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 AnnDataSingleCellDataLoaderConfig

AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C,B>

Nested classes/interfaces inherited from class SingleCellDataLoaderConfig

SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B>

Nested classes/interfaces inherited from class SequencingDataLoaderConfig

SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B>

Nested classes/interfaces inherited from class DataLoaderConfig

DataLoaderConfig.DataLoaderConfigBuilder<C,B>

Field Summary

Fields inherited from class 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 AnnDataSingleCellDataLoaderConfig

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

Methods inherited from class 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 SequencingDataLoaderConfig

getDefaultSequencingMetadata, getSequencingMetadataFile

Methods inherited from class DataLoaderConfig

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

Methods inherited from class 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.