Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataDoubleMatrix

java.lang.Object

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

ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix

All Implemented Interfaces:

Serializable, BulkExpressionDataMatrix<Double>, ExpressionDataMatrix<Double>, ExpressionDataPrimitiveDoubleMatrix

public class ExpressionDataDoubleMatrix
extends BaseExpressionDataMatrix<Double>
implements ExpressionDataPrimitiveDoubleMatrix

A data structure that holds a reference to the data for a given expression experiment. The data can be queried by row or column, returning data for a specific DesignElement or data for a specific BioAssay. This class is not database aware so the vectors provided must already be 'thawed'.

Author:

pavlidis, keshav

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.gemma.core.datastructure.matrix.BaseExpressionDataMatrix

bioAssayDimensions, columnAssayMap, columnBioAssayMapByInteger, columnBioMaterialMap, columnBioMaterialMapByInteger, expressionExperiment, quantitationTypes, rowDesignElementMapByInteger, rowElementMap

Constructor Summary

Constructors

Constructor	Description
ExpressionDataDoubleMatrix()	To comply with bean specifications.
ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> vectors)
ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> dataVectors, Collection<QuantitationType> quantitationTypes)
ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> dataVectors, QuantitationType quantitationType)
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<BioMaterial> columnsToUse, BioAssayDimension reorderedDim)	Create a matrix based on another one's selected columns.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, List<CompositeSequence> rowsToUse)	Create a matrix based on another one's selected rows.
ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix, DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix, Collection<QuantitationType> quantitationTypes)	Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.
ExpressionDataDoubleMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
ExpressionDataDoubleMatrix(ExpressionExperiment ee, QuantitationType qt, DoubleMatrix<CompositeSequence,BioMaterial> matrix)	Create a matrix given a 'raw' matrix that uses the same samples as the experiment.

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
Double	get(int row, int column)	Access a single value of the matrix by row and column.
Double[][]	get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)	Access a submatrix
Double	get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
double	getAsDouble(int row, int column)	Retrieve the value at the given row and column without boxing.
double[][]	getAsDoubles(List<CompositeSequence> designElements, List<BioAssay> bioAssays)
Double[]	getColumn(int index)	Access a single column of the matrix.
Double[]	getColumn(BioAssay bioAssay)	Access a single column of the matrix.
double[]	getColumnAsDoubles(int index)	Retrieve the given column without boxing.
double[]	getColumnAsDoubles(BioAssay bioAssay)	Retrieve the given column without boxing.
Double[][]	getColumns(List<BioAssay> bioAssays)	Access a submatrix slice by columns
DoubleMatrix<CompositeSequence,BioMaterial>	getMatrix()
Map<CompositeSequence,Double>	getRanks()
Double[][]	getRawMatrix()	Access the entire matrix.
double[][]	getRawMatrixAsDoubles()	Obtain the raw matrix without boxing.
Double[]	getRow(int index)	Access a single row of the matrix, by index.
Double[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
double[]	getRowAsDoubles(int index)	Retrieve a row without boxing.
double[]	getRowAsDoubles(CompositeSequence designElement)	Retrieve the row for the given design element without boxing.
List<CompositeSequence>	getRowNames()
boolean	hasMissingValues()
int	rows()
void	set(int row, int column, Double value)	Set a value in the matrix, by index
void	set(CompositeSequence designElement, BioAssay bioAssay, Double value)
void	setRow(int rowIndex, Double[] data)	Sets the row of matrix to the input data.
Collection<ProcessedExpressionDataVector>	toProcessedDataVectors()
Collection<RawExpressionDataVector>	toRawDataVectors()	Same as toProcessedDataVectors but uses RawExpressionDataVector
String	toString()
protected void	vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)	Populate this matrix from a given collection of BulkExpressionDataVectors.

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

addToRowMaps, columns, getBestBioAssayDimension, getBioAssayDimension, getBioAssayForColumn, getBioAssaysForColumn, getBioMaterialForColumn, getColumnIndex, getColumnIndex, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationType, getQuantitationTypes, getRowElement, getRowElement, getRowElements, getRowIndex, init, selectVectors, selectVectors, selectVectors, selectVectors, setMatBioAssayValues, setUpColumnElements

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.ExpressionDataMatrix

getDesignElementForRow, getDesignElements, getRowElement, getRowElement, getRowElements, getRowIndex

Constructor Detail

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix()

To comply with bean specifications. Not to be instantiated.

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> vectors)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionExperiment ee,
                                  Collection<? extends BulkExpressionDataVector> vectors)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> dataVectors,
                                  Collection<QuantitationType> quantitationTypes)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(Collection<? extends BulkExpressionDataVector> dataVectors,
                                  QuantitationType quantitationType)

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix,
                                  DoubleMatrix<CompositeSequence,BioMaterial> dataMatrix,
                                  Collection<QuantitationType> quantitationTypes)

Create a data matrix like sourceMatrix but use the values and quantitations from dataMatrix.

Note: The rows can be different from the original matrix, but the columns must be the same.

Parameters:

sourceMatrix - source matrix from which most of the meta-data will be imported

dataMatrix - data matrix to use

quantitationTypes - quantitation types used by the dataMatrix

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix,
                                  List<CompositeSequence> rowsToUse)

Create a matrix based on another one's selected rows.

Parameters:

rowsToUse - rows

sourceMatrix - matrix

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionExperiment ee,
                                  QuantitationType qt,
                                  DoubleMatrix<CompositeSequence,BioMaterial> matrix)

Create a matrix given a 'raw' matrix that uses the same samples as the experiment. Only simple situations are supported (one platform, not subsetting the dataset).

