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

Class GenericMetadataSingleCellDataLoader

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.metadata.GenericMetadataSingleCellDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader, SequencingDataLoader, SingleCellDataLoader

public class GenericMetadataSingleCellDataLoader
extends AbstractDelegatingSingleCellDataLoader
implements SingleCellDataLoader

A generic loader that can be used to load single-cell data with a tabular metadata file.

This loader supports cell type assignments and generic cell-level characteristics and fallback to a delegate if the corresponding path is unset.

Author:

poirigui

See Also:

• CellTypeAssignmentMetadataParser
• GenericCellLevelCharacteristicsMetadataParser

Constructor Summary

Constructors

Constructor	Description
GenericMetadataSingleCellDataLoader(SingleCellDataLoader delegate, Path cellTypeMetadataFile, List<String> otherCellLevelCharacteristicsNames, Path otherCellCharacteristicsMetadataFile)

Method Summary

Modifier and Type	Method	Description
Set<CellTypeAssignment>	getCellTypeAssignments(SingleCellDimension singleCellDimension)	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.
void	setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)	Set the strategy used for mapping BioAssay to sample names from the data.
void	setCellTypeAssignmentDescription(String cellTypeAssignmentDescription)
void	setCellTypeAssignmentName(String cellTypeAssignmentName)
void	setCellTypeAssignmentProtocol(Protocol cellTypeAssignmentProtocol)
void	setIgnoreUnmatchedCellIds(boolean ignoreUnmatchedCellIds)
void	setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)	Ignore unmatched samples from the data.
void	setInferSamplesFromCellIdsOverlap(boolean inferSamplesFromCellIdsOverlap)
void	setUseCellIdsIfSampleNameIsMissing(boolean useCellIdsIfSampleNameIsMissing)

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

getSequencingMetadata, getSingleCellDimension, loadVectors

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, setDesignElementToGeneMapper, setIgnoreUnmatchedDesignElements

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, setDesignElementToGeneMapper, setIgnoreUnmatchedDesignElements

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

getSequencingMetadata

Methods inherited from interface ubic.gemma.core.loader.expression.singleCell.SingleCellDataLoader

getSequencingMetadata, getSingleCellDimension, loadVectors

Constructor Details

GenericMetadataSingleCellDataLoader

public GenericMetadataSingleCellDataLoader(SingleCellDataLoader delegate,
 @Nullable
 Path cellTypeMetadataFile,
 @Nullable
 List<String> otherCellLevelCharacteristicsNames,
 @Nullable
 Path otherCellCharacteristicsMetadataFile)

Method Details

setIgnoreUnmatchedSamples

public void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)

Ignore unmatched samples from the data.

This defaults to true.

In addition, unmatched samples when parsing cell type assignment and other cell-level characteristics files will be ignored.

Specified by:

setIgnoreUnmatchedSamples in interface DataLoader

Overrides:

setIgnoreUnmatchedSamples in class AbstractDelegatingDataLoader

setCellTypeAssignmentName

public void setCellTypeAssignmentName(String cellTypeAssignmentName)

setCellTypeAssignmentDescription

public void setCellTypeAssignmentDescription(@Nullable
 String cellTypeAssignmentDescription)

setCellTypeAssignmentProtocol

public void setCellTypeAssignmentProtocol(@Nullable
 Protocol cellTypeAssignmentProtocol)

setBioAssayToSampleNameMapper

public void setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)

Description copied from interface: DataLoader

Set the strategy used for mapping BioAssay to sample names from the data.

Specified by:

setBioAssayToSampleNameMapper in interface DataLoader

Overrides:

setBioAssayToSampleNameMapper in class AbstractDelegatingDataLoader

getCellTypeAssignments

public Set<CellTypeAssignment> getCellTypeAssignments(SingleCellDimension singleCellDimension)
                                               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 AbstractDelegatingSingleCellDataLoader

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

Overrides:

getOtherCellLevelCharacteristics in class AbstractDelegatingSingleCellDataLoader

Throws:

IOException

setInferSamplesFromCellIdsOverlap

public void setInferSamplesFromCellIdsOverlap(boolean inferSamplesFromCellIdsOverlap)

setUseCellIdsIfSampleNameIsMissing

public void setUseCellIdsIfSampleNameIsMissing(boolean useCellIdsIfSampleNameIsMissing)

setIgnoreUnmatchedCellIds

public void setIgnoreUnmatchedCellIds(boolean ignoreUnmatchedCellIds)