Package ubic.gemma.core.loader.expression.sequencing

Class SequencingDataLoaderConfig

java.lang.Object

ubic.gemma.core.loader.expression.DataLoaderConfig

ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig

Direct Known Subclasses:

SingleCellDataLoaderConfig

public class SequencingDataLoaderConfig
extends DataLoaderConfig

Configuration for loading sequencing data.

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C extends SequencingDataLoaderConfig,B extends SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.DataLoaderConfig

DataLoaderConfig.DataLoaderConfigBuilder<C extends DataLoaderConfig,B extends DataLoaderConfig.DataLoaderConfigBuilder<C,B>>

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SequencingDataLoaderConfig(SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<?,?> b)

Method Summary

Modifier and Type	Method	Description
static SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<?,?>	builder()
SequencingMetadata	getDefaultSequencingMetadata()	Default sequencing metadata to use.
Path	getSequencingMetadataFile()	File containing per-assay sequencing metadata.

Methods inherited from class ubic.gemma.core.loader.expression.DataLoaderConfig

getDataPath, getQuantitationTypeName, getQuantitationTypeNewName, getQuantitationTypeNewScaleType, getQuantitationTypeNewType, getRenamingFile, isMarkQuantitationTypeAsPreferred, isMarkQuantitationTypeAsRecomputedFromRawData, isReplaceExistingQuantitationType

Methods inherited from class java.lang.Object

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

Constructor Details

SequencingDataLoaderConfig

protected SequencingDataLoaderConfig(SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<?,?> b)

Method Details

builder

public static SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<?,?> builder()

getDefaultSequencingMetadata

@Nullable
public SequencingMetadata getDefaultSequencingMetadata()

Default sequencing metadata to use.

This can be overwritten by the metadata file sequencingMetadataFile or by the delegate loader.

getSequencingMetadataFile

@Nullable
public Path getSequencingMetadataFile()

File containing per-assay sequencing metadata.

Values from the file overrides the default metadata and the metadata from the delegate loader if any.

See Also:

• SequencingMetadataFileDataLoader