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

Class MatrixWriter

java.lang.Object

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

All Implemented Interfaces:

BulkExpressionDataMatrixWriter, ExpressionDataMatrixWriter<BulkExpressionDataMatrix<?>,BulkExpressionDataVector>

@ParametersAreNonnullByDefault
public class MatrixWriter
extends Object
implements BulkExpressionDataMatrixWriter

Writes BulkExpressionDataMatrix to a tabular format.

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	setExcludeSampleIdentifiers(boolean excludeSampleIdentifiers)	Only include bioassays in the formed column name instead of prepending it with the sample name.
void	setScaleType(ScaleType scaleType)	Set the scale type to use when writing the matrix.
void	setUseBioAssayIds(boolean useBioAssayIds)	Use BioAssay IDs (and BioMaterial IDs) in the column names instead of names (or short names).
void	setUseRawColumnNames(boolean useRawColumnNames)	Do not make the column names R-friendly.
int	write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Writer writer)	Write the matrix to the given writer.
int	write(BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, Map<CompositeSequence,Collection<Gene>> geneAnnotations, Writer writer)
int	writeWithStringifiedGeneAnnotations(Writer writer, BulkExpressionDataMatrix<?> matrix, Class<? extends BulkExpressionDataVector> vectorType, 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.ExpressionDataMatrixWriter

write

Constructor Details

MatrixWriter

public MatrixWriter(EntityUrlBuilder entityUrlBuilder,
 BuildInfo buildInfo)

Method Details

write

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

Description copied from interface: ExpressionDataMatrixWriter

Write the matrix to the given writer.

Specified by:

write in interface ExpressionDataMatrixWriter<BulkExpressionDataMatrix<?>,BulkExpressionDataVector>

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(BulkExpressionDataMatrix<?> matrix,
 Class<? extends BulkExpressionDataVector> vectorType,
 @Nullable
 Map<CompositeSequence,Collection<Gene>> geneAnnotations,
 Writer writer)
          throws IOException

Parameters:

matrix - the matrix

vectorType - the type of vector to write

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.

writer - the writer to use

Throws:

IOException - when the write failed

writeWithStringifiedGeneAnnotations

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

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

Parameters:

writer - the writer to use

matrix - the matrix to write

vectorType - the type of vector to write

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

See Also:

• ArrayDesignAnnotationServiceImpl.readAnnotationFile(ArrayDesign)

setExcludeSampleIdentifiers

public void setExcludeSampleIdentifiers(boolean excludeSampleIdentifiers)

Only include bioassays in the formed column name instead of prepending it with the sample name.

setUseBioAssayIds

public void setUseBioAssayIds(boolean useBioAssayIds)

Use BioAssay IDs (and BioMaterial IDs) in the column names instead of names (or short names).

setUseRawColumnNames

public void setUseRawColumnNames(boolean useRawColumnNames)

Do not make the column names R-friendly.

See Also:

• StringUtil.makeNames(String)

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<BulkExpressionDataMatrix<?>,BulkExpressionDataVector>

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<BulkExpressionDataMatrix<?>,BulkExpressionDataVector>