Package ubic.gemma.core.loader.expression

Class AbstractDelegatingDataLoader

java.lang.Object

ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader

Direct Known Subclasses:

AbstractDelegatingSequencingDataLoader

public class AbstractDelegatingDataLoader
extends Object
implements DataLoader

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractDelegatingDataLoader(DataLoader delegate)

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.

Methods inherited from class java.lang.Object

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

Constructor Details

AbstractDelegatingDataLoader

protected AbstractDelegatingDataLoader(DataLoader delegate)

Method Details

setBioAssayToSampleNameMapper

public void setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMatcher)

Description copied from interface: DataLoader

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

Specified by:

setBioAssayToSampleNameMapper in interface DataLoader

setDesignElementToGeneMapper

public void setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)

Description copied from interface: DataLoader

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

Specified by:

setDesignElementToGeneMapper in interface DataLoader

setIgnoreUnmatchedSamples

public void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)

Description copied from interface: DataLoader

Ignore unmatched samples from the data.

This defaults to true.

Specified by:

setIgnoreUnmatchedSamples in interface DataLoader

setIgnoreUnmatchedDesignElements

public void setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)

Description copied from interface: DataLoader

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.

Specified by:

setIgnoreUnmatchedDesignElements in interface DataLoader

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

Throws:

IOException

getGenes

public Set<String> getGenes()
                     throws IOException

Description copied from interface: DataLoader

Load gene identifiers present in the data.

Specified by:

getGenes in interface DataLoader

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

Throws:

IOException

getFactors

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

Description copied from interface: DataLoader

Load experimental factors present in the data.

Specified by:

getFactors in interface DataLoader

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

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

Parameters:

samples - to use when determining which characteristics to load

Returns:

proposed characteristics grouped by sample

Throws:

IOException

close

public void close()
           throws IOException

Description copied from interface: DataLoader

Free any resources that the loaded has setup.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface DataLoader

Throws:

IOException