Class CellBrowserMetadataWriter
java.lang.Object
ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter
Write metadata file for the Cell Browser visualization tool.
- Author:
- poirigui
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidsetAutoFlush(boolean autoFlush) voidsetSeparateSampleFromAssayIdentifiers(boolean separateSampleFromAssayIdentifiers) If true, write the sample identifier and the assay identifiers in separate columns.voidsetUseBioAssayIds(boolean useBioAssayIds) This is only used for the cell ID and does not affect the 'Bioassay', 'Sample' and 'Assay' columns.voidsetUseRawColumnNames(boolean useRawColumnNames) If true, use column names as they appear in the database.voidwrite(ExpressionExperiment ee, SingleCellDimension singleCellDimension, Writer writer) voidwriteCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor, Map<BioMaterial, FactorValue>> factorValueMap, SortedMap<Category, Map<BioAssay, Characteristic>> bioAssayCharacteristics, SortedMap<Category, Map<BioMaterial, Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer)
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Constructor Details
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CellBrowserMetadataWriter
public CellBrowserMetadataWriter()
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Method Details
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write
public void write(ExpressionExperiment ee, SingleCellDimension singleCellDimension, Writer writer) throws IOException - Throws:
IOException
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writeCell
public void writeCell(BioAssay bioAssay, String cellId, int cellIndex, List<ExperimentalFactor> factors, Map<ExperimentalFactor, Map<BioMaterial, throws IOExceptionFactorValue>> factorValueMap, SortedMap<Category, Map<BioAssay, Characteristic>> bioAssayCharacteristics, SortedMap<Category, Map<BioMaterial, Characteristic>> sampleCharacteristics, List<CellLevelCharacteristics> clcs, Writer writer) - Throws:
IOException
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setSeparateSampleFromAssayIdentifiers
public void setSeparateSampleFromAssayIdentifiers(boolean separateSampleFromAssayIdentifiers) If true, write the sample identifier and the assay identifiers in separate columns.The column will be named "Sample" and "Assay" respectively.
The default column name for mangled sample and assay identifiers is "Bioassay".
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setUseBioAssayIds
public void setUseBioAssayIds(boolean useBioAssayIds) This is only used for the cell ID and does not affect the 'Bioassay', 'Sample' and 'Assay' columns. -
setUseRawColumnNames
public void setUseRawColumnNames(boolean useRawColumnNames) If true, use column names as they appear in the database. -
setAutoFlush
public void setAutoFlush(boolean autoFlush)
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