Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataDoubleMatrix

java.lang.Object

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

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

ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix

All Implemented Interfaces:

BulkExpressionDataMatrix<Double>, BulkExpressionDataPrimitiveDoubleMatrix, ExpressionDataMatrix<Double>, ExpressionDataPrimitiveDoubleMatrix, MultiAssayBulkExpressionDataMatrix<Double>

public class ExpressionDataDoubleMatrix
extends AbstractMultiAssayExpressionDataMatrix<Double>
implements BulkExpressionDataPrimitiveDoubleMatrix

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

Field Summary

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

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 dmatrix, DoubleMatrix<CompositeSequence,BioMaterial> copiedMatrix)
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.
protected String	format(int row, int column)	Format the value at the provided indices of the matrix.
Double	get(int row, int column)	Access a single value of the matrix by row and column.
double	getAsDouble(int row, int column)	Retrieve the value at the given row and column without boxing.
Double[]	getColumn(int index)	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.
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[]	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)	Deprecated.
void	set(CompositeSequence designElement, BioAssay bioAssay, Double value)
Collection<ProcessedExpressionDataVector>	toProcessedDataVectors()
Collection<RawExpressionDataVector>	toRawDataVectors()	Same as toProcessedDataVectors but uses RawExpressionDataVector
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.AbstractMultiAssayExpressionDataMatrix

addToRowMaps, columns, formatRepresentation, get, getBestBioAssayDimension, getBioAssayDimension, getBioAssayDimension, getBioAssayDimensions, getBioAssayForColumn, getBioAssaysForColumn, getBioMaterialForColumn, getColumn, getColumnIndex, getColumnIndex, getColumnLabel, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationType, getQuantitationTypes, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices, getRowLabel, selectVectors, selectVectors, selectVectors, setMatBioAssayValues, setUpColumnElements

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

format, format, 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

get, getBioAssayForColumn, getColumn, getColumnIndex

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

getDesignElementForRow, getDesignElements, getExpressionExperiment, getRow, getRowElement, getRowElements, getRowIndex, getRowIndices

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 dmatrix,
                                  DoubleMatrix<CompositeSequence,BioMaterial> copiedMatrix)

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(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)

getColumnAsDoubles

public double[] getColumnAsDoubles(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataPrimitiveDoubleMatrix

Retrieve the given column without boxing.

Specified by:

getColumnAsDoubles in interface BulkExpressionDataPrimitiveDoubleMatrix

See Also:

BulkExpressionDataMatrix.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)

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.

Specified by:

getRawMatrixAsDoubles in interface BulkExpressionDataPrimitiveDoubleMatrix

See Also:

getRawMatrix()

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 and floats); any other value that is considered missing.

rows

public int rows()

Specified by:

rows in interface ExpressionDataMatrix<Double>

Returns:

int

set

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

Deprecated.

Modifying the matrix directly is not recommended, make a copy instead.

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)

format

protected String format(int row,
                        int column)

Description copied from class: AbstractMultiAssayExpressionDataMatrix

Format the value at the provided indices of the matrix.

Specified by:

format in class AbstractMultiAssayExpressionDataMatrix<Double>

vectorsToMatrix

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

Populate this matrix from a given collection of BulkExpressionDataVectors.

Specified by:

vectorsToMatrix in class AbstractMultiAssayExpressionDataMatrix<Double>