OpenMS  2.8.0
IDFilter Member List

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

annotateBestPerPeptide(std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
annotateBestPerPeptidePerRun(MapType &prot_and_pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
annotateBestPerPeptidePerRun(const std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
annotateBestPerPeptidePerRunWithData(RunToSequenceToChargeToPepHitP &best_peps_per_run, std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
annotateBestPerPeptideWithData(SequenceToChargeToPepHitP &best_pep, PeptideIdentification &pep, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
ChargeToPepHitP typedefIDFilter
countHits(const std::vector< IdentificationType > &ids)IDFilterinlinestatic
extractPeptideSequences(const std::vector< PeptideIdentification > &peptides, std::set< String > &sequences, bool ignore_mods=false)IDFilterstatic
extractUnassignedProteins(ConsensusMap &cmap)IDFilterstatic
filterGroupsByScore(std::vector< ProteinIdentification::ProteinGroup > &grps, double threshold_score, bool higher_better)IDFilterstatic
filterHitsByRank(std::vector< IdentificationType > &ids, Size min_rank, Size max_rank)IDFilterinlinestatic
filterHitsByScore(std::vector< IdentificationType > &ids, double threshold_score)IDFilterinlinestatic
filterHitsByScore(IdentificationType &id, double threshold_score)IDFilterinlinestatic
filterHitsByScore(PeakMap &experiment, double peptide_threshold_score, double protein_threshold_score)IDFilterinlinestatic
filterObservationMatchesByFunctor(IdentificationData &id_data, PredicateType &&func, bool cleanup_affected=false)IDFilterinlinestatic
filterObservationMatchesByScore(IdentificationData &id_data, IdentificationData::ScoreTypeRef score_ref, double cutoff)IDFilterstatic
FilterPeptideEvidences(EvidenceFilter &filter, std::vector< PeptideIdentification > &peptides)IDFilterinlinestatic
filterPeptideEvidences(Filter &filter, std::vector< PeptideIdentification > &peptides)IDFilterstatic
filterPeptidesByCharge(std::vector< PeptideIdentification > &peptides, Int min_charge, Int max_charge)IDFilterstatic
filterPeptidesByLength(std::vector< PeptideIdentification > &peptides, Size min_length, Size max_length=UINT_MAX)IDFilterstatic
filterPeptidesByMZ(std::vector< PeptideIdentification > &peptides, double min_mz, double max_mz)IDFilterstatic
filterPeptidesByMZError(std::vector< PeptideIdentification > &peptides, double mass_error, bool unit_ppm)IDFilterstatic
filterPeptidesByRT(std::vector< PeptideIdentification > &peptides, double min_rt, double max_rt)IDFilterstatic
filterPeptidesByRTPredictPValue(std::vector< PeptideIdentification > &peptides, const String &metavalue_key, double threshold=0.05)IDFilterstatic
getBestHit(const std::vector< IdentificationType > &identifications, bool assume_sorted, typename IdentificationType::HitType &best_hit)IDFilterinlinestatic
IDFilter()=defaultIDFilter
keepBestMatchPerObservation(IdentificationData &id_data, IdentificationData::ScoreTypeRef score_ref)IDFilterstatic
keepBestPeptideHits(std::vector< PeptideIdentification > &peptides, bool strict=false)IDFilterstatic
keepBestPerPeptide(std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
keepBestPerPeptidePerRun(std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
keepBestPerPeptidePerRun(MapType &prot_and_pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)IDFilterinlinestatic
keepHitsMatchingProteins(std::vector< IdentificationType > &ids, const std::set< String > &accessions)IDFilterinlinestatic
keepHitsMatchingProteins(PeakMap &experiment, const std::vector< FASTAFile::FASTAEntry > &proteins)IDFilterinlinestatic
