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FeatureFinderIdentificationAlgorithm Member List

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

add_mass_offset_peptides_FeatureFinderIdentificationAlgorithmprotected
addOffsetPeptides_(std::vector< PeptideIdentification > &peptides, double offset)FeatureFinderIdentificationAlgorithmprotected
addPeptideRT_(TargetedExperiment::Peptide &peptide, double rt) constFeatureFinderIdentificationAlgorithmprotected
addPeptideToMap_(PeptideIdentification &peptide, PeptideMap &peptide_map, bool external=false)FeatureFinderIdentificationAlgorithmprotected
addSeeds_(std::vector< PeptideIdentification > &peptides, const FeatureMap &seeds)FeatureFinderIdentificationAlgorithmprotected
annotateFeatures_(FeatureMap &features, PeptideRefRTMap &ref_rt_map)FeatureFinderIdentificationAlgorithmprotected
annotateFeaturesFinalizeAssay_(FeatureMap &features, std::map< Size, std::vector< PeptideIdentification * > > &feat_ids, RTMap &rt_internal)FeatureFinderIdentificationAlgorithmprotected
batch_size_FeatureFinderIdentificationAlgorithmprotected
calculateFDR_(FeatureMap &features)FeatureFinderIdentificationAlgorithmprotected
candidates_out_FeatureFinderIdentificationAlgorithmprotected
ChargeMap typedefFeatureFinderIdentificationAlgorithmprotected
check_defaults_DefaultParamHandlerprotected
checkNumObservations_(Size n_pos, Size n_neg, const String &note="") constFeatureFinderIdentificationAlgorithmprotected
chrom_data_FeatureFinderIdentificationAlgorithmprotected
chunk_(It range_from, It range_to, const std::ptrdiff_t batch_size)FeatureFinderIdentificationAlgorithminlineprotected
classifyFeatures_(FeatureMap &features)FeatureFinderIdentificationAlgorithmprotected
createAssayLibrary_(const PeptideMap::iterator &begin, const PeptideMap::iterator &end, PeptideRefRTMap &ref_rt_map, bool clear_IDs=true)FeatureFinderIdentificationAlgorithmprotected
debug_level_FeatureFinderIdentificationAlgorithmprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
elution_model_FeatureFinderIdentificationAlgorithmprotected
ensureConvexHulls_(Feature &feature) constFeatureFinderIdentificationAlgorithmprotected
error_name_DefaultParamHandlerprotected
feat_finder_FeatureFinderIdentificationAlgorithmprotected
feature_compare_FeatureFinderIdentificationAlgorithmprotected
feature_filter_peptides_FeatureFinderIdentificationAlgorithmprotected
feature_filter_quality_FeatureFinderIdentificationAlgorithmprotected
FeatureFinderIdentificationAlgorithm()FeatureFinderIdentificationAlgorithm
filterFeatures_(FeatureMap &features, bool classified)FeatureFinderIdentificationAlgorithmprotected
filterFeaturesFinalizeAssay_(Feature &best_feature, double best_quality, const double quality_cutoff)FeatureFinderIdentificationAlgorithmprotected
generateTransitions_(const String &peptide_id, double mz, Int charge, const IsotopeDistribution &iso_dist)FeatureFinderIdentificationAlgorithmprotected
getChromatograms()FeatureFinderIdentificationAlgorithm
getChromatograms() constFeatureFinderIdentificationAlgorithm
getDefaults() constDefaultParamHandler
getLibrary()FeatureFinderIdentificationAlgorithm
getLibrary() constFeatureFinderIdentificationAlgorithm
getMSData()FeatureFinderIdentificationAlgorithm
getMSData() constFeatureFinderIdentificationAlgorithm
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getProgressLogger()FeatureFinderIdentificationAlgorithm
getProgressLogger() constFeatureFinderIdentificationAlgorithm
