65 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);
72 static std::vector<ResidueModification> getModificationsFromStringList(
StringList modNames);
94 static std::vector<OPXLDataStructs::AASeqWithMass> digestDatabase(std::vector<FASTAFile::FASTAEntry> fasta_db,
EnzymaticDigestion digestor,
Size min_peptide_length,
StringList cross_link_residue1,
StringList cross_link_residue2, std::vector<ResidueModification> fixed_modifications, std::vector<ResidueModification> variable_modifications,
Size max_variable_mods_per_peptide);
111 static std::vector <OPXLDataStructs::ProteinProteinCrossLink> buildCandidates(
const std::vector< OPXLDataStructs::XLPrecursor > & candidates,
112 const std::vector< int > & precursor_corrections,
113 const std::vector< int > & precursor_correction_positions,
114 const std::vector<OPXLDataStructs::AASeqWithMass> & peptide_masses,
117 double cross_link_mass,
119 const std::vector< double >& spectrum_precursor_vector,
120 const std::vector< double >& allowed_error_vector,
135 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);
147 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);
153 static void addProteinPositionMetaValues(std::vector< PeptideIdentification > & peptide_ids);
159 static bool filter_and_add_candidate(std::vector<OPXLDataStructs::XLPrecursor>& mass_to_candidates,
const std::vector< double >& spectrum_precursors, std::vector< int >& precursor_correction_positions,
bool precursor_mass_tolerance_unit_ppm,
double precursor_mass_tolerance,
OPXLDataStructs::XLPrecursor precursor);