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

Packages that use ExpressionExperimentSetValueObject

Package	Description
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.analysis.expression
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.web.controller.analysis.expression.diff
ubic.gemma.web.controller.expression.experiment

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

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

Modifier and Type	Class	Description
class	FreeTextExpressionExperimentResultsValueObject
class	SessionBoundExpressionExperimentSetValueObject

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

Modifier and Type	Method	Description
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentDetailsValueObject.getExpressionExperimentSets()	EE sets this experiment is part of.

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

Modifier and Type	Method	Description
int	ExpressionExperimentSetValueObject.compareTo(ExpressionExperimentSetValueObject arg0)

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

Modifier and Type	Method	Description
void	ExpressionExperimentDetailsValueObject.setExpressionExperimentSets(Collection<ExpressionExperimentSetValueObject> expressionExperimentSets)	EE sets this experiment is part of.

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

Methods in ubic.gemma.persistence.service.analysis.expression that return ExpressionExperimentSetValueObject

Modifier and Type	Method	Description
protected ExpressionExperimentSetValueObject	ExpressionExperimentSetDaoImpl.doLoadValueObject(ExpressionExperimentSet entity)
ExpressionExperimentSetValueObject	ExpressionExperimentSetDao.loadValueObject(Long id, boolean loadEEIds)
ExpressionExperimentSetValueObject	ExpressionExperimentSetDaoImpl.loadValueObject(Long id, boolean loadEEIds)

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

Modifier and Type	Method	Description
List<ExpressionExperimentSetValueObject>	ExpressionExperimentSetDaoImpl.doLoadValueObjects(Collection<ExpressionExperimentSet> entities)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetDao.loadAllValueObjects(boolean loadEEIds)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetDaoImpl.loadAllValueObjects(boolean loadEEIds)
List<ExpressionExperimentSetValueObject>	ExpressionExperimentSetDao.loadValueObjects(Collection<Long> eeSetIds, boolean loadEEIds)
List<ExpressionExperimentSetValueObject>	ExpressionExperimentSetDaoImpl.loadValueObjects(Collection<Long> eeSetIds, boolean loadEEIds)

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

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

Modifier and Type	Method	Description
ExpressionExperimentSetValueObject	ExpressionExperimentSetService.loadValueObjectById(Long id)
ExpressionExperimentSetValueObject	ExpressionExperimentSetService.loadValueObjectById(Long id, boolean loadEEIds)	Get a value object for the id param.
ExpressionExperimentSetValueObject	ExpressionExperimentSetServiceImpl.loadValueObjectById(Long id)
ExpressionExperimentSetValueObject	ExpressionExperimentSetServiceImpl.loadValueObjectById(Long id, boolean loadEEIds)
ExpressionExperimentSetValueObject	ExpressionExperimentSetValueObjectHelper.updateNameAndDescription(ExpressionExperimentSetValueObject eeSetVO, boolean loadEEIds)	Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
ExpressionExperimentSetValueObject	ExpressionExperimentSetValueObjectHelperImpl.updateNameAndDescription(ExpressionExperimentSetValueObject eeSetVO, boolean loadEEIds)

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

Modifier and Type	Method	Description
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetService.loadAllExperimentSetValueObjects(boolean loadEEIds)	Security filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetServiceImpl.loadAllExperimentSetValueObjects(boolean loadEEIds)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetService.loadMySetValueObjects(boolean loadEEIds)	load the user's sets
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetServiceImpl.loadMySetValueObjects(boolean loadEEIds)
List<ExpressionExperimentSetValueObject>	ExpressionExperimentSetService.loadValueObjectsByIds(Collection<Long> eeSetIds)
List<ExpressionExperimentSetValueObject>	ExpressionExperimentSetServiceImpl.loadValueObjectsByIds(Collection<Long> eeSetIds)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type ExpressionExperimentSetValueObject

