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

Class AnnDataSingleCellDataLoaderConfig

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

Direct Known Subclasses:

CellXGeneAnnDataSingleCellDataLoaderConfig

public class AnnDataSingleCellDataLoaderConfig
extends SingleCellDataLoaderConfig

A configuration for loading single-cell data form AnnData format.

See Also:

• AnnDataSingleCellDataLoader

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	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	AnnDataSingleCellDataLoaderConfig(AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<?,?> b)

Method Summary

Modifier and Type	Method	Description
static AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<?,?>	builder()
String	getCellTypeFactorName()
String	getCellTypeUriFactorName()
String	getSampleFactorName()
Boolean	getTranspose()
String	getUnknownCellTypeIndicator()
Boolean	getUseRawX()
boolean	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

AnnDataSingleCellDataLoaderConfig

protected AnnDataSingleCellDataLoaderConfig(AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<?,?> b)

Method Details

builder

public static AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<?,?> builder()

getSampleFactorName

@Nullable
public String getSampleFactorName()

getCellTypeFactorName

@Nullable
public String getCellTypeFactorName()

getCellTypeUriFactorName

@Nullable
public String getCellTypeUriFactorName()

isIgnoreCellTypeFactor

public boolean isIgnoreCellTypeFactor()

getUnknownCellTypeIndicator

@Nullable
public String getUnknownCellTypeIndicator()

getTranspose

@Nullable
public Boolean getTranspose()

getUseRawX

@Nullable
public Boolean getUseRawX()