Package ubic.gemma.core.datastructure.matrix

Class MatrixWriter

java.lang.Object

ubic.gemma.core.analysis.service.AbstractFileService<ExpressionDataMatrix<?>>

ubic.gemma.core.datastructure.matrix.MatrixWriter

All Implemented Interfaces:

FileService<ExpressionDataMatrix<?>>, JsonFileService<ExpressionDataMatrix<?>>, TsvFileService<ExpressionDataMatrix<?>>

@ParametersAreNonnullByDefault
public class MatrixWriter
extends AbstractFileService<ExpressionDataMatrix<?>>

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
MatrixWriter()

Method Summary

Modifier and Type	Method	Description
void	write(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, boolean writeHeader, boolean orderByDesign)
void	write(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,Collection<Gene>> geneAnnotations, boolean writeHeader, boolean writeSequence, boolean writeGeneInfo, boolean orderByDesign)
void	writeJSON(Writer writer, ExpressionDataMatrix<?> matrix)
void	writeTsv(ExpressionDataMatrix<?> entity, Writer writer)	Write the given entity to tabular format.
void	writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations, boolean writeHeader)	Alternate method that uses annotations in string form (e.g., read from another file).
void	writeWithStringifiedGeneAnnotations(Writer writer, ExpressionDataMatrix<?> matrix, Map<CompositeSequence,String[]> geneAnnotations, boolean writeHeader, boolean writeSequence, boolean writeGeneInfo, boolean orderByDesign)

Methods inherited from class ubic.gemma.core.analysis.service.AbstractFileService

escapeTsv, format, getSubDelimiter, getTsvFormatBuilder, write, write, writeJson

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MatrixWriter

public MatrixWriter()

Method Detail

write

public void write(Writer writer,
                  ExpressionDataMatrix<?> matrix,
                  @Nullable
                  Map<CompositeSequence,Collection<Gene>> geneAnnotations,
                  boolean writeHeader,
                  boolean orderByDesign)
           throws IOException

Throws:

IOException

writeWithStringifiedGeneAnnotations

public void writeWithStringifiedGeneAnnotations(Writer writer,
                                                ExpressionDataMatrix<?> matrix,
                                                Map<CompositeSequence,String[]> geneAnnotations,
                                                boolean writeHeader)
                                         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

writeHeader - the writer header

writer - the writer to use

Throws:

IOException - when the write failed

See Also:

ArrayDesignAnnotationServiceImpl.readAnnotationFileAsString(ArrayDesign)

writeWithStringifiedGeneAnnotations

public void writeWithStringifiedGeneAnnotations(Writer writer,
                                                ExpressionDataMatrix<?> matrix,
                                                @Nullable
                                                Map<CompositeSequence,String[]> geneAnnotations,
                                                boolean writeHeader,
                                                boolean writeSequence,
                                                boolean writeGeneInfo,
                                                boolean orderByDesign)
                                         throws IOException

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.

writeHeader - the writer header

matrix - the matrix

orderByDesign - if true, the columns are in the order defined by ExpressionDataMatrixColumnSort.orderByExperimentalDesign

writeGeneInfo - whether to write gene info

writer - the writer to use

writeSequence - whether to write sequence

Throws:

IOException - when the write failed

write

public void write(Writer writer,
                  ExpressionDataMatrix<?> matrix,
                  @Nullable
                  Map<CompositeSequence,Collection<Gene>> geneAnnotations,
                  boolean writeHeader,
                  boolean writeSequence,
                  boolean writeGeneInfo,
                  boolean orderByDesign)
           throws IOException

Parameters:

orderByDesign - if true, the columns are in the order defined by ExpressionDataMatrixColumnSort.orderByExperimentalDesign

writeSequence - whether to write sequence

writer - the writer to use

writeGeneInfo - whether to write gene info

matrix - the matrix

writeHeader - the writer header

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

writeJSON

public void writeJSON(Writer writer,
                      ExpressionDataMatrix<?> matrix)
               throws IOException

Throws:

IOException

writeTsv

public void writeTsv(ExpressionDataMatrix<?> entity,
                     Writer writer)
              throws IOException

Description copied from interface: TsvFileService

Write the given entity to tabular format.

Throws:

IOException