Parameters:

ee - to be associated with this

qt - to be associated with this

matrix - with valid row and column elements, and the data

ExpressionDataDoubleMatrix

public ExpressionDataDoubleMatrix(ExpressionDataDoubleMatrix sourceMatrix,
                                  List<BioMaterial> columnsToUse,
                                  BioAssayDimension reorderedDim)

Create a matrix based on another one's selected columns. The results will be somewhat butchered - only a single BioAssayDimension and the ranks will be copied over (not recomputed based on the selected columns).

Parameters:

columnsToUse - columns

sourceMatrix - matrix

reorderedDim - the reordered bioAssayDimension.

Method Detail

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Obtain the total number of columns.

Specified by:

columns in interface ExpressionDataMatrix<Double>

get

public Double 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 designelements 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<Double>

Parameters:

designElement - de

bioAssay - ba

Returns:

T t

get

public Double 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<Double>

getAsDouble

public double getAsDouble(int row,
                          int column)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the value at the given row and column without boxing.

Specified by:

getAsDouble in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

ExpressionDataMatrix.get(int, int)

get

public Double[][] get(List<CompositeSequence> designElements,
                      List<BioAssay> bioAssays)

Description copied from interface: BulkExpressionDataMatrix

Access a submatrix

Specified by:

get in interface BulkExpressionDataMatrix<Double>

Parameters:

designElements - de

bioAssays - bas

Returns:

T[][]

getAsDoubles

public double[][] getAsDoubles(List<CompositeSequence> designElements,
                               List<BioAssay> bioAssays)

getColumn

public Double[] getColumn(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataMatrix

Access a single column of the matrix.

Specified by:

getColumn in interface BulkExpressionDataMatrix<Double>

Parameters:

bioAssay - i

Returns:

T[]

getColumnAsDoubles

public double[] getColumnAsDoubles(BioAssay bioAssay)

Retrieve the given column without boxing.

See Also:

getColumn(BioAssay)

getColumn

public Double[] getColumn(int index)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Specified by:

getColumn in interface ExpressionDataMatrix<Double>

Parameters:

index - index

Returns:

T[]

getColumnAsDoubles

public double[] getColumnAsDoubles(int index)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the given column without boxing.

Specified by:

getColumnAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

ExpressionDataMatrix.getColumn(int)

getColumns

public Double[][] getColumns(List<BioAssay> bioAssays)

Description copied from interface: BulkExpressionDataMatrix

Access a submatrix slice by columns

Specified by:

getColumns in interface BulkExpressionDataMatrix<Double>

Parameters:

bioAssays - ba

Returns:

t[][]

getRawMatrix

public Double[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Specified by:

getRawMatrix in interface BulkExpressionDataMatrix<Double>

Returns:

T[][]

getRawMatrixAsDoubles

public double[][] getRawMatrixAsDoubles()

Obtain the raw matrix without boxing.

See Also:

getRawMatrix()

getRow

public Double[] getRow(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

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

Specified by:

getRow in interface ExpressionDataMatrix<Double>

Parameters:

designElement - de

Returns:

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

getRowAsDoubles

public double[] getRowAsDoubles(CompositeSequence designElement)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve the row for the given design element without boxing.

Specified by:

getRowAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

ExpressionDataMatrix.getRow(CompositeSequence)

getRow

public Double[] 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<Double>

Parameters:

index - i

Returns:

t[]

getRowAsDoubles

public double[] getRowAsDoubles(int index)

Description copied from interface: ExpressionDataPrimitiveDoubleMatrix

Retrieve a row without boxing.

Specified by:

getRowAsDoubles in interface ExpressionDataPrimitiveDoubleMatrix

See Also:

ExpressionDataMatrix.getRow(int)

hasMissingValues

public boolean hasMissingValues()

Specified by:

hasMissingValues in interface BulkExpressionDataMatrix<Double>

Returns:

true if any values are null or NaN (for Doubles); all other values are considered non-missing.

rows

public int rows()

Specified by:

rows in interface ExpressionDataMatrix<Double>

Returns:

int

set

public void set(int row,
                int column,
                @Nullable
                Double value)

Description copied from interface: BulkExpressionDataMatrix

Set a value in the matrix, by index

Specified by:

set in interface BulkExpressionDataMatrix<Double>

Parameters:

row - row

column - col

value - val

toProcessedDataVectors

public Collection<ProcessedExpressionDataVector> toProcessedDataVectors()

Returns:

Convert this to a collection of vectors.

toRawDataVectors

public Collection<RawExpressionDataVector> toRawDataVectors()

Same as toProcessedDataVectors but uses RawExpressionDataVector

Returns:

Convert this to a collection of vectors.

getMatrix

public DoubleMatrix<CompositeSequence,BioMaterial> getMatrix()

getRanks

public Map<CompositeSequence,Double> getRanks()

Returns:

The expression level ranks (based on mean signal intensity in the vectors); this will be empty if the vectors used to construct the matrix were not ProcessedExpressionDataVectors.

getRowNames

public List<CompositeSequence> getRowNames()

set

public void set(CompositeSequence designElement,
                BioAssay bioAssay,
                Double value)

setRow

public void setRow(int rowIndex,
                   Double[] data)

Sets the row of matrix to the input data.

Parameters:

rowIndex - The row index of the data in the matrix to be replaced.

data - The input data.

toString

public String toString()

Overrides:

toString in class Object

vectorsToMatrix

protected void vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)

Populate this matrix from a given collection of BulkExpressionDataVectors.

Specified by:

vectorsToMatrix in class BaseExpressionDataMatrix<Double>