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

Class AbstractDelegatingSingleCellDataLoader

java.lang.Object

ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader

ubic.gemma.core.loader.expression.sequencing.AbstractDelegatingSequencingDataLoader

ubic.gemma.core.loader.expression.singleCell.AbstractDelegatingSingleCellDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader, SequencingDataLoader, SingleCellDataLoader

Direct Known Subclasses:

GenericMetadataSingleCellDataLoader, SequencingMetadataFileSingleCellDataLoader

public abstract class AbstractDelegatingSingleCellDataLoader
extends AbstractDelegatingSequencingDataLoader
implements SingleCellDataLoader

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractDelegatingSingleCellDataLoader(SingleCellDataLoader delegate)

Method Summary

Modifier and Type	Method	Description
Set<CellTypeAssignment>	getCellTypeAssignments(SingleCellDimension dimension)	Load single-cell type assignments present in the data.
Set<CellLevelCharacteristics>	getOtherCellLevelCharacteristics(SingleCellDimension dimension)	Load cell-level characteristics that are not cell type assignments present in the data.
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(SingleCellDimension dimension)
SingleCellDimension	getSingleCellDimension(Collection<BioAssay> bioAssays)	Load the single-cell dimension present in the data.
Stream<SingleCellExpressionDataVector>	loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)	Produces a stream of single-cell expression data vectors for the given QuantitationType.

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

getSequencingMetadata

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

close, getFactors, getGenes, getQuantitationTypes, getSampleNames, getSamplesCharacteristics, setBioAssayToSampleNameMapper, setDesignElementToGeneMapper, setIgnoreUnmatchedDesignElements, setIgnoreUnmatchedSamples

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.loader.expression.DataLoader

close, getFactors, getGenes, getQuantitationTypes, getSampleNames, getSamplesCharacteristics, setBioAssayToSampleNameMapper, setDesignElementToGeneMapper, setIgnoreUnmatchedDesignElements, setIgnoreUnmatchedSamples

Methods inherited from interface ubic.gemma.core.loader.expression.sequencing.SequencingDataLoader

getSequencingMetadata

Constructor Details

AbstractDelegatingSingleCellDataLoader

protected AbstractDelegatingSingleCellDataLoader(SingleCellDataLoader delegate)

Method Details

getSingleCellDimension

public SingleCellDimension getSingleCellDimension(Collection<BioAssay> bioAssays)
                                           throws IOException,
IllegalArgumentException

Description copied from interface: SingleCellDataLoader

Load the single-cell dimension present in the data.

Not all samples might be present and thus the returned SingleCellDimension will have a expression data for a subset of the data.

Specified by:

getSingleCellDimension in interface SingleCellDataLoader

Parameters:

bioAssays - a set of bioassays to use when populating the dimension, not all bioassays may be used

Throws:

IllegalArgumentException - if a sample present in the data cannot be matched to one of the supplied BioAssay, ignored if DataLoader.setIgnoreUnmatchedSamples(boolean) is set to true.

IOException

getCellTypeAssignments

public Set<CellTypeAssignment> getCellTypeAssignments(SingleCellDimension dimension)
                                               throws IOException

Description copied from interface: SingleCellDataLoader

Load single-cell type assignments present in the data.

Specified by:

getCellTypeAssignments in interface SingleCellDataLoader

Throws:

IOException

getOtherCellLevelCharacteristics

public Set<CellLevelCharacteristics> getOtherCellLevelCharacteristics(SingleCellDimension dimension)
                                                               throws IOException

Description copied from interface: SingleCellDataLoader

Load cell-level characteristics that are not cell type assignments present in the data.

Specified by:

getOtherCellLevelCharacteristics in interface SingleCellDataLoader

Throws:

IOException

getSequencingMetadata

public Map<BioAssay,SequencingMetadata> getSequencingMetadata(SingleCellDimension dimension)
                                                       throws IOException

Specified by:

getSequencingMetadata in interface SingleCellDataLoader

Throws:

IOException

loadVectors

public Stream<SingleCellExpressionDataVector> loadVectors(Collection<CompositeSequence> designElements,
 SingleCellDimension dimension,
 QuantitationType quantitationType)
                                                   throws IOException,
IllegalArgumentException

Description copied from interface: SingleCellDataLoader

Produces a stream of single-cell expression data vectors for the given QuantitationType.

Specified by:

loadVectors in interface SingleCellDataLoader

Parameters:

designElements - a collection of design elements for mapping of element names used in the dataset to CompositeSequence

dimension - a dimension to use for creating vectors, may be loaded from the single-cell data with SingleCellDataLoader.getSingleCellDimension(Collection)

quantitationType - a quantitation type to extract from the data for, may be loaded from the single-cell data with DataLoader.getQuantitationTypes()

Returns:

a stream of single-cell expression data vectors that must be closed when done, preferably using a try-with-resource block.

Throws:

IllegalArgumentException - if a design element present in the data cannot be matched to one of the supplied elements, requires setting DataLoader.setIgnoreUnmatchedDesignElements(boolean) to false

IOException