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

Class MatrixWriter

java.lang.Object

ubic.gemma.core.datastructure.matrix.io.MatrixWriter

All Implemented Interfaces:

BulkExpressionDataMatrixWriter, ExpressionDataMatrixWriter

@ParametersAreNonnullByDefault
public class MatrixWriter
extends Object
implements BulkExpressionDataMatrixWriter

Writes BulkExpressionDataMatrix to various tabular formats.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
MatrixWriter(EntityUrlBuilder entityUrlBuilder, BuildInfo buildInfo)

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.
int	write(BulkExpressionDataMatrix<?> matrix, Writer writer)
int	write(BulkExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, Writer writer)
int	writeJSON(Writer writer, BulkExpressionDataMatrix<?> matrix)
int	writeWithStringifiedGeneAnnotations(Writer writer, BulkExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations)	Alternate method that uses annotations in string form (e.g., read from another file).

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.BulkExpressionDataMatrixWriter

write, write, write

Constructor Detail

MatrixWriter

public MatrixWriter(EntityUrlBuilder entityUrlBuilder,
                    BuildInfo buildInfo)

Method Detail

setAutoFlush

public void setAutoFlush(boolean autoFlush)

Flush every time a complete line is written.

This is only applicable to the tabular output.

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

write

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

Specified by:

write in interface BulkExpressionDataMatrixWriter

Throws:

IOException

write

public int write(BulkExpressionDataMatrix<?> matrix,
                 @Nullable
                 Map<CompositeSequence,Collection<Gene>> geneAnnotations,
                 Writer writer)
          throws IOException

Parameters:

writer - the writer to use

matrix - the matrix

geneAnnotations - Map of composite sequences to an array of delimited strings: [probe name,genes symbol, gene Name] -- these include the "|" to indicate multiple genes, and originate in the platform annotation files.

Throws:

IOException - when the write failed

writeWithStringifiedGeneAnnotations

public int writeWithStringifiedGeneAnnotations(Writer writer,
                                               BulkExpressionDataMatrix<?> matrix,
                                               @Nullable
                                               Map<CompositeSequence,String[]> geneAnnotations)
                                        throws IOException

Alternate method that uses annotations in string form (e.g., read from another file).

Parameters:

geneAnnotations - Map of composite sequences to an array of delimited strings: [probe name,genes symbol, gene Name] -- these include the "|" to indicate multiple genes, and originate in the platform annotation files.

matrix - the matrix to write

writer - the writer to use

Throws:

IOException - when the write failed

See Also:

ArrayDesignAnnotationServiceImpl.readAnnotationFile(ArrayDesign)

writeJSON

public int writeJSON(Writer writer,
                     BulkExpressionDataMatrix<?> matrix)
              throws IOException

Throws:

IOException