Package ubic.gemma.core.datastructure.matrix.io

Class TabularMatrixWriter

java.lang.Object

ubic.gemma.core.datastructure.matrix.io.TabularMatrixWriter

All Implemented Interfaces:

ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>,SingleCellExpressionDataVector>, SingleCellExpressionDataMatrixWriter

public class TabularMatrixWriter
extends Object
implements SingleCellExpressionDataMatrixWriter

Write a set of single-cell vectors to a simple tabular format.

The following column are written to disk:

- probe_id - probe_name - gene_(id|name|ncbi_id|official_symbol|official_name) if a cs2gene mapping is provided - sample_id - sample_name - cell_id - value

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
TabularMatrixWriter(EntityUrlBuilder entityUrlBuilder, BuildInfo buildInfo)

Method Summary

Modifier and Type	Method	Description
void	setAutoFlush(boolean autoFlush)	Flush every time a complete line is written.
void	setExcludeSampleIdentifiers(boolean excludeSampleIdentifiers)
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.
int	write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, Writer 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

TabularMatrixWriter

public TabularMatrixWriter(EntityUrlBuilder entityUrlBuilder,
 BuildInfo buildInfo)

Method Details

write

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

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:

IOException

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
 @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

write

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

Throws:

IOException

setExcludeSampleIdentifiers

public void setExcludeSampleIdentifiers(boolean excludeSampleIdentifiers)

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>