| OpenMS 2.5.0

XFDRAlgorithm Member List

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

arg_binsize_ | XFDRAlgorithm | private
arg_maxborder_ | XFDRAlgorithm | private
arg_minborder_ | XFDRAlgorithm | private
arg_mindeltas_ | XFDRAlgorithm | private
arg_minionsmatched_ | XFDRAlgorithm | private
arg_minscore_ | XFDRAlgorithm | private
arg_no_qvalues_ | XFDRAlgorithm | private
arg_uniquex_ | XFDRAlgorithm | private
assignTypes_(PeptideHit &ph, StringList &types) | XFDRAlgorithm | private static
calc_qfdr_(const std::vector< double > &fdr, std::vector< double > &qfdr) | XFDRAlgorithm | private static
check_defaults_ | DefaultParamHandler | protected
CMD enum value | ProgressLogger |
cross_link_classes_ | XFDRAlgorithm | private
crosslink_class_decoys_ | XFDRAlgorithm | private static
crosslink_class_fulldecoysinterlinks_ | XFDRAlgorithm | private static
crosslink_class_fulldecoysintralinks_ | XFDRAlgorithm | private static
crosslink_class_hybriddecoysinterlinks_ | XFDRAlgorithm | private static
crosslink_class_hybriddecoysintralinks_ | XFDRAlgorithm | private static
crosslink_class_interdecoys_ | XFDRAlgorithm | private static
crosslink_class_interlinks_ | XFDRAlgorithm | private static
crosslink_class_intradecoys_ | XFDRAlgorithm | private static
crosslink_class_intralinks_ | XFDRAlgorithm | private static
crosslink_class_monodecoys_ | XFDRAlgorithm | private static
crosslink_class_monolinks_ | XFDRAlgorithm | private static
crosslink_class_targets_ | XFDRAlgorithm | private static
current_logger_ | ProgressLogger | mutable protected
decoy_string_ | XFDRAlgorithm | private
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
endProgress() const | ProgressLogger |
error_name_ | DefaultParamHandler | protected
EXECUTION_OK enum value | XFDRAlgorithm |
ExitCodes enum name | XFDRAlgorithm |
fdr_xprophet_(std::map< String, Math::Histogram<> > &cum_histograms, const String &targetclass, const String &decoyclass, const String &fulldecoyclass, std::vector< double > &fdr, bool mono) | XFDRAlgorithm | private
findTopUniqueHits_(std::vector< PeptideIdentification > &peptide_ids) | XFDRAlgorithm | private
getDefaults() const | DefaultParamHandler |
getId_(const PeptideHit &ph) const | XFDRAlgorithm | private
getLogType() const | ProgressLogger |
getMinIonsMatched_(const PeptideHit &ph) | XFDRAlgorithm | inline private static
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
GUI enum value | ProgressLogger |
ILLEGAL_PARAMETERS enum value | XFDRAlgorithm |
initDataStructures_(std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id) | XFDRAlgorithm | private
isSameProtein_(String prot1, String prot2, const String &decoy_string) | XFDRAlgorithm | inline private static
last_invoke_ | ProgressLogger | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
max_score_ | XFDRAlgorithm | private
min_score_ | XFDRAlgorithm | private
nextProgress() const | ProgressLogger |
NONE enum value | ProgressLogger |
OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual
OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger |
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual
param_ | DefaultParamHandler | protected
param_binsize_ | XFDRAlgorithm | private static
param_decoy_string_ | XFDRAlgorithm | private static
param_maxborder_ | XFDRAlgorithm | private static
param_minborder_ | XFDRAlgorithm | private static
param_mindeltas_ | XFDRAlgorithm | private static
param_minionsmatched_ | XFDRAlgorithm | private static
param_minscore_ | XFDRAlgorithm | private static
param_no_qvalues_ | XFDRAlgorithm | private static
param_uniquexl_ | XFDRAlgorithm | private static
ProgressLogger() | ProgressLogger |
ProgressLogger(const ProgressLogger &other) | ProgressLogger |
recursion_depth_ | ProgressLogger | protected static
run(std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id) | XFDRAlgorithm |
setInterProtein_(PeptideHit &ph, const bool value) | XFDRAlgorithm | inline private static
setIntraProtein_(PeptideHit &ph, const bool value) | XFDRAlgorithm | inline private static
setLogType(LogType type) const | ProgressLogger |
setName(const String &name) | DefaultParamHandler |
setParameters(const Param &param) | DefaultParamHandler |
setProgress(SignedSize value) const | ProgressLogger |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger |
subsections_ | DefaultParamHandler | protected
type_ | ProgressLogger | mutable protected
UNEXPECTED_RESULT enum value | XFDRAlgorithm |
unique_id_scores_ | XFDRAlgorithm | private
unique_ids_ | XFDRAlgorithm | private
updateMembers_() override | XFDRAlgorithm | private virtual
validateClassArguments() const | XFDRAlgorithm |
warn_empty_defaults_ | DefaultParamHandler | protected
writeArgumentsLog_() const | XFDRAlgorithm | private
XFDRAlgorithm() | XFDRAlgorithm |
~DefaultParamHandler() | DefaultParamHandler | virtual
~ProgressLogger() | ProgressLogger |
~XFDRAlgorithm() override | XFDRAlgorithm |