| OpenMS 2.5.0

TransitionTSVFile Member List

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

addModification_(std::vector< TargetedExperiment::Peptide::Modification > &mods, int location, const ResidueModification &rmod) | TransitionTSVFile | private
check_defaults_ | DefaultParamHandler | protected
cleanupTransitions_(TSVTransition &mytransition) | TransitionTSVFile | private
CMD enum value | ProgressLogger |
convertTargetedExperimentToTSV(const char *filename, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVFile |
convertTransition_(const ReactionMonitoringTransition *it, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVFile | protected
convertTSVToTargetedExperiment(const char *filename, FileTypes::Type filetype, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVFile |
convertTSVToTargetedExperiment(const char *filename, FileTypes::Type filetype, OpenSwath::LightTargetedExperiment &targeted_exp) | TransitionTSVFile |
createCompound_(std::vector< TSVTransition >::const_iterator tr_it, OpenMS::TargetedExperiment::Compound &compound) | TransitionTSVFile | private
createPeptide_(std::vector< TSVTransition >::const_iterator tr_it, OpenMS::TargetedExperiment::Peptide &peptide) | TransitionTSVFile | private
createProtein_(String protein_name, String uniprot_id, OpenMS::TargetedExperiment::Protein &protein) | TransitionTSVFile | private
createTransition_(std::vector< TSVTransition >::iterator &tr_it, OpenMS::ReactionMonitoringTransition &rm_trans) | TransitionTSVFile | private
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
force_invalid_mods_ | TransitionTSVFile | private
getDefaults() const | DefaultParamHandler |
getLogType() const | ProgressLogger |
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
getTSVHeader_(const std::string &line, char &delimiter, std::map< std::string, int > &header_dict) const | TransitionTSVFile | private
GUI enum value | ProgressLogger |
header_names_ | TransitionTSVFile | private static
interpretRetentionTime_(std::vector< TargetedExperiment::RetentionTime > &retention_times, const OpenMS::DataValue rt_value) | TransitionTSVFile | private
last_invoke_ | ProgressLogger | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
nextProgress() const | ProgressLogger |
NONE enum value | ProgressLogger |
OpenMS::operator=(const ProgressLogger &other) | ProgressLogger |
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual
override_group_label_check_ | TransitionTSVFile | private
param_ | DefaultParamHandler | protected
PeptideVectorType typedef | TransitionTSVFile | private
ProgressLogger() | ProgressLogger |
ProgressLogger(const ProgressLogger &other) | ProgressLogger |
ProteinVectorType typedef | TransitionTSVFile | private
readUnstructuredTSVInput_(const char *filename, FileTypes::Type filetype, std::vector< TSVTransition > &transition_list) | TransitionTSVFile | private
recursion_depth_ | ProgressLogger | protected static
resolveMixedSequenceGroups_(std::vector< TSVTransition > &transition_list) const | TransitionTSVFile | private
retentionTimeInterpretation_ | TransitionTSVFile | private
setLogType(LogType type) const | ProgressLogger |
setName(const String &name) | DefaultParamHandler |
setParameters(const Param &param) | DefaultParamHandler |
setProgress(SignedSize value) const | ProgressLogger |
spectrastAnnotationExtract(const String str_inp, TSVTransition &mytransition) | TransitionTSVFile | private
spectrastRTExtract(const String str_inp, double &value, bool &spectrast_legacy) | TransitionTSVFile | private
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger |
strarray_ | TransitionTSVFile | private static
subsections_ | DefaultParamHandler | protected
TransitionTSVFile() | TransitionTSVFile |
TransitionVectorType typedef | TransitionTSVFile | private
TSVToTargetedExperiment_(std::vector< TSVTransition > &transition_list, OpenMS::TargetedExperiment &exp) | TransitionTSVFile | protected
TSVToTargetedExperiment_(std::vector< TSVTransition > &transition_list, OpenSwath::LightTargetedExperiment &exp) | TransitionTSVFile | protected
type_ | ProgressLogger | mutable protected
updateMembers_() override | TransitionTSVFile | protected virtual
validateTargetedExperiment(const OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVFile |
warn_empty_defaults_ | DefaultParamHandler | protected
writeTSVOutput_(const char *filename, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVFile | private
~DefaultParamHandler() | DefaultParamHandler | virtual
~ProgressLogger() | ProgressLogger |
~TransitionTSVFile() override | TransitionTSVFile |