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

Class NcbiGeneDomainObjectGenerator

java.lang.Object

ubic.gemma.core.loader.genome.gene.ncbi.NcbiGeneDomainObjectGenerator

public class NcbiGeneDomainObjectGenerator
extends Object

Combines information from the gene2accession and gene_info files from NCBI Gene.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
NcbiGeneDomainObjectGenerator(Collection<Taxon> taxa)

Method Summary

Modifier and Type	Method	Description
void	generate(BlockingQueue<NcbiGeneData> queue)
void	generateLocal(String geneInfoFilePath, String gene2AccesionFilePath, String geneHistoryFilePath, String geneEnsemblFilePath, BlockingQueue<NcbiGeneData> queue)
Collection<Taxon>	getSupportedTaxaWithNCBIGenes()	Those taxa that are supported by GEMMA and have genes in NCBI.
boolean	isDoDownload()
boolean	isProducerDone()
void	setDoDownload(boolean doDownload)
void	setProducerDoneFlag(AtomicBoolean flag)
void	setStartingNcbiId(Integer startingNcbiId)

Methods inherited from class java.lang.Object

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

Constructor Detail

NcbiGeneDomainObjectGenerator

public NcbiGeneDomainObjectGenerator(Collection<Taxon> taxa)

Method Detail

isDoDownload

public boolean isDoDownload()

setDoDownload

public void setDoDownload(boolean doDownload)

generate

public void generate(BlockingQueue<NcbiGeneData> queue)

Parameters:

queue - queue

generateLocal

public void generateLocal(String geneInfoFilePath,
                          String gene2AccesionFilePath,
                          String geneHistoryFilePath,
                          String geneEnsemblFilePath,
                          BlockingQueue<NcbiGeneData> queue)

isProducerDone

public boolean isProducerDone()

setProducerDoneFlag

public void setProducerDoneFlag(AtomicBoolean flag)

getSupportedTaxaWithNCBIGenes

public Collection<Taxon> getSupportedTaxaWithNCBIGenes()

Those taxa that are supported by GEMMA and have genes in NCBI.

Returns:

Collection of taxa that are supported by the GEMMA and have genes held by NCBI.

setStartingNcbiId

public void setStartingNcbiId(Integer startingNcbiId)