Class AnnDataSingleCellDataLoaderConfigurer

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.AbstractAnnDataSingleCellDataLoaderConfigurer

ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfigurer

All Implemented Interfaces:

DataLoaderConfigurer<AnnDataSingleCellDataLoader, SingleCellDataLoaderConfig>, SingleCellDataLoaderConfigurer<AnnDataSingleCellDataLoader>

public class AnnDataSingleCellDataLoaderConfigurer
extends AbstractAnnDataSingleCellDataLoaderConfigurer

Field Summary

Fields inherited from class AbstractAnnDataSingleCellDataLoaderConfigurer

CELL_ID_COLUMN_NAME_KEYWORDS

Constructor Summary

Constructors

Constructor	Description
AnnDataSingleCellDataLoaderConfigurer(Path annDataFile, Collection<BioAssay> bioAssays, BioAssayMapper bioAssayMapper, SingleCellDataTransformationFactory singleCellDataTransformationFactory)

Method Summary

Modifier and Type	Method	Description
AnnDataSingleCellDataLoader	configureLoader(SingleCellDataLoaderConfig config)	Automatically configure a loader for an AnnData file.
protected boolean	isSampleNameColumn(Dataframe.Column<?,String> column)	Check if a given dataframe column contains sample names.

Methods inherited from class AbstractAnnDataSingleCellDataLoaderConfigurer

getUnknownCellTypeIndicator, isCellIdColumn, isCellTypeColumn, isGeneColumn

Methods inherited from class Object

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

Constructor Details

AnnDataSingleCellDataLoaderConfigurer

public AnnDataSingleCellDataLoaderConfigurer(Path annDataFile,
 Collection<BioAssay> bioAssays,
 BioAssayMapper bioAssayMapper,
 @Nullable
 SingleCellDataTransformationFactory singleCellDataTransformationFactory)

Parameters:

bioAssays - a collection of BioAssay that are used to detect the sample column

bioAssayMapper - a mapper for BioAssay to sample name to interpret identifier in the file

Method Details

isSampleNameColumn

protected boolean isSampleNameColumn(Dataframe.Column<?,String> column)

Description copied from class: AbstractAnnDataSingleCellDataLoaderConfigurer

Check if a given dataframe column contains sample names.

Overrides:

isSampleNameColumn in class AbstractAnnDataSingleCellDataLoaderConfigurer

configureLoader

public AnnDataSingleCellDataLoader configureLoader(SingleCellDataLoaderConfig config)

Description copied from class: AbstractAnnDataSingleCellDataLoaderConfigurer

Automatically configure a loader for an AnnData file.

Specified by:

configureLoader in interface DataLoaderConfigurer<AnnDataSingleCellDataLoader, SingleCellDataLoaderConfig>

Overrides:

configureLoader in class AbstractAnnDataSingleCellDataLoaderConfigurer