PeakGroup.h

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//--------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI PeakGroup
  {
    typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak;
    typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine;
  public:
    PeakGroup() = default;
 
    explicit PeakGroup(const int min_abs_charge, const int max_abs_charge, const bool is_positive);
 
    ~PeakGroup();
 
    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 updateIsotopeCosineAndQScore(const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg, double min_cos, double iso_da_distance);
 
    //MSSpectrum getSubspectrumForMass(const MSSpectrum& spec, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg,  double mono_mass);
 
    void recruitAllPeaksInSpectrum(const MSSpectrum& spec, const double tol, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg,  double mono_mass, bool write_detail);
 
    void updateSNR();
 
    bool isSignalMZ(const double mz, const double tol) const;
 
    void setScanNumber(const int scan_number);
 
    void setChargeIsotopeCosine(const int abs_charge, const float cos);
 
 
    void setMaxQScoreMzRange(const double min, const double max);
 
    void setAbsChargeRange(const int min_abs_charge, const int max_abs_charge);
 
    void setIsotopeCosine(const float cos);
 
    void setRepAbsCharge(const int max_qscore_charge);
 
    void setQScore(const float qscore);
 
    void setChargeScore(const float charge_score);
 
    void setAvgPPMError(const float error);
 
    void setSNR(const float snr);
    void setChargeSNR(const int abs_charge, const float c_snr);
 
    void setTargeted();
 
    void setSecondBestMonsMass(const double mass);
 
    int getScanNumber() const;
 
    double getMonoMass() const;
 
    double getSecondBestMonoMass() const;
 
    double getIntensity() const;
 
    float getChargeSNR(const int abs_charge) const;
 
    float getChargeIsotopeCosine(const int abs_charge) const;
 
    float getChargeIntensity(const int abs_charge) const;
 
    std::tuple<double, double> getMaxQScoreMzRange() const;
 
    std::tuple<double, double> getMzRange(int abs_charge) const;
 
    std::tuple<int, int> getAbsChargeRange() const;
 
    std::vector<float> getIsotopeIntensities() const;
 
    float getIsotopeCosine() const;
 
    int getRepAbsCharge() const;
 
    float getQScore() const;
 
    float getSNR() const;
 
    float getChargeScore() const;
 
    float getAvgPPMError() const;
 
    bool isPositive() const;
 
    bool isTargeted() const;
 
    //float getDecoyQScore() const;
 
    //void setDecoyQScore(const float d);
 
    //float getDecoyIsoScore() const;
 
    //void setDecoyIsoScore(const float d);
 
    int getDecoyIndex() const;
 
    void setDecoyIndex(int index);
 
    float getQvalue() const;
 
    void setQvalue(const float q);
 
    float getQvalueWithChargeDecoyOnly() const;
 
    float getQvalueWithIsotopeDecoyOnly() const;
 
    float getQvalueWithNoiseDecoyOnly() const;
 
    void setQvalueWithChargeDecoyOnly(const float q);
 
    void setQvalueWithIsotopeDecoyOnly(const float q);
 
    void setQvalueWithNoiseDecoyOnly(const float q);
 
    void setIsotopeDaDistance(const double d);
 
    double getIsotopeDaDistance() 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[](const 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();
    std::vector<FLASHDeconvHelperStructs::LogMzPeak> noisy_peaks;
 
  private:
 
    void setChargePowers_(const int abs_charge, const double signal_pwr, const double noise_pwr, const double intensity);
    void updateChargeFitScoreAndChargeIntensities_();
    //update avg ppm error
    void updateAvgPPMError_(double iso_da_distance);
 
 
    std::vector<FLASHDeconvHelperStructs::LogMzPeak> logMzpeaks_;
 
 
    std::vector<float> per_charge_signal_pwr_;
    std::vector<float> per_charge_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_;
    double max_qscore_mz_end_, max_qscore_mz_start_;
    int min_abs_charge_ = 0, max_abs_charge_ = -1;
    int scan_number_;
    bool is_positive_;
    bool is_targeted_ = false;
    double monoisotopic_mass_ = -1.0;
    double second_best_monomass_ = -1.0;
    double intensity_;// total intensity
    int decoy_index_ = 0;
 
    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 snr_ = 0;
    float qvalue_ = 1.0;
 
    float qvalue_with_isotope_decoy_only_ = 1.0;
    float qvalue_with_noise_decoy_only_ = 1.0;
    float qvalue_with_charge_decoy_only_ = 1.0;
  };
}