Package ubic.gemma.core.datastructure.matrix

Class EmptySingleCellExpressionDataMatrix

java.lang.Object

ubic.gemma.core.datastructure.matrix.EmptySingleCellExpressionDataMatrix

All Implemented Interfaces:

ExpressionDataMatrix<Object>, SingleCellExpressionDataMatrix<Object>

public class EmptySingleCellExpressionDataMatrix
extends Object
implements SingleCellExpressionDataMatrix<Object>

Constructor Summary

Constructors

Constructor	Description
EmptySingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, SingleCellDimension dimension, QuantitationType quantitationType)

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
Object	get(int row, int column)	Access a single value of the matrix by row and column.
BioAssay	getBioAssayForColumn(int j)	Obtain a bioassay applicable to a given column.
List<BioAssay>	getBioAssays()	Obtain the list of bioassays.
BioMaterial	getBioMaterialForColumn(int j)
String	getCellIdForColumn(int j)	Obtain the cell ID of a given column.
List<String>	getCellIds()	Note: cell IDs are only unique within a given assay
Object[]	getColumn(int column)	Access a single 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()	Return the quantitation type for this matrix.
Object[]	getRow(int index)	Access a single row of the matrix, by index.
Object[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
ExpressionDataMatrixRowElement	getRowElement(int row)
List<ExpressionDataMatrixRowElement>	getRowElements()
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.
SingleCellDimension	getSingleCellDimension()	Return the single-cell dimension for this matrix.
int	rows()
ExpressionDataMatrix<Object>	sliceRows(List<CompositeSequence> designElements)

Methods inherited from class java.lang.Object

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

Constructor Details

EmptySingleCellExpressionDataMatrix

public EmptySingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment,
 SingleCellDimension dimension,
 QuantitationType quantitationType)

Method Details

getExpressionExperiment

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<Object>

getQuantitationType

public QuantitationType getQuantitationType()

Description copied from interface: SingleCellExpressionDataMatrix

Return the quantitation type for this matrix.

Specified by:

getQuantitationType in interface ExpressionDataMatrix<Object>

Specified by:

getQuantitationType in interface SingleCellExpressionDataMatrix<Object>

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<Object>

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<Object>

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Obtain the total number of columns.

Specified by:

columns in interface ExpressionDataMatrix<Object>

getSingleCellDimension

public SingleCellDimension getSingleCellDimension()

Description copied from interface: SingleCellExpressionDataMatrix

Return the single-cell dimension for this matrix.

Specified by:

getSingleCellDimension in interface SingleCellExpressionDataMatrix<Object>

getColumn

public Object[] getColumn(int column)

Description copied from interface: SingleCellExpressionDataMatrix

Access a single column of the matrix.

Important note: Retrieving a column is a O(n log m) operation where n is the number of vectors and m is the number of cells. Always favour row-oriented operations when possible.

Specified by:

getColumn in interface ExpressionDataMatrix<Object>

Specified by:

getColumn in interface SingleCellExpressionDataMatrix<Object>

Parameters:

column - index

Returns:

T[]

rows

public int rows()

Specified by:

rows in interface ExpressionDataMatrix<Object>

Returns:

int

getRow

public Object[] 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<Object>

Parameters:

index - i

Returns:

t[]

getRow

public Object[] getRow(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

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

Specified by:

getRow in interface ExpressionDataMatrix<Object>

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<Object>

Returns:

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

getRowIndices

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<Object>

sliceRows

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

Specified by:

sliceRows in interface ExpressionDataMatrix<Object>

getRowElements

public List<ExpressionDataMatrixRowElement> getRowElements()

Specified by:

getRowElements in interface ExpressionDataMatrix<Object>

Returns:

list of elements representing the row 'labels'.

getRowElement

public ExpressionDataMatrixRowElement getRowElement(int row)

Specified by:

getRowElement in interface ExpressionDataMatrix<Object>

get

public Object 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<Object>

getBioAssays

public List<BioAssay> getBioAssays()

Description copied from interface: SingleCellExpressionDataMatrix

Obtain the list of bioassays.

Specified by:

getBioAssays in interface SingleCellExpressionDataMatrix<Object>

getBioAssayForColumn

public BioAssay getBioAssayForColumn(int j)

Description copied from interface: SingleCellExpressionDataMatrix

Obtain a bioassay applicable to a given column.

Specified by:

getBioAssayForColumn in interface SingleCellExpressionDataMatrix<Object>

getBioMaterialForColumn

public BioMaterial getBioMaterialForColumn(int j)

Specified by:

getBioMaterialForColumn in interface SingleCellExpressionDataMatrix<Object>

getCellIds

public List<String> getCellIds()

Description copied from interface: SingleCellExpressionDataMatrix

Note: cell IDs are only unique within a given assay

Specified by:

getCellIds in interface SingleCellExpressionDataMatrix<Object>

getCellIdForColumn

public String getCellIdForColumn(int j)

Description copied from interface: SingleCellExpressionDataMatrix

Obtain the cell ID of a given column.

Specified by:

getCellIdForColumn in interface SingleCellExpressionDataMatrix<Object>