Package ubic.gemma.core.loader.expression.sequencing

Class SequencingMetadataFileDataLoader

java.lang.Object

ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader

ubic.gemma.core.loader.expression.sequencing.AbstractDelegatingSequencingDataLoader

ubic.gemma.core.loader.expression.sequencing.SequencingMetadataFileDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader, SequencingDataLoader

public class SequencingMetadataFileDataLoader
extends AbstractDelegatingSequencingDataLoader

Load sequencing metadata from a TSV file.

Author:

poirigui

See Also:

• SequencingMetadata

Constructor Summary

Constructors

Constructor	Description
SequencingMetadataFileDataLoader(SequencingDataLoader delegate, Path sequencingMetadataFile, SequencingMetadata defaultMetadata, BioAssayMapper bioAssayMapper)

Method Summary

Modifier and Type	Method	Description
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(Collection<BioAssay> bioAssays)	Retrieve various sequencing metadata if counting data is present.
void	setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)	Ignore unmatched samples from the data.

Methods inherited from class ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader

close, getFactors, getGenes, getQuantitationTypes, getSampleNames, getSamplesCharacteristics, setBioAssayToSampleNameMapper, 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, setBioAssayToSampleNameMapper, setDesignElementToGeneMapper, setIgnoreUnmatchedDesignElements

Constructor Details

SequencingMetadataFileDataLoader

public SequencingMetadataFileDataLoader(SequencingDataLoader delegate,
 @Nullable
 Path sequencingMetadataFile,
 @Nullable
 SequencingMetadata defaultMetadata,
 BioAssayMapper bioAssayMapper)

Parameters:

delegate - the delegate loader which may, or may not implement getSequencingMetadata(Collection)

sequencingMetadataFile - path to the TSV file containing the metadata

defaultMetadata - metadata to fill-in of there are no other values either from the file or supplied by the delegate

bioAssayMapper - a mapper to resolve BioAssays from the sample IDs in the file

Method Details

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

Overrides:

setIgnoreUnmatchedSamples in class AbstractDelegatingDataLoader

getSequencingMetadata

public Map<BioAssay,SequencingMetadata> getSequencingMetadata(Collection<BioAssay> bioAssays)
                                                       throws IOException

Description copied from interface: SequencingDataLoader

Retrieve various sequencing metadata if counting data is present.

Specified by:

getSequencingMetadata in interface SequencingDataLoader

Overrides:

getSequencingMetadata in class AbstractDelegatingSequencingDataLoader

Throws:

IOException