FFIDAlgoExternalIDHandler Member List

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

addDummyPeptideID_(Feature &feature, const PeptideIdentification *ext_id)	FFIDAlgoExternalIDHandler	private
addExternalPeptide(PeptideIdentification &peptide)	FFIDAlgoExternalIDHandler
addExternalPeptideToMap_(PeptideIdentification &peptide, std::map< AASequence, std::map< Int, std::pair< std::multimap< double, PeptideIdentification * >, std::multimap< double, PeptideIdentification * >>>> &peptide_map)	FFIDAlgoExternalIDHandler	private
adjustFDRForExternalFeatures_(std::vector< double > &fdr_probs, std::vector< double > &fdr_qvalues, Size n_internal_features)	FFIDAlgoExternalIDHandler	private
alignInternalAndExternalIDs(const std::vector< PeptideIdentification > &peptides_internal, const std::vector< PeptideIdentification > &peptides_external, double rt_quantile)	FFIDAlgoExternalIDHandler
annotateFeatureWithExternalIDs_(Feature &feature)	FFIDAlgoExternalIDHandler	private
calculateFDR(FeatureMap &features)	FFIDAlgoExternalIDHandler
checkNumObservations_(Size n_pos, Size n_neg, const String &note="") const	FFIDAlgoExternalIDHandler	private
classifyFeaturesWithSVM(FeatureMap &features, const Param &param)	FFIDAlgoExternalIDHandler
debug_level_	FFIDAlgoExternalIDHandler	private
external_peptide_map_	FFIDAlgoExternalIDHandler	private
ExternalChargeMap typedef	FFIDAlgoExternalIDHandler
ExternalPeptideMap typedef	FFIDAlgoExternalIDHandler
ExternalRTMap typedef	FFIDAlgoExternalIDHandler
FFIDAlgoExternalIDHandler()	FFIDAlgoExternalIDHandler
fillExternalRTMap_(const AASequence &sequence, Int charge, std::multimap< double, PeptideIdentification * > &rt_map)	FFIDAlgoExternalIDHandler	private
filterClassifiedFeatures(FeatureMap &features, double quality_cutoff)	FFIDAlgoExternalIDHandler
finalizeAssayFeatures_(Feature &best_feature, double best_quality, double quality_cutoff)	FFIDAlgoExternalIDHandler	private
getRandomSample_(std::map< Size, double > &training_labels)	FFIDAlgoExternalIDHandler	private
getRTTransformation() const	FFIDAlgoExternalIDHandler
getSVMProbsInternal() const	FFIDAlgoExternalIDHandler
getUnbiasedSample_(const std::multimap< double, std::pair< Size, bool > > &valid_obs, std::map< Size, double > &training_labels)	FFIDAlgoExternalIDHandler	private
handleExternalFeature_(Feature &feature, double prob_positive, double quality_cutoff)	FFIDAlgoExternalIDHandler	private
hasRTTransformation() const	FFIDAlgoExternalIDHandler
initSVMParameters_(const Param &param)	FFIDAlgoExternalIDHandler	private
n_external_features_	FFIDAlgoExternalIDHandler	private
n_external_peptides_	FFIDAlgoExternalIDHandler	private
n_internal_features_	FFIDAlgoExternalIDHandler	private
processExternalPeptides(std::vector< PeptideIdentification > &peptides_ext)	FFIDAlgoExternalIDHandler
reset()	FFIDAlgoExternalIDHandler
rt_transformation_	FFIDAlgoExternalIDHandler	private
svm_min_prob_	FFIDAlgoExternalIDHandler	private
svm_n_parts_	FFIDAlgoExternalIDHandler	private
svm_n_samples_	FFIDAlgoExternalIDHandler	private
svm_predictor_names_	FFIDAlgoExternalIDHandler	private
svm_probs_external_	FFIDAlgoExternalIDHandler	private
svm_probs_internal_	FFIDAlgoExternalIDHandler	private
svm_quality_cutoff	FFIDAlgoExternalIDHandler	private
svm_xval_out_	FFIDAlgoExternalIDHandler	private
transformRT(double rt) const	FFIDAlgoExternalIDHandler