Modifier and Type	Method	Description
ExpressionExperimentSet	ExpressionExperimentSetValueObjectHelper.convertToEntity(ExpressionExperimentSetValueObject eesvo)
ExpressionExperimentSet	ExpressionExperimentSetValueObjectHelperImpl.convertToEntity(ExpressionExperimentSetValueObject setVO)	Tries to load an existing experiment set with the param's id, if no experiment can be loaded, create a new one with id = null.
ExpressionExperimentSet	ExpressionExperimentSetValueObjectHelper.create(ExpressionExperimentSetValueObject eesvo)	Create an experiment set from a VO.
ExpressionExperimentSet	ExpressionExperimentSetValueObjectHelperImpl.create(ExpressionExperimentSetValueObject eesvo)
void	ExpressionExperimentSetValueObjectHelper.delete(ExpressionExperimentSetValueObject eesvo)	Delete the experiment set corresponding to the given VO.
void	ExpressionExperimentSetValueObjectHelperImpl.delete(ExpressionExperimentSetValueObject eesvo)
void	ExpressionExperimentSetValueObjectHelper.update(ExpressionExperimentSetValueObject eesvo)	Update corresponding entity based on value object
void	ExpressionExperimentSetValueObjectHelperImpl.update(ExpressionExperimentSetValueObject eesvo)
ExpressionExperimentSetValueObject	ExpressionExperimentSetValueObjectHelper.updateNameAndDescription(ExpressionExperimentSetValueObject eeSetVO, boolean loadEEIds)	Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
ExpressionExperimentSetValueObject	ExpressionExperimentSetValueObjectHelperImpl.updateNameAndDescription(ExpressionExperimentSetValueObject eeSetVO, boolean loadEEIds)

Uses of ExpressionExperimentSetValueObject in ubic.gemma.web.controller.analysis.expression.diff

Methods in ubic.gemma.web.controller.analysis.expression.diff with parameters of type ExpressionExperimentSetValueObject

Modifier and Type	Method	Description
String	DifferentialExpressionSearchController.scheduleDiffExpSearchTask(Long taxonId, ExpressionExperimentSetValueObject eevo, GeneSetValueObject gsvo)	AJAX - method used for main display metaheatmap.

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

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

Modifier and Type	Method	Description
ExpressionExperimentSetValueObject	ExpressionExperimentSetController.load(Long id)	AJAX
ExpressionExperimentSetValueObject	ExpressionExperimentSetController.loadByName(String name)
ExpressionExperimentSetValueObject	ExpressionExperimentSetController.updateNameDesc(ExpressionExperimentSetValueObject eeSetVO)	AJAX Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.

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

Modifier and Type	Method	Description
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.addUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> sets)	AJAX adds the experiment group to the session
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.create(Collection<ExpressionExperimentSetValueObject> entities)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.loadAll()	AJAX returns all available sets that have a taxon value (so not really all) sets can have *any* number of experiments
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.loadAllUserAndSessionGroups()	AJAX
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.loadAllUserOwnedAndSessionGroups()	AJAX
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.remove(Collection<ExpressionExperimentSetValueObject> entities)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.removeUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)	AJAX Given valid experiment groups will remove them from the session or the database appropriately.
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.update(Collection<ExpressionExperimentSetValueObject> entities)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.updateUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)	AJAX Updates the session group and user database groups.

Methods in ubic.gemma.web.controller.expression.experiment with parameters of type ExpressionExperimentSetValueObject

Modifier and Type	Method	Description
String	ExpressionExperimentSetController.canCurrentUserEditGroup(ExpressionExperimentSetValueObject eesvo)	AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
ExpressionExperimentSetValueObject	ExpressionExperimentSetController.updateNameDesc(ExpressionExperimentSetValueObject eeSetVO)	AJAX Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.

Method parameters in ubic.gemma.web.controller.expression.experiment with type arguments of type ExpressionExperimentSetValueObject

Modifier and Type	Method	Description
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.addUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> sets)	AJAX adds the experiment group to the session
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.create(Collection<ExpressionExperimentSetValueObject> entities)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.remove(Collection<ExpressionExperimentSetValueObject> entities)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.removeUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)	AJAX Given valid experiment groups will remove them from the session or the database appropriately.
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.update(Collection<ExpressionExperimentSetValueObject> entities)
Collection<ExpressionExperimentSetValueObject>	ExpressionExperimentSetController.updateUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)	AJAX Updates the session group and user database groups.