Package ubic.gemma.core.datastructure.matrix

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 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

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

get, getBioAssayDimension, getBioAssayForColumn, getBioMaterialForColumn, getBioMaterials, 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

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>