DeconvolvedSpectrum.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/KERNEL/MSSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <iomanip>
 
namespace OpenMS
{
  class PeakGroup;
 
  class OPENMS_DLLAPI DeconvolvedSpectrum
  {
  public:
    typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak;
 
    DeconvolvedSpectrum() = default;
 
    DeconvolvedSpectrum(const MSSpectrum& spectrum, const int scan_number);
 
    ~DeconvolvedSpectrum() = default;
 
    DeconvolvedSpectrum(const DeconvolvedSpectrum& ) = default;
 
    DeconvolvedSpectrum(DeconvolvedSpectrum&& other) = default;
 
    DeconvolvedSpectrum& operator=(const DeconvolvedSpectrum& deconvolved_spectrum) = default;
 
 
    MSSpectrum toSpectrum(const int to_charge, bool retain_undeconvolved = false);
 
    const MSSpectrum& getOriginalSpectrum() const;
 
    const PeakGroup& getPrecursorPeakGroup() const;
 
    int getPrecursorCharge() const;
 
    const Precursor& getPrecursor() const;
 
    void setPrecursorPeakGroupQvalue(const double qvalue_with_iso_decoy_only , const double qvalue_with_noise_decoy_only, const double qvalue_with_charge_decoy_only);
 
    double getCurrentMaxMass(const double max_mass) const;
 
    double getCurrentMinMass(const double min_mass) const;
 
    int getCurrentMaxAbsCharge(const int max_abs_charge) const;
 
    int getScanNumber() const;
 
    int getPrecursorScanNumber() const;
 
    const String& getActivationMethod() const;
 
    void setPrecursor(const Precursor& precursor);
 
    void setPrecursorIntensity(const double i);
 
    void setPrecursorScanNumber(const int scan_number);
 
    void setActivationMethod(const String& method);
 
    void setPrecursorPeakGroup(const PeakGroup& pg);
 
    void static updatePeakGroupQvalues(std::vector<DeconvolvedSpectrum>& deconvolved_spectra, std::vector<DeconvolvedSpectrum>& deconvolved_decoy_spectra);
 
 
    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;
    void push_back (const PeakGroup& pg);
    Size size() const noexcept;
    void clear();
    void reserve (Size n);
    bool empty() const;
    void swap (std::vector<PeakGroup>& x);
 
    void sort();
    void sortByQScore();
  private:
    std::vector<PeakGroup> peak_groups;
    MSSpectrum spec_;
    PeakGroup precursor_peak_group_;
    Precursor precursor_peak_;
    String activation_method_;
    int scan_number_ = 0, precursor_scan_number_ = 0;
 
  };
}