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

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

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

Modifier and Type	Method	Description
ArrayDesignValueObject	BioAssayValueObject.getArrayDesign()
ArrayDesignValueObject	BioAssayValueObject.getOriginalPlatform()

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

Modifier and Type	Method	Description
void	BioAssayValueObject.setArrayDesign(ArrayDesignValueObject arrayDesign)
void	BioAssayValueObject.setOriginalPlatform(ArrayDesignValueObject originalPlatform)

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)