Package org.biojava.bio.program.homologene

Class HomologeneTools

java.lang.Object

org.biojava.bio.program.homologene.HomologeneTools

public class HomologeneTools
extends Object

Homologene is a NCBI dataset that curates sets of orthologues from the reference model ogranisms.

This class is a Collection of methods for handling data from the Homologene dataset.

Author:

David Huen

Constructor Summary

Constructors

Constructor	Description
HomologeneTools()

Method Summary

Modifier and Type	Method	Description
static Taxon	createTaxon(int taxonID, String description)	add a Taxon
static Taxon	getTaxon(int taxonID)	get the Taxon corresponding to this Taxon ID
static void	instantiateDB(URL url, HomologeneBuilder builder)	instantiate a HomologeneDB.

Methods inherited from class java.lang.Object

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

Constructor Detail

HomologeneTools

public HomologeneTools()

Method Detail

getTaxon

public static Taxon getTaxon(int taxonID)

get the Taxon corresponding to this Taxon ID

createTaxon

public static Taxon createTaxon(int taxonID,
                                String description)
                         throws DuplicateTaxonException

add a Taxon

Throws:

DuplicateTaxonException

instantiateDB

public static void instantiateDB(URL url,
                                 HomologeneBuilder builder)
                          throws OperationNotSupportedException,
                                 FileNotFoundException,
                                 IOException

instantiate a HomologeneDB.

Currently, only file protocol support is available.

Throws:

OperationNotSupportedException

FileNotFoundException

IOException