AddressLookup typedef | IdentificationData | |
addScore(QueryMatchRef match_ref, ScoreTypeRef score_ref, double value) | IdentificationData | |
AppliedProcessingStep typedef | IdentificationData | |
AppliedProcessingSteps typedef | IdentificationData | |
calculateCoverages(bool check_molecule_length=false) | IdentificationData | |
checkAppliedProcessingSteps_(const AppliedProcessingSteps &steps_and_scores) const | IdentificationData | protected |
checkParentMatches_(const ParentMatches &matches, MoleculeType expected_type) const | IdentificationData | protected |
checkScoreTypes_(const std::map< ScoreTypeRef, double > &scores) const | IdentificationData | protected |
cleanup(bool require_query_match=true, bool require_identified_sequence=true, bool require_parent_match=true, bool require_parent_group=false, bool require_match_group=false) | IdentificationData | |
clearCurrentProcessingStep() | IdentificationData | |
clearMetaInfo() | MetaInfoInterface | |
createIfNotExists_() | MetaInfoInterface | inlineprotected |
current_step_ref_ | IdentificationData | protected |
data_queries_ | IdentificationData | protected |
data_query_lookup_ | IdentificationData | protected |
DataProcessingSoftware typedef | IdentificationData | |
DataProcessingSoftwares typedef | IdentificationData | |
DataProcessingStep typedef | IdentificationData | |
DataProcessingSteps typedef | IdentificationData | |
DataQueries typedef | IdentificationData | |
DataQuery typedef | IdentificationData | |
DataQueryRef typedef | IdentificationData | |
db_search_params_ | IdentificationData | protected |
db_search_steps_ | IdentificationData | protected |
DBSearchParam typedef | IdentificationData | |
DBSearchParams typedef | IdentificationData | |
DBSearchSteps typedef | IdentificationData | |
findScoreType(const String &score_name) const | IdentificationData | |
getBestMatchPerQuery(ScoreTypeRef score_ref) const | IdentificationData | |
getCurrentProcessingStep() | IdentificationData | |
getDataProcessingSoftwares() const | IdentificationData | inline |
getDataProcessingSteps() const | IdentificationData | inline |
getDataQueries() const | IdentificationData | inline |
getDBSearchParams() const | IdentificationData | inline |
getDBSearchSteps() const | IdentificationData | inline |
getIdentifiedCompounds() const | IdentificationData | inline |
getIdentifiedOligos() const | IdentificationData | inline |
getIdentifiedPeptides() const | IdentificationData | inline |
getInputFiles() const | IdentificationData | inline |
getKeys(std::vector< String > &keys) const | MetaInfoInterface | |
getKeys(std::vector< UInt > &keys) const | MetaInfoInterface | |
getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const | MetaInfoInterface | |
getMetaValue(UInt index, const DataValue &default_value=DataValue::EMPTY) const | MetaInfoInterface | |
getMoleculeQueryMatches() const | IdentificationData | inline |
getParentMoleculeGroupings() const | IdentificationData | inline |
getParentMolecules() const | IdentificationData | inline |
getQueryMatchGroups() const | IdentificationData | inline |
getScoreTypes() const | IdentificationData | inline |
IdentificationData() | IdentificationData | inline |
IdentificationData(const IdentificationData &other)=delete | IdentificationData | |
IdentificationData(IdentificationData &&other) | IdentificationData | inline |
identified_compound_lookup_ | IdentificationData | protected |
identified_compounds_ | IdentificationData | protected |
identified_oligo_lookup_ | IdentificationData | protected |
identified_oligos_ | IdentificationData | protected |
identified_peptide_lookup_ | IdentificationData | protected |
identified_peptides_ | IdentificationData | protected |
IdentifiedCompound typedef | IdentificationData | |
IdentifiedCompoundRef typedef | IdentificationData | |
IdentifiedCompounds typedef | IdentificationData | |
IdentifiedMoleculeRef typedef | IdentificationData | |
IdentifiedOligo typedef | IdentificationData | |
IdentifiedOligoRef typedef | IdentificationData | |
IdentifiedOligos typedef | IdentificationData | |
IdentifiedPeptide typedef | IdentificationData | |
IdentifiedPeptideRef typedef | IdentificationData | |
IdentifiedPeptides typedef | IdentificationData | |
IDFilter class | IdentificationData | friend |
input_files_ | IdentificationData | protected |
InputFileRef typedef | IdentificationData | |
InputFiles typedef | IdentificationData | |
insertIntoMultiIndex_(ContainerType &container, const ElementType &element) | IdentificationData | inlineprotected |
insertIntoMultiIndex_(ContainerType &container, const ElementType &element, AddressLookup &lookup) | IdentificationData | inlineprotected |
