Uses of Class
uk.ac.ebi.pride.utilities.pia.intermediate.IntermediateProtein

Packages that use IntermediateProtein

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

Uses of IntermediateProtein in uk.ac.ebi.pride.utilities.pia.intermediate

Methods in uk.ac.ebi.pride.utilities.pia.intermediate that return IntermediateProtein

Modifier and Type	Method and Description
IntermediateProtein	IntermediateStructureCreator.addProtein(IntermediateProtein protein) adds the given protein to the proteins map
IntermediateProtein	IntermediateStructureCreator.getProtein(Comparable proteinID) getter for the protein from the map with the given ID

Methods in uk.ac.ebi.pride.utilities.pia.intermediate that return types with arguments of type IntermediateProtein

Modifier and Type	Method and Description
Set<IntermediateProtein>	IntermediatePeptide.getAllProteins() Returns all proteins (if the group is assigned)
Set<IntermediateProtein>	IntermediateGroup.getAllProteins() Getter for the intermediateProtein of this group and all the parents.
Set<IntermediateProtein>	IntermediateGroup.getProteins() Getter for the proteins.

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

Modifier and Type	Method and Description
IntermediateProtein	IntermediateStructureCreator.addProtein(IntermediateProtein protein) adds the given protein to the proteins map
void	IntermediateGroup.addProtein(IntermediateProtein protein) Adds a new protein to the map of proteins.
void	IntermediateStructureCreator.addProteinInformation(String proteinAccession, IntermediateProtein newProtein) potentially adds further information to a protein, coming from e.g.
boolean	IntermediateGroup.directlyConnectedToProtein(IntermediateProtein protein) Returns true, if the group is directly connected to the dbSequence.
void	IntermediateGroup.removeProtein(IntermediateProtein protein) Removes the given dbSequence from the directly connected dbSequences

Method parameters in uk.ac.ebi.pride.utilities.pia.intermediate with type arguments of type IntermediateProtein

Modifier and Type	Method and Description
void	IntermediateStructureCreatorWorkerThread.insertIntoMap(IntermediatePeptide peptide, Set<IntermediateProtein> proteins, Map<Integer,IntermediateGroup> subGroups) Inserts the given peptide with its accessions into the intermediate format, which is then build up by the groups in subGroups.

Uses of IntermediateProtein in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl

Subclasses of IntermediateProtein in uk.ac.ebi.pride.utilities.pia.intermediate.prideimpl

Modifier and Type	Class and Description
class	PrideIntermediateProtein An intermediate class, which represents a protein

Uses of IntermediateProtein 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 IntermediateProtein

Modifier and Type	Method and Description
Set<IntermediateProtein>	InferenceProteinGroup.getProteins() Returns the set of proteins

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

Modifier and Type	Method and Description
boolean	InferenceProteinGroup.addProtein(IntermediateProtein protein) Adds one protein to the set of proteins