Uses of Class
ubic.gemma.model.common.description.Category

Packages that use Category

Package	Description
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.common.description
ubic.gemma.model.expression.bioAssay
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment

Uses of Category in ubic.gemma.core.visualization.cellbrowser

Method parameters in ubic.gemma.core.visualization.cellbrowser with type arguments of type Category

Modifier and Type	Method	Description
void	CellBrowserMetadataWriter.writeCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor,Map<BioMaterial,FactorValue>> factorValueMap, SortedMap<Category,Map<BioAssay,Characteristic>> bioAssayCharacteristics, SortedMap<Category,Map<BioMaterial,Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer)

Uses of Category in ubic.gemma.model.common.description

Fields in ubic.gemma.model.common.description declared as Category

Modifier and Type	Field	Description
static final Category	Categories.ASSAY
static final Category	Categories.BIOLOGICAL_SEX
static final Category	Categories.BLOCK
static final Category	Categories.CELL_TYPE
static final Category	Categories.GENOTYPE
static final Category	Categories.MASK	Represent a mask for a set of data.
static final Category	Categories.ORGANISM_PART
static final Category	Categories.TIMEPOINT
static final Category	Categories.TREATMENT
static final Category	Categories.UNCATEGORIZED	Indicate an uncategorized term.

Methods in ubic.gemma.model.common.description that return Category

Modifier and Type	Method	Description
static Category	CharacteristicUtils.getCategory(Characteristic t)	Create a new characteristic that represents the category of a given characteristic.

Methods in ubic.gemma.model.common.description with parameters of type Category

Modifier and Type	Method	Description
static boolean	CharacteristicUtils.hasCategory(Characteristic c, Category category)	Check if a given characteristics has a specific category.
static Characteristic	Characteristic.Factory.newInstance(Category category)
static Characteristic	Characteristic.Factory.newInstance(Category category, String value, String valueUri)
static Characteristic	Characteristic.Factory.newInstance(Category category, Value value)

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

Fields in ubic.gemma.model.expression.bioAssay declared as Category

Modifier and Type	Field	Description
static final Category	BioAssayCategories.IS_OUTLIER
static final Category	BioAssayCategories.NUMBER_OF_CELLS
static final Category	BioAssayCategories.NUMBER_OF_CELLS_BY_DESIGN_ELEMENTS
static final Category	BioAssayCategories.NUMBER_OF_DESIGN_ELEMENTS
static final Category	BioAssayCategories.PROCESSING_DATE
static final Category	BioAssayCategories.SEQUENCE_PAIRED_READS
static final Category	BioAssayCategories.SEQUENCE_READ_COUNT
static final Category	BioAssayCategories.SEQUENCE_READ_LENGTH

Methods in ubic.gemma.model.expression.bioAssay that return types with arguments of type Category

Modifier and Type	Method	Description
static Map<Category,Map<BioAssay,Collection<Characteristic>>>	BioAssayUtils.createCharacteristicMap(Collection<BioAssay> assays)	Create a mapping of biomaterial to characteristics for each category.

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

Fields in ubic.gemma.model.expression.experiment with type parameters of type Category

Modifier and Type	Field	Description
static final List<Category>	ExperimentFactorUtils.BATCH_FACTOR_CATEGORIES	A list of all categories considered to be batch.

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

Modifier and Type	Method	Description
static ExperimentalFactor	ExperimentalFactor.Factory.newInstance(String name, FactorType factorType, Category category)
static Statement	Statement.Factory.newInstance(Category category, String subject, String subjectUri)

Uses of Category in ubic.gemma.persistence.service.expression.biomaterial

Methods in ubic.gemma.persistence.service.expression.biomaterial that return types with arguments of type Category

Modifier and Type	Method	Description
static Map<Category,Map<BioMaterial,Collection<Characteristic>>>	BioMaterialUtils.createCharacteristicMap(Collection<BioMaterial> samples)	Create a mapping of biomaterial to characteristics for each category.

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

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

Modifier and Type	Method	Description
Category	ExpressionExperimentDao.getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)	Obtain the category of a cell-level characteristic.
Category	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentService.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)

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

Modifier and Type	Method	Description
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain all cell-level characteristics from all single-cell dimensions matching the given category.
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain CLC for given category.
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)