Package ubic.gemma.core.loader.expression

Class DataLoaderConfig

java.lang.Object

ubic.gemma.core.loader.expression.DataLoaderConfig

Direct Known Subclasses:

SequencingDataLoaderConfig

public class DataLoaderConfig
extends Object

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DataLoaderConfig.DataLoaderConfigBuilder<C extends DataLoaderConfig,B extends DataLoaderConfig.DataLoaderConfigBuilder<C,B>>

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	DataLoaderConfig(DataLoaderConfig.DataLoaderConfigBuilder<?,?> b)

Method Summary

Modifier and Type	Method	Description
static DataLoaderConfig.DataLoaderConfigBuilder<?,?>	builder()
Path	getDataPath()	Load data from that specific path instead of looking up standard locations.
String	getQuantitationTypeName()	Name of the QT to use if more than one is present in the data as per DataLoader.getQuantitationTypes().
String	getQuantitationTypeNewName()	Override the name of the resulting QT.
ScaleType	getQuantitationTypeNewScaleType()	Override the scale type of the resulting QT.
StandardQuantitationType	getQuantitationTypeNewType()	Override the type of the resulting QT.
Path	getRenamingFile()	A file containing a mapping of sample names to bioassay names.
boolean	isMarkQuantitationTypeAsPreferred()	Mark the QT as preferred.
boolean	isMarkQuantitationTypeAsRecomputedFromRawData()	Mark the quantitation type as recomputed from raw data.
boolean	isReplaceExistingQuantitationType()	Replace the vectors of an existing QT.

Methods inherited from class java.lang.Object

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

Constructor Details

DataLoaderConfig

protected DataLoaderConfig(DataLoaderConfig.DataLoaderConfigBuilder<?,?> b)

Method Details

builder

public static DataLoaderConfig.DataLoaderConfigBuilder<?,?> builder()

getDataPath

@Nullable
public Path getDataPath()

Load data from that specific path instead of looking up standard locations.

getQuantitationTypeName

@Nullable
public String getQuantitationTypeName()

Name of the QT to use if more than one is present in the data as per DataLoader.getQuantitationTypes().

This may be set to null, in which case the loader must only detect a single QT.

isReplaceExistingQuantitationType

public boolean isReplaceExistingQuantitationType()

Replace the vectors of an existing QT.

Requires quantitationTypeName to be set.

getQuantitationTypeNewName

@Nullable
public String getQuantitationTypeNewName()

Override the name of the resulting QT.

getQuantitationTypeNewType

@Nullable
public StandardQuantitationType getQuantitationTypeNewType()

Override the type of the resulting QT.

getQuantitationTypeNewScaleType

@Nullable
public ScaleType getQuantitationTypeNewScaleType()

Override the scale type of the resulting QT.

isMarkQuantitationTypeAsRecomputedFromRawData

public boolean isMarkQuantitationTypeAsRecomputedFromRawData()

Mark the quantitation type as recomputed from raw data.

See Also:

• QuantitationType.setIsRecomputedFromRawData(boolean)

isMarkQuantitationTypeAsPreferred

public boolean isMarkQuantitationTypeAsPreferred()

Mark the QT as preferred.

All other QTs of the same kind will be set to non-preferred as a result.

See Also:

• QuantitationType.setIsPreferred(boolean)
• QuantitationType.setIsSingleCellPreferred(boolean)
• QuantitationType.setIsMaskedPreferred(boolean)

getRenamingFile

@Nullable
public Path getRenamingFile()

A file containing a mapping of sample names to bioassay names.

See Also:

• RenamingBioAssayMapper