NuXLRTPrediction Struct Reference

Collaboration diagram for NuXLRTPrediction:

Public Member Functions
map< char, double >	encodeAAHist_ (const AASequence &aa_seq)
map< char, double >	encodeNAHist_ (const std::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
std::string	nucleotides = "CATGUXS"
std::string	amino_acids = "ACDEFGHIKLMNPQRSTVWYkmsty"

Member Function Documentation

annotatePredictions_()

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

inline

References MetaInfoInterface::setMetaValue().

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_(), PeptideHit::getCharge(), MetaInfoInterface::getMetaValue(), PeptideHit::getSequence(), nucleotides, OpenMS::RT, OpenMS::StringUtils::toStr(), and AASequence::toUnmodifiedString().

Referenced by predict().

buildPredictorsAndResponseFromIdentifiedFeatures_()

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

inline

References amino_acids, encodeAAHist_(), encodeNAHist_(), MetaInfoInterface::getMetaValue(), PeptideHit::getSequence(), nucleotides, OpenMS::RT, OpenMS::StringUtils::toStr(), and AASequence::toUnmodifiedString().

Referenced by train().

encodeAAHist_()

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

inline

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

encodeNAHist_()

map< char, double > encodeNAHist_ ( const std::string &  seq )

inline

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

predict()

void predict ( PeptideIdentificationList &  peptides )

inline

References annotatePredictions_(), buildPredictorsAndResponse_(), SimpleSVM::predict(), and svm.

train()

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

inline

References PeakFileOptions::addMSLevel(), buildPredictorsAndResponseFromIdentifiedFeatures_(), FeatureFinderIdentificationAlgorithm::getMSData(), MzMLFile::getOptions(), DefaultParamHandler::getParameters(), MzMLFile::load(), FeatureFinderIdentificationAlgorithm::run(), DefaultParamHandler::setParameters(), SimpleSVM::setup(), Param::setValue(), and svm.

Member Data Documentation

amino_acids

std::string amino_acids = "ACDEFGHIKLMNPQRSTVWYkmsty"

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

nucleotides

std::string nucleotides = "CATGUXS"

Referenced by buildPredictorsAndResponse_(), and buildPredictorsAndResponseFromIdentifiedFeatures_().

svm

SimpleSVM svm

Referenced by predict(), and train().