OpenMS  2.6.0
SpectrumAnnotator.h
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31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer $
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34 
35 #pragma once
36 
41 
42 #include <OpenMS/KERNEL/Peak1D.h>
43 
46 
47 #include <boost/regex.hpp>
48 
49 namespace OpenMS
50 {
60  class OPENMS_DLLAPI SpectrumAnnotator :
61  public DefaultParamHandler
62  {
63  public:
64 
70 
72  SpectrumAnnotator(const SpectrumAnnotator & source);
73 
75  ~SpectrumAnnotator() override;
77 
79  SpectrumAnnotator & operator=(const SpectrumAnnotator & tsg);
80 
84 
97  void annotateMatches(PeakSpectrum &spec, const PeptideHit& ph, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const;
98 
111  void addIonMatchStatistics(PeptideIdentification& pi, MSSpectrum &spec, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const;
112 
114  void updateMembers_() override;
115 
117 
118  protected:
127 
128  static const boost::regex nt_regex_;
129  static const boost::regex ct_regex_;
130  static const boost::regex noloss_regex_;
131  static const boost::regex seriesposition_regex_;
132 
133  };
134 }
135 
DefaultParamHandler.h
OpenMS::SpectrumAnnotator::list_of_ions_matched_
bool list_of_ions_matched_
Definition: SpectrumAnnotator.h:120
OpenMS::SpectrumAnnotator::ct_regex_
static const boost::regex ct_regex_
Definition: SpectrumAnnotator.h:129
OpenMS::SpectrumAnnotator::noloss_regex_
static const boost::regex noloss_regex_
Definition: SpectrumAnnotator.h:130
Peak1D.h
OpenMS::SpectrumAnnotator::max_series_
bool max_series_
Definition: SpectrumAnnotator.h:121
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::SpectrumAnnotator::SN_statistics_
bool SN_statistics_
Definition: SpectrumAnnotator.h:122
OpenMS::SpectrumAnnotator::fragmenterror_statistics_
bool fragmenterror_statistics_
Definition: SpectrumAnnotator.h:125
OpenMS::SpectrumAlignment
Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) ali...
Definition: SpectrumAlignment.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
PeptideHit.h
OpenMS::SpectrumAnnotator::nt_regex_
static const boost::regex nt_regex_
Definition: SpectrumAnnotator.h:128
OpenMS::SpectrumAnnotator::terminal_series_match_ratio_
bool terminal_series_match_ratio_
Definition: SpectrumAnnotator.h:126
OpenMS::SpectrumAnnotator::seriesposition_regex_
static const boost::regex seriesposition_regex_
Definition: SpectrumAnnotator.h:131
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:68
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::SpectrumAnnotator::basic_statistics_
bool basic_statistics_
Definition: SpectrumAnnotator.h:119
TheoreticalSpectrumGenerator.h
OpenMS::SpectrumAnnotator::topNmatch_fragmenterrors_
unsigned topNmatch_fragmenterrors_
Definition: SpectrumAnnotator.h:124
SpectrumAlignment.h
PeptideIdentification.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::SpectrumAnnotator::precursor_statistics_
bool precursor_statistics_
Definition: SpectrumAnnotator.h:123
OpenMS::SpectrumAnnotator
Annotates spectra from identifications and theoretical spectra or identifications from spectra and th...
Definition: SpectrumAnnotator.h:60
MSSpectrum.h
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55