Package ubic.gemma.core.datastructure.matrix

Class BaseExpressionDataMatrix<T>

java.lang.Object

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

All Implemented Interfaces:

Serializable, ExpressionDataMatrix<T>

Direct Known Subclasses:

EmptyExpressionMatrix, ExpressionDataBooleanMatrix, ExpressionDataDoubleMatrix, ExpressionDataIntegerMatrix, ExpressionDataStringMatrix

public abstract class BaseExpressionDataMatrix<T>
extends Object
implements ExpressionDataMatrix<T>, Serializable

Base class for ExpressionDataMatrix implementations. Implementation note: The underlying DoubleMatrixNamed is indexed by Integers, which are in turn mapped to BioAssays etc. held here. Thus the 'names' of the underlying matrix are just numbers.

Author:

pavlidis

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
BaseExpressionDataMatrix()

Method Summary

Modifier and Type	Method	Description
int	columns(CompositeSequence el)	Number of columns that use the given design element.
BioAssayDimension	getBestBioAssayDimension()
BioAssayDimension	getBioAssayDimension(CompositeSequence designElement)	Produce a BioAssayDimension representing the matrix columns for a specific row.
Collection<BioAssay>	getBioAssaysForColumn(int index)
BioMaterial	getBioMaterialForColumn(int index)
int	getColumnIndex(BioMaterial bioMaterial)
CompositeSequence	getDesignElementForRow(int index)
List<CompositeSequence>	getDesignElements()	Obtain all the design elements in this data matrix.
ExpressionExperiment	getExpressionExperiment()	The associated ExpressionExperiment, if known.
Collection<QuantitationType>	getQuantitationTypes()	Return the quantitation types for this matrix.
ExpressionDataMatrixRowElement	getRowElement(int index)
List<ExpressionDataMatrixRowElement>	getRowElements()
int	getRowIndex(CompositeSequence designElement)
protected abstract void	vectorsToMatrix(Collection<? extends DesignElementDataVector> vectors)

Methods inherited from class java.lang.Object

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

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

columns, get, get, get, getColumn, getColumn, getColumns, getRawMatrix, getRow, getRow, getRows, hasMissingValues, rows, set

Constructor Detail

BaseExpressionDataMatrix

public BaseExpressionDataMatrix()

Method Detail

columns

public int columns(CompositeSequence el)

Description copied from interface: ExpressionDataMatrix

Number of columns that use the given design element. Useful if the matrix includes data from more than one array design.

Specified by:

columns in interface ExpressionDataMatrix<T>

Parameters:

el - el

Returns:

int

getBestBioAssayDimension

public BioAssayDimension getBestBioAssayDimension()

Specified by:

getBestBioAssayDimension in interface ExpressionDataMatrix<T>

Returns:

The bioassaydimension that covers all the biomaterials in this matrix.

getBioAssayDimension

public BioAssayDimension getBioAssayDimension(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

Produce a BioAssayDimension representing the matrix columns for a specific row. The designelement argument is needed because a matrix can combine data from multiple array designs, each of which will generate its own bioassaydimension. Note that if this represents a subsetted data set, the return value may be a lightweight 'fake'.

Specified by:

getBioAssayDimension in interface ExpressionDataMatrix<T>

Parameters:

designElement - de

Returns:

bad

getBioAssaysForColumn

public Collection<BioAssay> getBioAssaysForColumn(int index)

Specified by:

getBioAssaysForColumn in interface ExpressionDataMatrix<T>

Parameters:

index - i

Returns:

bioassays that contribute data to the column. There can be multiple bioassays if more than one array was used in the study.

getBioMaterialForColumn

public BioMaterial getBioMaterialForColumn(int index)

Specified by:

getBioMaterialForColumn in interface ExpressionDataMatrix<T>

Parameters:

index - i

Returns:

BioMaterial. Note that if this represents a subsetted data set, the BioMaterial may be a lightweight 'fake'.

getColumnIndex

public int getColumnIndex(BioMaterial bioMaterial)

Specified by:

getColumnIndex in interface ExpressionDataMatrix<T>

Parameters:

bioMaterial - bm

Returns:

the index of the column for the data for the bioMaterial.

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)

Specified by:

getDesignElementForRow in interface ExpressionDataMatrix<T>

Parameters:

index - i

Returns:

cs

getExpressionExperiment

@Nullable
public ExpressionExperiment getExpressionExperiment()

The associated ExpressionExperiment, if known.

Specified by:

getExpressionExperiment in interface ExpressionDataMatrix<T>

Returns:

ee

getQuantitationTypes

public Collection<QuantitationType> getQuantitationTypes()

Description copied from interface: ExpressionDataMatrix

Return the quantitation types for this matrix. Often (usually) there will be just one.

Specified by:

getQuantitationTypes in interface ExpressionDataMatrix<T>

Returns:

qts

getRowElements

public List<ExpressionDataMatrixRowElement> getRowElements()

Specified by:

getRowElements in interface ExpressionDataMatrix<T>

Returns:

list of elements representing the row 'labels'.

getRowIndex

public int getRowIndex(CompositeSequence designElement)

Specified by:

getRowIndex in interface ExpressionDataMatrix<T>

getRowElement

public ExpressionDataMatrixRowElement getRowElement(int index)

vectorsToMatrix

protected abstract void vectorsToMatrix(Collection<? extends DesignElementDataVector> vectors)