Package ubic.gemma.core.datastructure.matrix

Class EmptyBulkExpressionDataMatrix

java.lang.Object

ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix<Object>

ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix<Object>

ubic.gemma.core.datastructure.matrix.EmptyBulkExpressionDataMatrix

All Implemented Interfaces:

BulkExpressionDataMatrix<Object>, ExpressionDataMatrix<Object>

public class EmptyBulkExpressionDataMatrix
extends AbstractBulkExpressionDataMatrix<Object>

An empty bulk expression data matrix.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
EmptyBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType quantitationType)

Method Summary

Modifier and Type	Method	Description
protected String	format(int i, int j)	Format a matrix entry at a particular row/column.
Object	get(int row, int column)	Access a single value of the matrix by row and column.
Object[]	getColumn(int column)	Access a single column of the matrix.
Object[][]	getRawMatrix()	Access the entire matrix.
Object[]	getRow(int index)	Access a single row of the matrix, by index.
boolean	hasMissingValues()
BulkExpressionDataMatrix<Object>	sliceColumns(List<BioMaterial> bioMaterials)	Slice the requested samples (columns) from this matrix.
EmptyBulkExpressionDataMatrix	sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)	Slice the requested samples (columns) from this matrix.
ExpressionDataMatrix<Object>	sliceRows(List<CompositeSequence> designElements)	Slice the given design elements (rows) from the matrix.

Methods inherited from class ubic.gemma.core.datastructure.matrix.AbstractBulkExpressionDataMatrix

columns, get, getBioAssayDimension, getBioAssayForColumn, getBioMaterialForColumn, getBioMaterials, getColumn, getColumnIndex, getColumnIndex, getColumnLabel, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationType, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, getRowLabel, rows

Methods inherited from class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix

format, format, formatRepresentation, toString

Methods inherited from class java.lang.Object

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

Constructor Details

EmptyBulkExpressionDataMatrix

public EmptyBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension,
 QuantitationType quantitationType)

Method Details

hasMissingValues

public boolean hasMissingValues()

Returns:

true if any values are null or NaN (for doubles and floats); any other value that is considered missing.

getRawMatrix

public Object[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Returns:

T[][]

sliceColumns

public BulkExpressionDataMatrix<Object> sliceColumns(List<BioMaterial> bioMaterials)

Description copied from interface: BulkExpressionDataMatrix

Slice the requested samples (columns) from this matrix.

Dimensions will be altered to reflect only the selected samples.

Parameters:

bioMaterials - samples to select from the matrix

sliceColumns

public EmptyBulkExpressionDataMatrix sliceColumns(List<BioMaterial> bioMaterials,
 BioAssayDimension dimension)

Description copied from interface: BulkExpressionDataMatrix

Slice the requested samples (columns) from this matrix.

This also allows specifying a new dimension for the columns that will be used for every design element (rows).

Parameters:

bioMaterials - samples to select from the matrix

dimension - the dimension to use

getColumn

public Object[] getColumn(int column)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Parameters:

column - index

Returns:

T[]

getRow

public Object[] getRow(int index)

Description copied from interface: ExpressionDataMatrix

Access a single row of the matrix, by index. A complete row is returned.

Parameters:

index - i

Returns:

t[]

sliceRows

public ExpressionDataMatrix<Object> sliceRows(List<CompositeSequence> designElements)

Description copied from interface: ExpressionDataMatrix

Slice the given design elements (rows) from the matrix.

get

public Object get(int row,
 int column)

Description copied from interface: ExpressionDataMatrix

Access a single value of the matrix by row and column.

format

protected String format(int i,
 int j)

Description copied from class: AbstractExpressionDataMatrix

Format a matrix entry at a particular row/column.

Specified by:

format in class AbstractExpressionDataMatrix<Object>