureIndex(uint findex);
 
    uint getIndex() const;
    uint getFeatureIndex() const;
 
    int getChargeRangeForDL()
    {
      return charge_range_for_DL_;
    };
    int getIsotopeRangeForDL()
    {
      return iso_range_for_DL_;
    };
    float getBinWidthDL()
    {
      return bin_width_DL_;
    }
 
    void calculateDLMatrices(const MSSpectrum& spec, double tol, const PrecalculatedAveragine& avg);
 
    Matrix<float> getDLMatrix(int index) const;
 
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator begin() const noexcept;
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator end() const noexcept;
 
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator begin() noexcept;
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator end() noexcept;
 
    const FLASHDeconvHelperStructs::LogMzPeak& operator[](Size i) const;
 
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator getNoisePeakBegin() const noexcept;
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator getNoisePeakEnd() const noexcept;
 
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator getNoisePeakBegin() noexcept;
    std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator getNoisePeakEnd() noexcept;
 
    void push_back(const FLASHDeconvHelperStructs::LogMzPeak& pg);
    FLASHDeconvHelperStructs::LogMzPeak& back();
    Size size() const noexcept;
 
    void reserve(Size n);
    bool empty() const;
    void swap(std::vector<FLASHDeconvHelperStructs::LogMzPeak>& x);
    void sort();
 
  private:
    void updateChargeFitScoreAndChargeIntensities_(bool is_low_charge);
    void updateAvgPPMError_();
    void updateAvgDaError_();
    float getAbsPPMError_(const LogMzPeak& p) const;
    float getAbsDaError_(const LogMzPeak& p) const;
    void updateSNR_();
    void clear_();
    void updatePerChargeInformation_(const std::vector<LogMzPeak>& noisy_peaks);
    void updateChargeRange_(std::vector<LogMzPeak>& noisy_peaks);
    void updatePerChargeCos_(const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg);
 
    float getNoisePeakPower_(const std::vector<LogMzPeak>& noisy_peaks, const std::vector<LogMzPeak>& signal_peaks, const int z) const;
    std::vector<Matrix<float>> dl_matrices_;
 
    std::vector<FLASHDeconvHelperStructs::LogMzPeak> logMzpeaks_;
    std::vector<FLASHDeconvHelperStructs::LogMzPeak> negative_iso_peaks_;
    std::vector<float> per_charge_sum_signal_squared_;
    std::vector<float> per_charge_noise_pwr_;
    std::vector<float> per_charge_cos_;
    std::vector<float> per_charge_int_;
    std::vector<float> per_charge_snr_;
    std::vector<float> per_isotope_int_;
    int min_abs_charge_ = 0, max_abs_charge_ = -1;
    uint index_ = 0;
    uint findex_ = 0;
    int scan_number_ = 0;
    bool is_positive_ = false;
    bool is_targeted_ = false;
    double monoisotopic_mass_ = -1.0;
    float intensity_ = 0; // total intensity
    PeakGroup::TargetDecoyType target_decoy_type_ = target;
    int min_negative_isotope_index_ = -1;
 
    int charge_range_for_DL_ = 7;
    float bin_width_DL_ = 0.25;
    int iso_range_for_DL_ = 21;
 
    double iso_da_distance_ = Constants::ISOTOPE_MASSDIFF_55K_U;
    int max_snr_abs_charge_ = -1;
    float isotope_cosine_score_ = 0;
    float charge_score_ = 0;
    double qscore_ = .0f;
    double qscore2D_ = -1.0f;
    float avg_ppm_error_ = 0;
    float avg_da_error_ = 0;
    float snr_ = 0;
    std::map<PeakGroup::TargetDecoyType, float> qvalue_;
  };
} // namespace OpenMS