Uses of Class
uk.ac.ebi.pride.utilities.pia.modeller.protein.inference.InferenceProteinGroup

Packages that use InferenceProteinGroup

Package	Description
uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl
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 InferenceProteinGroup in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl

Methods in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl with parameters of type InferenceProteinGroup

Modifier and Type	Method and Description
static uk.ac.ebi.pride.utilities.data.core.ProteinGroup	PrideUtilities.convertInferenceProteinGroup(InferenceProteinGroup piaGroup, boolean includingSubGroups, boolean completePrideProteins) Converts a InferenceProteinGroup from any protein inference into a PRIDE ProteinGroup.

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

Methods in uk.ac.ebi.pride.utilities.pia.modeller.protein that return types with arguments of type InferenceProteinGroup

Modifier and Type	Method and Description
List<InferenceProteinGroup>	ProteinModeller.getInferredProteins() Returns a list of the inferred protein groups.

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

Methods in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference that return types with arguments of type InferenceProteinGroup

Modifier and Type	Method and Description
List<InferenceProteinGroup>	ReportAllInference.calculateInference(boolean considerModifications)
List<InferenceProteinGroup>	OccamsRazorInference.calculateInference(boolean considerModifications)
abstract List<InferenceProteinGroup>	AbstractProteinInference.calculateInference(boolean considerModifications) calculateInference is the method of the abstract class which allows the class to compute the protein groups and create the List of different groups.
Set<InferenceProteinGroup>	InferenceProteinGroup.getSubGroups() Returns the set of sub-groups

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

Modifier and Type	Method and Description
boolean	InferenceProteinGroup.addSubgroup(InferenceProteinGroup proteinGroup) Adds a protein group to the subGroups of this group

Method parameters in uk.ac.ebi.pride.utilities.pia.modeller.protein.inference with type arguments of type InferenceProteinGroup

Modifier and Type	Method and Description
void	OccamsRazorInference.addToReports(List<InferenceProteinGroup> proteinGroups) Adds the proteinGroups to the list of reported ProteinGroups.

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

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

Modifier and Type	Method and Description
Double	ProteinScoringMultiplicative.calculateProteinScore(InferenceProteinGroup proteinGroup)
Double	ProteinScoringAdditive.calculateProteinScore(InferenceProteinGroup proteinGroup)
abstract Double	ProteinScoring.calculateProteinScore(InferenceProteinGroup proteinGroup) Calculates the protein score for the inference group.