Package ubic.basecode.io.writer

Class MatrixWriter<R,C>

java.lang.Object

ubic.basecode.io.writer.MatrixWriter<R,C>

public class MatrixWriter<R,C>
extends Object

Class for writing matrices to disk

Author:

Raymond Lim, paul

Field Summary

Fields

Modifier and Type	Field	Description
protected Map<C,String>	colNameMap
static String	DEFAULT_SEP
static String	DEFAULT_TOP_LEFT
protected Format	formatter
protected Writer	out
protected Map<R,String>	rowNameMap
protected String	sep
protected Map<?,String>	sliceNameMap
protected String	topLeft

Constructor Summary

Constructors

Constructor	Description
MatrixWriter(OutputStream out)
MatrixWriter(OutputStream out, Format formatter)
MatrixWriter(OutputStream out, Format formatter, String sep)
MatrixWriter(Writer out)
MatrixWriter(Writer out, String sep)
MatrixWriter(Writer out, Format formatter)
MatrixWriter(Writer out, Format formatter, String sep)
MatrixWriter(String fileName, Format formatter)
MatrixWriter(String fileName, Format formatter, String sep)

Method Summary

Modifier and Type	Method	Description
void	setColNameMap(Map<C,String> colNameMap)	Use to customize the labels instead of relying on the toString method of the column object
void	setRowNameMap(Map<R,String> rowNameMap)	Use to customize the labels instead of relying on the toString method of the row object
void	setSep(String sep)
void	setSliceNameMap(Map<?,String> sliceNameMap)
void	setTopLeft(String topLeft)
void	writeMatrix(cern.colt.matrix.DoubleMatrix1D coltMatrix)	Write a bare 1D matrix (one value per line)
void	writeMatrix(cern.colt.matrix.DoubleMatrix2D coltMatrix)	Write a bare matrix without row names or columns
<V> void	writeMatrix(Matrix2D<R,C,V> matrix, boolean printNames)
<S,V> void	writeMatrix(Matrix3D<R,C,S,V> matrix, boolean printNames)	Writes a 3d matrix, collapsing the rows and columns

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SEP

public static final String DEFAULT_SEP

See Also:

Constant Field Values

DEFAULT_TOP_LEFT

public static final String DEFAULT_TOP_LEFT

See Also:

Constant Field Values

colNameMap

protected Map<C,String> colNameMap

formatter

protected Format formatter

out

protected Writer out

rowNameMap

protected Map<R,String> rowNameMap

sep

protected String sep

sliceNameMap

protected Map<?,String> sliceNameMap

topLeft

protected String topLeft

Constructor Detail

MatrixWriter

public MatrixWriter(OutputStream out)

MatrixWriter

public MatrixWriter(OutputStream out,
                    Format formatter)

MatrixWriter

public MatrixWriter(OutputStream out,
                    Format formatter,
                    String sep)

MatrixWriter

public MatrixWriter(String fileName,
                    Format formatter)
             throws IOException

Throws:

IOException

MatrixWriter

public MatrixWriter(String fileName,
                    Format formatter,
                    String sep)
             throws IOException

Throws:

IOException

MatrixWriter

public MatrixWriter(Writer out)

MatrixWriter

public MatrixWriter(Writer out,
                    Format formatter)

MatrixWriter

public MatrixWriter(Writer out,
                    Format formatter,
                    String sep)

MatrixWriter

public MatrixWriter(Writer out,
                    String sep)

Method Detail

setColNameMap

public void setColNameMap(Map<C,String> colNameMap)

Use to customize the labels instead of relying on the toString method of the column object

Parameters:

colNameMap -

setRowNameMap

public void setRowNameMap(Map<R,String> rowNameMap)

Use to customize the labels instead of relying on the toString method of the row object

Parameters:

rowNameMap -

setSep

public void setSep(String sep)

setSliceNameMap

public void setSliceNameMap(Map<?,String> sliceNameMap)

setTopLeft

public void setTopLeft(String topLeft)

writeMatrix

public <V> void writeMatrix(Matrix2D<R,C,V> matrix,
                            boolean printNames)
                     throws IOException

Type Parameters:

V -

Parameters:

matrix -

printNames - Should the row and column names be included; FIXME this fails if names aren't provided

Throws:

IOException

writeMatrix

public void writeMatrix(cern.colt.matrix.DoubleMatrix2D coltMatrix)
                 throws IOException

Write a bare matrix without row names or columns

Parameters:

coltMatrix -

Throws:

IOException

writeMatrix

public void writeMatrix(cern.colt.matrix.DoubleMatrix1D coltMatrix)
                 throws IOException

Write a bare 1D matrix (one value per line)

Parameters:

coltMatrix -

Throws:

IOException

writeMatrix

public <S,V> void writeMatrix(Matrix3D<R,C,S,V> matrix,
                                    boolean printNames)
                             throws IOException

Writes a 3d matrix, collapsing the rows and columns

Parameters:

matrix -

printNames -

Throws:

IOException