Uses of Class
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject

Packages that use ArrayDesignValueObject

Package	Description
ubic.gemma.core.analysis.report
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.designElement
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of ArrayDesignValueObject in ubic.gemma.core.analysis.report

Methods in ubic.gemma.core.analysis.report that return ArrayDesignValueObject

Modifier and Type	Method	Description
ArrayDesignValueObject	ArrayDesignReportService.generateArrayDesignReport(Long id)
ArrayDesignValueObject	ArrayDesignReportServiceImpl.generateArrayDesignReport(Long id)
ArrayDesignValueObject	ArrayDesignReportService.getSummaryObject()
ArrayDesignValueObject	ArrayDesignReportService.getSummaryObject(Long id)
ArrayDesignValueObject	ArrayDesignReportServiceImpl.getSummaryObject()	Get the cached summary object that represents all platforms.
ArrayDesignValueObject	ArrayDesignReportServiceImpl.getSummaryObject(Long id)	Get a specific cached summary object

Methods in ubic.gemma.core.analysis.report that return types with arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
Collection<ArrayDesignValueObject>	ArrayDesignReportService.getSummaryObject(Collection<Long> ids)
Collection<ArrayDesignValueObject>	ArrayDesignReportServiceImpl.getSummaryObject(Collection<Long> ids)	Get the cached summary objects

Methods in ubic.gemma.core.analysis.report with parameters of type ArrayDesignValueObject

Modifier and Type	Method	Description
void	ArrayDesignReportService.generateArrayDesignReport(ArrayDesignValueObject adVo)
void	ArrayDesignReportServiceImpl.generateArrayDesignReport(ArrayDesignValueObject adVo)

Method parameters in ubic.gemma.core.analysis.report with type arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
void	ArrayDesignReportService.fillEventInformation(Collection<ArrayDesignValueObject> adVos)
void	ArrayDesignReportServiceImpl.fillEventInformation(Collection<ArrayDesignValueObject> adVos)	Fill in event information
void	ArrayDesignReportService.fillInSubsumptionInfo(Collection<ArrayDesignValueObject> valueObjects)
void	ArrayDesignReportServiceImpl.fillInSubsumptionInfo(Collection<ArrayDesignValueObject> valueObjects)
void	ArrayDesignReportService.fillInValueObjects(Collection<ArrayDesignValueObject> adVos)
void	ArrayDesignReportServiceImpl.fillInValueObjects(Collection<ArrayDesignValueObject> adVos)	Fill in the probe summary statistics

Uses of ArrayDesignValueObject in ubic.gemma.model.expression.arrayDesign

Subclasses with type arguments of type ArrayDesignValueObject in ubic.gemma.model.expression.arrayDesign

Modifier and Type	Class	Description
static class	ArrayDesignReferenceValueObject.FromArrayDesignValueObject	Project a full ArrayDesignValueObject down to this shape at serialization time.

Methods in ubic.gemma.model.expression.arrayDesign that return types with arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
static Collection<ArrayDesignValueObject>	ArrayDesignValueObject.create(Collection<ArrayDesign> subsumees)

Methods in ubic.gemma.model.expression.arrayDesign with parameters of type ArrayDesignValueObject

Modifier and Type	Method	Description
ArrayDesignReferenceValueObject	ArrayDesignReferenceValueObject.FromArrayDesignValueObject.convert(ArrayDesignValueObject value)

Constructors in ubic.gemma.model.expression.arrayDesign with parameters of type ArrayDesignValueObject

Modifier	Constructor	Description
protected	ArrayDesignValueObject(ArrayDesignValueObject arrayDesignValueObject)	Copies constructor from other ArrayDesignValueObject

Uses of ArrayDesignValueObject in ubic.gemma.model.expression.bioAssay

Methods in ubic.gemma.model.expression.bioAssay that return ArrayDesignValueObject

Modifier and Type	Method	Description
ArrayDesignValueObject	BioAssayValueObject.getArrayDesign()	The platform this assay was run on, serialized as ArrayDesignReferenceValueObject — id, shortName, name, technologyType.
ArrayDesignValueObject	BioAssayValueObject.getOriginalPlatform()	The platform this assay was originally run on before a platform switch, or null if it was never switched.

