Uses of Class
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

Packages that use ExpressionExperimentValueObject

Package	Description
ubic.gemma.core.tasks.visualization
ubic.gemma.model.common.description
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of ExpressionExperimentValueObject in ubic.gemma.core.tasks.visualization

Constructors in ubic.gemma.core.tasks.visualization with parameters of type ExpressionExperimentValueObject

Modifier	Constructor	Description
	Condition(ExpressionExperimentValueObject experiment, DifferentialExpressionAnalysisValueObject analysis, DiffExResultSetSummaryValueObject resultSet, FactorValueValueObject factorValue)

Uses of ExpressionExperimentValueObject in ubic.gemma.model.common.description

Methods in ubic.gemma.model.common.description that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
Collection<ExpressionExperimentValueObject>	BibliographicReferenceValueObject.getExperiments()

Method parameters in ubic.gemma.model.common.description with type arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
void	BibliographicReferenceValueObject.setExperiments(Collection<ExpressionExperimentValueObject> experiments)

Constructor parameters in ubic.gemma.model.common.description with type arguments of type ExpressionExperimentValueObject

Modifier	Constructor	Description
	BibliographicReferenceValueObject(Long id, String abstractText, String authorList, String issue, String pages, String pubAccession, String publication, Date publicationDate, String publisher, String title, String volume, Collection<ExpressionExperimentValueObject> experiments)

Uses of ExpressionExperimentValueObject in ubic.gemma.model.expression.bioAssayData

Constructors in ubic.gemma.model.expression.bioAssayData with parameters of type ExpressionExperimentValueObject

Modifier	Constructor	Description
	BooleanVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject badvo, ArrayDesignValueObject advo)
protected	DataVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtVo, BioAssayDimensionValueObject badvo, ArrayDesignValueObject advo, Collection<Long> genes)
	DoubleVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject badVo, ArrayDesignValueObject advo, Collection<Long> genes)
	DoubleVectorValueObject(BulkExpressionDataVector dedv, ExpressionExperimentValueObject eevo, QuantitationTypeValueObject qtvo, BioAssayDimensionValueObject vectorsBadVo, ArrayDesignValueObject advo, Collection<Long> genes, BioAssayDimensionValueObject dimToMatch)	Create a vector where we expect to have to create one or more gaps to match other vectors, defined by dimToMatch.

Uses of ExpressionExperimentValueObject in ubic.gemma.model.expression.experiment

Subclasses of ExpressionExperimentValueObject in ubic.gemma.model.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentDetailsValueObject

Methods in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
static void	ExpressionExperimentValueObject.populateAclInfo(ExpressionExperimentValueObject vo, AclObjectIdentity aoi, AclSid sid)	Apply ACL-derived flags (isPublic, userCanWrite, isShared, userOwned) onto an existing VO.

Constructors in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperimentValueObject

Modifier	Constructor	Description
	ExpressionExperimentDetailsValueObject(ExpressionExperimentValueObject vo)
protected	ExpressionExperimentValueObject(ExpressionExperimentValueObject vo)

Uses of ExpressionExperimentValueObject in ubic.gemma.persistence.service.expression.experiment

Subclasses with type arguments of type ExpressionExperimentValueObject in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentDaoImpl
class	ExpressionExperimentServiceImpl

Subinterfaces with type arguments of type ExpressionExperimentValueObject in ubic.gemma.persistence.service.expression.experiment

Modifier and Type	Interface	Description
interface	ExpressionExperimentDao	Created by tesarst on 13/03/17.
interface	ExpressionExperimentService

Methods in ubic.gemma.persistence.service.expression.experiment that return ExpressionExperimentValueObject

Modifier and Type	Method	Description
protected ExpressionExperimentValueObject	ExpressionExperimentDaoImpl.doLoadValueObject(ExpressionExperiment entity)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
protected TypedResultTransformer<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.getValueObjectTransformer()
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentDao.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted-experiment view.
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentReadService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
List<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
List<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)
List<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)
List<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)	Variant of BaseVoEnabledService.loadValueObjectsByIds(Collection) that preserve its input order.
List<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)
List<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)
List<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)
List<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)	Load VOs for the given dataset IDs and initialize their relations like SecurableFilteringVoEnabledService.load(Filters, Sort).
List<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchService.searchExpressionExperiments(String query)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchService.searchExpressionExperiments(List<String> value)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchServiceImpl.searchExpressionExperiments(String query)
Collection<ExpressionExperimentValueObject>	ExpressionExperimentSearchServiceImpl.searchExpressionExperiments(List<String> query)

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
protected void	ExpressionExperimentDaoImpl.postProcessValueObjects(List<ExpressionExperimentValueObject> results)

Uses of ExpressionExperimentValueObject in ubic.gemma.rest

Subclasses of ExpressionExperimentValueObject in ubic.gemma.rest

Modifier and Type	Class	Description
static final class	DatasetsWebService.ExpressionExperimentWithSearchResultValueObject

Subclasses with type arguments of type ExpressionExperimentValueObject in ubic.gemma.rest

Modifier and Type	Class	Description
static class	DatasetsWebService.FilteredAndInferredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject	Cursor shape for DatasetsWebService.getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) / DatasetsWebService.getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg).
static class	DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject	Legacy shape for DatasetsWebService.getDatasetsByIds(DatasetArrayArg, FilterArg, OffsetArg, LimitArg, SortArg, CursorArg) / DatasetsWebService.getBlacklistedDatasets(FilterArg, SortArg, OffsetArg, LimitArg, CursorArg).
static class	DatasetsWebService.ResponseDataObjectExpressionExperimentValueObject

Methods in ubic.gemma.rest that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
SearchWebService.SearchResultValueObject<ExpressionExperimentValueObject>	DatasetsWebService.ExpressionExperimentWithSearchResultValueObject.getSearchResult()
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasets(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)	Does a search for datasets containing characteristics matching the given string.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasetsByQueryInPath(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)
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)

Constructors in ubic.gemma.rest with parameters of type ExpressionExperimentValueObject

Modifier	Constructor	Description
	DatasetSearchHitValueObject(ExpressionExperimentValueObject vo, Double score)
	ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject vo)
	ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject vo, SearchResult<ExpressionExperiment> result, String resultObjectUrl, boolean resultObjectUrlExternal)
	ResponseDataObjectExpressionExperimentValueObject(ExpressionExperimentValueObject payload)

Constructor parameters in ubic.gemma.rest with type arguments of type ExpressionExperimentValueObject

Modifier	Constructor	Description
	FilteredAndInferredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject(CursorPage<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject(Slice<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)

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

Methods in ubic.gemma.rest.util.args that return types with arguments of type ExpressionExperimentValueObject

Modifier and Type	Method	Description
CursorPage<ExpressionExperimentValueObject>	DatasetArgService.getBlacklistedDatasetsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ExpressionExperimentValueObject>	DatasetArgService.getDatasetsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to SecurableFilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int).
Slice<ExpressionExperimentValueObject>	PlatformArgService.getExperiments(PlatformArg<?> arg, int limit, int offset)	Retrieves the Datasets of the Platform that this argument represents.
CursorPage<ExpressionExperimentValueObject>	PlatformArgService.getExperimentsByCursor(PlatformArg<?> arg, Cursor cursor, int limit)	Cursor-mode counterpart to PlatformArgService.getExperiments(PlatformArg, int, int): keyset pagination over the datasets that use a single platform, always sorted by ascending id (the primary key, indexed and unique) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1f.