PeptideAndProteinQuant Member List

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

aggregateAbundances_(const std::vector< double > &abundances, const String &method) const	PeptideAndProteinQuant	private
annotateQuantificationsToProteins(const ProteinQuant &protein_quants, ProteinIdentification &proteins, bool remove_unquantified=true)	PeptideAndProteinQuant
calculateFileAndChannelLevelProteinAbundances_(const String &protein_accession, const std::vector< String > &selected_peptides, const String &aggregate_method, Size top_n, bool include_all, const std::map< String, String > &accession_to_leader)	PeptideAndProteinQuant	private
calculateProteinAbundances_(const String &protein_accession, const std::vector< String > &selected_peptides, const String &aggregate_method, Size top_n, bool include_all)	PeptideAndProteinQuant	private
check_defaults_	DefaultParamHandler	protected
countPeptides_(PeptideIdentificationList &peptides)	PeptideAndProteinQuant	private
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
DefaultParamHandler()	DefaultParamHandler	private
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
error_name_	DefaultParamHandler	protected
experimental_design_	PeptideAndProteinQuant	private
getAccession_(const std::set< String > &pep_accessions, const std::map< String, String > &accession_to_leader) const	PeptideAndProteinQuant	private
getAnnotation_(PeptideIdentificationList &peptides)	PeptideAndProteinQuant	private
getBest_(const std::map< Int, std::map< String, std::map< Int, std::map< Int, double >>>> &peptide_abundances, std::tuple< size_t, String, size_t, Int > &best)	PeptideAndProteinQuant	private
getDefaults() const	DefaultParamHandler
getName() const	DefaultParamHandler
getParameters() const	DefaultParamHandler
getPeptideResults()	PeptideAndProteinQuant
getProteinResults()	PeptideAndProteinQuant
getSampleIDFromFilenameAndChannel_(const String &filename, Int channel_or_label, const ExperimentalDesign &ed) const	PeptideAndProteinQuant	private
getStatistics()	PeptideAndProteinQuant
getSubsections() const	DefaultParamHandler
mapAccessionToLeader(const OpenMS::ProteinIdentification &proteins) const	PeptideAndProteinQuant
normalizePeptides_()	PeptideAndProteinQuant	private
operator=(const DefaultParamHandler &rhs)	DefaultParamHandler
operator==(const DefaultParamHandler &rhs) const	DefaultParamHandler	virtual
orderBest_(const std::map< T, SampleAbundances > &abundances, std::vector< T > &result)	PeptideAndProteinQuant	inlineprivate
param_	DefaultParamHandler	protected
pep_quant_	PeptideAndProteinQuant	private
PeptideAndProteinQuant()	PeptideAndProteinQuant
PeptideQuant typedef	PeptideAndProteinQuant
performIbaqNormalization_(const ProteinIdentification &proteins)	PeptideAndProteinQuant	private
prot_quant_	PeptideAndProteinQuant	private
ProteinQuant typedef	PeptideAndProteinQuant
quantifyFeature_(const FeatureHandle &feature, size_t fraction, const String &filename, const PeptideHit &hit, Int channel_or_label)	PeptideAndProteinQuant	private
quantifyPeptides(const PeptideIdentificationList &peptides=PeptideIdentificationList())	PeptideAndProteinQuant
quantifyProteins(const ProteinIdentification &proteins=ProteinIdentification())	PeptideAndProteinQuant
readQuantData(FeatureMap &features, const ExperimentalDesign &ed)	PeptideAndProteinQuant
readQuantData(ConsensusMap &consensus, const ExperimentalDesign &ed)	PeptideAndProteinQuant
readQuantData(std::vector< ProteinIdentification > &proteins, PeptideIdentificationList &peptides, const ExperimentalDesign &ed)	PeptideAndProteinQuant
SampleAbundances typedef	PeptideAndProteinQuant
selectPeptidesForQuantification_(const String &protein_accession, Size top_n, bool fix_peptides)	PeptideAndProteinQuant	private
setName(const String &name)	DefaultParamHandler
setParameters(const Param &param)	DefaultParamHandler
stats_	PeptideAndProteinQuant	private
subsections_	DefaultParamHandler	protected
transferPeptideDataToProteins_(const ProteinIdentification &proteins)	PeptideAndProteinQuant	private
updateMembers_() override	PeptideAndProteinQuant	privatevirtual
warn_empty_defaults_	DefaultParamHandler	protected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")	DefaultParamHandler	static
~DefaultParamHandler()	DefaultParamHandler	virtual
~PeptideAndProteinQuant() override	PeptideAndProteinQuant	inline