Uses of Class
ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject
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Packages that use Ensembl2NcbiValueObject Package Description ubic.gemma.core.loader.util.biomart -
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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 differencesMethods 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 fileMap<String,Ensembl2NcbiValueObject>
BiomartEnsemblNcbiObjectGenerator. parseTaxonBiomartFile(Taxon taxon, File taxonBiomartFile)
Method calls the parse method to parse a biomart file.
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