keepMatchingItems(Container &items, const Predicate &pred)IDFilterinlinestatic
keepMatchingItemsUnroll(IDContainer &items, const Predicate &pred)IDFilterinlinestatic
keepMatchingPeptideHits(MapType &prot_and_pep_ids, Predicate &pred)IDFilterinlinestatic
keepNBestHits(std::vector< IdentificationType > &ids, Size n)IDFilterinlinestatic
keepNBestHits(PeakMap &experiment, Size n)IDFilterinlinestatic
keepNBestPeptideHits(MapType &map, Size n)IDFilterinlinestatic
keepNBestSpectra(std::vector< PeptideIdentification > &peptides, Size n)IDFilterstatic
keepPeptidesWithMatchingModifications(std::vector< PeptideIdentification > &peptides, const std::set< String > &modifications)IDFilterstatic
keepPeptidesWithMatchingSequences(std::vector< PeptideIdentification > &peptides, const std::vector< PeptideIdentification > &good_peptides, bool ignore_mods=false)IDFilterstatic
keepUniquePeptidesPerProtein(std::vector< PeptideIdentification > &peptides)IDFilterstatic
moveMatchingItems(Container &items, const Predicate &pred, Container &target)IDFilterinlinestatic
removeDecoyHits(std::vector< IdentificationType > &ids)IDFilterinlinestatic
removeDecoys(IdentificationData &id_data)IDFilterstatic
removeDuplicatePeptideHits(std::vector< PeptideIdentification > &peptides, bool seq_only=false)IDFilterstatic
removeEmptyIdentifications(std::vector< IdentificationType > &ids)IDFilterinlinestatic
removeEmptyIdentifications(MapType &prot_and_pep_ids)IDFilterinlinestatic
removeHitsMatchingProteins(std::vector< IdentificationType > &ids, const std::set< String > accessions)IDFilterinlinestatic
removeMatchingItems(Container &items, const Predicate &pred)IDFilterinlinestatic
removeMatchingItemsUnroll(IDContainer &items, const Predicate &pred)IDFilterinlinestatic
removeMatchingPeptideHits(MapType &prot_and_pep_ids, Predicate &pred)IDFilterinlinestatic
removeMatchingPeptideIdentifications(MapType &prot_and_pep_ids, Predicate &pred)IDFilterinlinestatic
removePeptidesWithMatchingModifications(std::vector< PeptideIdentification > &peptides, const std::set< String > &modifications)IDFilterstatic
removePeptidesWithMatchingRegEx(std::vector< PeptideIdentification > &peptides, const String &regex)IDFilterstatic
removePeptidesWithMatchingSequences(std::vector< PeptideIdentification > &peptides, const std::vector< PeptideIdentification > &bad_peptides, bool ignore_mods=false)IDFilterstatic
removeUngroupedProteins(const std::vector< ProteinIdentification::ProteinGroup > &groups, std::vector< ProteinHit > &hits)IDFilterstatic
removeUnreferencedProteins(ConsensusMap &cmap, bool include_unassigned)IDFilterstatic
removeUnreferencedProteins(std::vector< ProteinIdentification > &proteins, const std::vector< PeptideIdentification > &peptides)IDFilterstatic
removeUnreferencedProteins(ProteinIdentification &proteins, const std::vector< PeptideIdentification > &peptides)IDFilterstatic
RunToSequenceToChargeToPepHitP typedefIDFilter
SequenceToChargeToPepHitP typedefIDFilter
updateHitRanks(std::vector< IdentificationType > &ids)IDFilterinlinestatic
updateProteinGroups(std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &hits)IDFilterstatic
updateProteinReferences(std::vector< PeptideIdentification > &peptides, const std::vector< ProteinIdentification > &proteins, bool remove_peptides_without_reference=false)IDFilterstatic
updateProteinReferences(ConsensusMap &cmap, bool remove_peptides_without_reference=false)IDFilterstatic
updateProteinReferences(ConsensusMap &cmap, const ProteinIdentification &ref_run, bool remove_peptides_without_reference=false)IDFilterstatic
~IDFilter()=defaultIDFiltervirtual