| OpenMS 2.5.0

OPXLHelper Member List

This is the complete list of members for OPXLHelper, including all inherited members.

addBetaAccessions(std::vector< PeptideIdentification > &peptide_ids) | OPXLHelper | static
addPercolatorFeatureList(ProteinIdentification &prot_id) | OPXLHelper | static
addProteinPositionMetaValues(std::vector< PeptideIdentification > &peptide_ids) | OPXLHelper | static
addXLTargetDecoyMV(std::vector< PeptideIdentification > &peptide_ids) | OPXLHelper | static
buildCandidates(const std::vector< OPXLDataStructs::XLPrecursor > &candidates, const std::vector< int > &precursor_corrections, const std::vector< int > &precursor_correction_positions, const std::vector< OPXLDataStructs::AASeqWithMass > &peptide_masses, const StringList &cross_link_residue1, const StringList &cross_link_residue2, double cross_link_mass, const DoubleList &cross_link_mass_mono_link, const std::vector< double > &spectrum_precursor_vector, const std::vector< double > &allowed_error_vector, String cross_link_name) | OPXLHelper | static
buildFragmentAnnotations(std::vector< PeptideHit::PeakAnnotation > &frag_annotations, const std::vector< std::pair< Size, Size > > &matching, const PeakSpectrum &theoretical_spectrum, const PeakSpectrum &experiment_spectrum) | OPXLHelper | static
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) | OPXLHelper | static
collectPrecursorCandidates(const IntList &precursor_correction_steps, double precursor_mass, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, const std::vector< OPXLDataStructs::AASeqWithMass > &filtered_peptide_masses, double cross_link_mass, DoubleList cross_link_mass_mono_link, StringList cross_link_residue1, StringList cross_link_residue2, String cross_link_name, bool use_sequence_tags=false, const std::vector< std::string > &tags=std::vector< std::string >()) | OPXLHelper | static
combineTopRanksFromPairs(std::vector< PeptideIdentification > &peptide_ids, Size number_top_hits) | OPXLHelper | static
computeDeltaScores(std::vector< PeptideIdentification > &peptide_ids) | OPXLHelper | static
computePrecursorError(OPXLDataStructs::CrossLinkSpectrumMatch csm, double precursor_mz, int precursor_charge) | OPXLHelper | static
digestDatabase(std::vector< FASTAFile::FASTAEntry > fasta_db, EnzymaticDigestion digestor, Size min_peptide_length, StringList cross_link_residue1, StringList cross_link_residue2, const ModifiedPeptideGenerator::MapToResidueType &fixed_modifications, const ModifiedPeptideGenerator::MapToResidueType &variable_modifications, Size max_variable_mods_per_peptide) | OPXLHelper | static
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) | OPXLHelper | static
filterPrecursorsByTags(std::vector< OPXLDataStructs::XLPrecursor > &candidates, std::vector< int > &precursor_correction_positions, const std::vector< std::string > &tags) | OPXLHelper | static
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) | OPXLHelper | static
removeBetaPeptideHits(std::vector< PeptideIdentification > &peptide_ids) | OPXLHelper | static