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

Class AbstractMexSingleCellDataLoaderConfigurer

java.lang.Object

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

All Implemented Interfaces:

DataLoaderConfigurer<MexSingleCellDataLoader,SingleCellDataLoaderConfig>, SingleCellDataLoaderConfigurer<MexSingleCellDataLoader>

Direct Known Subclasses:

GeoMexSingleCellDataLoaderConfigurer, MexSingleCellDataLoaderConfigurer

public abstract class AbstractMexSingleCellDataLoaderConfigurer
extends Object
implements SingleCellDataLoaderConfigurer<MexSingleCellDataLoader>

Field Summary

Fields

Modifier and Type	Field	Description
protected final org.apache.commons.logging.Log	log

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractMexSingleCellDataLoaderConfigurer(Path cellRangerPrefix)

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 abstract String	detect10xChemistry(String sampleName, Path sampleDir)	Detect the chemistry used by a 10x dataset.
protected abstract 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 abstract List<Path>	getSampleDirs()
protected abstract List<String>	getSampleNames()

Methods inherited from class java.lang.Object

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

Field Details

log

protected final org.apache.commons.logging.Log log

Constructor Details

AbstractMexSingleCellDataLoaderConfigurer

protected AbstractMexSingleCellDataLoaderConfigurer(@Nullable
 Path cellRangerPrefix)

Parameters:

cellRangerPrefix - path to an installation of Cell Ranger, required if 10x filtering is deemed necessary, MexSingleCellDataLoaderConfig.getApply10xFilter().

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>

getSampleNames

protected abstract List<String> getSampleNames()

getSampleDirs

protected abstract List<Path> getSampleDirs()

detect10x

protected boolean detect10x(String sampleName,
 Path sampleDir)

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

detectUnfiltered

protected boolean detectUnfiltered(String sampleName,
 Path sampleDir)

Detect if a MEX dataset is unfiltered.

detect10xGenome

protected abstract String detect10xGenome(String sampleName,
 Path sampleDir)

Detect the genome used by a 10x dataset.

detect10xChemistry

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

Detect the chemistry used by a 10x dataset.