OpenMS
DeconvolvedSpectrum.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Kyowon Jeong, Jihyung Kim $
6 // $Authors: Kyowon Jeong, Jihyung Kim $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
14 #include <iomanip>
15 
16 namespace OpenMS
17 {
18  class PeakGroup;
19 
29  class OPENMS_DLLAPI DeconvolvedSpectrum
30  {
31  public:
33 
35  DeconvolvedSpectrum() = default;
36 
41  explicit DeconvolvedSpectrum(int scan_number);
42 
44  ~DeconvolvedSpectrum() = default;
45 
48 
50  DeconvolvedSpectrum(DeconvolvedSpectrum&& other) noexcept = default;
51 
53  DeconvolvedSpectrum& operator=(const DeconvolvedSpectrum& deconvolved_spectrum) = default;
54 
55 
61  MSSpectrum toSpectrum(int to_charge, uint min_ms_level, double tol = 10.0, bool retain_undeconvolved = false);
62 
65 
68 
70  int getPrecursorCharge() const;
71 
73  const Precursor& getPrecursor() const;
74 
78  double getCurrentMaxMass(double max_mass) const;
79 
83  double getCurrentMinMass(double min_mass) const;
84 
88  int getCurrentMaxAbsCharge(int max_abs_charge) const;
89 
91  int getScanNumber() const;
92 
95 
98 
100  void setPrecursor(const Precursor& precursor);
101 
103  void setPrecursorIntensity(float i);
104 
106  void setPrecursorScanNumber(int scan_number);
107 
110 
113 
115  void setOriginalSpectrum(const MSSpectrum& spec);
116 
118  void setPeakGroups(std::vector<PeakGroup>& x);
119 
121  std::vector<PeakGroup>::const_iterator begin() const noexcept;
122  std::vector<PeakGroup>::const_iterator end() const noexcept;
123 
124  std::vector<PeakGroup>::iterator begin() noexcept;
125  std::vector<PeakGroup>::iterator end() noexcept;
126 
127  const PeakGroup& operator[](Size i) const;
128  PeakGroup& operator[](Size i);
129  void push_back(const PeakGroup& pg);
130  Size size() const noexcept;
131  void clear();
132  void reserve(Size n);
133  bool empty() const;
134 
136  void sort();
138  void sortByQscore();
139 
140  private:
142  std::vector<PeakGroup> peak_groups_;
144  MSSpectrum spec_;
146  PeakGroup precursor_peak_group_;
148  Precursor precursor_peak_;
150  Precursor::ActivationMethod activation_method_ = Precursor::ActivationMethod::CID;
152  int scan_number_ = 0, precursor_scan_number_ = 0;
153  };
154 } // namespace OpenMS
A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups representing ...
Definition: DeconvolvedSpectrum.h:30
void setPrecursor(const Precursor &precursor)
set precursor for MSn for n>1
void setOriginalSpectrum(const MSSpectrum &spec)
original spectrum setter
const MSSpectrum & getOriginalSpectrum() const
original spectrum getter
std::vector< PeakGroup >::const_iterator begin() const noexcept
iterators and vector operators for std::vector<PeakGroup> peak_groups_ in this spectrum
void setPrecursorIntensity(float i)
set precursor peak intensity
FLASHDeconvHelperStructs::LogMzPeak LogMzPeak
Definition: DeconvolvedSpectrum.h:32
void setPeakGroups(std::vector< PeakGroup > &x)
set peak groups in this spectrum
DeconvolvedSpectrum(int scan_number)
Constructor for DeconvolvedSpectrum. Takes the spectrum and scan number calculated from outside.
int getPrecursorCharge() const
precursor charge getter (set in registerPrecursor)
~DeconvolvedSpectrum()=default
default destructor
int getCurrentMaxAbsCharge(int max_abs_charge) const
DeconvolvedSpectrum(DeconvolvedSpectrum &&other) noexcept=default
move constructor
double getCurrentMinMass(double min_mass) const
double getCurrentMaxMass(double max_mass) const
void setPrecursorPeakGroup(const PeakGroup &pg)
set precursor peakGroup
DeconvolvedSpectrum(const DeconvolvedSpectrum &)=default
copy constructor
void setPrecursorScanNumber(int scan_number)
set precursor scan number
MSSpectrum toSpectrum(int to_charge, uint min_ms_level, double tol=10.0, bool retain_undeconvolved=false)
int getScanNumber() const
get scan number of the original spectrum
PeakGroup & getPrecursorPeakGroup()
get precursor peak group for MSn (n>1) spectrum. It returns an empty peak group if no peak group is r...
const Precursor::ActivationMethod & getActivationMethod() const
get activation method
DeconvolvedSpectrum()=default
default constructor
const Precursor & getPrecursor() const
get precursor peak
void setActivationMethod(const Precursor::ActivationMethod &method)
set activation method
DeconvolvedSpectrum & operator=(const DeconvolvedSpectrum &deconvolved_spectrum)=default
assignment operator
int getPrecursorScanNumber() const
get precursor scan number - only if it is registered. Otherwise return 0
log transformed peak. After deconvolution, all necessary information from deconvolution such as charg...
Definition: FLASHDeconvHelperStructs.h:139
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
Class describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and ...
Definition: PeakGroup.h:26
Precursor meta information.
Definition: Precursor.h:35
ActivationMethod
Method of activation.
Definition: Precursor.h:59
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19