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

Packages that use Parser

Package	Description
ubic.gemma.core.loader.association
ubic.gemma.core.loader.expression.arrayDesign
ubic.gemma.core.loader.expression.geo
ubic.gemma.core.loader.genome
ubic.gemma.core.loader.genome.gene
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
ubic.gemma.core.util.concurrent

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

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

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

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

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

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 Parser in ubic.gemma.core.loader.expression.geo

Classes in ubic.gemma.core.loader.expression.geo that implement Parser

Modifier and Type	Class	Description
class	GeoFamilyParser	Class for parsing GSE and GDS files from NCBI GEO.

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

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

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

Uses of Parser in ubic.gemma.core.loader.genome.gene

Classes in ubic.gemma.core.loader.genome.gene that implement Parser

Modifier and Type	Class	Description
class	SwissProtParser	This does a very minimal parse of Swissprot records, just to get mRNAs associated with a single protein.

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

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

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 Parser in ubic.gemma.core.loader.genome.taxon

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

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

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

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

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

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

Subinterfaces of Parser in ubic.gemma.core.loader.util.parser

Modifier and Type	Interface	Description
interface	LineParser<T>	A Parser that processes its input line-by-line.

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

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.
class	RecordParser<T>	Abstract record-based parser.

Uses of Parser in ubic.gemma.core.util.concurrent

Constructors in ubic.gemma.core.util.concurrent with parameters of type Parser

Constructor	Description
ParsingStreamConsumer(Parser<T> parser, InputStream is)