OpenMS
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)TransitionTSVFileprivate
check_defaults_DefaultParamHandlerprotected
cleanupTransitions_(TSVTransition &mytransition)TransitionTSVFileprivate
CMD enum valueProgressLogger
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)TransitionTSVFileprotected
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)TransitionTSVFileprivate
createPeptide_(std::vector< TSVTransition >::const_iterator tr_it, OpenMS::TargetedExperiment::Peptide &peptide)TransitionTSVFileprivate
createProtein_(String protein_name, const String &uniprot_id, OpenMS::TargetedExperiment::Protein &protein)TransitionTSVFileprivate
createTransition_(std::vector< TSVTransition >::iterator &tr_it, OpenMS::ReactionMonitoringTransition &rm_trans)TransitionTSVFileprivate
current_logger_ProgressLoggermutableprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
endProgress() constProgressLogger
error_name_DefaultParamHandlerprotected
force_invalid_mods_TransitionTSVFileprivate
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
getTSVHeader_(const std::string &line, char &delimiter, std::map< std::string, int > &header_dict) constTransitionTSVFileprivate
GUI enum valueProgressLogger
header_names_TransitionTSVFileprivatestatic
interpretRetentionTime_(std::vector< TargetedExperiment::RetentionTime > &retention_times, const OpenMS::DataValue &rt_value)TransitionTSVFileprivate
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
nextProgress() constProgressLogger
NONE enum valueProgressLogger
OpenMS::operator=(const ProgressLogger &other)ProgressLogger
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
override_group_label_check_TransitionTSVFileprivate
param_DefaultParamHandlerprotected
PeptideVectorType typedefTransitionTSVFileprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
ProteinVectorType typedefTransitionTSVFileprivate
readPQPInput_(const char *filename, std::vector< TSVTransition > &transition_list, bool legacy_traml_id=false)TransitionPQPFileprivate
readUnstructuredTSVInput_(const char *filename, FileTypes::Type filetype, std::vector< TSVTransition > &transition_list)TransitionTSVFileprivate
recursion_depth_ProgressLoggerprotectedstatic
resolveMixedSequenceGroups_(std::vector< TSVTransition > &transition_list) constTransitionTSVFileprivate
retentionTimeInterpretation_TransitionTSVFileprivate
setLogType(LogType type) constProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
spectrastAnnotationExtract(const String &str_inp, TSVTransition &mytransition)TransitionTSVFileprivate
spectrastRTExtract(const String &str_inp, double &value, bool &spectrast_legacy)TransitionTSVFileprivate
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
strarray_TransitionTSVFileprivatestatic
subsections_DefaultParamHandlerprotected
TransitionPQPFile()TransitionPQPFile
TransitionTSVFile()TransitionTSVFile
TransitionVectorType typedefTransitionTSVFileprivate
TSVToTargetedExperiment_(std::vector< TSVTransition > &transition_list, OpenMS::TargetedExperiment &exp)TransitionTSVFileprotected
TSVToTargetedExperiment_(std::vector< TSVTransition > &transition_list, OpenSwath::LightTargetedExperiment &exp)TransitionTSVFileprotected
type_ProgressLoggermutableprotected
updateMembers_() overrideTransitionTSVFileprotectedvirtual
validateTargetedExperiment(const OpenMS::TargetedExperiment &targeted_exp)TransitionTSVFile
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
writePQPOutput_(const char *filename, OpenMS::TargetedExperiment &targeted_exp)TransitionPQPFileprivate
writeTSVOutput_(const char *filename, OpenMS::TargetedExperiment &targeted_exp)TransitionTSVFileprivate
~DefaultParamHandler()DefaultParamHandlervirtual
~ProgressLogger()ProgressLoggervirtual
~TransitionPQPFile() overrideTransitionPQPFile
~TransitionTSVFile() overrideTransitionTSVFile