Package ubic.gemma.core.datastructure.matrix

Class AbstractBulkExpressionDataMatrix<T>

java.lang.Object

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

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

Type Parameters:

T -

All Implemented Interfaces:

BulkExpressionDataMatrix<T>, ExpressionDataMatrix<T>

Direct Known Subclasses:

BulkExpressionDataDoubleMatrix, BulkExpressionDataIntMatrix, EmptyBulkExpressionDataMatrix

public abstract class AbstractBulkExpressionDataMatrix<T>
extends AbstractExpressionDataMatrix<T>
implements BulkExpressionDataMatrix<T>

Base class for bulk expression data matrices.

If you need to handle multiple BioAssay per BioMaterial, use AbstractMultiAssayExpressionDataMatrix instead.

Author:

poirigui

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractBulkExpressionDataMatrix(List<? extends BulkExpressionDataVector> vectors)
protected	AbstractBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType quantitationType, List<CompositeSequence> designElements)

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
T	get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
BioAssayDimension	getBioAssayDimension()	Obtain the dimension for the columns of this matrix.
BioAssay	getBioAssayForColumn(int index)	Obtain an assay corresponding to a given column.
BioMaterial	getBioMaterialForColumn(int index)	Obtain a biomaterial corresponding to a column.
T[]	getColumn(BioAssay bioAssay)	Access a single column of the matrix.
int	getColumnIndex(BioAssay bioAssay)
int	getColumnIndex(BioMaterial bioMaterial)
protected String	getColumnLabel(int j)	Obtain a label suitable for describing a 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()	Obtain the quantitation type for this matrix.
T[]	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.
protected String	getRowLabel(int i)	Obtain a label suitable for describing a row of the matrix.
int	rows()

Methods inherited from class ubic.gemma.core.datastructure.matrix.AbstractExpressionDataMatrix

format, 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

getRawMatrix, hasMissingValues

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

get, getColumn, getRow

Constructor Details

AbstractBulkExpressionDataMatrix

protected AbstractBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension,
 QuantitationType quantitationType,
 List<CompositeSequence> designElements)

AbstractBulkExpressionDataMatrix

protected AbstractBulkExpressionDataMatrix(List<? extends BulkExpressionDataVector> vectors)

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<T>

getQuantitationType

public QuantitationType getQuantitationType()

Description copied from interface: ExpressionDataMatrix

Obtain the quantitation type for this matrix.

Specified by:

getQuantitationType in interface ExpressionDataMatrix<T>

getBioAssayDimension

public BioAssayDimension getBioAssayDimension()

Description copied from interface: BulkExpressionDataMatrix

Obtain the dimension for the columns of this matrix.

Specified by:

getBioAssayDimension in interface BulkExpressionDataMatrix<T>

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Obtain the total number of columns.

Specified by:

columns in interface ExpressionDataMatrix<T>

getColumn

public T[] getColumn(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataMatrix

Access a single column of the matrix.

Specified by:

getColumn in interface BulkExpressionDataMatrix<T>

Returns:

a vector for the given column, or null if the column is not present

getColumnIndex

public int getColumnIndex(BioAssay bioAssay)

Specified by:

getColumnIndex in interface BulkExpressionDataMatrix<T>

Returns:

the index of the column for the data for the bioAssay, or -1 if missing

getColumnIndex

public int getColumnIndex(BioMaterial bioMaterial)

Specified by:

getColumnIndex in interface BulkExpressionDataMatrix<T>

getBioAssayForColumn

public BioAssay getBioAssayForColumn(int index)

Description copied from interface: BulkExpressionDataMatrix

Obtain an assay corresponding to a given column.

Specified by:

getBioAssayForColumn in interface BulkExpressionDataMatrix<T>

getBioMaterialForColumn

public BioMaterial getBioMaterialForColumn(int index)

Description copied from interface: BulkExpressionDataMatrix

Obtain a biomaterial corresponding to a column.

Specified by:

getBioMaterialForColumn in interface BulkExpressionDataMatrix<T>

rows

public int rows()

Specified by:

rows in interface ExpressionDataMatrix<T>

Returns:

int

getRow

public T[] getRow(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

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

Specified by:

getRow in interface ExpressionDataMatrix<T>

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<T>

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<T>

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<T>

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<T>

get

public T get(CompositeSequence designElement,
 BioAssay bioAssay)

Description copied from interface: BulkExpressionDataMatrix

Access a single value of the matrix. Note that because there can be multiple bioassays per column and multiple design elements per row, it is possible for this method to retrieve a data that does not come from the bioassay and/or designelement arguments.

Specified by:

get in interface BulkExpressionDataMatrix<T>

Parameters:

designElement - de

bioAssay - ba

Returns:

the value at the given design element and bioassay, or null if the value is missing

getRowElements

public List<ExpressionDataMatrixRowElement> getRowElements()

Specified by:

getRowElements in interface ExpressionDataMatrix<T>

Returns:

list of elements representing the row 'labels'.

getRowElement

public ExpressionDataMatrixRowElement getRowElement(int row)

Specified by:

getRowElement in interface ExpressionDataMatrix<T>

getRowLabel

protected String getRowLabel(int i)

Description copied from class: AbstractExpressionDataMatrix

Obtain a label suitable for describing a row of the matrix.

Specified by:

getRowLabel in class AbstractExpressionDataMatrix<T>

getColumnLabel

protected String getColumnLabel(int j)

Description copied from class: AbstractExpressionDataMatrix

Obtain a label suitable for describing a column of the matrix.

Specified by:

getColumnLabel in class AbstractExpressionDataMatrix<T>