Uses of Class
ubic.gemma.model.common.protocol.Protocol

Packages that use Protocol

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.expression.singleCell.metadata	This package contains classes for loading single-cell metadata such as cell type assignment and cell-level characteristics.
ubic.gemma.model.analysis
ubic.gemma.model.common.protocol
ubic.gemma.persistence.persister
ubic.gemma.persistence.service.common.protocol
ubic.gemma.persistence.service.expression.experiment

Uses of Protocol in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util that return Protocol

Modifier and Type	Method	Description
Protocol	EntityLocator.locateProtocol(String protocolName)
Protocol	EntityLocatorImpl.locateProtocol(String protocolName)

Uses of Protocol in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell that return Protocol

Modifier and Type	Method	Description
Protocol	SingleCellDataLoaderConfig.getCellTypeAssignmentProtocol()	A protocol to use for the cell type assignment.

Methods in ubic.gemma.core.loader.expression.singleCell with parameters of type Protocol

Modifier and Type	Method	Description
B	SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder.cellTypeAssignmentProtocol(Protocol cellTypeAssignmentProtocol)	A protocol to use for the cell type assignment.

Uses of Protocol in ubic.gemma.core.loader.expression.singleCell.metadata

Methods in ubic.gemma.core.loader.expression.singleCell.metadata with parameters of type Protocol

Modifier and Type	Method	Description
void	GenericMetadataSingleCellDataLoader.setCellTypeAssignmentProtocol(Protocol cellTypeAssignmentProtocol)

Uses of Protocol in ubic.gemma.model.analysis

Methods in ubic.gemma.model.analysis that return Protocol

Modifier and Type	Method	Description
Protocol	Analysis.getProtocol()

Methods in ubic.gemma.model.analysis with parameters of type Protocol

Modifier and Type	Method	Description
void	Analysis.setProtocol(Protocol protocol)

Constructors in ubic.gemma.model.analysis with parameters of type Protocol

Modifier	Constructor	Description
	ProtocolValueObject(Protocol protocol)

Uses of Protocol in ubic.gemma.model.common.protocol

Methods in ubic.gemma.model.common.protocol that return Protocol

Modifier and Type	Method	Description
static Protocol	Protocol.Factory.newInstance()

Uses of Protocol in ubic.gemma.persistence.persister

Methods in ubic.gemma.persistence.persister that return Protocol

Modifier and Type	Method	Description
protected Protocol	CommonPersister.persistProtocol(Protocol protocol)

Methods in ubic.gemma.persistence.persister with parameters of type Protocol

Modifier and Type	Method	Description
protected Protocol	CommonPersister.persistProtocol(Protocol protocol)

Uses of Protocol in ubic.gemma.persistence.service.common.protocol

Methods in ubic.gemma.persistence.service.common.protocol that return Protocol

Modifier and Type	Method	Description
Protocol	ProtocolDaoImpl.find(Protocol protocol)
Protocol	ProtocolDao.findByName(String protocolName)
Protocol	ProtocolDaoImpl.findByName(String protocolName)
Protocol	ProtocolService.findByName(String protocolName)
Protocol	ProtocolServiceImpl.findByName(String protocolName)

Methods in ubic.gemma.persistence.service.common.protocol that return types with arguments of type Protocol

Modifier and Type	Method	Description
List<Protocol>	ProtocolDao.loadAllUniqueByName()	Load all protocols that are unique by name.
List<Protocol>	ProtocolDaoImpl.loadAllUniqueByName()
List<Protocol>	ProtocolService.loadAllUniqueByName()
List<Protocol>	ProtocolServiceImpl.loadAllUniqueByName()

Methods in ubic.gemma.persistence.service.common.protocol with parameters of type Protocol

Modifier and Type	Method	Description
Protocol	ProtocolDaoImpl.find(Protocol protocol)

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

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

Modifier and Type	Method	Description
Collection<Protocol>	ExpressionExperimentDao.getCellTypeAssignmentProtocols()	Obtain all cell type assignment protocols currently used.
Collection<Protocol>	ExpressionExperimentDaoImpl.getCellTypeAssignmentProtocols()
Collection<Protocol>	SingleCellExpressionExperimentService.getCellTypeAssignmentProtocols()	Obtain a collection of protocols used to assign cell types to single-cell vectors.
Collection<Protocol>	SingleCellExpressionExperimentServiceImpl.getCellTypeAssignmentProtocols()

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

Modifier and Type	Method	Description
CellTypeAssignment	SingleCellExpressionExperimentService.relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol labellingProtocol, String description)	Relabel the cell types of an existing set of single-cell vectors.
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol protocol, String description)