Package org.biopax.paxtools.pattern.miner

Class CommonIDFetcher

java.lang.Object

org.biopax.paxtools.pattern.miner.CommonIDFetcher

All Implemented Interfaces:

IDFetcher

public class CommonIDFetcher
extends Object
implements IDFetcher

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).

Author:

Ozgun Babur et al.

Constructor Summary

Constructors

Constructor	Description
CommonIDFetcher()

Method Summary

Modifier and Type	Method	Description
Set<String>	fetchID(BioPAXElement ele)	Finds a String ID for the given element.
void	setUseUniprotIDs(boolean useUniprotIDs)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CommonIDFetcher

public CommonIDFetcher()

Method Details

fetchID

public Set<String> fetchID(BioPAXElement ele)

Description copied from interface: IDFetcher

Finds a String ID for the given element.

Specified by:

fetchID in interface IDFetcher

Parameters:

ele - element to fecth the ID from

Returns:

ID

setUseUniprotIDs

public void setUseUniprotIDs(boolean useUniprotIDs)