Uses of Class
ubic.gemma.rest.util.ResponseDataObject

Packages that use ResponseDataObject

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

Uses of ResponseDataObject in ubic.gemma.rest

Subclasses of ResponseDataObject in ubic.gemma.rest

Modifier and Type	Class	Description
static class	AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject	Similar to PaginatedResponseDataObject, but the data.results is paginated instead of data
static class	DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<T>
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<T>
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<T>
static class	DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject
static class	DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject<T>
static class	DatasetsWebService.ResponseDataObjectCellTypeAssignmentValueObject
static class	DatasetsWebService.ResponseDataObjectExpressionExperimentValueObject
static class	DatasetsWebService.ResponseDataObjectListCellLevelCharacteristicsValueObject
static class	DatasetsWebService.ResponseDataObjectSingleCellDimensionValueObject
static class	SearchWebService.SearchResultsResponseDataObject

Methods in ubic.gemma.rest that return ResponseDataObject

Modifier and Type	Method	Description
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	AnnotationsWebService.getAnnotationsChildren(String termUri, boolean direct)	Obtain the children of a given annotation.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	AnnotationsWebService.getAnnotationsParents(String termUri, boolean direct)
ResponseDataObject<RootWebService.ApiInfoValueObject>	RootWebService.getApiInfo(javax.ws.rs.core.UriInfo uriInfo)	Returns an object with API information.
ResponseDataObject<List<BibliographicReferenceValueObject>>	DatasetsWebService.getDatasetAllPublications(DatasetArg<?> datasetArg)
ResponseDataObject<Set<AnnotationValueObject>>	DatasetsWebService.getDatasetAnnotations(DatasetArg<?> datasetArg)	Retrieves the annotations for the given dataset.
ResponseDataObject<DatasetsWebService.BatchInformationValueObject>	DatasetsWebService.getDatasetBatchInformation(DatasetArg<?> datasetArg)
ResponseDataObject<List<DifferentialExpressionAnalysisValueObject>>	DatasetsWebService.getDatasetDifferentialExpressionAnalyses(DatasetArg<?> datasetArg, OffsetArg offsetArg, LimitArg limitArg)	Retrieves the differential analysis results for the given dataset.
ResponseDataObject<Boolean>	DatasetsWebService.getDatasetHasBatchInformation(DatasetArg<?> datasetArg)	Indicate if the experiment has batch information.
ResponseDataObject<List<ArrayDesignValueObject>>	DatasetsWebService.getDatasetPlatforms(DatasetArg<?> datasetArg)	Retrieves platforms for the given dataset.
ResponseDataObject<Set<QuantitationTypeValueObject>>	DatasetsWebService.getDatasetQuantitationTypes(DatasetArg<?> datasetArg)	Retrieve all available quantitation types for a dataset.
ResponseDataObject<List<BioAssayValueObject>>	DatasetsWebService.getDatasetSamples(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, boolean useProcessedQuantitationType)	Retrieves the samples for the given dataset.
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsDifferentialExpression(DatasetArrayArg datasets, Long diffExSet, Double threshold, LimitArg limit, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)	Retrieves the expression levels of genes highly expressed in the given component on given datasets.
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsExpressionLevelsForGenes(DatasetArrayArg datasets, GeneArrayArg genes, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)
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<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsExpressionPca(DatasetArrayArg datasets, Integer component, LimitArg limit, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate)	Retrieves the expression levels of genes highly expressed in the given component on given datasets.
