Class BulkExpressionDataDoubleMatrix

java.lang.Object

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

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

ubic.gemma.core.datastructure.matrix.BulkExpressionDataDoubleMatrix

All Implemented Interfaces:

BulkExpressionDataMatrix<Double>, BulkExpressionDataPrimitiveDoubleMatrix, ExpressionDataMatrix<Double>, ExpressionDataPrimitiveDoubleMatrix

public class BulkExpressionDataDoubleMatrix
extends AbstractBulkExpressionDataMatrix<Double>
implements BulkExpressionDataPrimitiveDoubleMatrix

Constructor Summary

Constructors

Constructor	Description
BulkExpressionDataDoubleMatrix(List<? extends BulkExpressionDataVector> vectors)

Method Summary

Modifier and Type	Method	Description
protected String	format(int i, int j)	Format a matrix entry at a particular row/column.
Double	get(int row, int column)	Access a single value of the matrix by row and column.
double	getAsDouble(int row, int column)	Retrieve the value at the given row and column without boxing.
Double[]	getColumn(int column)	Access a single column of the matrix.
double[]	getColumnAsDoubles(int column)	Retrieve the given column without boxing.
double[]	getColumnAsDoubles(BioAssay bioAssay)	Retrieve the given column without boxing, or null if the assay is not part of this matrix.
Double[][]	getRawMatrix()	Access the entire matrix.
double[][]	getRawMatrixAsDoubles()	Obtain the raw matrix as a double array.
Double[]	getRow(int index)	Access a single row of the matrix, by index.
double[]	getRowAsDoubles(int index)	Retrieve a row without boxing.
double[]	getRowAsDoubles(CompositeSequence designElement)	Retrieve the row for the given design element without boxing.
boolean	hasMissingValues()
BulkExpressionDataMatrix<Double>	sliceColumns(List<BioMaterial> bioMaterials)	Slice the requested samples (columns) from this matrix.
BulkExpressionDataDoubleMatrix	sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)	Slice the requested samples (columns) from this matrix.
ExpressionDataMatrix<Double>	sliceRows(List<CompositeSequence> designElements)	Slice the given design elements (rows) from the matrix.

Methods inherited from class 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 AbstractExpressionDataMatrix

format, format, formatRepresentation, toString

Methods inherited from class Object

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

Methods inherited from interface BulkExpressionDataMatrix

get, getBioAssayDimension, getBioAssayForColumn, getBioMaterialForColumn, getBioMaterials, getColumn, getColumnIndex, getColumnIndex

Methods inherited from interface ExpressionDataMatrix

columns, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationType, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, rows

Constructor Details

BulkExpressionDataDoubleMatrix

public BulkExpressionDataDoubleMatrix(List<? extends BulkExpressionDataVector> vectors)

Method Details

hasMissingValues

public boolean hasMissingValues()

Specified by:

hasMissingValues in interface BulkExpressionDataMatrix<Double>

Returns:

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

getColumn

public Double[] getColumn(int column)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Specified by:

getColumn in interface ExpressionDataMatrix<Double>

Parameters:

column - index

Returns:

T[]

getColumnAsDoubles

public double[] getColumnAsDoubles(int column)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the given column without boxing.

Specified by:

getColumnAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.getColumn(int)

getColumnAsDoubles

@Nullable
public double[] getColumnAsDoubles(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataPrimitiveDoubleMatrix

Retrieve the given column without boxing, or null if the assay is not part of this matrix.

Specified by:

getColumnAsDoubles in interface BulkExpressionDataPrimitiveDoubleMatrix

See Also:

• BulkExpressionDataMatrix.getColumn(BioAssay)

getRow

public Double[] 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<Double>

Parameters:

index - i

Returns:

t[]

sliceRows

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

Description copied from interface: ExpressionDataMatrix

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

Specified by:

sliceRows in interface ExpressionDataMatrix<Double>

getRowAsDoubles

public double[] getRowAsDoubles(int index)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve a row without boxing.

Specified by:

getRowAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.getRow(int)

getRowAsDoubles

@Nullable
public double[] getRowAsDoubles(CompositeSequence designElement)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the row for the given design element without boxing.

Specified by:

getRowAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.getRow(CompositeSequence)

get

public Double 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<Double>

getAsDouble

public double getAsDouble(int row,
 int column)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the value at the given row and column without boxing.

Specified by:

getAsDouble in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

• ExpressionDataMatrix.get(int, int)

getRawMatrix

public Double[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Specified by:

getRawMatrix in interface BulkExpressionDataMatrix<Double>

Returns:

T[][]

sliceColumns

public BulkExpressionDataMatrix<Double> 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.

Specified by:

sliceColumns in interface BulkExpressionDataMatrix<Double>

Parameters:

bioMaterials - samples to select from the matrix

sliceColumns

public BulkExpressionDataDoubleMatrix 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).

Specified by:

sliceColumns in interface BulkExpressionDataMatrix<Double>

Parameters:

bioMaterials - samples to select from the matrix

dimension - the dimension to use

getRawMatrixAsDoubles

public double[][] getRawMatrixAsDoubles()

Description copied from interface: BulkExpressionDataPrimitiveDoubleMatrix

Obtain the raw matrix as a double array.

Specified by:

getRawMatrixAsDoubles in interface BulkExpressionDataPrimitiveDoubleMatrix

See Also:

• BulkExpressionDataMatrix.getRawMatrix()

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<Double>