Package ubic.gemma.cli.options

Class DesignFileOptionValue

java.lang.Object

ubic.gemma.cli.options.DataFileOptionValue

ubic.gemma.cli.options.DesignFileOptionValue

public class DesignFileOptionValue
extends DataFileOptionValue

Options to write an experimental design file.

Rows are samples/assays and columns are factors, sample characteristics or assay characteristics.

Author:

poirigui

Field Summary

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

outputDir, outputFile, standardLocation, standardOutput

Constructor Summary

Constructors

Constructor	Description
DesignFileOptionValue(boolean standardLocation, boolean standardOutput, Path outputFile, Path outputDir, boolean useMultipleRowsForAssays, boolean separateSampleFromAssaysIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames, String forceOption, boolean force)
DesignFileOptionValue(DataFileOptionValue dfov, boolean useMultipleRowsForAssays, boolean separateSampleFromAssaysIdentifiers, boolean useBioAssayIds, boolean useRawColumnNames)

Method Summary

Modifier and Type	Method	Description
boolean	isSeparateSampleFromAssaysIdentifiers()
boolean	isUseBioAssayIds()
boolean	isUseMultipleRowsForAssays()
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

Constructor Details

DesignFileOptionValue

public DesignFileOptionValue(DataFileOptionValue dfov,
 boolean useMultipleRowsForAssays,
 boolean separateSampleFromAssaysIdentifiers,
 boolean useBioAssayIds,
 boolean useRawColumnNames)

DesignFileOptionValue

public DesignFileOptionValue(boolean standardLocation,
 boolean standardOutput,
 @Nullable
 Path outputFile,
 @Nullable
 Path outputDir,
 boolean useMultipleRowsForAssays,
 boolean separateSampleFromAssaysIdentifiers,
 boolean useBioAssayIds,
 boolean useRawColumnNames,
 @Nullable
 String forceOption,
 boolean force)

Method Details

isUseMultipleRowsForAssays

public boolean isUseMultipleRowsForAssays()

isSeparateSampleFromAssaysIdentifiers

public boolean isSeparateSampleFromAssaysIdentifiers()

isUseBioAssayIds

public boolean isUseBioAssayIds()

isUseRawColumnNames

public boolean isUseRawColumnNames()