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

Class CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C extends CellXGeneAnnDataSingleCellDataLoaderConfig,B extends CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>>

java.lang.Object

ubic.gemma.core.loader.expression.DataLoaderConfig.DataLoaderConfigBuilder<C,B>

ubic.gemma.core.loader.expression.sequencing.SequencingDataLoaderConfig.SequencingDataLoaderConfigBuilder<C,B>

ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoaderConfig.SingleCellDataLoaderConfigBuilder<C,B>

ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C,B>

ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>

Enclosing class:

CellXGeneAnnDataSingleCellDataLoaderConfig

public abstract static class CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C extends CellXGeneAnnDataSingleCellDataLoaderConfig,B extends CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>>
extends AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C,B>

Constructor Summary

Constructors

Constructor	Description
CellXGeneAnnDataSingleCellDataLoaderConfigBuilder()

Method Summary

Modifier and Type	Method	Description
abstract C	build()
B	keepPooledSample(boolean keepPooledSample)	Keep the pooled sample (if any) in the dataset.
B	keepUnknownSample(boolean keepUnknownSample)	Keep the unknown sample (if any) in the dataset.
protected abstract B	self()
String	toString()

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

cellTypeFactorName, cellTypeUriFactorName, ignoreCellTypeFactor, sampleFactorName, transpose, unknownCellTypeIndicator, useRawX

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

cellTypeAssignmentDescription, cellTypeAssignmentFile, cellTypeAssignmentName, cellTypeAssignmentProtocol, console, discardEmptyCells, ignoreCompatibleCellTypeFactor, ignoreDataVectors, ignoreExistingCellTypeAssignment, ignoreExistingOtherCellLevelCharacteristics, ignoreSamplesLackingData, ignoreUnmatchedCellIds, inferSamplesFromCellIdsOverlap, markSingleCellTypeAssignmentAsPreferred, otherCellLevelCharacteristicsDefaultValues, otherCellLevelCharacteristicsDefaultValueUris, otherCellLevelCharacteristicsFile, otherCellLevelCharacteristicsNames, preferredCellTypeAssignmentName, preferSinglePrecision, recreateCellTypeFactorIfNecessary, replaceExistingCellTypeAssignment, replaceExistingOtherCellLevelCharacteristics, transformExecutor, useCellIdsIfSampleNameIsMissing

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

defaultSequencingMetadata, sequencingMetadataFile

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

dataPath, markQuantitationTypeAsPreferred, markQuantitationTypeAsRecomputedFromRawData, quantitationTypeName, quantitationTypeNewName, quantitationTypeNewScaleType, quantitationTypeNewType, renamingFile, replaceExistingQuantitationType

Methods inherited from class java.lang.Object

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

Constructor Details

CellXGeneAnnDataSingleCellDataLoaderConfigBuilder

public CellXGeneAnnDataSingleCellDataLoaderConfigBuilder()

Method Details

keepPooledSample

public B keepPooledSample(boolean keepPooledSample)

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

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

Returns:

this.

keepUnknownSample

public B keepUnknownSample(boolean keepUnknownSample)

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

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

Returns:

this.

self

protected abstract B self()

Specified by:

self in class AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C extends CellXGeneAnnDataSingleCellDataLoaderConfig,B extends CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>>

build

public abstract C build()

Specified by:

build in class AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C extends CellXGeneAnnDataSingleCellDataLoaderConfig,B extends CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>>

toString

public String toString()

Overrides:

toString in class AnnDataSingleCellDataLoaderConfig.AnnDataSingleCellDataLoaderConfigBuilder<C extends CellXGeneAnnDataSingleCellDataLoaderConfig,B extends CellXGeneAnnDataSingleCellDataLoaderConfig.CellXGeneAnnDataSingleCellDataLoaderConfigBuilder<C,B>>