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

Class SequencingMetadataFileSingleCellDataLoader

java.lang.Object

ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader

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

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

ubic.gemma.core.loader.expression.singleCell.SequencingMetadataFileSingleCellDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader, SequencingDataLoader, SingleCellDataLoader

public class SequencingMetadataFileSingleCellDataLoader
extends AbstractDelegatingSingleCellDataLoader

Adapt a SequencingMetadataFileDataLoader so that it can be used as a SingleCellDataLoader.

Author:

poirigui

See Also:

• SequencingMetadataFileDataLoader

Constructor Summary

Constructors

Constructor	Description
SequencingMetadataFileSingleCellDataLoader(SingleCellDataLoader delegate, Path sequencingMetadataFile, SequencingMetadata defaultMetadata, BioAssayMapper bioAssayMapper)

Method Summary

Modifier and Type	Method	Description
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(Collection<BioAssay> samples)	Retrieve various sequencing metadata if counting data is present.
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(SingleCellDimension dimension)

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

getCellTypeAssignments, getOtherCellLevelCharacteristics, getSingleCellDimension, loadVectors

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

Constructor Details

SequencingMetadataFileSingleCellDataLoader

public SequencingMetadataFileSingleCellDataLoader(SingleCellDataLoader delegate,
 Path sequencingMetadataFile,
 @Nullable
 SequencingMetadata defaultMetadata,
 BioAssayMapper bioAssayMapper)

Method Details

getSequencingMetadata

public Map<BioAssay,SequencingMetadata> getSequencingMetadata(Collection<BioAssay> samples)
                                                       throws IOException

Description copied from interface: SequencingDataLoader

Retrieve various sequencing metadata if counting data is present.

Specified by:

getSequencingMetadata in interface SequencingDataLoader

Overrides:

getSequencingMetadata in class AbstractDelegatingSequencingDataLoader

Throws:

IOException

getSequencingMetadata

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

Specified by:

getSequencingMetadata in interface SingleCellDataLoader

Overrides:

getSequencingMetadata in class AbstractDelegatingSingleCellDataLoader

Throws:

IOException