MRMDecoy Member List

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

AASequenceIdentity(const String &sequence, const String &decoy) const	MRMDecoy
check_defaults_	DefaultParamHandler	protected
CMD enum value	ProgressLogger
current_logger_	ProgressLogger	mutableprotected
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
DefaultParamHandler()	DefaultParamHandler	private
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
endProgress(UInt64 bytes_processed=0) const	ProgressLogger
error_name_	DefaultParamHandler	protected
findFixedAndTermResidues_(const std::string &sequence) const	MRMDecoy	protected
findFixedResidues(const std::string &sequence, bool keepN, bool keepC, const OpenMS::String &keep_const_pattern)	MRMDecoy	static
findFixedResidues_(const std::string &sequence) const	MRMDecoy	protected
generateDecoys(const OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, const String &method, const double aim_decoy_fraction, const bool switchKR, const String &decoy_tag, const int max_attempts, const double identity_threshold, const double precursor_mz_shift, const double product_mz_shift, const double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) const	MRMDecoy
getDefaults() const	DefaultParamHandler
getLogType() const	ProgressLogger
getModifiedPeptideSequence_(const OpenMS::TargetedExperiment::Peptide &pep) const	MRMDecoy	protected
getName() const	DefaultParamHandler
getParameters() const	DefaultParamHandler
getSubsections() const	DefaultParamHandler
GUI enum value	ProgressLogger
hasCNterminalMods_(const OpenMS::TargetedExperiment::Peptide &peptide, bool checkCterminalAA) const	MRMDecoy	protected
IndexType typedef	MRMDecoy
keep_const_pattern_	MRMDecoy	protected
keepC_	MRMDecoy	protected
keepN_	MRMDecoy	protected
last_invoke_	ProgressLogger	mutableprotected
LogType enum name	ProgressLogger
MRMDecoy()	MRMDecoy
nextProgress() const	ProgressLogger
NONE enum value	ProgressLogger
OpenMS::operator=(const DefaultParamHandler &rhs)	DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)	ProgressLogger
operator==(const DefaultParamHandler &rhs) const	DefaultParamHandler	virtual
param_	DefaultParamHandler	protected
PeptideTransitionMapType typedef	MRMDecoy
PeptideVectorType typedef	MRMDecoy
ProgressLogger()	ProgressLogger
ProgressLogger(const ProgressLogger &other)	ProgressLogger
ProteinVectorType typedef	MRMDecoy
pseudoreversePeptide_(const OpenMS::TargetedExperiment::Peptide &peptide) const	MRMDecoy	protected
recursion_depth_	ProgressLogger	protectedstatic
reversePeptide(const OpenMS::TargetedExperiment::Peptide &peptide, const bool keepN, const bool keepC, const String &const_pattern=String())	MRMDecoy	static
reversePeptide_(const OpenMS::TargetedExperiment::Peptide &peptide) const	MRMDecoy	protected
setLogger(ProgressLoggerImpl *logger)	ProgressLogger
setLogType(LogType type) const	ProgressLogger
setName(const String &name)	DefaultParamHandler
setParameters(const Param &param)	DefaultParamHandler
setProgress(SignedSize value) const	ProgressLogger
shufflePeptide(OpenMS::TargetedExperiment::Peptide peptide, const double identity_threshold, int seed=-1, const int max_attempts=100) const	MRMDecoy
startProgress(SignedSize begin, SignedSize end, const String &label) const	ProgressLogger
subsections_	DefaultParamHandler	protected
switchKR(OpenMS::TargetedExperiment::Peptide &peptide) const	MRMDecoy
TransitionVectorType typedef	MRMDecoy
type_	ProgressLogger	mutableprotected
updateMembers_() override	MRMDecoy	protectedvirtual
warn_empty_defaults_	DefaultParamHandler	protected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")	DefaultParamHandler	static
~DefaultParamHandler()	DefaultParamHandler	virtual
~ProgressLogger()	ProgressLogger	virtual