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SpectrumAnnotator.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/KERNEL/MSSpectrum.h>
39 #include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
40 #include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
41
42 #include <OpenMS/KERNEL/Peak1D.h>
43
44 #include <OpenMS/METADATA/PeptideHit.h>
45 #include <OpenMS/METADATA/PeptideIdentification.h>
46
47 #include <boost/regex.hpp>
48
49 namespace OpenMS
50 {
60 class OPENMS_DLLAPI SpectrumAnnotator :
61 public DefaultParamHandler
62 {
63 public:
64
68 SpectrumAnnotator();
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:
119 bool basic_statistics_;
120 bool list_of_ions_matched_;
121 bool max_series_;
122 bool SN_statistics_;
123 bool precursor_statistics_;
124 unsigned topNmatch_fragmenterrors_;
125 bool fragmenterror_statistics_;
126 bool terminal_series_match_ratio_;
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
OpenMS::SpectrumAnnotator::precursor_statistics_
bool precursor_statistics_
Definition: SpectrumAnnotator.h:123
OpenMS::SpectrumAnnotator::seriesposition_regex_
static const boost::regex seriesposition_regex_
Definition: SpectrumAnnotator.h:131
OpenMS::SpectrumAnnotator::fragmenterror_statistics_
bool fragmenterror_statistics_
Definition: SpectrumAnnotator.h:125
OpenMS::SpectrumAnnotator::list_of_ions_matched_
bool list_of_ions_matched_
Definition: SpectrumAnnotator.h:120
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Peak1D.h
OpenMS::SpectrumAnnotator::SN_statistics_
bool SN_statistics_
Definition: SpectrumAnnotator.h:122
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
PeptideHit.h
OpenMS::SpectrumAnnotator::noloss_regex_
static const boost::regex noloss_regex_
Definition: SpectrumAnnotator.h:130
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::SpectrumAnnotator::nt_regex_
static const boost::regex nt_regex_
Definition: SpectrumAnnotator.h:128
OpenMS::SpectrumAnnotator::basic_statistics_
bool basic_statistics_
Definition: SpectrumAnnotator.h:119
DefaultParamHandler.h
MSSpectrum.h
OpenMS::SpectrumAnnotator
Annotates spectra from identifications and theoretical spectra or identifications from spectra and th...
Definition: SpectrumAnnotator.h:60
OpenMS::SpectrumAlignment
Aligns the peaks of two sorted spectra Method 1: Using a banded (width via &#39;tolerance&#39; parameter) ali...
Definition: SpectrumAlignment.h:67
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:67
OpenMS::SpectrumAnnotator::ct_regex_
static const boost::regex ct_regex_
Definition: SpectrumAnnotator.h:129
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
SpectrumAlignment.h
OpenMS::SpectrumAnnotator::topNmatch_fragmenterrors_
unsigned topNmatch_fragmenterrors_
Definition: SpectrumAnnotator.h:124
TheoreticalSpectrumGenerator.h
OpenMS::SpectrumAnnotator::terminal_series_match_ratio_
bool terminal_series_match_ratio_
Definition: SpectrumAnnotator.h:126
OpenMS::SpectrumAnnotator::max_series_
bool max_series_
Definition: SpectrumAnnotator.h:121