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

Class TabularMatrixWriter

java.lang.Object

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

All Implemented Interfaces:

ExpressionDataMatrixWriter, 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
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, Writer 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

setScaleType

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

write, write, write

Constructor Detail

TabularMatrixWriter

public TabularMatrixWriter(EntityUrlBuilder entityUrlBuilder,
                           BuildInfo buildInfo)

Method Detail

write

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

Specified by:

write in interface SingleCellExpressionDataMatrixWriter

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