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

Class NcbiGeneConverter

java.lang.Object

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

All Implemented Interfaces:

Converter<Object,Object>

public class NcbiGeneConverter
extends Object
implements Converter<Object,Object>

Convert NCBIGene2Accession objects into Gemma Gene objects with associated GeneProducts. Genes without products are ignored.

Author:

pavlidis, jrsantos

Constructor Summary

Constructors

Constructor	Description
NcbiGeneConverter()

Method Summary

Modifier and Type	Method	Description
Object	convert(Object sourceDomainObject)
Collection<Object>	convert(Collection<?> sourceDomainObjects)
void	convert(BlockingQueue<NcbiGeneData> geneInfoQueue, BlockingQueue<Gene> geneQueue)
Collection<GeneProduct>	convert(NCBIGene2Accession acc, Gene gene)
Gene	convert(NCBIGeneInfo info)
Gene	convert(NcbiGeneData data)
static ExternalDatabase	getEnsembl()
static ExternalDatabase	getGenbank()
boolean	isProducerDone()
void	setProducerDoneFlag(AtomicBoolean flag)
void	setSourceDoneFlag(AtomicBoolean flag)

Methods inherited from class java.lang.Object

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

Constructor Details

NcbiGeneConverter

public NcbiGeneConverter()

Method Details

getGenbank

public static ExternalDatabase getGenbank()

Returns:

the genBank

getEnsembl

public static ExternalDatabase getEnsembl()

Returns:

the ensembl

convert

public Collection<Object> convert(Collection<?> sourceDomainObjects)

Specified by:

convert in interface Converter<Object,Object>

convert

public Object convert(Object sourceDomainObject)

Specified by:

convert in interface Converter<Object,Object>

convert

public Gene convert(NCBIGeneInfo info)

convert

public Collection<GeneProduct> convert(NCBIGene2Accession acc,
 Gene gene)

convert

public Gene convert(NcbiGeneData data)

convert

public void convert(BlockingQueue<NcbiGeneData> geneInfoQueue,
 BlockingQueue<Gene> geneQueue)

isProducerDone

public boolean isProducerDone()

setProducerDoneFlag

public void setProducerDoneFlag(AtomicBoolean flag)

setSourceDoneFlag

public void setSourceDoneFlag(AtomicBoolean flag)