Package ubic.gemma.core.loader.genome.gene.ncbi.homology

Class HomologeneServiceImpl

java.lang.Object

ubic.gemma.core.loader.genome.gene.ncbi.homology.HomologeneServiceImpl

All Implemented Interfaces:

HomologeneService

public class HomologeneServiceImpl
extends Object
implements HomologeneService

Reads in the homologene list as specified in the Gemmea.properties file. Loads the list at startup and keeps a mapping off.

You almost certainly want to call refresh() before using this service. This is done automatically if you use the

invalid reference

HomologeneServiceFactory

to lazy-load this service.

Author:

kelsey

See Also:

• invalid reference

  HomologeneServiceFactory

Constructor Summary

Constructors

Constructor	Description
HomologeneServiceImpl(GeneService geneService, TaxonService taxonService, org.springframework.core.io.Resource homologeneFile)

Method Summary

Modifier and Type	Method	Description
Gene	getHomologue(Gene gene, Taxon taxon)
Collection<Long>	getHomologues(Long ncbiId)
Collection<Gene>	getHomologues(Gene gene)
GeneValueObject	getHomologueValueObject(Long geneId, String taxonCommonName)
Collection<Long>	getNCBIGeneIdsInGroup(long homologeneGroupId)	Given an NCBI Homologene Group ID returns a list of all the NCBI Gene Ids in the given group
void	refresh()	Refresh homologene data.

Methods inherited from class java.lang.Object

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

Constructor Details

HomologeneServiceImpl

public HomologeneServiceImpl(GeneService geneService,
 TaxonService taxonService,
 org.springframework.core.io.Resource homologeneFile)

Method Details

getHomologue

public Gene getHomologue(Gene gene,
 Taxon taxon)

Specified by:

getHomologue in interface HomologeneService

Parameters:

gene - gene

taxon - desired taxon to find homologue in

Returns:

Finds the homologue of the given gene for the taxon specified, or null if there is no homologue

getHomologues

public Collection<Gene> getHomologues(Gene gene)

Specified by:

getHomologues in interface HomologeneService

Parameters:

gene - gene

Returns:

Collection of genes found in Gemma that are homologous with the given gene. Empty if no homologues or gene lacks homologue information, or null if not ready.

getHomologues

public Collection<Long> getHomologues(Long ncbiId)

Specified by:

getHomologues in interface HomologeneService

Parameters:

ncbiId - gene ncbi id

Returns:

A collection of NCBI gene ids that are homologous with the given NCBI Gene Id

refresh

public void refresh()
             throws IOException

Description copied from interface: HomologeneService

Refresh homologene data.

Specified by:

refresh in interface HomologeneService

Throws:

IOException

getHomologueValueObject

public GeneValueObject getHomologueValueObject(Long geneId,
 String taxonCommonName)

Specified by:

getHomologueValueObject in interface HomologeneService

Parameters:

geneId - gene id

taxonCommonName - desired taxon to find homologue in

Returns:

Finds the homologue of the given gene for the taxon specified, or null if there is no homologue

getNCBIGeneIdsInGroup

public Collection<Long> getNCBIGeneIdsInGroup(long homologeneGroupId)

Given an NCBI Homologene Group ID returns a list of all the NCBI Gene Ids in the given group

Specified by:

getNCBIGeneIdsInGroup in interface HomologeneService

Returns:

Collection of NCBI Gene Ids, or null if not ready.