Uses of Class
uk.ac.ebi.pride.utilities.pia.modeller.scores.protein.ProteinScoring

Packages that use ProteinScoring

Package	Description
uk.ac.ebi.pride.utilities.pia.modeller.protein
uk.ac.ebi.pride.utilities.pia.modeller.protein.inference
uk.ac.ebi.pride.utilities.pia.modeller.scores.protein

Uses of ProteinScoring in uk.ac.ebi.pride.utilities.pia.modeller.protein

Methods in uk.ac.ebi.pride.utilities.pia.modeller.protein with parameters of type ProteinScoring

Modifier and Type	Method and Description
void	ProteinModeller.infereProteins(PeptideScoring peptideScoring, ProteinScoring proteinScoring, Class<? extends AbstractProteinInference> proteinInferenceClass, List<AbstractFilter> filters, boolean considerModifications) Runs the protein inference with the given settings and stores the protein groups in a list, which can be returned by ProteinModeller.getInferredProteins()

Uses of ProteinScoring in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference

Fields in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference declared as ProteinScoring

Modifier and Type	Field and Description
protected ProteinScoring	AbstractProteinInference.proteinScoring the currently set protein scoring

Constructors in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference with parameters of type ProteinScoring

Constructor and Description
AbstractProteinInference(IntermediateStructure intermediateStructure, PeptideScoring peptideScoring, ProteinScoring proteinScoring, List<AbstractFilter> filters, Integer nrThreads) The constructor works using a DataAccessController.
OccamsRazorInference(IntermediateStructure intermediateStructure, PeptideScoring peptideScoring, ProteinScoring proteinScoring, List<AbstractFilter> filters, Integer nrThreads)
ReportAllInference(IntermediateStructure intermediateStructure, PeptideScoring peptideScoring, ProteinScoring proteinScoring, List<AbstractFilter> filters, Integer nrThreads)

Uses of ProteinScoring in uk.ac.ebi.pride.utilities.pia.modeller.scores.protein

Subclasses of ProteinScoring in uk.ac.ebi.pride.utilities.pia.modeller.scores.protein

Modifier and Type	Class and Description
class	ProteinScoringAdditive Calculates the score of the protein by adding up the scores of peptides.
class	ProteinScoringMultiplicative Calculates the score of the protein by multiplying up the scores of peptides and returning the -log10 of the score (log for numeric reasons, minus to get higherScoreBetter)