FeatureFinderIdentificationAlgorithm Member List

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

addPeptideRT_(TargetedExperiment::Peptide &peptide, double rt) const	FeatureFinderIdentificationAlgorithm	protected
addPeptideToMap_(PeptideIdentification &peptide, PeptideMap &peptide_map, bool external=false)	FeatureFinderIdentificationAlgorithm	protected
annotateFeatures_(FeatureMap &features, PeptideRefRTMap &ref_rt_map)	FeatureFinderIdentificationAlgorithm	protected
annotateFeaturesFinalizeAssay_(FeatureMap &features, std::map< Size, std::vector< PeptideIdentification * > > &feat_ids, RTMap &rt_internal)	FeatureFinderIdentificationAlgorithm	protected
batch_size_	FeatureFinderIdentificationAlgorithm	protected
calculateFDR_(FeatureMap &features)	FeatureFinderIdentificationAlgorithm	protected
candidates_out_	FeatureFinderIdentificationAlgorithm	protected
ChargeMap typedef	FeatureFinderIdentificationAlgorithm	protected
check_defaults_	DefaultParamHandler	protected
checkNumObservations_(Size n_pos, Size n_neg, const String &note="") const	FeatureFinderIdentificationAlgorithm	protected
chrom_data_	FeatureFinderIdentificationAlgorithm	protected
chunk_(It range_from, It range_to, const std::ptrdiff_t batch_size)	FeatureFinderIdentificationAlgorithm	inlineprotected
classifyFeatures_(FeatureMap &features)	FeatureFinderIdentificationAlgorithm	protected
createAssayLibrary_(const PeptideMap::iterator &begin, const PeptideMap::iterator &end, PeptideRefRTMap &ref_rt_map, bool clear_IDs=true)	FeatureFinderIdentificationAlgorithm	protected
debug_level_	FeatureFinderIdentificationAlgorithm	protected
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
DefaultParamHandler()	DefaultParamHandler	private
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
elution_model_	FeatureFinderIdentificationAlgorithm	protected
ensureConvexHulls_(Feature &feature) const	FeatureFinderIdentificationAlgorithm	protected
error_name_	DefaultParamHandler	protected
feat_finder_	FeatureFinderIdentificationAlgorithm	protected
feature_compare_	FeatureFinderIdentificationAlgorithm	protected
feature_filter_peptides_	FeatureFinderIdentificationAlgorithm	protected
feature_filter_quality_	FeatureFinderIdentificationAlgorithm	protected
FeatureFinderIdentificationAlgorithm()	FeatureFinderIdentificationAlgorithm
filterFeatures_(FeatureMap &features, bool classified)	FeatureFinderIdentificationAlgorithm	protected
filterFeaturesFinalizeAssay_(Feature &best_feature, double best_quality, const double quality_cutoff)	FeatureFinderIdentificationAlgorithm	protected
generateTransitions_(const String &peptide_id, double mz, Int charge, const IsotopeDistribution &iso_dist)	FeatureFinderIdentificationAlgorithm	protected
getChromatograms()	FeatureFinderIdentificationAlgorithm
getChromatograms() const	FeatureFinderIdentificationAlgorithm
getDefaults() const	DefaultParamHandler
getLibrary()	FeatureFinderIdentificationAlgorithm
getLibrary() const	FeatureFinderIdentificationAlgorithm
getMSData()	FeatureFinderIdentificationAlgorithm
getMSData() const	FeatureFinderIdentificationAlgorithm
getName() const	DefaultParamHandler
getParameters() const	DefaultParamHandler
getProgressLogger()	FeatureFinderIdentificationAlgorithm
getProgressLogger() const	FeatureFinderIdentificationAlgorithm
getRandomSample_(std::map< Size, double > &training_labels) const	FeatureFinderIdentificationAlgorithm	protected
getRTRegions_(ChargeMap &peptide_data, std::vector< RTRegion > &rt_regions, bool clear_IDs=true) const	FeatureFinderIdentificationAlgorithm	protected
getSubsections() const	DefaultParamHandler
getUnbiasedSample_(const std::multimap< double, std::pair< Size, bool > > &valid_obs, std::map< Size, double > &training_labels)	FeatureFinderIdentificationAlgorithm	protected
