| OpenMS 2.5.0

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 | mutable protected
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
endProgress() 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 |
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 | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
MRMDecoy() | MRMDecoy |
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
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 | protected static
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
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
TransitionVectorType typedef | MRMDecoy |
type_ | ProgressLogger | mutable protected
updateMembers_() override | MRMDecoy | protected virtual
warn_empty_defaults_ | DefaultParamHandler | protected
~DefaultParamHandler() | DefaultParamHandler | virtual
~ProgressLogger() | ProgressLogger |