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

Class MexMatrixWriter

java.lang.Object

ubic.gemma.core.datastructure.matrix.io.MexMatrixWriter

All Implemented Interfaces:

ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>>, SingleCellExpressionDataMatrixWriter

public class MexMatrixWriter
extends Object
implements SingleCellExpressionDataMatrixWriter

Writes SingleCellExpressionDataMatrix to the 10x MEX format.

The data is written as a TAR archive containing the following entries for each bioassay: {bioAssayName}/barcodes.tsv, {bioAssayName}/features.tsv, {bioAssayName}/matrix.mtx. If using the directory output, individual files are compressed and will have a .gz extension.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
MexMatrixWriter()

Method Summary

Modifier and Type	Method	Description
int	write(Stream<SingleCellExpressionDataVector> vectors, int numVecs, Map<BioAssay,Long> nnzBySample, Map<CompositeSequence,Set<Gene>> cs2gene, Path outputDir)	Writes a stream of vectors to a directory.
int	write(SingleCellExpressionDataMatrix<?> matrix, OutputStream stream)	Write the matrix to the given output stream.
int	write(SingleCellExpressionDataMatrix<?> matrix, Writer stream)	Write the matrix to the given writer.
int	write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, OutputStream stream)	Write a MEX matrix as a TAR archive to the given output stream.
int	write(SingleCellExpressionDataMatrix<?> matrix, Map<CompositeSequence,Set<Gene>> cs2gene, Path outputDir)	Write a matrix to a directory.

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

setAutoFlush, setScaleType

Constructor Detail

MexMatrixWriter

public MexMatrixWriter()

Method Detail

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
                 Writer stream)
          throws IOException

Description copied from interface: ExpressionDataMatrixWriter

Write the matrix to the given writer.

Specified by:

write in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>>

Returns:

the number of vectors written

Throws:

IOException

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
                 OutputStream stream)
          throws IOException

Description copied from interface: ExpressionDataMatrixWriter

Write the matrix to the given output stream.

Specified by:

write in interface ExpressionDataMatrixWriter<SingleCellExpressionDataMatrix<?>>

Returns:

the number of vectors written

Throws:

IOException

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
                 @Nullable
                 Map<CompositeSequence,Set<Gene>> cs2gene,
                 OutputStream stream)
          throws IOException

Write a MEX matrix as a TAR archive to the given output stream.

Throws:

IOException

write

public int write(SingleCellExpressionDataMatrix<?> matrix,
                 @Nullable
                 Map<CompositeSequence,Set<Gene>> cs2gene,
                 Path outputDir)
          throws IOException

Write a matrix to a directory.

Throws:

IOException

write

public int write(Stream<SingleCellExpressionDataVector> vectors,
                 int numVecs,
                 Map<BioAssay,Long> nnzBySample,
                 @Nullable
                 Map<CompositeSequence,Set<Gene>> cs2gene,
                 Path outputDir)
          throws IOException

Writes a stream of vectors to a directory.

Parameters:

vectors - a stream of vectors

numVecs - the total number of vectors to write

nnzBySample - the number of non-zeroes by sample

cs2gene - a mapping of design elements to their corresponding gene(s)

Throws:

IOException