Methods in ubic.gemma.model.expression.bioAssay with parameters of type ArrayDesignValueObject

Modifier and Type	Method	Description
void	BioAssayValueObject.setArrayDesign(ArrayDesignValueObject arrayDesign)	The platform this assay was run on, serialized as ArrayDesignReferenceValueObject — id, shortName, name, technologyType.
void	BioAssayValueObject.setOriginalPlatform(ArrayDesignValueObject originalPlatform)	The platform this assay was originally run on before a platform switch, or null if it was never switched.

Constructor parameters in ubic.gemma.model.expression.bioAssay with type arguments of type ArrayDesignValueObject

Modifier	Constructor	Description
	BioAssayValueObject(BioAssay bioAssay, Map<ArrayDesign, ArrayDesignValueObject> ad2vo, BioAssay sourceBioAssay, boolean basic, boolean allFactorValues)

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

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

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 ArrayDesignValueObject in ubic.gemma.model.expression.designElement

Methods in ubic.gemma.model.expression.designElement that return ArrayDesignValueObject

Modifier and Type	Method	Description
ArrayDesignValueObject	CompositeSequenceValueObject.getArrayDesign()

Methods in ubic.gemma.model.expression.designElement with parameters of type ArrayDesignValueObject

Modifier and Type	Method	Description
void	CompositeSequenceValueObject.setArrayDesign(ArrayDesignValueObject arrayDesign)

Constructors in ubic.gemma.model.expression.designElement with parameters of type ArrayDesignValueObject

Modifier	Constructor	Description
	CompositeSequenceValueObject(CompositeSequence cs, ArrayDesignValueObject arrayDesign)	Constructor that reuses an existing ArrayDesignValueObject.

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

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
Collection<ArrayDesignValueObject>	ExpressionExperimentDetailsValueObject.getArrayDesigns()

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
void	ExpressionExperimentDetailsValueObject.setArrayDesigns(Collection<ArrayDesignValueObject> arrayDesigns)	As a side effect, sets the technology type and taxon of this based on the first arrayDesign.

Constructor parameters in ubic.gemma.model.expression.experiment with type arguments of type ArrayDesignValueObject

Modifier	Constructor	Description
	ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees, Map<ArrayDesign, ArrayDesignValueObject> arrayDesignValueObjectsById, Map<BioAssay,BioAssay> bioAssay2SourceBioAssayMap, boolean includeAssays, boolean basic, boolean allFactorValues)

Uses of ArrayDesignValueObject in ubic.gemma.persistence.service.expression.arrayDesign

Subclasses with type arguments of type ArrayDesignValueObject in ubic.gemma.persistence.service.expression.arrayDesign

Modifier and Type	Class	Description
class	ArrayDesignDaoImpl
class	ArrayDesignServiceImpl

Subinterfaces with type arguments of type ArrayDesignValueObject in ubic.gemma.persistence.service.expression.arrayDesign

Modifier and Type	Interface	Description
interface	ArrayDesignDao	Created by tesarst on 13/03/17.
interface	ArrayDesignService

Methods in ubic.gemma.persistence.service.expression.arrayDesign that return ArrayDesignValueObject

Modifier and Type	Method	Description
protected ArrayDesignValueObject	ArrayDesignDaoImpl.doLoadValueObject(ArrayDesign ad)	Loads a single value objects for the given array design.

