Class BulkExpressionDataIntMatrix

java.lang.Object

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

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

ubic.gemma.core.datastructure.matrix.BulkExpressionDataIntMatrix

All Implemented Interfaces:

BulkExpressionDataMatrix<Integer>, BulkExpressionDataPrimitiveIntMatrix, ExpressionDataMatrix<Integer>, ExpressionDataPrimitiveIntMatrix

public class BulkExpressionDataIntMatrix
extends AbstractBulkExpressionDataMatrix<Integer>
implements BulkExpressionDataPrimitiveIntMatrix

A bulk expression data matrix that can be efficiently accessed as a primitive int matrix.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
BulkExpressionDataIntMatrix(List<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.
Integer	get(int row, int column)	Access a single value of the matrix by row and column.
int	getAsInt(int row, int column)	Retrieve the value at the given row and column without boxing.
Integer[]	getColumn(int column)	Access a single column of the matrix.
int[]	getColumnAsInts(int column)	Retrieve the given column without boxing.
int[]	getColumnAsInts(BioAssay bioAssay)	Retrieve the given column without boxing.
Integer[][]	getRawMatrix()	Access the entire matrix.
int[][]	getRawMatrixAsInts()	Obtain the raw matrix as a int array.
Integer[]	getRow(int index)	Access a single row of the matrix, by index.
int[]	getRowAsInts(int index)	Retrieve a row without boxing.
int[]	getRowAsInts(CompositeSequence designElement)	Retrieve the row for the given design element without boxing.
boolean	hasMissingValues()
BulkExpressionDataMatrix<Integer>	sliceColumns(List<BioMaterial> bioMaterials)	Slice the requested samples (columns) from this matrix.
BulkExpressionDataIntMatrix	sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)	Slice the requested samples (columns) from this matrix.
BulkExpressionDataIntMatrix	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

BulkExpressionDataIntMatrix

public BulkExpressionDataIntMatrix(List<BulkExpressionDataVector> vectors)

Method Details

hasMissingValues

public boolean hasMissingValues()

Specified by:

hasMissingValues in interface BulkExpressionDataMatrix<Integer>

Returns:

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

getRawMatrix

public Integer[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Specified by:

getRawMatrix in interface BulkExpressionDataMatrix<Integer>

Returns:

T[][]

sliceColumns

public BulkExpressionDataMatrix<Integer> 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<Integer>

Parameters:

bioMaterials - samples to select from the matrix

sliceColumns

public BulkExpressionDataIntMatrix 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<Integer>

Parameters:

bioMaterials - samples to select from the matrix

dimension - the dimension to use

getRawMatrixAsInts

public int[][] getRawMatrixAsInts()

Description copied from interface: BulkExpressionDataPrimitiveIntMatrix

Obtain the raw matrix as a int array.

Specified by:

getRawMatrixAsInts in interface BulkExpressionDataPrimitiveIntMatrix

See Also:

• BulkExpressionDataMatrix.getRawMatrix()

getColumn

public Integer[] getColumn(int column)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Specified by:

getColumn in interface ExpressionDataMatrix<Integer>

Parameters:

column - index

Returns:

T[]

getColumnAsInts

public int[] getColumnAsInts(int column)

Description copied from interface: ExpressionDataPrimitiveIntMatrix

Retrieve the given column without boxing.

Specified by:

getColumnAsInts in interface ExpressionDataPrimitiveIntMatrix

See Also:

• ExpressionDataMatrix.getColumn(int)

getColumnAsInts

public int[] getColumnAsInts(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataPrimitiveIntMatrix

Retrieve the given column without boxing.

Specified by:

getColumnAsInts in interface BulkExpressionDataPrimitiveIntMatrix

See Also:

• ExpressionDataMatrix.getColumn(int)

getRow

public Integer[] 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<Integer>

Parameters:

index - i

Returns:

t[]

sliceRows

public BulkExpressionDataIntMatrix sliceRows(List<CompositeSequence> designElements)

Description copied from interface: ExpressionDataMatrix

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

Specified by:

sliceRows in interface ExpressionDataMatrix<Integer>

getRowAsInts

public int[] getRowAsInts(int index)

Description copied from interface: ExpressionDataPrimitiveIntMatrix

Retrieve a row without boxing.

Specified by:

getRowAsInts in interface ExpressionDataPrimitiveIntMatrix

See Also:

• ExpressionDataMatrix.getRow(int)

getRowAsInts

public int[] getRowAsInts(CompositeSequence designElement)

Description copied from interface: ExpressionDataPrimitiveIntMatrix

Retrieve the row for the given design element without boxing.

Specified by:

getRowAsInts in interface ExpressionDataPrimitiveIntMatrix

See Also:

• ExpressionDataMatrix.getRow(CompositeSequence)

get

public Integer 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<Integer>

getAsInt

public int getAsInt(int row,
 int column)

Description copied from interface: ExpressionDataPrimitiveIntMatrix

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

Specified by:

getAsInt in interface ExpressionDataPrimitiveIntMatrix

See Also:

• ExpressionDataMatrix.get(int, int)

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<Integer>