OpenMS
MRMDecoy Member List

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

AASequenceIdentity(const String &sequence, const String &decoy) constMRMDecoy
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
current_logger_ProgressLoggermutableprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
endProgress() constProgressLogger
error_name_DefaultParamHandlerprotected
findFixedAndTermResidues_(const std::string &sequence) constMRMDecoyprotected
findFixedResidues(const std::string &sequence, bool keepN, bool keepC, const OpenMS::String &keep_const_pattern)MRMDecoystatic
findFixedResidues_(const std::string &sequence) constMRMDecoyprotected
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) constMRMDecoy
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getModifiedPeptideSequence_(const OpenMS::TargetedExperiment::Peptide &pep) constMRMDecoyprotected
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
hasCNterminalMods_(const OpenMS::TargetedExperiment::Peptide &peptide, bool checkCterminalAA) constMRMDecoyprotected
IndexType typedefMRMDecoy
keep_const_pattern_MRMDecoyprotected
keepC_MRMDecoyprotected
keepN_MRMDecoyprotected
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
MRMDecoy()MRMDecoy
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
PeptideTransitionMapType typedefMRMDecoy
PeptideVectorType typedefMRMDecoy
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
ProteinVectorType typedefMRMDecoy
pseudoreversePeptide_(const OpenMS::TargetedExperiment::Peptide &peptide) constMRMDecoyprotected
recursion_depth_ProgressLoggerprotectedstatic
reversePeptide(const OpenMS::TargetedExperiment::Peptide &peptide, const bool keepN, const bool keepC, const String &const_pattern=String())MRMDecoystatic
reversePeptide_(const OpenMS::TargetedExperiment::Peptide &peptide) constMRMDecoyprotected
setLogType(LogType type) constProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
shufflePeptide(OpenMS::TargetedExperiment::Peptide peptide, const double identity_threshold, int seed=-1, const int max_attempts=100) constMRMDecoy
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
subsections_DefaultParamHandlerprotected
switchKR(OpenMS::TargetedExperiment::Peptide &peptide) constMRMDecoy
TransitionVectorType typedefMRMDecoy
type_ProgressLoggermutableprotected
updateMembers_() overrideMRMDecoyprotectedvirtual
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~ProgressLogger()ProgressLoggervirtual