Package ubic.gemma.cli.options

Class ExpressionDataFileOptionValue

java.lang.Object

ubic.gemma.cli.options.DataFileOptionValue

ubic.gemma.cli.options.ExpressionDataFileOptionValue

Direct Known Subclasses:

SingleCellExpressionDataFileOptionValue

public class ExpressionDataFileOptionValue
extends DataFileOptionValue

Options to write an expression data file.

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

Author:

poirigui

Field Summary

Fields

Modifier and Type	Field	Description
protected final boolean	excludeSampleIdentifiers
protected final ubic.gemma.model.common.quantitationtype.ScaleType	scaleType
protected final boolean	useBioAssayIds
protected final boolean	useRawColumnNames

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

outputDir, outputFile, standardLocation, standardOutput

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
ubic.gemma.model.common.quantitationtype.ScaleType	getScaleType()
boolean	isExcludeSampleIdentifiers()
boolean	isUseBioAssayIds()
boolean	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

Field Details

excludeSampleIdentifiers

protected final boolean excludeSampleIdentifiers

useBioAssayIds

protected final boolean useBioAssayIds

useRawColumnNames

protected final boolean useRawColumnNames

scaleType

@Nullable
protected final ubic.gemma.model.common.quantitationtype.ScaleType scaleType

Constructor Details

ExpressionDataFileOptionValue

public ExpressionDataFileOptionValue(DataFileOptionValue dfov,
 boolean excludeSampleIdentifiers,
 boolean useBioAssayIds,
 boolean useRawColumnNames,
 @Nullable
 ubic.gemma.model.common.quantitationtype.ScaleType scaleType)

ExpressionDataFileOptionValue

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

Method Details

isExcludeSampleIdentifiers

public boolean isExcludeSampleIdentifiers()

isUseBioAssayIds

public boolean isUseBioAssayIds()

isUseRawColumnNames

public boolean isUseRawColumnNames()

getScaleType

@Nullable
public ubic.gemma.model.common.quantitationtype.ScaleType getScaleType()