Package ubic.gemma.core.datastructure.matrix

Class MaskedExpressionDataMatrix<T>

java.lang.Object

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

ubic.gemma.core.datastructure.matrix.MaskedExpressionDataMatrix<T>

Type Parameters:

T - the type of data in the matrix

All Implemented Interfaces:

ExpressionDataMatrix<T>

public class MaskedExpressionDataMatrix<T>
extends AbstractExpressionDataMatrix<T>
implements ExpressionDataMatrix<T>

A wrapper for an ExpressionDataMatrix that applies a mask to the data, allowing selective access to the underlying matrix.

See Also:

• MatrixMask

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
protected String	format(int row, int column)	Format a matrix entry at a particular row/column.
T	get(int row, int column)	Access a single value of the matrix by row and column.
T[]	getColumn(int column)	Access a single column of the matrix.
protected String	getColumnLabel(int j)	Obtain a label suitable for describing a column of the matrix.
CompositeSequence	getDesignElementForRow(int index)	Return a design element for a given index.
List<CompositeSequence>	getDesignElements()	Obtain all the design elements in this data matrix.
ExpressionExperiment	getExpressionExperiment()	Return the expression experiment this matrix is holding data for, if known.
QuantitationType	getQuantitationType()	Obtain the quantitation type for this matrix.
T[]	getRow(int index)	Access a single row of the matrix, by index.
T[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
ExpressionDataMatrixRowElement	getRowElement(int row)	Deprecated.
List<ExpressionDataMatrixRowElement>	getRowElements()	Deprecated.
int	getRowIndex(CompositeSequence designElement)
int[]	getRowIndices(CompositeSequence designElement)	Obtain all the rows that correspond to the given design element, or null if the design element is not found.
protected String	getRowLabel(int i)	Obtain a label suitable for describing a row of the matrix.
MaskedExpressionDataMatrix<T>	inverted()
static <T> MaskedExpressionDataMatrix<T>	maskColumns(ExpressionDataMatrix<T> matrix, boolean[] columnMask, T maskedValue)	Mask whole columns of the given matrix.
static <T> MaskedExpressionDataMatrix<T>	maskElements(ExpressionDataMatrix<T> matrix, boolean[][] mask, T maskedValue)	Mask individual elements of the given matrix.
static <T> MaskedExpressionDataMatrix<T>	maskElements(ExpressionDataMatrix<T> matrix, int[] i, int[] j, T maskedValue)	Mask individual elements of the given matrix at the specified coordinates.
static <T> MaskedExpressionDataMatrix<T>	maskRows(ExpressionDataMatrix<T> matrix, boolean[] rowMask, T maskedValue)	Mask whole rows of the given matrix.
int	rows()
ExpressionDataMatrix<T>	sliceRows(List<CompositeSequence> designElements)

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

Method Details

maskElements

public static <T> MaskedExpressionDataMatrix<T> maskElements(ExpressionDataMatrix<T> matrix,
 boolean[][] mask,
 @Nullable
 T maskedValue)

Mask individual elements of the given matrix.

Parameters:

maskedValue - value to use for masked elements, usually null

See Also:

• MatrixMask.maskElements(int, int, boolean[][])

maskElements

public static <T> MaskedExpressionDataMatrix<T> maskElements(ExpressionDataMatrix<T> matrix,
 int[] i,
 int[] j,
 @Nullable
 T maskedValue)

Mask individual elements of the given matrix at the specified coordinates.

This uses a sparse representation internally, which is more efficient for large matrices with few masked elements.

See Also:

• MatrixMask.maskElements(int, int, int[], int[])

maskRows

public static <T> MaskedExpressionDataMatrix<T> maskRows(ExpressionDataMatrix<T> matrix,
 boolean[] rowMask,
 @Nullable
 T maskedValue)

Mask whole rows of the given matrix.

