Uses of Interface
org.biopax.paxtools.pattern.miner.IDFetcher

Packages that use IDFetcher

Package	Description
org.biopax.paxtools.pattern.constraint	Package for constraints.
org.biopax.paxtools.pattern.miner	Package for pattern miner utility.

Uses of IDFetcher in org.biopax.paxtools.pattern.constraint

Constructors in org.biopax.paxtools.pattern.constraint with parameters of type IDFetcher

Modifier	Constructor	Description
	HasAnID(IDFetcher fetcher, Map<BioPAXElement,Set<String>> idMap)	Constructor with the ID fetcher.

Uses of IDFetcher in org.biopax.paxtools.pattern.miner

Classes in org.biopax.paxtools.pattern.miner that implement IDFetcher

Modifier and Type	Class	Description
class	CommonIDFetcher	Tries to get Gene Symbols or UniProt IDs for genes and - display names for small molecules; This id-fetcher is mainly to use with the BioPAX pathway data from Pathway Commons (PC2) db (normalized and enriched with xrefs).
class	ConfigurableIDFetcher	Tries to get preferred type IDs of an entity reference.
class	SimpleIDFetcher	Simple gets the URI (of an entity reference);

Fields in org.biopax.paxtools.pattern.miner declared as IDFetcher

Modifier and Type	Field	Description
protected IDFetcher	MinerAdapter.idFetcher	ID fetcher is used for skipping objects that cannot generate a valid ID during the search.

Methods in org.biopax.paxtools.pattern.miner with parameters of type IDFetcher

Modifier and Type	Method	Description
Set<SIFInteraction>	MinerAdapter.createSIFInteraction(Match m, IDFetcher fetcher)	Creates a SIF interaction for the given match.
Set<SIFInteraction>	SIFMiner.createSIFInteraction(Match m, IDFetcher fetcher)	Creates SIF interactions for the given match.
protected Set<String>	MinerAdapter.fetchIDs(BioPAXElement ele, IDFetcher fetcher)
void	MinerAdapter.setIDFetcher(IDFetcher idFetcher)	Sets the ID fetcher to use during SIF search.
void	SIFMiner.setIDFetcher(IDFetcher idFetcher)	Sets the idFetcher that helps to fasten the search.

Constructors in org.biopax.paxtools.pattern.miner with parameters of type IDFetcher

Modifier	Constructor	Description
	SIFSearcher(IDFetcher idFetcher, SIFMiner... miners)	Constructor with ID fetcher and miners.
	SIFSearcher(IDFetcher idFetcher, SIFType... types)	Constructor with ID fetcher and binary interaction types.