Uses of Class
ubic.gemma.model.common.description.LocalFile

Packages that use LocalFile

Package	Description
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.loader.association
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.arrayExpress
ubic.gemma.core.loader.expression.geo.fetcher
ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.loader.util.fetcher
ubic.gemma.model.common.description
ubic.gemma.persistence.util

Uses of LocalFile in ubic.gemma.core.analysis.preprocess.batcheffects

Method parameters in ubic.gemma.core.analysis.preprocess.batcheffects with type arguments of type LocalFile

Modifier and Type	Method	Description
Map<BioMaterial,Date>	BatchInfoParser.getBatchInfo(ExpressionExperiment ee, Collection<LocalFile> files)

Uses of LocalFile in ubic.gemma.core.loader.association

Methods in ubic.gemma.core.loader.association with parameters of type LocalFile

Modifier and Type	Method	Description
void	NCBIGene2GOAssociationLoader.load(LocalFile ncbiFile)

Uses of LocalFile in ubic.gemma.core.loader.expression.arrayDesign

Method parameters in ubic.gemma.core.loader.expression.arrayDesign with type arguments of type LocalFile

Modifier and Type	Method	Description
static Map<BioAssay,String>	AffyChipTypeExtractor.getChipTypes(ExpressionExperiment ee, Collection<LocalFile> files)	Extract a string like "Rat230_2" from CEL files.

Uses of LocalFile in ubic.gemma.core.loader.expression.arrayExpress

Methods in ubic.gemma.core.loader.expression.arrayExpress that return LocalFile

Modifier and Type	Method	Description
LocalFile	DataFileFetcher.getMageMlFile(Collection<LocalFile> files)

Methods in ubic.gemma.core.loader.expression.arrayExpress that return types with arguments of type LocalFile

Modifier and Type	Method	Description
Collection<LocalFile>	DataFileFetcher.fetch(String identifier)

Method parameters in ubic.gemma.core.loader.expression.arrayExpress with type arguments of type LocalFile

Modifier and Type	Method	Description
LocalFile	DataFileFetcher.getMageMlFile(Collection<LocalFile> files)

Uses of LocalFile in ubic.gemma.core.loader.expression.geo.fetcher

Methods in ubic.gemma.core.loader.expression.geo.fetcher that return types with arguments of type LocalFile

Modifier and Type	Method	Description
Collection<LocalFile>	LocalDatasetFetcher.fetch(String accession)
Collection<LocalFile>	LocalSeriesFetcher.fetch(String accession)
Collection<LocalFile>	RawDataFetcher.fetch(String identifier)

Uses of LocalFile in ubic.gemma.core.loader.genome.taxon

Methods in ubic.gemma.core.loader.genome.taxon that return types with arguments of type LocalFile

Modifier and Type	Method	Description
Collection<LocalFile>	TaxonFetcher.fetch()	Fetch the Taxon bundle from NCBI.

Uses of LocalFile in ubic.gemma.core.loader.util.fetcher

Methods in ubic.gemma.core.loader.util.fetcher that return LocalFile

Modifier and Type	Method	Description
protected LocalFile	AbstractFetcher.fetchedFile(String seekFile)
protected LocalFile	AbstractFetcher.fetchedFile(String seekFilePath, String outputFilePath)

Methods in ubic.gemma.core.loader.util.fetcher that return types with arguments of type LocalFile

Modifier and Type	Method	Description
protected Collection<LocalFile>	FtpArchiveFetcher.doTask(FutureTask<Boolean> future, long expectedSize, String seekFileName, String outputFileName)
protected Collection<LocalFile>	FtpFetcher.doTask(FutureTask<Boolean> future, long expectedSize, String seekFileName, String outputFileName)
protected Collection<LocalFile>	HttpFetcher.doTask(FutureTask<Boolean> future, String seekFile, String outputFileName)
Collection<LocalFile>	Fetcher.fetch(String identifier)	Fetch files according to the identifier provided.
Collection<LocalFile>	FtpFetcher.fetch(String identifier)
protected Collection<LocalFile>	FtpFetcher.fetch(String identifier, String seekFile)
Collection<LocalFile>	HttpFetcher.fetch(String url)
Collection<LocalFile>	HttpFetcher.fetch(String url, String outputFileName)
protected Collection<LocalFile>	AbstractFetcher.getExistingFile(File existingFile, String seekFile)	Wrap the existing file in the required Collection<LocalFile>
protected Collection<LocalFile>	FtpArchiveFetcher.listFiles(String remoteFile, File newDir, Collection<LocalFile> result)
protected Collection<LocalFile>	HttpFetcher.listFiles(String seekFile, String outputFileName)

Method parameters in ubic.gemma.core.loader.util.fetcher with type arguments of type LocalFile

Modifier and Type	Method	Description
protected Collection<LocalFile>	FtpArchiveFetcher.listFiles(String remoteFile, File newDir, Collection<LocalFile> result)
File	HttpArchiveFetcherInterface.unPackFile(Collection<LocalFile> localFile)

Uses of LocalFile in ubic.gemma.model.common.description

Methods in ubic.gemma.model.common.description that return LocalFile

Modifier and Type	Method	Description
static LocalFile	LocalFile.Factory.newInstance()

Uses of LocalFile in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type LocalFile

Modifier and Type	Method	Description
static void	BusinessKey.checkValidKey(LocalFile localFile)