Uses of Class ubic.gemma.rest.util.args.TaxonArg (Gemma 1.31.13 API)

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
`ResponseDataObject<Set<GeneEvidenceValueObject>>`	TaxaWebService.`findCandidateGenesInTaxon(TaxonArg<?> taxonArg, StringArrayArg phenotypes, Boolean editableOnly)`	Deprecated.
`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.
`ResponseDataObject<List<GeneEvidenceValueObject>>`	TaxaWebService.`getGenesEvidenceInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg)`	Deprecated.
`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.
`ResponseDataObject<Collection<?>>`	TaxaWebService.`getTaxonPhenotypes(TaxonArg<?> taxonArg, Boolean editableOnly, Boolean tree)`	Loads all phenotypes for the given taxon.
`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.