TransitionPQPFile Member List

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, const 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(UInt64 bytes_processed=0) const	ProgressLogger
error_name_	DefaultParamHandler	protected
force_invalid_mods_	TransitionTSVFile	private
getDefaults() const	DefaultParamHandler
getLogType() const	ProgressLogger
getName() const	DefaultParamHandler
getParameters() const	DefaultParamHandler
getPQPIDToTraMLIDMap(const char *filename, std::string tableName)	TransitionPQPFile
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
nextProgress() const	ProgressLogger
NONE enum value	ProgressLogger
OpenMS::operator=(const ProgressLogger &other)	ProgressLogger
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)	DefaultParamHandler
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
setLogger(ProgressLoggerImpl *logger)	ProgressLogger
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	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 &key_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	virtual
~TransitionPQPFile() override	TransitionPQPFile
~TransitionTSVFile() override	TransitionTSVFile