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
ubic.gemma.web.controller.expression.arrayDesign
ubic.gemma.web.taglib.arrayDesign

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

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)

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

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()
Collection<ArrayDesignValueObject>	ExpressionExperimentDetailsValueObject.getOriginalPlatforms()

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.
void	ExpressionExperimentDetailsValueObject.setOriginalPlatforms(Collection<ArrayDesignValueObject> originalPlatforms)

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

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
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>	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)
List<ArrayDesignValueObject>	ArrayDesignDao.loadValueObjectsForEE(Long eeId)
List<ArrayDesignValueObject>	ArrayDesignDaoImpl.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>	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 class	DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject

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

Modifier and Type	Method	Description
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getBlacklistedPlatforms(FilterArg<ArrayDesign> filter, SortArg<ArrayDesign> sort, OffsetArg offset, LimitArg limit)
ResponseDataObject<List<ArrayDesignValueObject>>	DatasetsWebService.getDatasetPlatforms(DatasetArg<?> datasetArg)	Retrieves platforms for the given dataset.
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getPlatforms(FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)
FilteredAndPaginatedResponseDataObject<ArrayDesignValueObject>	PlatformsWebService.getPlatformsByIds(PlatformArrayArg platformsArg, FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort)	Retrieves all datasets matching the given identifiers.

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
List<ArrayDesignValueObject>	DatasetArgService.getPlatforms(DatasetArg<?> arg)	Retrieves the Platforms of the Dataset that this argument represents.

Uses of ArrayDesignValueObject in ubic.gemma.web.controller.expression.arrayDesign

Subclasses of ArrayDesignValueObject in ubic.gemma.web.controller.expression.arrayDesign

Modifier and Type	Class	Description
class	ArrayDesignValueObjectExt	Extended value object to carry more data to client.

Methods in ubic.gemma.web.controller.expression.arrayDesign that return ArrayDesignValueObject

Modifier and Type	Method	Description
ArrayDesignValueObject	ArrayDesignValueObjectExt.getAlternative()
ArrayDesignValueObject	ArrayDesignValueObjectExt.getMerger()
ArrayDesignValueObject	ArrayDesignValueObjectExt.getSubsumer()
ArrayDesignValueObject	ArrayDesignController.loadArrayDesignsSummary()

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

Modifier and Type	Method	Description
JsonReaderResponse<ArrayDesignValueObject>	ArrayDesignController.browse(ListBatchCommand batch, Long[] ids, boolean showMerged, boolean showOrphans)
Collection<ArrayDesignValueObject>	ArrayDesignController.getArrayDesigns(Long[] arrayDesignIds, boolean showMergees, boolean showOrphans)
Collection<ArrayDesignValueObject>	ArrayDesignValueObjectExt.getMergees()
Collection<ArrayDesignValueObject>	ArrayDesignValueObjectExt.getSubsumees()
Collection<ArrayDesignValueObject>	ArrayDesignController.loadArrayDesignsForShowAll(Long[] arrayDesignIds)

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

Modifier and Type	Method	Description
void	ArrayDesignValueObjectExt.setAlternative(ArrayDesignValueObject alternative)
void	ArrayDesignValueObjectExt.setMerger(ArrayDesignValueObject arrayDesignValueObject)
void	ArrayDesignValueObjectExt.setSubsumer(ArrayDesignValueObject arrayDesignValueObject)

Method parameters in ubic.gemma.web.controller.expression.arrayDesign with type arguments of type ArrayDesignValueObject

Modifier and Type	Method	Description
void	ArrayDesignValueObjectExt.setMergees(Collection<ArrayDesignValueObject> mergees)
void	ArrayDesignValueObjectExt.setSubsumees(Collection<ArrayDesignValueObject> subsumees)

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

Modifier	Constructor	Description
	ArrayDesignValueObjectExt(ArrayDesignValueObject vo)

Uses of ArrayDesignValueObject in ubic.gemma.web.taglib.arrayDesign

Methods in ubic.gemma.web.taglib.arrayDesign with parameters of type ArrayDesignValueObject

Modifier and Type	Method	Description
static String	ArrayDesignHtmlUtil.getSummaryHtml(ArrayDesignValueObject object)	Generate a pretty HTML table with the array design stats summary, used for AJAX version.