Package ubic.gemma.core.visualization.cellbrowser

Class CellBrowserMetadataWriter

java.lang.Object

ubic.gemma.core.visualization.cellbrowser.CellBrowserMetadataWriter

public class CellBrowserMetadataWriter
extends Object

Write metadata file for the Cell Browser visualization tool.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
CellBrowserMetadataWriter()

Method Summary

Modifier and Type	Method	Description
void	setAutoFlush(boolean autoFlush)
void	setSeparateSampleFromAssayIdentifiers(boolean separateSampleFromAssayIdentifiers)	If true, write the sample identifier and the assay identifiers in separate columns.
void	setUseBioAssayIds(boolean useBioAssayIds)	This is only used for the cell ID and does not affect the 'Bioassay', 'Sample' and 'Assay' columns.
void	setUseRawColumnNames(boolean useRawColumnNames)	If true, use column names as they appear in the database.
void	write(ExpressionExperiment ee, SingleCellDimension singleCellDimension, Writer writer)
void	writeCell(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)

Methods inherited from class java.lang.Object

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

Constructor Details

CellBrowserMetadataWriter

public CellBrowserMetadataWriter()

Method Details

write

public void write(ExpressionExperiment ee,
 SingleCellDimension singleCellDimension,
 Writer writer)
           throws IOException

Throws:

IOException

writeCell

public void writeCell(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)
               throws IOException

Throws:

IOException

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".

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)