Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataBooleanMatrix

java.lang.Object

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

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

ubic.gemma.core.datastructure.matrix.ExpressionDataBooleanMatrix

All Implemented Interfaces:

BulkExpressionDataMatrix<Boolean>, ExpressionDataMatrix<Boolean>, MultiAssayBulkExpressionDataMatrix<Boolean>

public class ExpressionDataBooleanMatrix
extends AbstractMultiAssayExpressionDataMatrix<Boolean>

Matrix of booleans mapped from an ExpressionExperiment.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
ExpressionDataBooleanMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors)
ExpressionDataBooleanMatrix(ExpressionExperiment ee, Collection<? extends BulkExpressionDataVector> vectors, List<QuantitationType> qtypes)

Method Summary

Modifier and Type	Method	Description
protected String	format(int row, int column)	Format the value at the provided indices of the matrix.
Boolean	get(int row, int column)	Access a single value of the matrix by row and column.
Boolean[]	getColumn(int column)	Access a single column of the matrix.
Boolean[][]	getRawMatrix()	Access the entire matrix.
Boolean[]	getRow(int index)	Access a single row of the matrix, by index.
boolean	hasMissingValues()
BulkExpressionDataMatrix<Boolean>	sliceColumns(List<BioMaterial> bioMaterials)	Slice the requested samples (columns) from this matrix.
ExpressionDataBooleanMatrix	sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)	Slice the requested samples (columns) from this matrix.
ExpressionDataBooleanMatrix	sliceRows(List<CompositeSequence> designElements)	Slice the given design elements (rows) from the matrix.

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

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

Constructor Details

ExpressionDataBooleanMatrix

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

ExpressionDataBooleanMatrix

public ExpressionDataBooleanMatrix(ExpressionExperiment ee,
 Collection<? extends BulkExpressionDataVector> vectors,
 List<QuantitationType> qtypes)

Method Details

get

public Boolean get(int row,
 int column)

Description copied from interface: ExpressionDataMatrix

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

getColumn

public Boolean[] getColumn(int column)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Parameters:

column - index

Returns:

T[]

getRawMatrix

public Boolean[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Returns:

T[][]

sliceColumns

public BulkExpressionDataMatrix<Boolean> sliceColumns(List<BioMaterial> bioMaterials)

Description copied from interface: BulkExpressionDataMatrix

Slice the requested samples (columns) from this matrix.

Dimensions will be altered to reflect only the selected samples.

Parameters:

bioMaterials - samples to select from the matrix

sliceColumns

public ExpressionDataBooleanMatrix sliceColumns(List<BioMaterial> bioMaterials,
 BioAssayDimension dimension)

Description copied from interface: BulkExpressionDataMatrix

Slice the requested samples (columns) from this matrix.

This also allows specifying a new dimension for the columns that will be used for every design element (rows).

Parameters:

bioMaterials - samples to select from the matrix

dimension - the dimension to use

getRow

public Boolean[] getRow(int index)

Description copied from interface: ExpressionDataMatrix

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

Parameters:

index - i

Returns:

t[]

sliceRows

public ExpressionDataBooleanMatrix sliceRows(List<CompositeSequence> designElements)

Description copied from interface: ExpressionDataMatrix

Slice the given design elements (rows) from the matrix.

hasMissingValues

public boolean hasMissingValues()

Returns:

true if any values are null or NaN (for doubles and floats); any other value that is considered missing.

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<Boolean>