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

Class NcbiGeneLoader

java.lang.Object

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

public class NcbiGeneLoader
extends Object

Load or update information about genes from the NCBI Gene database.

Author:

jsantos, paul

Constructor Summary

Constructors

Constructor	Description
NcbiGeneLoader()
NcbiGeneLoader(Persister persisterHelper)

Method Summary

Modifier and Type	Method	Description
int	getLoadedGeneCount()
boolean	isLoaderDone()
void	load(boolean filterTaxa)	download the gene_info and gene2accession files, then call load
void	load(String geneInfoFile, String gene2AccFile, String geneHistoryFile, String geneEnsemblFile, boolean filterTaxa)
void	load(String geneInfoFile, String gene2AccFile, String geneHistoryFile, String geneEnsemblFile, Taxon t)
void	load(Taxon t)
void	setPersisterHelper(Persister persisterHelper)
void	setSkipDownload(boolean skipDownload)	Set to true to avoid downloading the files, if copies already exist (not recommended if you want an update!)
void	setStartingNcbiId(Integer startNcbiid)	Indicate
void	setTaxonService(TaxonService bean)
void	updateTaxaWithGenesUsable(Collection<Taxon> taxaGenesLoaded)	Method to update taxon to indicate that genes have been loaded for that taxon are are usable.

Methods inherited from class java.lang.Object

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

Constructor Detail

NcbiGeneLoader

public NcbiGeneLoader()

NcbiGeneLoader

public NcbiGeneLoader(Persister persisterHelper)

Method Detail

getLoadedGeneCount

public int getLoadedGeneCount()

Returns:

the loadedGeneCount

isLoaderDone

public boolean isLoaderDone()

load

public void load(boolean filterTaxa)

download the gene_info and gene2accession files, then call load

Parameters:

filterTaxa - filter taxa

load

public void load(String geneInfoFile,
                 String gene2AccFile,
                 String geneHistoryFile,
                 String geneEnsemblFile,
                 boolean filterTaxa)

Parameters:

geneInfoFile - the gene_info file

gene2AccFile - the gene2accession file

geneHistoryFile - history file

geneEnsemblFile - mapping file

filterTaxa - should we filter out taxa we're not supporting

load

public void load(String geneInfoFile,
                 String gene2AccFile,
                 String geneHistoryFile,
                 String geneEnsemblFile,
                 Taxon t)

load

public void load(Taxon t)

setPersisterHelper

public void setPersisterHelper(Persister persisterHelper)

Parameters:

persisterHelper - the persisterHelper to set

setTaxonService

public void setTaxonService(TaxonService bean)

updateTaxaWithGenesUsable

public void updateTaxaWithGenesUsable(Collection<Taxon> taxaGenesLoaded)

Method to update taxon to indicate that genes have been loaded for that taxon are are usable. If there is a parent taxon for this species and it has genes loaded against it then use that parent's taxons genes rather than the species found in NCBI. Set the flag genesUSable to false for that child taxon that was found in ncbi.

Parameters:

taxaGenesLoaded - List of taxa that have had genes loaded into GEMMA from NCBI.

setSkipDownload

public void setSkipDownload(boolean skipDownload)

Set to true to avoid downloading the files, if copies already exist (not recommended if you want an update!)

Parameters:

skipDownload - skip download

setStartingNcbiId

public void setStartingNcbiId(Integer startNcbiid)

Indicate

Parameters:

startNcbiid - start ncbi id