| addModification_(std::vector< TargetedExperiment::Peptide::Modification > &mods, int location, const ResidueModification &rmod) | TransitionTSVReader | private |
| check_defaults_ | DefaultParamHandler | protected |
| cleanupTransitions_(TSVTransition &mytransition) | TransitionTSVReader | private |
| CMD enum value | ProgressLogger | |
| convertTargetedExperimentToTSV(const char *filename, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVReader | |
| convertTransition_(const ReactionMonitoringTransition *it, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVReader | protected |
| convertTSVToTargetedExperiment(const char *filename, FileTypes::Type filetype, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVReader | |
| convertTSVToTargetedExperiment(const char *filename, FileTypes::Type filetype, OpenSwath::LightTargetedExperiment &targeted_exp) | TransitionTSVReader | |
| createCompound_(std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Compound &compound) | TransitionTSVReader | private |
| createPeptide_(std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Peptide &peptide) | TransitionTSVReader | private |
| createProtein_(std::vector< TSVTransition >::iterator &tr_it, OpenMS::TargetedExperiment::Protein &protein) | TransitionTSVReader | private |
| createTransition_(std::vector< TSVTransition >::iterator &tr_it, OpenMS::ReactionMonitoringTransition &rm_trans) | TransitionTSVReader | private |
| current_logger_ | ProgressLogger | mutableprotected |
| 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_ | TransitionTSVReader | private |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| getTSVHeader_(const std::string &line, char &delimiter, std::vector< std::string > header, std::map< std::string, int > &header_dict) | TransitionTSVReader | private |
| GUI enum value | ProgressLogger | |
| header_names_ | TransitionTSVReader | privatestatic |
| interpretRetentionTime_(std::vector< TargetedExperiment::RetentionTime > &retention_times, const OpenMS::DataValue rt_value) | TransitionTSVReader | private |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| 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_ | TransitionTSVReader | private |
| param_ | DefaultParamHandler | protected |
| PeptideVectorType typedef | TransitionTSVReader | private |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| ProteinVectorType typedef | TransitionTSVReader | private |
| readUnstructuredTSVInput_(const char *filename, FileTypes::Type filetype, std::vector< TSVTransition > &transition_list) | TransitionTSVReader | private |
| recursion_depth_ | ProgressLogger | protectedstatic |
| resolveMixedSequenceGroups_(std::vector< TSVTransition > &transition_list) | TransitionTSVReader | private |
| retentionTimeInterpretation_ | TransitionTSVReader | private |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| strarray_ | TransitionTSVReader | privatestatic |
| subsections_ | DefaultParamHandler | protected |
| TransitionTSVReader() | TransitionTSVReader | |
| TransitionVectorType typedef | TransitionTSVReader | private |
| TSVToTargetedExperiment_(std::vector< TSVTransition > &transition_list, OpenMS::TargetedExperiment &exp) | TransitionTSVReader | protected |
| TSVToTargetedExperiment_(std::vector< TSVTransition > &transition_list, OpenSwath::LightTargetedExperiment &exp) | TransitionTSVReader | protected |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() | TransitionTSVReader | protectedvirtual |
| validateTargetedExperiment(OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVReader | |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeTSVOutput_(const char *filename, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVReader | private |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ProgressLogger() | ProgressLogger | |
| ~TransitionTSVReader() | TransitionTSVReader | |