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

Class GeoMexSingleCellDataLoaderConfigurer

java.lang.Object

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

ubic.gemma.core.loader.expression.geo.singleCell.GeoMexSingleCellDataLoaderConfigurer

All Implemented Interfaces:

DataLoaderConfigurer<MexSingleCellDataLoader,SingleCellDataLoaderConfig>, SingleCellDataLoaderConfigurer<MexSingleCellDataLoader>

public class GeoMexSingleCellDataLoaderConfigurer
extends AbstractMexSingleCellDataLoaderConfigurer

Constructor Summary

Constructors

Constructor	Description
GeoMexSingleCellDataLoaderConfigurer(Path mexDir, GeoSeries series, Path cellRangerPrefix)

Method Summary

Modifier and Type	Method	Description
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 ubic.gemma.core.loader.expression.singleCell.AbstractMexSingleCellDataLoaderConfigurer

configureLoader

Methods inherited from class java.lang.Object

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

Constructor Details

GeoMexSingleCellDataLoaderConfigurer

public GeoMexSingleCellDataLoaderConfigurer(Path mexDir,
 GeoSeries series,
 @Nullable
 Path cellRangerPrefix)

Method Details

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

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