Package ubic.gemma.core.datastructure.matrix

Class MatrixWriter

java.lang.Object

ubic.gemma.core.datastructure.matrix.MatrixWriter

public class MatrixWriter
extends Object

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	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 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,
                  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,
                                                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,
                  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