getRandomSample_(std::map< Size, double > &training_labels) constFeatureFinderIdentificationAlgorithmprotected
getRTRegions_(ChargeMap &peptide_data, std::vector< RTRegion > &rt_regions, bool clear_IDs=true) constFeatureFinderIdentificationAlgorithmprotected
getSubsections() constDefaultParamHandler
getUnbiasedSample_(const std::multimap< double, std::pair< Size, bool > > &valid_obs, std::map< Size, double > &training_labels)FeatureFinderIdentificationAlgorithmprotected
isotope_pmin_FeatureFinderIdentificationAlgorithmprotected
isotope_probs_FeatureFinderIdentificationAlgorithmprotected
library_FeatureFinderIdentificationAlgorithmprotected
mapping_tolerance_FeatureFinderIdentificationAlgorithmprotected
MassTrace typedefFeatureFinderIdentificationAlgorithmprotected
MassTraces typedefFeatureFinderIdentificationAlgorithmprotected
min_peak_width_FeatureFinderIdentificationAlgorithmprotected
ms_data_FeatureFinderIdentificationAlgorithmprotected
mz_window_FeatureFinderIdentificationAlgorithmprotected
mz_window_ppm_FeatureFinderIdentificationAlgorithmprotected
n_external_features_FeatureFinderIdentificationAlgorithmprotected
n_external_peps_FeatureFinderIdentificationAlgorithmprotected
n_internal_features_FeatureFinderIdentificationAlgorithmprotected
n_internal_peps_FeatureFinderIdentificationAlgorithmprotected
n_isotopes_FeatureFinderIdentificationAlgorithmprotected
operator=(const DefaultParamHandler &rhs)DefaultParamHandler
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
peak_width_FeatureFinderIdentificationAlgorithmprotected
peptide_compare_FeatureFinderIdentificationAlgorithmprotected
peptide_map_FeatureFinderIdentificationAlgorithmprotected
PeptideMap typedefFeatureFinderIdentificationAlgorithmprotected
PeptideRefRTMap typedefFeatureFinderIdentificationAlgorithmprotected
postProcess_(FeatureMap &features, bool with_external_ids)FeatureFinderIdentificationAlgorithmprotected
prog_log_FeatureFinderIdentificationAlgorithmprotected
psm_score_cutoff_FeatureFinderIdentificationAlgorithmprotected
quantify_decoys_FeatureFinderIdentificationAlgorithmprotected
rt_quantile_FeatureFinderIdentificationAlgorithmprotected
rt_window_FeatureFinderIdentificationAlgorithmprotected
RTMap typedefFeatureFinderIdentificationAlgorithmprotected
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_FeatureFinderIdentificationAlgorithmprotected
setMSData(const PeakMap &ms_data)FeatureFinderIdentificationAlgorithm
setMSData(PeakMap &&ms_data)FeatureFinderIdentificationAlgorithm
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
signal_to_noise_FeatureFinderIdentificationAlgorithmprotected
statistics_(const FeatureMap &features) constFeatureFinderIdentificationAlgorithmprotected
subsections_DefaultParamHandlerprotected
svm_min_prob_FeatureFinderIdentificationAlgorithmprotected
svm_n_parts_FeatureFinderIdentificationAlgorithmprotected
svm_n_samples_FeatureFinderIdentificationAlgorithmprotected
svm_predictor_names_FeatureFinderIdentificationAlgorithmprotected
svm_probs_external_FeatureFinderIdentificationAlgorithmprotected
svm_probs_internal_FeatureFinderIdentificationAlgorithmprotected
svm_quality_cutoffFeatureFinderIdentificationAlgorithmprotected
svm_xval_out_FeatureFinderIdentificationAlgorithmprotected
trafo_external_FeatureFinderIdentificationAlgorithmprotected
unassignedIDs_FeatureFinderIdentificationAlgorithmprotected
updateMembers_() overrideFeatureFinderIdentificationAlgorithmprotectedvirtual
use_psm_cutoff_FeatureFinderIdentificationAlgorithmprotected
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual