NuXLRTPrediction Struct Reference

Collaboration diagram for NuXLRTPrediction:

Public Member Functions
map< char, double >	encodeAAHist_ (const AASequence &aa_seq)
map< char, double >	encodeNAHist_ (const String &seq)
std::tuple< SimpleSVM::PredictorMap, map< size_t, double > >	buildPredictorsAndResponseFromIdentifiedFeatures_ (const FeatureMap &features)
std::tuple< SimpleSVM::PredictorMap, map< size_t, double > >	buildPredictorsAndResponse_ (const PeptideIdentificationList &peptides, bool all_hits)
void	train (const std::string &spectra_filename, PeptideIdentificationList peptides, const vector< ProteinIdentification > &proteins)
void	annotatePredictions_ (const vector< SimpleSVM::Prediction > &preds, PeptideIdentificationList &peptides, bool all_hits)
void	predict (PeptideIdentificationList &peptides)

Public Attributes
SimpleSVM	svm
String	nucleotides = "CATGUXS"
String	amino_acids = "ACDEFGHIKLMNPQRSTVWYkmsty"

Member Function Documentation

annotatePredictions_()

void annotatePredictions_ ( const vector< SimpleSVM::Prediction > & preds, PeptideIdentificationList & peptides, bool all_hits )

inline

Referenced by predict().

buildPredictorsAndResponse_()

std::tuple< SimpleSVM::PredictorMap, map< size_t, double > > buildPredictorsAndResponse_ ( const PeptideIdentificationList & peptides, bool all_hits )

inline

References amino_acids, encodeAAHist_(), encodeNAHist_(), and nucleotides.

Referenced by predict().

buildPredictorsAndResponseFromIdentifiedFeatures_()

std::tuple< SimpleSVM::PredictorMap, map< size_t, double > > buildPredictorsAndResponseFromIdentifiedFeatures_ ( const FeatureMap & features )

inline

References amino_acids, encodeAAHist_(), encodeNAHist_(), and nucleotides.

Referenced by train().

encodeAAHist_()

map< char, double > encodeAAHist_ ( const AASequence & aa_seq )

inline

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

encodeNAHist_()

map< char, double > encodeNAHist_ ( const String & seq )

inline

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

predict()

void predict ( PeptideIdentificationList & peptides )

inline

References annotatePredictions_(), buildPredictorsAndResponse_(), and svm.

train()

void train ( const std::string & spectra_filename, PeptideIdentificationList peptides, const vector< ProteinIdentification > & proteins )

inline

References buildPredictorsAndResponseFromIdentifiedFeatures_(), and svm.

Member Data Documentation

amino_acids

String amino_acids = "ACDEFGHIKLMNPQRSTVWYkmsty"

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

nucleotides

String nucleotides = "CATGUXS"

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

svm

SimpleSVM svm

Referenced by predict(), and train().