PeakGroup.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/FLASHDeconvHelperStructs.h>
#include <OpenMS/DATASTRUCTURES//Matrix.h>

namespace OpenMS
{
  class OPENMS_DLLAPI PeakGroup
  {
    typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak;
    typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine;
  public:

    enum DecoyFlag
    {
      target = 0,
      charge_decoy,
      noise_decoy,
      isotope_decoy
    };

    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();

    void updateIsotopeCosineSNRAvgErrorAndQScore(const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg, double min_cos);

    std::vector<LogMzPeak> recruitAllPeaksInSpectrum(const MSSpectrum& spec, double tol, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg,  double mono_mass, const std::unordered_set<int>& excluded_integer_mzs_, int charge_offset = 0, double charge_multiple = 1.0, double mz_off = .0);

    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_qscore_charge);

    void setQScore(float 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;

    float getQScore() const;

    float getSNR() const;

    float getChargeScore() const;

    float getAvgPPMError() const;

    float getAvgDaError() const;

    bool isPositive() const;

    bool isTargeted() const;

    PeakGroup::DecoyFlag getDecoyFlag() const;

    void setDecoyFlag(PeakGroup::DecoyFlag index);

    float getQvalue(PeakGroup::DecoyFlag flag = PeakGroup::DecoyFlag::target) const;

    void setQvalue(float q, PeakGroup::DecoyFlag flag);

    void setIsotopeDaDistance(double d);

    double getIsotopeDaDistance() const;

    void setIndex(uint i);

    uint getIndex() 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;

    void push_back (const FLASHDeconvHelperStructs::LogMzPeak& pg);
    Size size() const noexcept;
    void clear();
    void reserve (Size n);
    bool empty() const;
    void swap (std::vector<FLASHDeconvHelperStructs::LogMzPeak>& x);
    void shrink_to_fit();
    void sort();

  private:
    void setChargePowers_(int abs_charge, float signal_pwr, float noise_pwr, float intensity);
    void updateChargeFitScoreAndChargeIntensities_();
    void updateAvgPPMError_();
    void updateAvgDaError_();
    float getAbsPPMError_(const LogMzPeak& p) const;
    float getAbsDaError_(LogMzPeak& p) const;
    void updateSNR_();

    std::vector<Matrix<float>> dl_matrices_;

    std::vector<FLASHDeconvHelperStructs::LogMzPeak> logMzpeaks_;

    std::vector<float> per_charge_signal_pwr_;
    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;
    int scan_number_;
    bool is_positive_;
    bool is_targeted_ = false;
    double monoisotopic_mass_ = -1.0;
    float intensity_;// total intensity
    PeakGroup::DecoyFlag decoy_flag_ = target;

    double iso_da_distance_ = Constants::ISOTOPE_MASSDIFF_55K_U;
    int max_qscore_abs_charge_ = -1;
    float isotope_cosine_score_ = 0;
    float charge_score_;
    float qscore_ = .0f;
    float avg_ppm_error_ = 0;
    float avg_da_error_ = 0;
    float snr_ = 0;
    std::map<PeakGroup::DecoyFlag, float> qvalue_;
  };
}