Package ubic.gemma.cli.options

Class SingleCellExpressionDataFileOptionValue

java.lang.Object

ubic.gemma.cli.options.DataFileOptionValue

ubic.gemma.cli.options.ExpressionDataFileOptionValue

ubic.gemma.cli.options.SingleCellExpressionDataFileOptionValue

public class SingleCellExpressionDataFileOptionValue
extends ExpressionDataFileOptionValue

Rows are probes/genes, columns are samples/assays.

Author:

poirigui

Field Summary

Fields inherited from class ubic.gemma.cli.options.ExpressionDataFileOptionValue

excludeSampleIdentifiers, scaleType, useBioAssayIds, useRawColumnNames

Fields inherited from class ubic.gemma.cli.options.DataFileOptionValue

outputDir, outputFile, standardLocation, standardOutput

Constructor Summary

Constructors

Constructor	Description
SingleCellExpressionDataFileOptionValue(boolean standardLocation, boolean standardOutput, Path outputFile, Path outputDir, boolean excludeSampleIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, ubic.gemma.model.common.quantitationtype.ScaleType scaleType, boolean useEnsemblIds, String forceOption, boolean force)
SingleCellExpressionDataFileOptionValue(ExpressionDataFileOptionValue dfov, boolean useEnsemblIds)

Method Summary

Modifier and Type	Method	Description
boolean	isUseEnsemblIds()

Methods inherited from class ubic.gemma.cli.options.ExpressionDataFileOptionValue

getScaleType, isExcludeSampleIdentifiers, isUseBioAssayIds, isUseRawColumnNames

Methods inherited from class ubic.gemma.cli.options.DataFileOptionValue

getForceOption, getOutputDir, getOutputFile, getOutputFile, isForce, isStandardLocation, isStandardOutput

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SingleCellExpressionDataFileOptionValue

public SingleCellExpressionDataFileOptionValue(ExpressionDataFileOptionValue dfov,
 boolean useEnsemblIds)

SingleCellExpressionDataFileOptionValue

public SingleCellExpressionDataFileOptionValue(boolean standardLocation,
 boolean standardOutput,
 @Nullable
 Path outputFile,
 @Nullable
 Path outputDir,
 boolean excludeSampleIdentifiers,
 boolean useBioAssayIds,
 boolean useRawColumnNames,
 @Nullable
 ubic.gemma.model.common.quantitationtype.ScaleType scaleType,
 boolean useEnsemblIds,
 @Nullable
 String forceOption,
 boolean force)

Method Details

isUseEnsemblIds

public boolean isUseEnsemblIds()