isotope_pmin_	FeatureFinderIdentificationAlgorithm	protected
isotope_probs_	FeatureFinderIdentificationAlgorithm	protected
library_	FeatureFinderIdentificationAlgorithm	protected
mapping_tolerance_	FeatureFinderIdentificationAlgorithm	protected
MassTrace typedef	FeatureFinderIdentificationAlgorithm	protected
MassTraces typedef	FeatureFinderIdentificationAlgorithm	protected
min_peak_width_	FeatureFinderIdentificationAlgorithm	protected
ms_data_	FeatureFinderIdentificationAlgorithm	protected
mz_window_	FeatureFinderIdentificationAlgorithm	protected
mz_window_ppm_	FeatureFinderIdentificationAlgorithm	protected
n_external_features_	FeatureFinderIdentificationAlgorithm	protected
n_external_peps_	FeatureFinderIdentificationAlgorithm	protected
n_internal_features_	FeatureFinderIdentificationAlgorithm	protected
n_internal_peps_	FeatureFinderIdentificationAlgorithm	protected
n_isotopes_	FeatureFinderIdentificationAlgorithm	protected
operator=(const DefaultParamHandler &rhs)	DefaultParamHandler
operator==(const DefaultParamHandler &rhs) const	DefaultParamHandler	virtual
param_	DefaultParamHandler	protected
peak_width_	FeatureFinderIdentificationAlgorithm	protected
peptide_compare_	FeatureFinderIdentificationAlgorithm	protected
peptide_map_	FeatureFinderIdentificationAlgorithm	protected
PeptideMap typedef	FeatureFinderIdentificationAlgorithm	protected
PeptideRefRTMap typedef	FeatureFinderIdentificationAlgorithm	protected
postProcess_(FeatureMap &features, bool with_external_ids)	FeatureFinderIdentificationAlgorithm	protected
prog_log_	FeatureFinderIdentificationAlgorithm	protected
psm_score_cutoff_	FeatureFinderIdentificationAlgorithm	protected
quantify_decoys_	FeatureFinderIdentificationAlgorithm	protected
rt_quantile_	FeatureFinderIdentificationAlgorithm	protected
rt_window_	FeatureFinderIdentificationAlgorithm	protected
RTMap typedef	FeatureFinderIdentificationAlgorithm	protected
run(std::vector< PeptideIdentification > peptides, const std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features, const FeatureMap &seeds=FeatureMap(), const String &spectra_file="")	FeatureFinderIdentificationAlgorithm
runOnCandidates(FeatureMap &features)	FeatureFinderIdentificationAlgorithm
seed_rt_window_	FeatureFinderIdentificationAlgorithm	protected
setMSData(const PeakMap &ms_data)	FeatureFinderIdentificationAlgorithm
setMSData(PeakMap &&ms_data)	FeatureFinderIdentificationAlgorithm
setName(const String &name)	DefaultParamHandler
setParameters(const Param &param)	DefaultParamHandler
signal_to_noise_	FeatureFinderIdentificationAlgorithm	protected
statistics_(const FeatureMap &features) const	FeatureFinderIdentificationAlgorithm	protected
subsections_	DefaultParamHandler	protected
svm_min_prob_	FeatureFinderIdentificationAlgorithm	protected
svm_n_parts_	FeatureFinderIdentificationAlgorithm	protected
svm_n_samples_	FeatureFinderIdentificationAlgorithm	protected
svm_predictor_names_	FeatureFinderIdentificationAlgorithm	protected
svm_probs_external_	FeatureFinderIdentificationAlgorithm	protected
svm_probs_internal_	FeatureFinderIdentificationAlgorithm	protected
svm_quality_cutoff	FeatureFinderIdentificationAlgorithm	protected
svm_xval_out_	FeatureFinderIdentificationAlgorithm	protected
trafo_external_	FeatureFinderIdentificationAlgorithm	protected
unassignedIDs_	FeatureFinderIdentificationAlgorithm	protected
updateMembers_() override	FeatureFinderIdentificationAlgorithm	protectedvirtual
use_psm_cutoff_	FeatureFinderIdentificationAlgorithm	protected
warn_empty_defaults_	DefaultParamHandler	protected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")	DefaultParamHandler	static
~DefaultParamHandler()	DefaultParamHandler	virtual