ResponseDataObject<DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject>	DatasetsWebService.getDatasetSubSetById(DatasetArg<?> datasetArg, Long subSetId)
ResponseDataObject<DatasetsWebService.ExpressionExperimentSubSetGroupValueObject>	DatasetsWebService.getDatasetSubSetGroup(DatasetArg<?> datasetArg, Long bioAssayDimensionId)
ResponseDataObject<List<DatasetsWebService.ExpressionExperimentSubSetGroupValueObject>>	DatasetsWebService.getDatasetSubSetGroups(DatasetArg<?> datasetArg)	Retrieve all the "groups" of subsets of a dataset.
ResponseDataObject<List<DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject>>	DatasetsWebService.getDatasetSubSets(DatasetArg<?> datasetArg)
ResponseDataObject<List<BioAssayValueObject>>	DatasetsWebService.getDatasetSubSetSamples(DatasetArg<?> datasetArg, Long subSetId)
ResponseDataObject<DatasetsWebService.SimpleSVDValueObject>	DatasetsWebService.getDatasetSvd(DatasetArg<?> datasetArg)	Retrieves the design for the given dataset.
ResponseDataObject<List<CoexpressionValueObjectExt>>	GeneWebService.getGeneGeneCoexpression(GeneArg<?> geneArg, GeneArg<?> with, LimitArg limit, Integer stringency)	Retrieves the coexpression of two given genes.
ResponseDataObject<List<GeneOntologyTermValueObject>>	GeneWebService.getGeneGoTerms(GeneArg<?> geneArg)	Retrieves the GO terms of the given gene.
ResponseDataObject<List<PhysicalLocationValueObject>>	GeneWebService.getGeneLocations(GeneArg<?> geneArg)	Retrieves the physical location of the given gene.
ResponseDataObject<List<GeneValueObject>>	GeneWebService.getGenesByIds(GeneArrayArg genes)	Retrieves all genes matching the identifier.
ResponseDataObject<RootWebService.UserValueObject>	RootWebService.getMyself()	Retrieve user information for the current user.
ResponseDataObject<Long>	DatasetsWebService.getNumberOfDatasets(QueryArg query, FilterArg<ExpressionExperiment> filter)
ResponseDataObject<Long>	PlatformsWebService.getNumberOfPlatforms(FilterArg<ArrayDesign> filter)
ResponseDataObject<Long>	AnalysisResultSetsWebService.getNumberOfResultSets(FilterArg<ExpressionAnalysisResultSet> filter)
ResponseDataObject<List<TaxonValueObject>>	TaxaWebService.getTaxa()	Lists all available taxa.
ResponseDataObject<List<TaxonValueObject>>	TaxaWebService.getTaxaByIds(TaxonArrayArg taxaArg)	Retrieves single taxon based on the given identifier.
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.
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<RootWebService.UserValueObject>	RootWebService.getUser(String username)	Retrieve user information.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	AnnotationsWebService.searchAnnotations(StringArrayArg query)	Does a search for annotation tags based on the given string.
ResponseDataObject<List<AnnotationsWebService.AnnotationSearchResultValueObject>>	AnnotationsWebService.searchAnnotationsByPathQuery(StringArrayArg query)

Uses of ResponseDataObject in ubic.gemma.rest.util

Subclasses of ResponseDataObject in ubic.gemma.rest.util

Modifier and Type	Class	Description
class	FilteredAndLimitedResponseDataObject<T>
class	FilteredAndPaginatedResponseDataObject<T>
class	FilteredResponseDataObject<T>
class	PaginatedResponseDataObject<T>	Represents paginated results with offset and limit.
class	QueriedAndFilteredAndLimitedResponseDataObject<T>	Represents a payload with a limited number of results.
class	QueriedAndFilteredAndPaginatedResponseDataObject<T>
class	QueriedAndFilteredResponseDataObject<T>

Methods in ubic.gemma.rest.util with type parameters of type ResponseDataObject

Modifier and Type	Method	Description
<S extends ResponseDataObject<T>> S	ResponseDataObject.addWarnings(Iterable<Throwable> throwables, String location, LocationType locationType)	Add a bunch of warnings to invalid reference #getWarnings() .

Methods in ubic.gemma.rest.util that return ResponseDataObject

Modifier and Type	Method	Description
static <T> ResponseDataObject<T>	Responders.respond(T payload)	Produce a ResponseDataObject that wraps the given argument.