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