OpenMS
2.6.0
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This is the complete list of members for TransitionPQPFile, 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 | |
convertPQPToTargetedExperiment(const char *filename, OpenMS::TargetedExperiment &targeted_exp, bool legacy_traml_id=false) | TransitionPQPFile | |
convertPQPToTargetedExperiment(const char *filename, OpenSwath::LightTargetedExperiment &targeted_exp, bool legacy_traml_id=false) | TransitionPQPFile | |
convertTargetedExperimentToPQP(const char *filename, OpenMS::TargetedExperiment &targeted_exp) | TransitionPQPFile | |
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 | mutableprotected |
DefaultParamHandler(const String &name) | DefaultParamHandler | |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
DefaultParamHandler() | DefaultParamHandler | private |
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 | privatestatic |
interpretRetentionTime_(std::vector< TargetedExperiment::RetentionTime > &retention_times, const OpenMS::DataValue rt_value) | TransitionTSVFile | private |
last_invoke_ | ProgressLogger | mutableprotected |
LogType enum name | ProgressLogger | |
logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
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 |
readPQPInput_(const char *filename, std::vector< TSVTransition > &transition_list, bool legacy_traml_id=false) | TransitionPQPFile | private |
readUnstructuredTSVInput_(const char *filename, FileTypes::Type filetype, std::vector< TSVTransition > &transition_list) | TransitionTSVFile | private |
recursion_depth_ | ProgressLogger | protectedstatic |
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 ¶m) | 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 | privatestatic |
subsections_ | DefaultParamHandler | protected |
TransitionPQPFile() | TransitionPQPFile | |
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 | mutableprotected |
updateMembers_() override | TransitionTSVFile | protectedvirtual |
validateTargetedExperiment(const OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVFile | |
warn_empty_defaults_ | DefaultParamHandler | protected |
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") | DefaultParamHandler | static |
writePQPOutput_(const char *filename, OpenMS::TargetedExperiment &targeted_exp) | TransitionPQPFile | private |
writeTSVOutput_(const char *filename, OpenMS::TargetedExperiment &targeted_exp) | TransitionTSVFile | private |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~ProgressLogger() | ProgressLogger | |
~TransitionPQPFile() override | TransitionPQPFile | |
~TransitionTSVFile() override | TransitionTSVFile |