Package ubic.gemma.core.loader.expression.cellxgene

Class CellXGeneAnnDataSingleCellDataLoaderConfig

java.lang.Object

ubic.gemma.core.loader.expression.DataLoaderConfig

ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig

ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig

ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig

ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig

public class CellXGeneAnnDataSingleCellDataLoaderConfig
extends AnnDataSingleCellDataLoaderConfig

A configuration for loading CELLxGENE data from AnnData files.

Author:

poirigui

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C extends CellXGeneAnnDataSingleCellDataLoaderConfig,B extends CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig

AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C extends AnnDataSingleCellDataLoaderConfig,B extends AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig

SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C extends SingleCellDataLoaderConfig,B extends SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig

SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C extends SequencingDataLoaderConfig,B extends SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B>>

Nested classes/interfaces inherited from class ubic.gemma.core.loader.expression.DataLoaderConfig

DataLoaderConfig.DataLoaderConfigBuilder<C extends DataLoaderConfig,B extends DataLoaderConfig.DataLoaderConfigBuilder<C,B>>

Field Summary

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

transformExecutor

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	CellXGeneAnnDataSingleCellDataLoaderConfig(CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<?,?> b)

Method Summary

Modifier and Type	Method	Description
static CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<?,?>	builder()
boolean	isKeepPooledSample()	Keep the pooled sample (if any) in the dataset.
boolean	isKeepUnknownSample()	Keep the unknown sample (if any) in the dataset.

Methods inherited from class ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig

getCellTypeFactorName, getCellTypeUriFactorName, getSampleFactorName, getTranspose, getUnknownCellTypeIndicator, getUseRawX, isIgnoreCellTypeFactor

Methods inherited from class ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig

getCellTypeAssignmentDescription, getCellTypeAssignmentFile, getCellTypeAssignmentName, getCellTypeAssignmentProtocol, getConsole, getDiscardEmptyCells, getOtherCellLevelCharacteristicsDefaultValues, getOtherCellLevelCharacteristicsDefaultValueUris, getOtherCellLevelCharacteristicsFile, getOtherCellLevelCharacteristicsNames, getPreferredCellTypeAssignmentName, getTransformExecutor, isIgnoreCompatibleCellTypeFactor, isIgnoreDataVectors, isIgnoreExistingCellTypeAssignment, isIgnoreExistingOtherCellLevelCharacteristics, isIgnoreSamplesLackingData, isIgnoreUnmatchedCellIds, isInferSamplesFromCellIdsOverlap, isMarkSingleCellTypeAssignmentAsPreferred, isPreferSinglePrecision, isRecreateCellTypeFactorIfNecessary, isReplaceExistingCellTypeAssignment, isReplaceExistingOtherCellLevelCharacteristics, isUseCellIdsIfSampleNameIsMissing

Methods inherited from class ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig

getDefaultSequencingMetadata, getSequencingMetadataFile

Methods inherited from class ubic.gemma.core.loader.expression.DataLoaderConfig

getDataPath, getQuantitationTypeName, getQuantitationTypeNewName, getQuantitationTypeNewScaleType, getQuantitationTypeNewType, getRenamingFile, isMarkQuantitationTypeAsPreferred, isMarkQuantitationTypeAsRecomputedFromRawData, isReplaceExistingQuantitationType

Methods inherited from class java.lang.Object

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

Constructor Details

CellXGeneAnnDataSingleCellDataLoaderConfig

protected CellXGeneAnnDataSingleCellDataLoaderConfig(CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<?,?> b)

Method Details

builder

public static CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<?,?> builder()

isKeepPooledSample

public boolean isKeepPooledSample()

Keep the pooled sample (if any) in the dataset.

This sample uses the "pooled" indicator as donor ID.

isKeepUnknownSample

public boolean isKeepUnknownSample()

Keep the unknown sample (if any) in the dataset.

This sample uses the "unknown" indicator as donor ID.