Class CellBrowserTabularMatrixWriter

java.lang.Object

ubic.gemma.core.visualization.cellbrowser.CellBrowserTabularMatrixWriter

All Implemented Interfaces:

ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>, SingleCellExpressionDataVector>, SingleCellExpressionDataMatrixWriter

public class CellBrowserTabularMatrixWriter
extends Object
implements SingleCellExpressionDataMatrixWriter

Generate a tabular matrix format compatible with Cell Browser.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
CellBrowserTabularMatrixWriter()

Method Summary

Modifier and Type	Method	Description
void	setAutoFlush(boolean autoFlush)	Flush every time a complete line is written.
void	setScaleType(ScaleType scaleType)	Set the scale type to use when writing the matrix.
void	setUseBioAssayIds(boolean useBioAssayIds)
void	setUseRawColumnNames(boolean useRawColumnNames)
int	write(Collection<SingleCellExpressionDataVector> vectors, Map<CompositeSequence, Set<Gene>> cs2gene, Writer writer)
int	write(Stream<SingleCellExpressionDataVector> vectors, Map<CompositeSequence, Set<Gene>> cs2gene, Writer writer)
int	write(SingleCellExpressionDataMatrix<?> matrix, Class<? extends SingleCellExpressionDataVector> vectorType, Writer writer)	Write the matrix to the given writer.

Methods inherited from class Object

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

Methods inherited from interface ExpressionDataMatrixWriter

write

Methods inherited from interface SingleCellExpressionDataMatrixWriter

write, write

Constructor Details

CellBrowserTabularMatrixWriter

public CellBrowserTabularMatrixWriter()

Method Details

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
 Class<? extends SingleCellExpressionDataVector> vectorType,
 Writer writer)
          throws IOException,
UnsupportedOperationException

Description copied from interface: ExpressionDataMatrixWriter

Write the matrix to the given writer.

Specified by:

write in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>, SingleCellExpressionDataVector>

Parameters:

vectorType - the type of vectors to write. This helps the writer determine how the QuantitationType of the matrix should be interpreted.

Returns:

the number of vectors written

Throws:

UnsupportedOperationException - if the matrix cannot be written to a text output (i.e. if this is a binary format).

IOException

write

public int write(Stream<SingleCellExpressionDataVector> vectors,
 @Nullable
 Map<CompositeSequence, Set<Gene>> cs2gene,
 Writer writer)
          throws IOException

Throws:

IOException

write

public int write(Collection<SingleCellExpressionDataVector> vectors,
 @Nullable
 Map<CompositeSequence, Set<Gene>> cs2gene,
 Writer writer)
          throws IOException

Throws:

IOException

setUseBioAssayIds

public void setUseBioAssayIds(boolean useBioAssayIds)

setUseRawColumnNames

public void setUseRawColumnNames(boolean useRawColumnNames)

setAutoFlush

public void setAutoFlush(boolean autoFlush)

Description copied from interface: ExpressionDataMatrixWriter

Flush every time a complete line is written.

This is not very efficient, but it can be used to view the output of a matrix as it is being written.

Specified by:

setAutoFlush in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>, SingleCellExpressionDataVector>

setScaleType

public void setScaleType(@Nullable
 ScaleType scaleType)

Description copied from interface: ExpressionDataMatrixWriter

Set the scale type to use when writing the matrix.

When null, the original values must be used.

Specified by:

setScaleType in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>, SingleCellExpressionDataVector>