Class AbstractDelegatingDataLoader
java.lang.Object
ubic.gemma.core.loader.expression.AbstractDelegatingDataLoader
- All Implemented Interfaces:
Closeable,AutoCloseable,DataLoader
- Direct Known Subclasses:
AbstractDelegatingSequencingDataLoader
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidclose()Free any resources that the loaded has setup.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 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.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.
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Constructor Details
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AbstractDelegatingDataLoader
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Method Details
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setBioAssayToSampleNameMapper
Description copied from interface:DataLoaderSet the strategy used for mappingBioAssayto sample names from the data.- Specified by:
setBioAssayToSampleNameMapperin interfaceDataLoader
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setDesignElementToGeneMapper
Description copied from interface:DataLoaderSet the strategy used for mappingCompositeSequenceto gene identifiers from the data.- Specified by:
setDesignElementToGeneMapperin interfaceDataLoader
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setIgnoreUnmatchedSamples
public void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples) Description copied from interface:DataLoaderIgnore unmatched samples from the data.This defaults to true.
- Specified by:
setIgnoreUnmatchedSamplesin interfaceDataLoader
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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
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getSampleNames
Description copied from interface:DataLoaderObtain the sample names present in the data.- Specified by:
getSampleNamesin interfaceDataLoader- Throws:
IOException
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getGenes
Description copied from interface:DataLoaderLoad gene identifiers present in the data.- Specified by:
getGenesin interfaceDataLoader- Throws:
IOException
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getQuantitationTypes
Description copied from interface:DataLoaderLoad quantitation types present in the data.- Specified by:
getQuantitationTypesin interfaceDataLoader- Throws:
IOException
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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
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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
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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
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