OpenMS
XFDRAlgorithm Member List

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

arg_binsize_XFDRAlgorithmprivate
arg_maxborder_XFDRAlgorithmprivate
arg_minborder_XFDRAlgorithmprivate
arg_mindeltas_XFDRAlgorithmprivate
arg_minionsmatched_XFDRAlgorithmprivate
arg_minscore_XFDRAlgorithmprivate
arg_no_qvalues_XFDRAlgorithmprivate
arg_uniquex_XFDRAlgorithmprivate
assignTypes_(PeptideHit &pep_id, StringList &types)XFDRAlgorithmprivatestatic
calc_qfdr_(const std::vector< double > &fdr, std::vector< double > &qfdr)XFDRAlgorithmprivatestatic
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
cross_link_classes_XFDRAlgorithmprivate
crosslink_class_decoys_XFDRAlgorithmprivatestatic
crosslink_class_fulldecoysinterlinks_XFDRAlgorithmprivatestatic
crosslink_class_fulldecoysintralinks_XFDRAlgorithmprivatestatic
crosslink_class_hybriddecoysinterlinks_XFDRAlgorithmprivatestatic
crosslink_class_hybriddecoysintralinks_XFDRAlgorithmprivatestatic
crosslink_class_interdecoys_XFDRAlgorithmprivatestatic
crosslink_class_interlinks_XFDRAlgorithmprivatestatic
crosslink_class_intradecoys_XFDRAlgorithmprivatestatic
crosslink_class_intralinks_XFDRAlgorithmprivatestatic
crosslink_class_monodecoys_XFDRAlgorithmprivatestatic
crosslink_class_monolinks_XFDRAlgorithmprivatestatic
crosslink_class_targets_XFDRAlgorithmprivatestatic
current_logger_ProgressLoggermutableprotected
decoy_string_XFDRAlgorithmprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
endProgress(UInt64 bytes_processed=0) constProgressLogger
error_name_DefaultParamHandlerprotected
EXECUTION_OK enum valueXFDRAlgorithm
ExitCodes enum nameXFDRAlgorithm
fdr_xprophet_(std::map< String, Math::Histogram<> > &cum_histograms, const String &targetclass, const String &decoyclass, const String &fulldecoyclass, std::vector< double > &fdr, bool mono) constXFDRAlgorithmprivate
findTopUniqueHits_(std::vector< PeptideIdentification > &peptide_ids)XFDRAlgorithmprivate
getDefaults() constDefaultParamHandler
getId_(const PeptideHit &ph) constXFDRAlgorithmprivate
getLogType() constProgressLogger
getMinIonsMatched_(const PeptideHit &ph)XFDRAlgorithminlineprivatestatic
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
ILLEGAL_PARAMETERS enum valueXFDRAlgorithm
initDataStructures_(std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id)XFDRAlgorithmprivate
isSameProtein_(String prot1, String prot2, const String &decoy_string)XFDRAlgorithminlineprivatestatic
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
max_score_XFDRAlgorithmprivate
min_score_XFDRAlgorithmprivate
nextProgress() constProgressLogger
NONE enum valueProgressLogger
OpenMS::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
param_binsize_XFDRAlgorithmprivatestatic
param_decoy_string_XFDRAlgorithmprivatestatic
param_maxborder_XFDRAlgorithmprivatestatic
param_minborder_XFDRAlgorithmprivatestatic
param_mindeltas_XFDRAlgorithmprivatestatic
param_minionsmatched_XFDRAlgorithmprivatestatic
param_minscore_XFDRAlgorithmprivatestatic
param_no_qvalues_XFDRAlgorithmprivatestatic
param_uniquexl_XFDRAlgorithmprivatestatic
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
run(std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id)XFDRAlgorithm
setInterProtein_(PeptideHit &ph, const bool value)XFDRAlgorithminlineprivatestatic
setIntraProtein_(PeptideHit &ph, const bool value)XFDRAlgorithminlineprivatestatic
setLogger(ProgressLoggerImpl *logger)ProgressLogger
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
UNEXPECTED_RESULT enum valueXFDRAlgorithm
unique_id_scores_XFDRAlgorithmprivate
unique_ids_XFDRAlgorithmprivate
updateMembers_() overrideXFDRAlgorithmprivatevirtual
validateClassArguments() constXFDRAlgorithm
warn_empty_defaults_DefaultParamHandlerprotected
writeArgumentsLog_() constXFDRAlgorithmprivate
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
XFDRAlgorithm()XFDRAlgorithm
~DefaultParamHandler()DefaultParamHandlervirtual
~ProgressLogger()ProgressLoggervirtual
~XFDRAlgorithm() overrideXFDRAlgorithm