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

Class MexSingleCellDataLoaderConfigurer

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer

ubic.gemma.core.loader.expression.singleCell.MexSingleCellDataLoaderConfigurer

All Implemented Interfaces:

DataLoaderConfigurer<MexSingleCellDataLoader,SingleCellDataLoaderConfig>, SingleCellDataLoaderConfigurer<MexSingleCellDataLoader>

public class MexSingleCellDataLoaderConfigurer
extends AbstractMexSingleCellDataLoaderConfigurer

Configure a MexSingleCellDataLoader for a given directory and collection of BioAssays.

Author:

poirigui

Field Summary

Fields inherited from class ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer

log

Constructor Summary

Constructors

Constructor	Description
MexSingleCellDataLoaderConfigurer(Path mexDir, Collection<BioAssay> bioAssays, BioAssayMapper bioAssayMapper, Path cellRangerPrefix, GeoSeries geoSeries)

Method Summary

Modifier and Type	Method	Description
MexSingleCellDataLoader	configureLoader(SingleCellDataLoaderConfig config)	Create a DataLoader from the given configuration.
protected boolean	detect10x(String sampleName, Path sampleDir)	Detect if a MEX dataset is using the 10x Chromium Sequencing platform.
protected String	detect10xChemistry(String sampleName, Path sampleDir)	Detect the chemistry used by a 10x dataset.
protected String	detect10xGenome(String sampleName, Path sampleDir)	Detect the genome used by a 10x dataset.
protected boolean	detectUnfiltered(String sampleName, Path sampleDir)	Detect if a MEX dataset is unfiltered.
protected List<Path>	getSampleDirs()
protected List<String>	getSampleNames()

Methods inherited from class java.lang.Object

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

Constructor Details

MexSingleCellDataLoaderConfigurer

public MexSingleCellDataLoaderConfigurer(Path mexDir,
 Collection<BioAssay> bioAssays,
 BioAssayMapper bioAssayMapper,
 @Nullable
 Path cellRangerPrefix,
 @Nullable
 GeoSeries geoSeries)

Parameters:

geoSeries - GEO series metadata, optional, but can be used to infer the 10x chemistry

Method Details

configureLoader

public MexSingleCellDataLoader configureLoader(SingleCellDataLoaderConfig config)

Description copied from interface: DataLoaderConfigurer

Create a DataLoader from the given configuration.

Specified by:

configureLoader in interface DataLoaderConfigurer<MexSingleCellDataLoader,SingleCellDataLoaderConfig>

Overrides:

configureLoader in class AbstractMexSingleCellDataLoaderConfigurer

getSampleNames

protected List<String> getSampleNames()

Specified by:

getSampleNames in class AbstractMexSingleCellDataLoaderConfigurer

getSampleDirs

protected List<Path> getSampleDirs()

Specified by:

getSampleDirs in class AbstractMexSingleCellDataLoaderConfigurer

detect10x

protected boolean detect10x(String sampleName,
 Path sampleDir)

Description copied from class: AbstractMexSingleCellDataLoaderConfigurer

Detect if a MEX dataset is using the 10x Chromium Sequencing platform.

Overrides:

detect10x in class AbstractMexSingleCellDataLoaderConfigurer

detectUnfiltered

protected boolean detectUnfiltered(String sampleName,
 Path sampleDir)

Description copied from class: AbstractMexSingleCellDataLoaderConfigurer

Detect if a MEX dataset is unfiltered.

Overrides:

detectUnfiltered in class AbstractMexSingleCellDataLoaderConfigurer

detect10xGenome

protected String detect10xGenome(String sampleName,
 Path sampleDir)

Description copied from class: AbstractMexSingleCellDataLoaderConfigurer

Detect the genome used by a 10x dataset.

Specified by:

detect10xGenome in class AbstractMexSingleCellDataLoaderConfigurer

detect10xChemistry

@Nullable
protected String detect10xChemistry(String sampleName,
 Path sampleDir)

Description copied from class: AbstractMexSingleCellDataLoaderConfigurer

Detect the chemistry used by a 10x dataset.

Specified by:

detect10xChemistry in class AbstractMexSingleCellDataLoaderConfigurer