| OpenMS 2.5.0

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) const | 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 | inline protected
classifyFeatures_(FeatureMap &features) | FeatureFinderIdentificationAlgorithm | protected
createAssayLibrary_(const PeptideMap::iterator &begin, const PeptideMap::iterator &end, PeptideRefRTMap &ref_rt_map) | FeatureFinderIdentificationAlgorithm | protected
debug_level_ | FeatureFinderIdentificationAlgorithm | protected
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
elution_model_ | FeatureFinderIdentificationAlgorithm | protected
ensureConvexHulls_(Feature &feature) | 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 | inline
getChromatograms() const | FeatureFinderIdentificationAlgorithm | inline
getDefaults() const | DefaultParamHandler |
getLibrary() | FeatureFinderIdentificationAlgorithm | inline
getLibrary() const | FeatureFinderIdentificationAlgorithm | inline
getMSData() | FeatureFinderIdentificationAlgorithm | inline
getMSData() const | FeatureFinderIdentificationAlgorithm | inline
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getProgressLogger() | FeatureFinderIdentificationAlgorithm | inline
getProgressLogger() const | FeatureFinderIdentificationAlgorithm | inline
getRandomSample_(std::map< Size, Int > &training_labels) | FeatureFinderIdentificationAlgorithm | protected
getRTRegions_(ChargeMap &peptide_data, std::vector< RTRegion > &rt_regions) const | FeatureFinderIdentificationAlgorithm | protected
getSubsections() const | DefaultParamHandler |
getUnbiasedSample_(const std::multimap< double, std::pair< Size, bool > > &valid_obs, std::map< Size, Int > &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 | virtual
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
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()) | FeatureFinderIdentificationAlgorithm |
runOnCandidates(FeatureMap &features) | 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
updateMembers_() override | FeatureFinderIdentificationAlgorithm | protected virtual
warn_empty_defaults_ | DefaultParamHandler | protected
~DefaultParamHandler() | DefaultParamHandler | virtual