75 return a.
getHits()[0].getScore() < b;
86 return a < b.
getHits()[0].getScore();
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);
134 static std::vector<OPXLDataStructs::AASeqWithMass> digestDatabase(std::vector<FASTAFile::FASTAEntry> fasta_db,
138 Size max_variable_mods_per_peptide);
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,
161 double cross_link_mass,
163 const std::vector< double >& spectrum_precursor_vector,
164 const std::vector< double >& allowed_error_vector,
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);
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);
197 static void addProteinPositionMetaValues(std::vector< PeptideIdentification > & peptide_ids);
203 static void addXLTargetDecoyMV(std::vector< PeptideIdentification > & peptide_ids);
209 static void addBetaAccessions(std::vector< PeptideIdentification > & peptide_ids);
215 static void removeBetaPeptideHits(std::vector< PeptideIdentification > & peptide_ids);
227 static void computeDeltaScores(std::vector< PeptideIdentification >& peptide_ids);
239 static std::vector< PeptideIdentification > combineTopRanksFromPairs(std::vector< PeptideIdentification > & peptide_ids,
Size number_top_hits);
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,
270 bool use_sequence_tags =
false,
271 const std::vector<std::string>& tags = std::vector<std::string>());
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);
297 static void filterPrecursorsByTags(std::vector <OPXLDataStructs::XLPrecursor>& candidates, std::vector< int >& precursor_correction_positions,
const std::vector<std::string>& tags);