Package ubic.gemma.core.visualization.cellbrowser

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 java.lang.Object

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

Methods inherited from interface ubic.gemma.core.datastructure.matrix.io.ExpressionDataMatrixWriter

write

Methods inherited from interface ubic.gemma.core.datastructure.matrix.io.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>