Package ubic.gemma.core.datastructure.matrix

Interface ExpressionDataMatrix<T>

Type Parameters:

T - type of scalar held in the matrix

All Known Subinterfaces:

BulkExpressionDataMatrix<T>, ExpressionDataPrimitiveDoubleMatrix, ExpressionDataPrimitiveIntMatrix, SingleCellExpressionDataMatrix<T>

All Known Implementing Classes:

BaseExpressionDataMatrix, EmptyExpressionMatrix, ExpressionDataBooleanMatrix, ExpressionDataDoubleMatrix, ExpressionDataIntegerMatrix, ExpressionDataStringMatrix, SingleCellExpressionDataDoubleMatrix, SingleCellExpressionDataIntMatrix

public interface ExpressionDataMatrix<T>

Represents a matrix of data from an ExpressionExperiment.

The rows of this matrix represent design elements.

Author:

pavlidis, keshav

See Also:

BulkExpressionDataMatrix, SingleCellExpressionDataMatrix

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
T	get(int row, int column)	Access a single value of the matrix by row and column.
T[]	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.
T[]	getRow(int index)	Access a single row of the matrix, by index.
T[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
ExpressionDataMatrixRowElement	getRowElement(int row)
ExpressionDataMatrixRowElement	getRowElement(CompositeSequence designElement)
List<ExpressionDataMatrixRowElement>	getRowElements()
int	getRowIndex(CompositeSequence designElement)
int	rows()

Method Detail

getExpressionExperiment

ExpressionExperiment getExpressionExperiment()

Return the expression experiment this matrix is holding data for.

getDesignElements

List<CompositeSequence> getDesignElements()

Obtain all the design elements in this data matrix.

getDesignElementForRow

CompositeSequence getDesignElementForRow(int index)

Return a design element for a given index.

Throws:

IndexOutOfBoundsException - if the supplied index is not within zero and rows()

columns

int columns()

Obtain the total number of columns.

getColumn

T[] getColumn(int column)

Access a single column of the matrix.

Parameters:

column - index

Returns:

T[]

Throws:

IndexOutOfBoundsException - if the supplied index is not within zero and columns()

rows

int rows()

Returns:

int

getRow

T[] getRow(int index)

Access a single row of the matrix, by index. A complete row is returned.

Parameters:

index - i

Returns:

t[]

Throws:

IndexOutOfBoundsException - if the supplied index is not within zero and rows()

getRow

@Nullable
T[] getRow(CompositeSequence designElement)

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

Parameters:

designElement - de

Returns:

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

getRowIndex

int getRowIndex(CompositeSequence designElement)

Returns:

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

getRowElements

List<ExpressionDataMatrixRowElement> getRowElements()

Returns:

list of elements representing the row 'labels'.

getRowElement

ExpressionDataMatrixRowElement getRowElement(int row)

getRowElement

@Nullable
ExpressionDataMatrixRowElement getRowElement(CompositeSequence designElement)

get

T get(int row,
      int column)

Access a single value of the matrix by row and column.

Throws:

IndexOutOfBoundsException - if either the row or column is outside the matrix bounds