OpenMS  3.0.0
OPXLHelper.h
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34 
35 #pragma once
36 
43 #include <numeric>
44 
45 namespace OpenMS
46 {
50  class OPENMS_DLLAPI OPXLHelper
51  {
52  public:
53 
59  {
60  bool operator() (const PeptideIdentification& a, const PeptideIdentification& b) const
61  {
62  if (!a.getHits().empty() && !b.getHits().empty())
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().empty())
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().empty())
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::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
EnzymaticDigestion.h
OpenMS::OPXLHelper::PeptideIDScoreComparator
A comparator for PeptideIdentifications that compares the scores in the first PeptideHit.
Definition: OPXLHelper.h:58
OpenMS::OPXLDataStructs::CrossLinkSpectrumMatch
The CrossLinkSpectrumMatch struct represents a PSM between a ProteinProteinCrossLink and a spectrum i...
Definition: OPXLDataStructs.h:112
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:66
OpenMS::DoubleList
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OPXLDataStructs.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
FASTAFile.h
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::OPXLHelper
The OPXLHelper class contains functions needed by OpenPepXL and OpenPepXLLF to reduce duplicated code...
Definition: OPXLHelper.h:50
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::ModifiedPeptideGenerator::MapToResidueType
Definition: ModifiedPeptideGenerator.h:58
ModifiedPeptideGenerator.h
ResidueModification.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h