OpenMS
SpectrumAnnotator.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: Mathias Walzer $
6 // $Authors: Mathias Walzer $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
15 
16 #include <OpenMS/KERNEL/Peak1D.h>
17 
20 
21 #include <boost/regex.hpp>
22 
23 namespace OpenMS
24 {
34  class OPENMS_DLLAPI SpectrumAnnotator :
35  public DefaultParamHandler
36  {
37  public:
38 
44 
47 
49  ~SpectrumAnnotator() override;
51 
54 
58 
70  void annotateMatches(PeakSpectrum &spec, const PeptideHit& ph, const TheoreticalSpectrumGenerator& tg, const SpectrumAlignment& sa) const;
71 
84 
86  void updateMembers_() override;
87 
89 
90  protected:
99 
100  static const boost::regex nt_regex_;
101  static const boost::regex ct_regex_;
102  static const boost::regex noloss_regex_;
103  static const boost::regex seriesposition_regex_;
104  };
105 }
106 
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
Representation of a peptide hit.
Definition: PeptideHit.h:31
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:39
Aligns the peaks of two sorted spectra Method 1: Using a banded (width via 'tolerance' parameter) ali...
Definition: SpectrumAlignment.h:43
Annotates spectra from identifications and theoretical spectra or identifications from spectra and th...
Definition: SpectrumAnnotator.h:36
unsigned topNmatch_fragmenterrors_
Definition: SpectrumAnnotator.h:96
void annotateMatches(PeakSpectrum &spec, const PeptideHit &ph, const TheoreticalSpectrumGenerator &tg, const SpectrumAlignment &sa) const
Adds ion match annotation to the spec input spectrum.
static const boost::regex noloss_regex_
Definition: SpectrumAnnotator.h:102
bool fragmenterror_statistics_
Definition: SpectrumAnnotator.h:97
SpectrumAnnotator(const SpectrumAnnotator &source)
copy constructor
bool basic_statistics_
Definition: SpectrumAnnotator.h:91
static const boost::regex seriesposition_regex_
Definition: SpectrumAnnotator.h:103
void addIonMatchStatistics(PeptideIdentification &pi, MSSpectrum &spec, const TheoreticalSpectrumGenerator &tg, const SpectrumAlignment &sa) const
Adds ion match statistics to pi PeptideIdentifcation.
~SpectrumAnnotator() override
destructor
static const boost::regex nt_regex_
Definition: SpectrumAnnotator.h:100
bool precursor_statistics_
Definition: SpectrumAnnotator.h:95
void updateMembers_() override
overwrite
SpectrumAnnotator & operator=(const SpectrumAnnotator &tsg)
assignment operator
bool terminal_series_match_ratio_
Definition: SpectrumAnnotator.h:98
bool max_series_
Definition: SpectrumAnnotator.h:93
SpectrumAnnotator()
default constructor
bool list_of_ions_matched_
Definition: SpectrumAnnotator.h:92
static const boost::regex ct_regex_
Definition: SpectrumAnnotator.h:101
bool SN_statistics_
Definition: SpectrumAnnotator.h:94
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:45
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19