DeconvolvedSpectrum.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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// $Maintainer: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <OpenMS/KERNEL/MSSpectrum.h>

#include <iomanip>

namespace OpenMS
{
  class PeakGroup;

  class OPENMS_DLLAPI DeconvolvedSpectrum
  {
  public:
    typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak;

    DeconvolvedSpectrum() = default;

    explicit DeconvolvedSpectrum(int scan_number);

    ~DeconvolvedSpectrum() = default;

    DeconvolvedSpectrum(const DeconvolvedSpectrum& ) = default;

    DeconvolvedSpectrum(DeconvolvedSpectrum&& other) noexcept = default;

    DeconvolvedSpectrum& operator=(const DeconvolvedSpectrum& deconvolved_spectrum) = default;


    MSSpectrum toSpectrum(int to_charge, double tol = 10.0, bool retain_undeconvolved = false);

    const MSSpectrum& getOriginalSpectrum() const;

    const PeakGroup& getPrecursorPeakGroup() const;

    int getPrecursorCharge() const;

    const Precursor& getPrecursor() const;

    double getCurrentMaxMass(double max_mass) const;

    double getCurrentMinMass(double min_mass) const;

    int getCurrentMaxAbsCharge(int max_abs_charge) const;

    int getScanNumber() const;

    int getPrecursorScanNumber() const;

    const Precursor::ActivationMethod& getActivationMethod() const;

    void setPrecursor(const Precursor& precursor);

    void setPrecursorIntensity(float i);

    void setPrecursorScanNumber(int scan_number);

    void setActivationMethod(const Precursor::ActivationMethod& method);

    void setPrecursorPeakGroup(const PeakGroup& pg);

    void setOriginalSpectrum(const MSSpectrum& spec);

    void static updatePeakGroupQvalues(std::vector<DeconvolvedSpectrum>& deconvolved_spectra, std::vector<DeconvolvedSpectrum>& deconvolved_decoy_spectra);

    void setPeakGroups (std::vector<PeakGroup>& x);

    std::vector<PeakGroup>::const_iterator begin() const noexcept;
    std::vector<PeakGroup>::const_iterator end() const noexcept;

    std::vector<PeakGroup>::iterator begin() noexcept;
    std::vector<PeakGroup>::iterator end() noexcept;

    const PeakGroup& operator[](Size i) const;
    PeakGroup& operator[](Size i);
    void push_back (const PeakGroup& pg);
    Size size() const noexcept;
    void clear();
    void reserve (Size n);
    bool empty() const;

    void sort();
    void sortByQScore();
  private:
    std::vector<PeakGroup> peak_groups_;
    MSSpectrum spec_;
    PeakGroup precursor_peak_group_;
    Precursor precursor_peak_;
    Precursor::ActivationMethod activation_method_;
    int scan_number_ = 0, precursor_scan_number_ = 0;

  };
}