| OpenMS 2.5.0

OPXLHelper.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 2002-2020.
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: Eugen Netz $
32 // $Authors: Eugen Netz $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>
39 #include <OpenMS/CHEMISTRY/ResidueModification.h>
40 #include <OpenMS/FORMAT/FASTAFile.h>
41 #include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
42 #include <OpenMS/ANALYSIS/RNPXL/ModifiedPeptideGenerator.h>
43 #include <numeric>
44
45 namespace OpenMS
46 {
50 class OPENMS_DLLAPI OPXLHelper
51 {
52 public:
53
58 struct PeptideIDScoreComparator
59 {
60 bool operator() (const PeptideIdentification& a, const PeptideIdentification& b) const
61 {
62 if (a.getHits().size() > 0 && b.getHits().size() > 0)
63 {
64 return a.getHits()[0].getScore() < b.getHits()[0].getScore();
65 }
66 else
67 {
68 return false;
69 }
70 }
71 bool operator() (const PeptideIdentification& a, const double& b) const
72 {
73 if (a.getHits().size() > 0)
74 {
75 return a.getHits()[0].getScore() < b;
76 }
77 else
78 {
79 return false;
80 }
81 }
82 bool operator() (const double& a, const PeptideIdentification& b) const
83 {
84 if (b.getHits().size() > 0)
85 {
86 return a < b.getHits()[0].getScore();
87 }
88 else
89 {
90 return false;
91 }
92 }
93 };
94
112 static std::vector<OPXLDataStructs::XLPrecursor> enumerateCrossLinksAndMasses(const std::vector<OPXLDataStructs::AASeqWithMass>& peptides, double cross_link_mass_light, const DoubleList& cross_link_mass_mono_link, const StringList& cross_link_residue1, const StringList& cross_link_residue2, const std::vector< double >& spectrum_precursors, std::vector< int >& precursor_correction_positions, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm);
113
134 static std::vector<OPXLDataStructs::AASeqWithMass> digestDatabase(std::vector<FASTAFile::FASTAEntry> fasta_db,
135 EnzymaticDigestion digestor, Size min_peptide_length, StringList cross_link_residue1, StringList cross_link_residue2,
136 const ModifiedPeptideGenerator::MapToResidueType& fixed_modifications,
137 const ModifiedPeptideGenerator::MapToResidueType& variable_modifications,
138 Size max_variable_mods_per_peptide);
139
155 static std::vector <OPXLDataStructs::ProteinProteinCrossLink> buildCandidates(const std::vector< OPXLDataStructs::XLPrecursor > & candidates,
156 const std::vector< int > & precursor_corrections,
157 const std::vector< int > & precursor_correction_positions,
158 const std::vector<OPXLDataStructs::AASeqWithMass> & peptide_masses,
159 const StringList & cross_link_residue1,
160 const StringList & cross_link_residue2,
161 double cross_link_mass,
162 const DoubleList & cross_link_mass_mono_link,
163 const std::vector< double >& spectrum_precursor_vector,
164 const std::vector< double >& allowed_error_vector,
165 String cross_link_name);
166
179 static void buildFragmentAnnotations(std::vector<PeptideHit::PeakAnnotation> & frag_annotations, const std::vector< std::pair< Size, Size > > & matching, const PeakSpectrum & theoretical_spectrum, const PeakSpectrum & experiment_spectrum);
180
191 static void buildPeptideIDs(std::vector<PeptideIdentification> & peptide_ids, const std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > & top_csms_spectrum, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > & all_top_csms, Size all_top_csms_current_index, const PeakMap & spectra, Size scan_index, Size scan_index_heavy);
192
197 static void addProteinPositionMetaValues(std::vector< PeptideIdentification > & peptide_ids);
198
203 static void addXLTargetDecoyMV(std::vector< PeptideIdentification > & peptide_ids);
204
209 static void addBetaAccessions(std::vector< PeptideIdentification > & peptide_ids);
210
215 static void removeBetaPeptideHits(std::vector< PeptideIdentification > & peptide_ids);
216
221 static void addPercolatorFeatureList(ProteinIdentification& prot_id);
222
227 static void computeDeltaScores(std::vector< PeptideIdentification >& peptide_ids);
228
239 static std::vector< PeptideIdentification > combineTopRanksFromPairs(std::vector< PeptideIdentification > & peptide_ids, Size number_top_hits);
240
260 static std::vector <OPXLDataStructs::ProteinProteinCrossLink> collectPrecursorCandidates(const IntList& precursor_correction_steps,
261 double precursor_mass,
262 double precursor_mass_tolerance,
263 bool precursor_mass_tolerance_unit_ppm,
264 const std::vector<OPXLDataStructs::AASeqWithMass>& filtered_peptide_masses,
265 double cross_link_mass,
266 DoubleList cross_link_mass_mono_link,
267 StringList cross_link_residue1,
268 StringList cross_link_residue2,
269 String cross_link_name,
270 bool use_sequence_tags = false,
271 const std::vector<std::string>& tags = std::vector<std::string>());
272
280 static double computePrecursorError(OPXLDataStructs::CrossLinkSpectrumMatch csm, double precursor_mz, int precursor_charge);
281
289 static void isoPeakMeans(OPXLDataStructs::CrossLinkSpectrumMatch& csm, DataArrays::IntegerDataArray& num_iso_peaks_array, std::vector< std::pair< Size, Size > >& matched_spec_linear_alpha, std::vector< std::pair< Size, Size > >& matched_spec_linear_beta, std::vector< std::pair< Size, Size > >& matched_spec_xlinks_alpha, std::vector< std::pair< Size, Size > >& matched_spec_xlinks_beta);
290
297 static void filterPrecursorsByTags(std::vector <OPXLDataStructs::XLPrecursor>& candidates, std::vector< int >& precursor_correction_positions, const std::vector<std::string>& tags);
298 };
299 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch
The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum i...
Definition: OPXLDataStructs.h:112
OpenMS::ModifiedPeptideGenerator::MapToResidueType
Definition: ModifiedPeptideGenerator.h:58
OPXLDataStructs.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
StandardTypes.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::OPXLHelper
The OPXLHelper class contains functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code...
Definition: OPXLHelper.h:50
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
FASTAFile.h
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:62
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
OpenMS::OPXLHelper::PeptideIDScoreComparator
A comparator for PeptideIdentifications that compares the scores in the first PeptideHit.
Definition: OPXLHelper.h:58
ModifiedPeptideGenerator.h
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
EnzymaticDigestion.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ResidueModification.h