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

Class CellXGeneAnnDataSingleCellDataLoader

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader

ubic.gemma.core.loader.expression.cellxgene.CellXGeneAnnDataSingleCellDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader, SequencingDataLoader, SingleCellDataLoader

public class CellXGeneAnnDataSingleCellDataLoader
extends AnnDataSingleCellDataLoader

Constructor Summary

Constructors

Constructor	Description
CellXGeneAnnDataSingleCellDataLoader(Path file, boolean keepPooledSample, boolean keepUnknownSample)

Method Summary

Modifier and Type	Method	Description
Set<CellTypeAssignment>	getCellTypeAssignments(SingleCellDimension dimension)	Load single-cell type assignments present in the data.
Set<QuantitationType>	getQuantitationTypes()	Load quantitation types present in the data.
Set<String>	getSampleNames()	Obtain the sample names present in the data.
Map<BioMaterial,Set<Characteristic>>	getSamplesCharacteristics(Collection<BioAssay> samples)	Load samples characteristics present in the data.

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

close, getFactors, getGenes, getGenes, getOtherCellLevelCharacteristics, getSequencingMetadata, getSequencingMetadata, getSingleCellDimension, loadVectors, setBioAssayToSampleNameMapper, setCellTypeFactorName, setCellTypeUriFactorName, setDesignElementToGeneMapper, setIgnoreCellTypeFactor, setIgnoreDataVectors, setIgnoreUnmatchedDesignElements, setIgnoreUnmatchedSamples, setMaxCharacteristics, setSampleFactorName, setTranspose, setUnknownCellTypeIndicator, setUseRawX

Methods inherited from class java.lang.Object

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

Constructor Details

CellXGeneAnnDataSingleCellDataLoader

public CellXGeneAnnDataSingleCellDataLoader(Path file,
 boolean keepPooledSample,
 boolean keepUnknownSample)

Method Details

getSampleNames

public Set<String> getSampleNames()
                           throws IOException

Description copied from interface: DataLoader

Obtain the sample names present in the data.

Specified by:

getSampleNames in interface DataLoader

Overrides:

getSampleNames in class AnnDataSingleCellDataLoader

Throws:

IOException

getSamplesCharacteristics

public Map<BioMaterial,Set<Characteristic>> getSamplesCharacteristics(Collection<BioAssay> samples)
                                                               throws IOException

Description copied from interface: DataLoader

Load samples characteristics present in the data.

Specified by:

getSamplesCharacteristics in interface DataLoader

Overrides:

getSamplesCharacteristics in class AnnDataSingleCellDataLoader

Parameters:

samples - to use when determining which characteristics to load

Returns:

proposed characteristics grouped by sample

Throws:

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

Overrides:

getCellTypeAssignments in class AnnDataSingleCellDataLoader

Throws:

IOException

getQuantitationTypes

public Set<QuantitationType> getQuantitationTypes()
                                           throws IOException

Description copied from interface: DataLoader

Load quantitation types present in the data.

Specified by:

getQuantitationTypes in interface DataLoader

Overrides:

getQuantitationTypes in class AnnDataSingleCellDataLoader

Throws:

IOException