Uses of Class
ubic.gemma.rest.util.args.TaxonArg

Packages that use TaxonArg

Package	Description
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of TaxonArg in ubic.gemma.rest

Methods in ubic.gemma.rest with parameters of type TaxonArg

Modifier and Type	Method	Description
Object	DatasetsWebService.getDatasetsDifferentialExpressionAnalysisResultsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offsetArg, LimitArg limitArg, Double threshold, javax.ws.rs.core.HttpHeaders headers)	Obtain differential expression analysis results for a given gene in a given taxon.
PaginatedResponseDataObject<ExperimentExpressionLevelsValueObject>	DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)	Retrieve the expression levels of a given gene and taxon across all datasets.
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsExpressionLevelsForGenesInTaxon(DatasetArrayArg datasets, TaxonArg<?> taxonArg, GeneArrayArg genes, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)	Retrieves the expression levels of given genes on given datasets.
FilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	TaxaWebService.getTaxonDatasets(TaxonArg<?> taxonArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Retrieves datasets for the given taxon.
ResponseDataObject<List<GeneOntologyTermValueObject>>	TaxaWebService.getTaxonGeneGoTerms(TaxonArg<?> taxonArg, GeneArg<?> geneArg)
ResponseDataObject<List<PhysicalLocationValueObject>>	TaxaWebService.getTaxonGeneLocations(TaxonArg<?> taxonArg, GeneArg<?> geneArg)	Retrieves gene location for the gene on the given taxon.
PaginatedResponseDataObject<CompositeSequenceValueObject>	TaxaWebService.getTaxonGeneProbes(TaxonArg<?> taxonArg, GeneArg<?> geneArg, OffsetArg offsetArg, LimitArg limitArg)
PaginatedResponseDataObject<GeneValueObject>	TaxaWebService.getTaxonGenes(TaxonArg<?> taxonArg, OffsetArg offsetArg, LimitArg limitArg)
ResponseDataObject<List<GeneValueObject>>	TaxaWebService.getTaxonGenesByIds(TaxonArg<?> taxonArg, GeneArrayArg geneArg)	Retrieves genes matching the identifier on the given taxon.
ResponseDataObject<List<GeneValueObject>>	TaxaWebService.getTaxonGenesOverlappingChromosome(TaxonArg<?> taxonArg, String chromosomeName, String strand, Long start, Integer size)	Finds genes overlapping a given region.
SearchWebService.SearchResultsResponseDataObject	SearchWebService.search(QueryArg query, TaxonArg<?> taxonArg, PlatformArg<?> platformArg, List<String> resultTypes, LimitArg limit, ExcludeArg<SearchResult<?>> excludeArg)	Search everything subject to taxon and platform constraints.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasets(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasetsByQueryInPath(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)

Uses of TaxonArg in ubic.gemma.rest.util.args

Subclasses of TaxonArg in ubic.gemma.rest.util.args

Modifier and Type	Class	Description
class	TaxonIdArg	Long argument type for taxon API, referencing the Taxon ID.
class	TaxonNameArg	String argument type for taxon API, referencing the Taxon scientific name or common name.
class	TaxonNcbiIdArg	Long argument type for taxon API, referencing the Taxon ID.

Methods in ubic.gemma.rest.util.args that return TaxonArg

Modifier and Type	Method	Description
static TaxonArg<?>	TaxonArg.valueOf(String s)	Used by RS to parse value of request parameters.

Methods in ubic.gemma.rest.util.args with parameters of type TaxonArg

Modifier and Type	Method	Description
List<GeneValueObject>	TaxonArgService.getGenesOnChromosome(TaxonArg<?> arg, String chromosomeName, String strand, long start, int size)	Lists Genes overlapping a location on a specific chromosome on a taxon that this TaxonArg represents.