OpenMS  2.8.0
BasicProteinInferenceAlgorithm Member List

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

aggFromString_(const std::string &method_string) constBasicProteinInferenceAlgorithmprivate
aggFunFromEnum_(const BasicProteinInferenceAlgorithm::AggregationMethod &agg_method, bool higher_better) constBasicProteinInferenceAlgorithmprivate
aggregatePeptideScores_(SequenceToChargeToPSM &best_pep, std::vector< PeptideIdentification > &pep_ids, const String &overall_score_type, bool higher_better, const std::string &run_id) constBasicProteinInferenceAlgorithmprivate
AggregationMethod enum nameBasicProteinInferenceAlgorithm
BasicProteinInferenceAlgorithm()BasicProteinInferenceAlgorithm
check_defaults_DefaultParamHandlerprotected
checkCompat_(const String &score_type, const AggregationMethod &aggregation_method) constBasicProteinInferenceAlgorithmprivate
CMD enum valueProgressLogger
current_logger_ProgressLoggermutableprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
endProgress() constProgressLogger
error_name_DefaultParamHandlerprotected
fptr typedefBasicProteinInferenceAlgorithmprivate
getDefaults() constDefaultParamHandler
getInitScoreForAggMethod_(const AggregationMethod &aggregation_method, bool higher_better) constBasicProteinInferenceAlgorithmprivate
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
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
processRun_(std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &acc_to_protein_hitP_and_count, SequenceToChargeToPSM &best_pep, ProteinIdentification &prot_run, std::vector< PeptideIdentification > &pep_ids) constBasicProteinInferenceAlgorithmprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
run(std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids) constBasicProteinInferenceAlgorithm
run(std::vector< PeptideIdentification > &pep_ids, ProteinIdentification &prot_id) constBasicProteinInferenceAlgorithm
run(ConsensusMap &cmap, ProteinIdentification &prot_id, bool include_unassigned) constBasicProteinInferenceAlgorithm
SequenceToChargeToPSM typedefBasicProteinInferenceAlgorithm
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_()DefaultParamHandlerprotectedvirtual
updateProteinScores_(std::unordered_map< std::string, std::pair< ProteinHit *, Size >> &acc_to_protein_hitP_and_count, const SequenceToChargeToPSM &best_pep, bool pep_scores, bool higher_better) constBasicProteinInferenceAlgorithmprivate
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~ProgressLogger()ProgressLoggervirtual