Package ubic.gemma.core.loader.expression.singleCell

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

CELL_ID_COLUMN_NAME_KEYWORDS

Constructor Summary

Constructors

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

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

getUnknownCellTypeIndicator, isCellIdColumn, isCellTypeColumn, isGeneColumn, setPythonExecutable, setScratchDir

Methods inherited from class java.lang.Object

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

Constructor Details

AnnDataSingleCellDataLoaderConfigurer

public AnnDataSingleCellDataLoaderConfigurer(Path annDataFile,
 Collection<BioAssay> bioAssays,
 BioAssayMapper bioAssayMapper)

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