Uses of Class
ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject

Packages that use Ensembl2NcbiValueObject

Package	Description
ubic.gemma.core.loader.util.biomart

Uses of Ensembl2NcbiValueObject in ubic.gemma.core.loader.util.biomart

Fields in ubic.gemma.core.loader.util.biomart with type parameters of type Ensembl2NcbiValueObject

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

Methods in ubic.gemma.core.loader.util.biomart that return Ensembl2NcbiValueObject

Modifier and Type	Method	Description
Ensembl2NcbiValueObject	BiomartEnsembleNcbiParser.createBioMartEnsembleNcbi(String[] fields)	Given an array of strings representing the line to parse then create a BioMartEnsembleNcbi value object with some validation.
Ensembl2NcbiValueObject	BiomartEnsembleNcbiParser.get(String key)	Method that returns a particular BioMartEnsembleNcbi based on a peptide id.
Ensembl2NcbiValueObject	BiomartEnsembleNcbiParser.parseOneLine(String line)	Method to parse one biomart line, note that there is a many to many relationship between ensemble ids and entrez gene ids.

Methods in ubic.gemma.core.loader.util.biomart that return types with arguments of type Ensembl2NcbiValueObject

Modifier and Type	Method	Description
Map<String,Ensembl2NcbiValueObject>	BiomartEnsemblNcbiObjectGenerator.generate(Collection<Taxon> validTaxa)	Main method to generate a map of biomartEnsembleNcbiIds, involves optional fetch from biomart if no file is provided then returns results of parse method.
Map<String,Ensembl2NcbiValueObject>	BiomartEnsemblNcbiObjectGenerator.generateRemote(Collection<Taxon> validTaxa)
Map<String,Ensembl2NcbiValueObject>	BiomartEnsembleNcbiParser.getMap()
Collection<Ensembl2NcbiValueObject>	BiomartEnsembleNcbiParser.getResults()	Getter for values in map that is BioMartEnsembleNcbi value objects associated with the parsing of this file
Map<String,Ensembl2NcbiValueObject>	BiomartEnsemblNcbiObjectGenerator.parseTaxonBiomartFile(Taxon taxon, File taxonBiomartFile)	Method calls the parse method to parse a biomart file.