OpenMS  3.0.0
SpectrumAnnotator.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2022.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: Mathias Walzer $
33 // --------------------------------------------------------------------------
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:47
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:63
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:66
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