OpenMS  2.8.0
AccurateMassSearchEngine Member List

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

AccurateMassSearchEngine()AccurateMassSearchEngine
addMatchesToID_(IdentificationData &id, const std::vector< AccurateMassSearchResult > &amr, const IdentificationData::InputFileRef &file_ref, const IdentificationData::ScoreTypeRef &mass_error_ppm_score_ref, const IdentificationData::ScoreTypeRef &mass_error_Da_score_ref, const IdentificationData::ProcessingStepRef &step_ref, BaseFeature &f) constAccurateMassSearchEngineprivate
annotate_(const std::vector< AccurateMassSearchResult > &, BaseFeature &) constAccurateMassSearchEngineprivate
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
computeCosineSim_(const std::vector< double > &x, const std::vector< double > &y) constAccurateMassSearchEngineprivate
computeIsotopePatternSimilarity_(const Feature &feat, const EmpiricalFormula &form) constAccurateMassSearchEngineprivate
current_logger_ProgressLoggermutableprotected
database_location_AccurateMassSearchEngineprivate
database_name_AccurateMassSearchEngineprivate
database_version_AccurateMassSearchEngineprivate
db_mapping_file_AccurateMassSearchEngineprivate
db_struct_file_AccurateMassSearchEngineprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
endProgress() constProgressLogger
error_name_DefaultParamHandlerprotected
exportMzTab_(const QueryResultsTable &overall_results, const Size number_of_maps, MzTab &mztab_out, const std::vector< String > &file_locations) constAccurateMassSearchEngineprivate
exportMzTabM_(const FeatureMap &fmap, MzTabM &mztabm_out) constAccurateMassSearchEngineprivate
extractQueryResults_(const Feature &feature, const Size &feature_index, const String &ion_mode_internal, Size &dummy_count) constAccurateMassSearchEngineprivate
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
hmdb_properties_mapping_AccurateMassSearchEngineprivate
HMDBPropsMapping typedefAccurateMassSearchEngineprivate
init()AccurateMassSearchEngine
ion_mode_AccurateMassSearchEngineprivate
is_initialized_AccurateMassSearchEngineprivate
iso_similarity_AccurateMassSearchEngineprivate
keep_unidentified_masses_AccurateMassSearchEngineprivate
last_invoke_ProgressLoggermutableprotected
legacyID_AccurateMassSearchEngineprivate
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
mass_error_unit_AccurateMassSearchEngineprivate
mass_error_value_AccurateMassSearchEngineprivate
mass_mappings_AccurateMassSearchEngineprivate
MassIDMapping typedefAccurateMassSearchEngineprivate
neg_adducts_AccurateMassSearchEngineprivate
neg_adducts_fname_AccurateMassSearchEngineprivate
nextProgress() constProgressLogger
NONE enum valueProgressLogger
OpenMS::operator=(const DefaultParamHandler &rhs)DefaultParamHandlervirtual
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
parseAdductsFile_(const String &filename, std::vector< AdductInfo > &result)AccurateMassSearchEngineprivate
parseMappingFile_(const StringList &)AccurateMassSearchEngineprivate
parseStructMappingFile_(const StringList &)AccurateMassSearchEngineprivate
pos_adducts_AccurateMassSearchEngineprivate
pos_adducts_fname_AccurateMassSearchEngineprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
queryByConsensusFeature(const ConsensusFeature &cfeat, const Size &cf_index, const Size &number_of_maps, const String &ion_mode, std::vector< AccurateMassSearchResult > &results) constAccurateMassSearchEngine
queryByFeature(const Feature &feature, const Size &feature_index, const String &ion_mode, std::vector< AccurateMassSearchResult > &results) constAccurateMassSearchEngine
queryByMZ(const double &observed_mz, const Int &observed_charge, const String &ion_mode, std::vector< AccurateMassSearchResult > &results, const EmpiricalFormula &observed_adduct=EmpiricalFormula()) constAccurateMassSearchEngine
QueryResultsTable typedefAccurateMassSearchEngineprivate
recursion_depth_ProgressLoggerprotectedstatic
resolveAutoMode_(const MAPTYPE &map) constAccurateMassSearchEngineinlineprivate
run(FeatureMap &, MzTab &) constAccurateMassSearchEngine
run(FeatureMap &, MzTabM &) constAccurateMassSearchEngine
run(ConsensusMap &, MzTab &) constAccurateMassSearchEngine
search_engine_identifierAccurateMassSearchEnginestatic
searchMass_(double neutral_query_mass, double diff_mass, std::pair< Size, Size > &hit_indices) constAccurateMassSearchEngineprivate
setLogType(LogType type) constProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
subsections_DefaultParamHandlerprotected
type_ProgressLoggermutableprotected
updateMembers_() overrideAccurateMassSearchEngineprotectedvirtual
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~AccurateMassSearchEngine() overrideAccurateMassSearchEngine
~DefaultParamHandler()DefaultParamHandlervirtual
~ProgressLogger()ProgressLoggervirtual
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