Package ubic.gemma.core.datastructure.matrix

Class SingleCellExpressionDataIntMatrix

java.lang.Object

ubic.gemma.core.datastructure.matrix.SingleCellExpressionDataIntMatrix

All Implemented Interfaces:

ExpressionDataMatrix<Integer>, ExpressionDataPrimitiveIntMatrix, SingleCellExpressionDataMatrix<Integer>

public class SingleCellExpressionDataIntMatrix
extends Object
implements SingleCellExpressionDataMatrix<Integer>, ExpressionDataPrimitiveIntMatrix

Constructor Summary

Constructors

Constructor	Description
SingleCellExpressionDataIntMatrix(Collection<SingleCellExpressionDataVector> vectors)

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
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.
BioAssay	getBioAssayForColumn(int j)	Obtain a bioassay applicable to a given column.
List<BioAssay>	getBioAssays()	Obtain the list of bioassays.
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
Integer[]	getColumn(int column)	Access a single column of the matrix.
int[]	getColumnAsInts(int column)	Retrieve the given column without boxing.
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.
no.uib.cipr.matrix.sparse.CompRowMatrix	getMatrix()	Obtain the sparse matrix underlying this.
QuantitationType	getQuantitationType()	Return the quantitation type for this matrix.
Integer[]	getRow(int index)	Access a single row of the matrix, by index.
Integer[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
int[]	getRowAsInts(int index)	Retrieve a row without boxing.
int[]	getRowAsInts(CompositeSequence designElement)	Retrieve the row for the given design element without boxing.
ExpressionDataMatrixRowElement	getRowElement(int row)
ExpressionDataMatrixRowElement	getRowElement(CompositeSequence designElement)
List<ExpressionDataMatrixRowElement>	getRowElements()
int	getRowIndex(CompositeSequence designElement)
SingleCellDimension	getSingleCellDimension()	Return the single-cell dimension for this matrix.
int	rows()

Methods inherited from class java.lang.Object

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

Constructor Detail

SingleCellExpressionDataIntMatrix

public SingleCellExpressionDataIntMatrix(Collection<SingleCellExpressionDataVector> vectors)

Method Detail

getMatrix

public no.uib.cipr.matrix.sparse.CompRowMatrix getMatrix()

Obtain the sparse matrix underlying this.

getExpressionExperiment

public ExpressionExperiment getExpressionExperiment()

Description copied from interface: ExpressionDataMatrix

Return the expression experiment this matrix is holding data for.

Specified by:

getExpressionExperiment in interface ExpressionDataMatrix<Integer>

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Obtain the total number of columns.

Specified by:

columns in interface ExpressionDataMatrix<Integer>

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)

getColumn

public Integer[] 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<Integer>

Specified by:

getColumn in interface SingleCellExpressionDataMatrix<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)

getBioAssays

public List<BioAssay> getBioAssays()

Description copied from interface: SingleCellExpressionDataMatrix

Obtain the list of bioassays.

Specified by:

getBioAssays in interface SingleCellExpressionDataMatrix<Integer>

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<Integer>

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<Integer>

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<Integer>

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<Integer>

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<Integer>

getRow

public Integer[] getRow(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

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

Specified by:

getRow in interface ExpressionDataMatrix<Integer>

Parameters:

designElement - de

Returns:

the corresponding row or null if the design element is not found in the matrix

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)

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[]

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)

getRowIndex

public int getRowIndex(CompositeSequence designElement)

Specified by:

getRowIndex in interface ExpressionDataMatrix<Integer>

Returns:

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

getRowElements

public List<ExpressionDataMatrixRowElement> getRowElements()

Specified by:

getRowElements in interface ExpressionDataMatrix<Integer>

Returns:

list of elements representing the row 'labels'.

getRowElement

public ExpressionDataMatrixRowElement getRowElement(int row)

Specified by:

getRowElement in interface ExpressionDataMatrix<Integer>

getRowElement

@Nullable
public ExpressionDataMatrixRowElement getRowElement(CompositeSequence designElement)

Specified by:

getRowElement in interface ExpressionDataMatrix<Integer>

rows

public int rows()

Specified by:

rows in interface ExpressionDataMatrix<Integer>

Returns:

int

getQuantitationType

public QuantitationType getQuantitationType()

Description copied from interface: SingleCellExpressionDataMatrix

Return the quantitation type for this matrix.

Specified by:

getQuantitationType in interface SingleCellExpressionDataMatrix<Integer>

getSingleCellDimension

public SingleCellDimension getSingleCellDimension()

Description copied from interface: SingleCellExpressionDataMatrix

Return the single-cell dimension for this matrix.

Specified by:

getSingleCellDimension in interface SingleCellExpressionDataMatrix<Integer>