See Also:

• MatrixMask.maskRows(int, int, boolean[])

maskColumns

public static <T> MaskedExpressionDataMatrix<T> maskColumns(ExpressionDataMatrix<T> matrix,
 boolean[] columnMask,
 @Nullable
 T maskedValue)

Mask whole columns of the given matrix.

See Also:

• MatrixMask.maskColumns(int, int, boolean[])

getExpressionExperiment

@Nullable
public ExpressionExperiment getExpressionExperiment()

Description copied from interface: ExpressionDataMatrix

Return the expression experiment this matrix is holding data for, if known.

Specified by:

getExpressionExperiment in interface ExpressionDataMatrix<T>

getQuantitationType

public QuantitationType getQuantitationType()

Description copied from interface: ExpressionDataMatrix

Obtain the quantitation type for this matrix.

Specified by:

getQuantitationType in interface ExpressionDataMatrix<T>

getDesignElements

public List<CompositeSequence> getDesignElements()

Description copied from interface: ExpressionDataMatrix

Obtain all the design elements in this data matrix.

Specified by:

getDesignElements in interface ExpressionDataMatrix<T>

getDesignElementForRow

public CompositeSequence getDesignElementForRow(int index)

Description copied from interface: ExpressionDataMatrix

Return a design element for a given index.

Specified by:

getDesignElementForRow in interface ExpressionDataMatrix<T>

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Obtain the total number of columns.

Specified by:

columns in interface ExpressionDataMatrix<T>

getColumn

public T[] getColumn(int column)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Specified by:

getColumn in interface ExpressionDataMatrix<T>

Parameters:

column - index

Returns:

T[]

rows

public int rows()

Specified by:

rows in interface ExpressionDataMatrix<T>

Returns:

int

getRow

public T[] getRow(int index)

Description copied from interface: ExpressionDataMatrix

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

Specified by:

getRow in interface ExpressionDataMatrix<T>

Parameters:

index - i

Returns:

t[]

getRow

@Nullable
public T[] getRow(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

Return a row that 'came from' the given design element.

Specified by:

getRow in interface ExpressionDataMatrix<T>

Parameters:

designElement - de

Returns:

the corresponding row or null if the design element is not found in the matrix

getRowIndex

public int getRowIndex(CompositeSequence designElement)

Specified by:

getRowIndex in interface ExpressionDataMatrix<T>

Returns:

the index for the given design element, or -1 if not found

getRowIndices

@Nullable
public int[] getRowIndices(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

Obtain all the rows that correspond to the given design element, or null if the design element is not found.

Specified by:

getRowIndices in interface ExpressionDataMatrix<T>

sliceRows

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

Specified by:

sliceRows in interface ExpressionDataMatrix<T>

getRowElements

@Deprecated
public List<ExpressionDataMatrixRowElement> getRowElements()

Deprecated.

Specified by:

getRowElements in interface ExpressionDataMatrix<T>

Returns:

list of elements representing the row 'labels'.

getRowElement

@Deprecated
public ExpressionDataMatrixRowElement getRowElement(int row)

Deprecated.

Specified by:

getRowElement in interface ExpressionDataMatrix<T>

get

public T get(int row,
 int column)

Description copied from interface: ExpressionDataMatrix

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

Specified by:

get in interface ExpressionDataMatrix<T>

inverted

public MaskedExpressionDataMatrix<T> inverted()

getRowLabel

protected String getRowLabel(int i)

Description copied from class: AbstractExpressionDataMatrix

Obtain a label suitable for describing a row of the matrix.

Specified by:

getRowLabel in class AbstractExpressionDataMatrix<T>

getColumnLabel

protected String getColumnLabel(int j)

Description copied from class: AbstractExpressionDataMatrix

Obtain a label suitable for describing a column of the matrix.

Specified by:

getColumnLabel in class AbstractExpressionDataMatrix<T>

format

protected String format(int row,
 int column)

Description copied from class: AbstractExpressionDataMatrix

Format a matrix entry at a particular row/column.

Specified by:

format in class AbstractExpressionDataMatrix<T>