PeptideIndexing Member List

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

aaa_max_	PeptideIndexing	protected
addHits_(AhoCorasickAmbiguous &fuzzyAC, const AhoCorasickAmbiguous::FuzzyACPattern &pattern, const AhoCorasickAmbiguous::PeptideDB &pep_DB, const String &prot, const String &full_prot, SignedSize idx_prot, Int offset, FoundProteinFunctor &func_threads) const	PeptideIndexing	inlineprotected
AUTO_MODE	PeptideIndexing	static
check_defaults_	DefaultParamHandler	protected
CMD enum value	ProgressLogger
current_logger_	ProgressLogger	mutableprotected
DATABASE_EMPTY enum value	PeptideIndexing
decoy_string_	PeptideIndexing	protected
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
DefaultParamHandler()	DefaultParamHandler	private
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
endProgress() const	ProgressLogger
enzyme_name_	PeptideIndexing	protected
enzyme_specificity_	PeptideIndexing	protected
error_name_	DefaultParamHandler	protected
EXECUTION_OK enum value	PeptideIndexing
ExitCodes enum name	PeptideIndexing
getDecoyString() const	PeptideIndexing
getDefaults() const	DefaultParamHandler
getLogType() const	ProgressLogger
getName() const	DefaultParamHandler
getParameters() const	DefaultParamHandler
getSubsections() const	DefaultParamHandler
GUI enum value	ProgressLogger
IL_equivalent_	PeptideIndexing	protected
ILLEGAL_PARAMETERS enum value	PeptideIndexing
isPrefix() const	PeptideIndexing
keep_unreferenced_proteins_	PeptideIndexing	protected
last_invoke_	ProgressLogger	mutableprotected
LogType enum name	ProgressLogger
logTypeToFactoryName_(LogType type)	ProgressLogger	protectedstatic
missing_decoy_action_	PeptideIndexing	protected
MissingDecoy enum name	PeptideIndexing
mm_max_	PeptideIndexing	protected
names_of_missing_decoy	PeptideIndexing	static
names_of_unmatched	PeptideIndexing	static
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
PEPTIDE_IDS_EMPTY enum value	PeptideIndexing
PeptideIndexing()	PeptideIndexing
prefix_	PeptideIndexing	protected
ProgressLogger()	ProgressLogger
ProgressLogger(const ProgressLogger &other)	ProgressLogger
recursion_depth_	ProgressLogger	protectedstatic
run(std::vector< FASTAFile::FASTAEntry > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)	PeptideIndexing	inline
run(FASTAContainer< T > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)	PeptideIndexing	inline
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	mutableprotected
UNEXPECTED_RESULT enum value	PeptideIndexing
Unmatched enum name	PeptideIndexing
unmatched_action_	PeptideIndexing	protected
updateMembers_() override	PeptideIndexing	protectedvirtual
warn_empty_defaults_	DefaultParamHandler	protected
write_protein_description_	PeptideIndexing	protected
write_protein_sequence_	PeptideIndexing	protected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")	DefaultParamHandler	static
~DefaultParamHandler()	DefaultParamHandler	virtual
~PeptideIndexing() override	PeptideIndexing
~ProgressLogger()	ProgressLogger	virtual