Uses of Interface
ubic.gemma.core.loader.util.parser.LineParser

Packages that use LineParser

Package	Description
ubic.gemma.core.loader.association
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.core.loader.genome.taxon
ubic.gemma.core.loader.util.biomart
ubic.gemma.core.loader.util.parser

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

Classes in ubic.gemma.core.loader.association that implement LineParser

Modifier and Type	Class	Description
class	NCBIGene2GOAssociationParser	This parses GO annotations from NCBI.

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

Classes in ubic.gemma.core.loader.expression.arrayDesign that implement LineParser

Modifier and Type	Class	Description
class	AffyProbeReader	Reads Affymetrix Probe files, including exon arrays.
class	ArrayDesignParser	Deprecated.
class	CompositeSequenceParser	Parse the "old" array description format.
class	IlluminaProbeReader	Parse an Illumina "manifest.txt" file (tab-delimited).

Uses of LineParser in ubic.gemma.core.loader.genome

Classes in ubic.gemma.core.loader.genome that implement LineParser

Modifier and Type	Class	Description
class	BlatResultParser	Loader to handle results generated by Jim Kent's Blat.
class	ProbeSequenceParser	Parse probes from a tabular file.

Uses of LineParser in ubic.gemma.core.loader.genome.gene.ncbi

Classes in ubic.gemma.core.loader.genome.gene.ncbi that implement LineParser

Modifier and Type	Class	Description
class	NcbiGene2AccessionParser	Class to parse the NCBI gene2accession files.
class	NcbiGeneEnsemblFileParser
class	NcbiGeneHistoryParser	Parse the NCBI "gene_history" file.
class	NcbiGeneInfoParser	Class to parse the gene_info file from NCBI Gene.

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

Classes in ubic.gemma.core.loader.genome.taxon that implement LineParser

Modifier and Type	Class	Description
class	TaxonParser	Parse the "names.dmp" file from NCBI, ftp://ftp.ncbi.nih.gov/pub/taxonomy/.

Uses of LineParser in ubic.gemma.core.loader.util.biomart

Classes in ubic.gemma.core.loader.util.biomart that implement LineParser

Modifier and Type	Class	Description
class	BiomartEnsembleNcbiParser	Parser for BioMart file.

Fields in ubic.gemma.core.loader.util.biomart declared as LineParser

Modifier and Type	Field	Description
protected LineParser<Ensembl2NcbiValueObject>	BiomartEnsemblNcbiObjectGenerator.bioMartEnsemblNcbiParser	A biomart parser which is constructed a new for each taxon due to slight file taxon differences

Uses of LineParser in ubic.gemma.core.loader.util.parser

Classes in ubic.gemma.core.loader.util.parser that implement LineParser

Modifier and Type	Class	Description
class	BasicLineMapParser<K,T>	A line parser that produces a Map instead of a Collection.
class	BasicLineParser<T>	A simple LineParser implementation that doesn't do anything.
class	LineMapParser<K,T>	The difference between this class and BasicLineMapParser is more flexibility in how keys are provided.