Methods in ubic.gemma.persistence.service.expression.arrayDesign that return types with arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
protected TypedResultTransformer<ArrayDesignValueObject>	ArrayDesignDaoImpl.getValueObjectTransformer()
Slice<ArrayDesignValueObject>	ArrayDesignDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignReadService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)	No need for ACL_VALUE_OBJECT_COLLECTION_READ because the filtering is done in the query.
Slice<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ArrayDesignValueObject>	ArrayDesignDao.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted platforms, applying the same shortName/accession blacklist filter that the offset-mode variant composes — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.
CursorPage<ArrayDesignValueObject>	ArrayDesignDaoImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ArrayDesignValueObject>	ArrayDesignReadService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignReadService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ArrayDesignValueObject>	ArrayDesignService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignService.loadBlacklistedValueObjects(Filters, Sort, int, int) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.
CursorPage<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
List<ArrayDesignValueObject>	ArrayDesignDao.loadOriginalPlatformValueObjectsForEE(Long eeId)	Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
List<ArrayDesignValueObject>	ArrayDesignDaoImpl.loadOriginalPlatformValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignReadService.loadOriginalPlatformValueObjectsForEE(Long eeId)	Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
List<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadOriginalPlatformValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignService.loadOriginalPlatformValueObjectsForEE(Long eeId)	Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
List<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadOriginalPlatformValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignDao.loadValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignDaoImpl.loadValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignReadService.loadValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignService.loadValueObjectsForEE(Long eeId)	Loads the Value Objects for array designs used by expression experiment with the given ID
List<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadValueObjectsForEE(Long eeId)
Collection<ArrayDesignValueObject>	ArrayDesignReadService.loadValueObjectsWithCache(Filters filters, Sort sort)
Collection<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort)
Collection<ArrayDesignValueObject>	ArrayDesignService.loadValueObjectsWithCache(Filters filters, Sort sort)
Collection<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort)

Method parameters in ubic.gemma.persistence.service.expression.arrayDesign with type arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
protected void	ArrayDesignDaoImpl.postProcessValueObjects(List<ArrayDesignValueObject> results)

Uses of ArrayDesignValueObject in ubic.gemma.persistence.service.expression.bioAssay

Method parameters in ubic.gemma.persistence.service.expression.bioAssay with type arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
List<BioAssayValueObject>	BioAssayDao.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign, ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
List<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjects(Collection<BioAssay> entities, Map<ArrayDesign, ArrayDesignValueObject> ad2vo, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)

Uses of ArrayDesignValueObject in ubic.gemma.rest

Subclasses of ArrayDesignValueObject in ubic.gemma.rest

Modifier and Type	Class	Description
static final class	DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject

Methods in ubic.gemma.rest that return ArrayDesignValueObject

Modifier and Type	Method	Description
ArrayDesignValueObject	SearchWebService.SearchSettingsValueObject.getPlatform()

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

Modifier and Type	Method	Description
ResponseDataObject<List<ArrayDesignValueObject>>	DatasetsWebService.getDatasetPlatforms(DatasetArg<?> datasetArg, Boolean original)	Retrieves platforms for the given dataset.
ResponseDataObject<ArrayDesignValueObject>	AdminWebService.regeneratePlatformReport(PlatformArg<?> platformArg)	Regenerate the cached report for ONE platform, synchronously.

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

Modifier	Constructor	Description
	ArrayDesignWithUsageStatisticsValueObject(ArrayDesignValueObject arrayDesign, Long numberOfExpressionExperiments, Long numberOfExpressionExperimentsForTechnologyType)

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

Modifier	Constructor	Description
	ExpressionExperimentSubsetWithFactorValuesObject(ExpressionExperimentSubSet subset, Set<FactorValue> factorValues, Map<ArrayDesign, ArrayDesignValueObject> id2advo, boolean includeAssays, Map<BioAssay,BioAssay> assay2sourceAssayMap)

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

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

Modifier and Type	Method	Description
CursorPage<ArrayDesignValueObject>	PlatformArgService.getBlacklistedPlatformsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignService.loadBlacklistedValueObjects(Filters, Sort, int, int).
List<ArrayDesignValueObject>	DatasetArgService.getOriginalPlatforms(DatasetArg<?> arg)	The platforms the dataset was originally submitted on, before any switch — empty when it was never switched.
List<ArrayDesignValueObject>	DatasetArgService.getPlatforms(DatasetArg<?> arg)	Retrieves the Platforms of the Dataset that this argument represents.
CursorPage<ArrayDesignValueObject>	PlatformArgService.getPlatformsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to SecurableFilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int).