Class NullSingleCellDataLoader
java.lang.Object
ubic.gemma.core.loader.expression.singleCell.NullSingleCellDataLoader
- All Implemented Interfaces:
Closeable,AutoCloseable,DataLoader,SequencingDataLoader,SingleCellDataLoader
Single-cell data loader used when no data is available.
This is useful to use as a base loader for an AbstractDelegatingSingleCellDataLoader implementation.
- Author:
- poirigui
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidclose()Free any resources that the loaded has setup.getCellTypeAssignments(SingleCellDimension dimension) Load single-cell type assignments present in the data.getFactors(Collection<BioAssay> samples, Map<BioMaterial, Set<FactorValue>> factorValueAssignments) Load experimental factors present in the data.getGenes()Load gene identifiers present in the data.Load cell-level characteristics that are not cell type assignments present in the data.Load quantitation types present in the data.Obtain the sample names present in the data.getSamplesCharacteristics(Collection<BioAssay> samples) Load samples characteristics present in the data.getSequencingMetadata(Collection<BioAssay> samples) Retrieve various sequencing metadata if counting data is present.getSequencingMetadata(SingleCellDimension dimension) getSingleCellDimension(Collection<BioAssay> bioAssays) Load the single-cell dimension present in the data.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType) Produces a stream of single-cell expression data vectors for the givenQuantitationType.voidsetBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher) Set the strategy used for mappingBioAssayto sample names from the data.voidsetDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper) Set the strategy used for mappingCompositeSequenceto gene identifiers from the data.voidsetIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements) Ignore unmatched design elements from the data when creating vectors.voidsetIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples) Ignore unmatched samples from the data.
-
Constructor Details
-
NullSingleCellDataLoader
public NullSingleCellDataLoader()
-
-
Method Details
-
setBioAssayToSampleNameMapper
Description copied from interface:DataLoaderSet the strategy used for mappingBioAssayto sample names from the data.- Specified by:
setBioAssayToSampleNameMapperin interfaceDataLoader
-
setDesignElementToGeneMapper
Description copied from interface:DataLoaderSet the strategy used for mappingCompositeSequenceto gene identifiers from the data.- Specified by:
setDesignElementToGeneMapperin interfaceDataLoader
-
setIgnoreUnmatchedSamples
public void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples) Description copied from interface:DataLoaderIgnore unmatched samples from the data.This defaults to true.
- Specified by:
setIgnoreUnmatchedSamplesin interfaceDataLoader
-
setIgnoreUnmatchedDesignElements
public void setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements) Description copied from interface:DataLoaderIgnore unmatched design elements from the data when creating vectors.This defaults to true.
There's a discussions to make this default in false in general for sequencing data.
- Specified by:
setIgnoreUnmatchedDesignElementsin interfaceDataLoader
-
getSampleNames
Description copied from interface:DataLoaderObtain the sample names present in the data.- Specified by:
getSampleNamesin interfaceDataLoader- Throws:
IOException
-
getSingleCellDimension
public SingleCellDimension getSingleCellDimension(Collection<BioAssay> bioAssays) throws IOException, IllegalArgumentException Description copied from interface:SingleCellDataLoaderLoad the single-cell dimension present in the data.Not all samples might be present and thus the returned
SingleCellDimensionwill have a expression data for a subset of the data.- Specified by:
getSingleCellDimensionin interfaceSingleCellDataLoader- 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 suppliedBioAssay, ignored ifDataLoader.setIgnoreUnmatchedSamples(boolean)is set to true.IOException
-
getQuantitationTypes
Description copied from interface:DataLoaderLoad quantitation types present in the data.- Specified by:
getQuantitationTypesin interfaceDataLoader- Throws:
IOException
-
getCellTypeAssignments
public Set<CellTypeAssignment> getCellTypeAssignments(SingleCellDimension dimension) throws IOException Description copied from interface:SingleCellDataLoaderLoad single-cell type assignments present in the data.- Specified by:
getCellTypeAssignmentsin interfaceSingleCellDataLoader- Throws:
IOException
-
getOtherCellLevelCharacteristics
public Set<CellLevelCharacteristics> getOtherCellLevelCharacteristics(SingleCellDimension dimension) throws IOException Description copied from interface:SingleCellDataLoaderLoad cell-level characteristics that are not cell type assignments present in the data.- Specified by:
getOtherCellLevelCharacteristicsin interfaceSingleCellDataLoader- Throws:
IOException
-
getFactors
public Set<ExperimentalFactor> getFactors(Collection<BioAssay> samples, @Nullable Map<BioMaterial, Set<FactorValue>> factorValueAssignments) throws IOExceptionDescription copied from interface:DataLoaderLoad experimental factors present in the data.- Specified by:
getFactorsin interfaceDataLoader- Parameters:
samples- samples to use when determining which factors to loadfactorValueAssignments- if non-null, the proposed assignment of factor values to samples are populated in the mapping.- Returns:
- a set of factors present in the data
- Throws:
IOException
-
getSamplesCharacteristics
public Map<BioMaterial,Set<Characteristic>> getSamplesCharacteristics(Collection<BioAssay> samples) throws IOException Description copied from interface:DataLoaderLoad samples characteristics present in the data.- Specified by:
getSamplesCharacteristicsin interfaceDataLoader- Parameters:
samples- to use when determining which characteristics to load- Returns:
- proposed characteristics grouped by sample
- Throws:
IOException
-
getGenes
Description copied from interface:DataLoaderLoad gene identifiers present in the data.- Specified by:
getGenesin interfaceDataLoader- Throws:
IOException
-
getSequencingMetadata
public Map<BioAssay,SequencingMetadata> getSequencingMetadata(Collection<BioAssay> samples) throws IOException Description copied from interface:SequencingDataLoaderRetrieve various sequencing metadata if counting data is present.- Specified by:
getSequencingMetadatain interfaceSequencingDataLoader- Throws:
IOException
-
getSequencingMetadata
public Map<BioAssay,SequencingMetadata> getSequencingMetadata(SingleCellDimension dimension) throws IOException - Specified by:
getSequencingMetadatain interfaceSingleCellDataLoader- Throws:
IOException
-
loadVectors
public Stream<SingleCellExpressionDataVector> loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType) throws IOException, IllegalArgumentException Description copied from interface:SingleCellDataLoaderProduces a stream of single-cell expression data vectors for the givenQuantitationType.- Specified by:
loadVectorsin interfaceSingleCellDataLoader- Parameters:
designElements- a collection of design elements for mapping of element names used in the dataset toCompositeSequencedimension- a dimension to use for creating vectors, may be loaded from the single-cell data withSingleCellDataLoader.getSingleCellDimension(Collection)quantitationType- a quantitation type to extract from the data for, may be loaded from the single-cell data withDataLoader.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 settingDataLoader.setIgnoreUnmatchedDesignElements(boolean)to falseIOException
-
close
Description copied from interface:DataLoaderFree any resources that the loaded has setup.- Specified by:
closein interfaceAutoCloseable- Specified by:
closein interfaceCloseable- Specified by:
closein interfaceDataLoader- Throws:
IOException
-