isBetterScore(double first, double second, bool higher_better) | IdentificationData | inlinestatic |
isMetaEmpty() const | MetaInfoInterface | |
isValidHashedReference_(RefType ref, const AddressLookup &lookup) | IdentificationData | inlineprotectedstatic |
isValidReference_(RefType ref, ContainerType &container) | IdentificationData | inlineprotectedstatic |
MassType typedef | IdentificationData | |
MatchGroupRef typedef | IdentificationData | |
meta_ | MetaInfoInterface | protected |
MetaInfoInterface() | MetaInfoInterface | |
MetaInfoInterface(const MetaInfoInterface &rhs) | MetaInfoInterface | |
MetaInfoInterface(MetaInfoInterface &&) noexcept | MetaInfoInterface | |
metaRegistry() | MetaInfoInterface | static |
metaValueExists(const String &name) const | MetaInfoInterface | |
metaValueExists(UInt index) const | MetaInfoInterface | |
MoleculeParentMatch typedef | IdentificationData | |
MoleculeQueryMatch typedef | IdentificationData | |
MoleculeQueryMatches typedef | IdentificationData | |
MoleculeType typedef | IdentificationData | |
operator!=(const MetaInfoInterface &rhs) const | MetaInfoInterface | |
operator=(const MetaInfoInterface &rhs) | MetaInfoInterface | |
operator=(MetaInfoInterface &&) noexcept | MetaInfoInterface | |
operator==(const MetaInfoInterface &rhs) const | MetaInfoInterface | |
parent_molecule_groupings_ | IdentificationData | protected |
parent_molecule_lookup_ | IdentificationData | protected |
parent_molecules_ | IdentificationData | protected |
ParentGroupRef typedef | IdentificationData | |
ParentMatches typedef | IdentificationData | |
ParentMolecule typedef | IdentificationData | |
ParentMoleculeGroup typedef | IdentificationData | |
ParentMoleculeGrouping typedef | IdentificationData | |
ParentMoleculeGroupings typedef | IdentificationData | |
ParentMoleculeGroups typedef | IdentificationData | |
ParentMoleculeRef typedef | IdentificationData | |
ParentMolecules typedef | IdentificationData | |
PeakAnnotations typedef | IdentificationData | |
processing_softwares_ | IdentificationData | protected |
processing_steps_ | IdentificationData | protected |
ProcessingSoftwareRef typedef | IdentificationData | |
ProcessingStepRef typedef | IdentificationData | |
query_match_groups_ | IdentificationData | protected |
query_match_lookup_ | IdentificationData | protected |
query_matches_ | IdentificationData | protected |
QueryMatchGroup typedef | IdentificationData | |
QueryMatchGroups typedef | IdentificationData | |
QueryMatchRef typedef | IdentificationData | |
registerDataProcessingSoftware(const DataProcessingSoftware &software) | IdentificationData | |
registerDataProcessingStep(const DataProcessingStep &step) | IdentificationData | |
registerDataProcessingStep(const DataProcessingStep &step, SearchParamRef search_ref) | IdentificationData | |
registerDataQuery(const DataQuery &query) | IdentificationData | |
registerDBSearchParam(const DBSearchParam ¶m) | IdentificationData | |
registerIdentifiedCompound(const IdentifiedCompound &compound) | IdentificationData | |
registerIdentifiedOligo(const IdentifiedOligo &oligo) | IdentificationData | |
registerIdentifiedPeptide(const IdentifiedPeptide &peptide) | IdentificationData | |
registerInputFile(const String &file) | IdentificationData | |
registerMoleculeQueryMatch(const MoleculeQueryMatch &match) | IdentificationData | |
registerParentMolecule(const ParentMolecule &parent) | IdentificationData | |
registerParentMoleculeGrouping(const ParentMoleculeGrouping &grouping) | IdentificationData | |
registerQueryMatchGroup(const QueryMatchGroup &group) | IdentificationData | |
registerScoreType(const ScoreType &score) | IdentificationData | |
removeFromSetIf_(ContainerType &container, PredicateType predicate) | IdentificationData | inlineprotectedstatic |
removeFromSetIfNotHashed_(ContainerType &container, const AddressLookup &lookup) | IdentificationData | inlineprotectedstatic |
removeMetaValue(const String &name) | MetaInfoInterface | |
removeMetaValue(UInt index) | MetaInfoInterface | |
score_types_ | IdentificationData | protected |
ScoreType typedef | IdentificationData | |
ScoreTypeRef typedef | IdentificationData | |
ScoreTypes typedef | IdentificationData | |
SearchParamRef typedef | IdentificationData | |
setCurrentProcessingStep(ProcessingStepRef step_ref) | IdentificationData | |
setMetaValue(const String &name, const DataValue &value) | MetaInfoInterface | |
setMetaValue(UInt index, const DataValue &value) | MetaInfoInterface | |
updateAddressLookup_(const ContainerType &container, AddressLookup &lookup) | IdentificationData | inlineprotectedstatic |
~MetaInfoInterface() | MetaInfoInterface | |