Uses of Class
ubic.gemma.cli.options.DataFileOptionValue

Packages that use DataFileOptionValue

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.cli.options	This package contains reusable command line options.

Uses of DataFileOptionValue in ubic.gemma.apps

Methods in ubic.gemma.apps that return DataFileOptionValue

Modifier and Type	Method	Description
protected DataFileOptionValue	ExpressionExperimentManipulatingCLI.getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation)
protected DataFileOptionValue	ExpressionExperimentManipulatingCLI.getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, boolean allowStdout, boolean allowCurrentDirectory)

Uses of DataFileOptionValue in ubic.gemma.cli.options

Subclasses of DataFileOptionValue in ubic.gemma.cli.options

Modifier and Type	Class	Description
class	CellMetadataFileOptionValue	Options to write cell metadata file.
class	DesignFileOptionValue	Options to write an experimental design file.
class	ExpressionDataFileOptionValue	Options to write an expression data file.
class	SingleCellExpressionDataFileOptionValue	Rows are probes/genes, columns are samples/assays.

Methods in ubic.gemma.cli.options that return DataFileOptionValue

Modifier and Type	Method	Description
static DataFileOptionValue	DataFileOptionsUtils.getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, boolean allowStdout, boolean allowCurrentDirectory, String forceOption, boolean force)	Obtain the result of the data file options added by DataFileOptionsUtils.addDataFileOptions(Options, String, boolean, boolean, boolean, boolean, boolean, BiConsumer)
static DataFileOptionValue	DataFileOptionsUtils.getDataFileOptionValue(org.apache.commons.cli.CommandLine commandLine, boolean allowStandardLocation, String forceOption, boolean force)

Constructors in ubic.gemma.cli.options with parameters of type DataFileOptionValue

Modifier	Constructor	Description
	CellMetadataFileOptionValue(DataFileOptionValue dfov, boolean separateSampleFromAssaysIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames)
	DesignFileOptionValue(DataFileOptionValue dfov, boolean useMultipleRowsForAssays, boolean separateSampleFromAssaysIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames)
	ExpressionDataFileOptionValue(DataFileOptionValue dfov, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, ubic.gemma.model.common.quantitationtype.ScaleType scaleType)