Package ubic.gemma.core.loader.expression

Interface DataLoader

All Superinterfaces:

AutoCloseable, Closeable

All Known Subinterfaces:

SequencingDataLoader, SingleCellDataLoader

All Known Implementing Classes:

AbstractDelegatingDataLoader, AbstractDelegatingSequencingDataLoader, AbstractDelegatingSingleCellDataLoader, AnnDataSingleCellDataLoader, GenericMetadataSingleCellDataLoader, MexSingleCellDataLoader, NullSingleCellDataLoader, SequencingMetadataFileDataLoader, SequencingMetadataFileSingleCellDataLoader

public interface DataLoader
extends Closeable

Base interface for loading expression data in Gemma.

Author:

poirigui

Method Summary

Modifier and Type	Method	Description
void	close()	Free any resources that the loaded has setup.
Set<ExperimentalFactor>	getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)	Load experimental factors present in the data.
Set<String>	getGenes()	Load gene identifiers 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.
void	setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher)	Set the strategy used for mapping BioAssay to sample names from the data.
void	setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)	Set the strategy used for mapping CompositeSequence to gene identifiers from the data.
void	setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)	Ignore unmatched design elements from the data when creating vectors.
void	setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)	Ignore unmatched samples from the data.

Method Detail

setBioAssayToSampleNameMapper

void setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher)

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

setIgnoreUnmatchedSamples

void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)

Ignore unmatched samples from the data.

This defaults to true.

setDesignElementToGeneMapper

void setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)

Set the strategy used for mapping CompositeSequence to gene identifiers from the data.

setIgnoreUnmatchedDesignElements

void setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)

Ignore 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.

getSampleNames

Set<String> getSampleNames()
                    throws IOException

Obtain the sample names present in the data.

Throws:

IOException

getQuantitationTypes

Set<QuantitationType> getQuantitationTypes()
                                    throws IOException

Load quantitation types present in the data.

Throws:

IOException

getFactors

Set<ExperimentalFactor> getFactors(Collection<BioAssay> samples,
                                   @Nullable
                                   Map<BioMaterial,Set<FactorValue>> factorValueAssignments)
                            throws IOException

Load experimental factors present in the data.

Parameters:

samples - samples to use when determining which factors to load

factorValueAssignments - 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

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

Load samples characteristics present in the data.

Parameters:

samples - to use when determining which characteristics to load

Returns:

proposed characteristics grouped by sample

Throws:

IOException

getGenes

Set<String> getGenes()
              throws IOException

Load gene identifiers present in the data.

Throws:

IOException

close

void close()
    throws IOException

Free any resources that the loaded has setup.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Throws:

IOException