Package ubic.gemma.core.datastructure.matrix

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

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

columns, get, getBioAssayDimension, getBioAssayForColumn, getBioMaterialForColumn, 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

Methods inherited from interface ubic.gemma.core.datastructure.matrix.BulkExpressionDataMatrix

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

Methods inherited from interface ubic.gemma.core.datastructure.matrix.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

public double[] getColumnAsDoubles(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataPrimitiveDoubleMatrix

Retrieve the given column without boxing.

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)

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[][]

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>