PeakGroup.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/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 TargetDummyType
    {
      target = 0,
      charge_dummy,
      noise_dummy,
      isotope_dummy
    };


    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, int allowed_iso_error = 1);

    std::vector<LogMzPeak> recruitAllPeaksInSpectrum(const MSSpectrum& spec, double tol, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg, double mono_mass,
                                                     const std::unordered_set<double>& excluded_peak_mzs);

    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 Qscore(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::TargetDummyType getTargetDummyType() const;

    void setTargetDummyType(PeakGroup::TargetDummyType index);

    float getQvalue(PeakGroup::TargetDummyType target_dummy_type = PeakGroup::TargetDummyType::target) const;

    void setQvalue(float q, PeakGroup::TargetDummyType target_dummy_type);

    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;

    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);
    Size size() const noexcept;

    void reserve(Size n);
    bool empty() const;
    void swap(std::vector<FLASHDeconvHelperStructs::LogMzPeak>& x);
    void sort();

    static const int isotope_int_shift = 1;

  private:
    void updateChargeFitScoreAndChargeIntensities_();
    void updateAvgPPMError_();
    void updateAvgDaError_();
    float getAbsPPMError_(const LogMzPeak& p) const;
    float getAbsDaError_(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;

    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;
    int scan_number_ = 0;
    bool is_positive_;
    bool is_targeted_ = false;
    double monoisotopic_mass_ = -1.0;
    float intensity_ = 0; // total intensity
    PeakGroup::TargetDummyType target_dummy_type_ = target;

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