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

Packages that use ExpressionExperimentDetailsValueObject

Package	Description
ubic.gemma.core.analysis.report
ubic.gemma.core.tasks.visualization
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.web.controller.expression.experiment
ubic.gemma.web.controller.visualization
ubic.gemma.web.persistence

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

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

Modifier and Type	Method	Description
ExpressionExperimentDetailsValueObject	ExpressionExperimentReportService.generateSummary(Long id)	Generate a value object that contain summary information about links, biomaterials, and datavectors
ExpressionExperimentDetailsValueObject	ExpressionExperimentReportServiceImpl.generateSummary(Long id)

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

Modifier and Type	Method	Description
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentReportService.generateSummaryObjects()	Generates reports on ALL experiments, including 'private' ones.
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentReportServiceImpl.generateSummaryObjects()
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentReportService.retrieveSummaryObjects(Collection<Long> ids)	retrieves a collection of cached value objects containing summary information
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentReportServiceImpl.retrieveSummaryObjects(Collection<Long> ids)

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

Modifier and Type	Method	Description
void	ExpressionExperimentReportService.getAnnotationInformation(Collection<ExpressionExperimentDetailsValueObject> vos)
void	ExpressionExperimentReportServiceImpl.getAnnotationInformation(Collection<ExpressionExperimentDetailsValueObject> vos)	Populate information about how many annotations there are, and how many factor values there are.
void	ExpressionExperimentReportService.populateEventInformation(Collection<ExpressionExperimentDetailsValueObject> vos)
void	ExpressionExperimentReportServiceImpl.populateEventInformation(Collection<ExpressionExperimentDetailsValueObject> vos)	Fills in event and security information from the database.
void	ExpressionExperimentReportService.populateReportInformation(Collection<ExpressionExperimentDetailsValueObject> vos)	Fills in link analysis and differential expression analysis summaries, and other info from the report.
void	ExpressionExperimentReportServiceImpl.populateReportInformation(Collection<ExpressionExperimentDetailsValueObject> vos)

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

Methods in ubic.gemma.core.tasks.visualization that return types with arguments of type ExpressionExperimentDetailsValueObject

Modifier and Type	Method	Description
Collection<ExpressionExperimentDetailsValueObject>	DifferentialExpressionSearchTaskCommand.getExperimentGroup()

Uses of ExpressionExperimentDetailsValueObject in ubic.gemma.persistence.service.analysis.expression

Methods in ubic.gemma.persistence.service.analysis.expression that return types with arguments of type ExpressionExperimentDetailsValueObject

Modifier and Type	Method	Description
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentSetDao.getExperimentValueObjectsInSet(Long id)
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentSetDaoImpl.getExperimentValueObjectsInSet(Long id)

Uses of ExpressionExperimentDetailsValueObject in ubic.gemma.persistence.service.analysis.expression.diff

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return types with arguments of type ExpressionExperimentDetailsValueObject

Modifier and Type	Method	Description
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	DifferentialExpressionAnalysisService.getAnalysesByExperiment(Collection<Long> ids)	Given a set of ids, find experiments or experimentsubsets that have differential expression analyses.
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	DifferentialExpressionAnalysisService.getAnalysesByExperiment(Collection<Long> ids, int offset, int limit)
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	DifferentialExpressionAnalysisServiceImpl.getAnalysesByExperiment(Collection<Long> ids)
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	DifferentialExpressionAnalysisServiceImpl.getAnalysesByExperiment(Collection<Long> ids, int offset, int limit)

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

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

Modifier and Type	Method	Description
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentSetService.getExperimentValueObjectsInSet(Long id)	Get the member experiment value objects for the set id; security filtered.
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentSetServiceImpl.getExperimentValueObjectsInSet(Long id)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Special method for front-end access.
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection<Long> ids)	Like ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjectsByIds(Collection<Long> ids)
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjectsByIds(Collection<Long> ids)
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjectsByIds(Collection<Long> ids)
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)	Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDao.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentDaoImpl.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
List<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentService.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
Slice<ExpressionExperimentDetailsValueObject>	ExpressionExperimentServiceImpl.loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)

Uses of ExpressionExperimentDetailsValueObject in ubic.gemma.web.controller.expression.experiment

Subclasses of ExpressionExperimentDetailsValueObject in ubic.gemma.web.controller.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentEditValueObject

Methods in ubic.gemma.web.controller.expression.experiment that return ExpressionExperimentDetailsValueObject

Modifier and Type	Method	Description
ExpressionExperimentDetailsValueObject	ExpressionExperimentController.loadExpressionExperimentDetails(Long id)	AJAX; Populate all the details.
ExpressionExperimentDetailsValueObject	ExpressionExperimentController.updateBasics(UpdateEEDetailsCommand command)

Methods in ubic.gemma.web.controller.expression.experiment that return types with arguments of type ExpressionExperimentDetailsValueObject

Modifier and Type	Method	Description
JsonReaderResponse<ExpressionExperimentDetailsValueObject>	ExpressionExperimentController.browse(ListBatchCommand batch)	AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level.
JsonReaderResponse<ExpressionExperimentDetailsValueObject>	ExpressionExperimentController.browseByTaxon(ListBatchCommand batch, Long taxonId)
JsonReaderResponse<ExpressionExperimentDetailsValueObject>	ExpressionExperimentController.browseSpecificIds(ListBatchCommand batch, Collection<Long> ids)	AJAX call for remote paging store
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentSetController.getExperimentsInSet(Long groupId, Integer limit)
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentController.loadDetailedExpressionExperiments(Collection<Long> ids)	AJAX - for display in tables.
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentController.loadExperimentsForPlatform(Long id)	AJAX get experiments that used a given platform.
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentController.loadExpressionExperiments(List<Long> ids)	AJAX - for display in tables.
Collection<ExpressionExperimentDetailsValueObject>	ExpressionExperimentController.loadStatusSummaries(Long taxonId, List<Long> ids, Integer limit, Integer filter, Boolean showPublic)	AJAX.

Uses of ExpressionExperimentDetailsValueObject in ubic.gemma.web.controller.visualization

Methods in ubic.gemma.web.controller.visualization with parameters of type ExpressionExperimentDetailsValueObject

Modifier and Type	Method	Description
void	VisualizationValueObject.setEevo(ExpressionExperimentDetailsValueObject eevo)
void	VisualizationValueObject.setEEwithPvalue(ExpressionExperimentDetailsValueObject ee, Double minP)

Uses of ExpressionExperimentDetailsValueObject in ubic.gemma.web.persistence

Methods in ubic.gemma.web.persistence that return types with arguments of type ExpressionExperimentDetailsValueObject

Modifier and Type	Method	Description
Collection<ExpressionExperimentDetailsValueObject>	SessionListManager.getExperimentsInSet(Long id)
Collection<ExpressionExperimentDetailsValueObject>	SessionListManagerImpl.getExperimentsInSet(Long id)