Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataStringMatrix

java.lang.Object

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

ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix

All Implemented Interfaces:

Serializable, BulkExpressionDataMatrix<String>, ExpressionDataMatrix<String>

public class ExpressionDataStringMatrix
extends BaseExpressionDataMatrix<String>

Author:

pavlidis

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
ExpressionDataStringMatrix(Collection<? extends BulkExpressionDataVector> vectors)
ExpressionDataStringMatrix(Collection<? extends BulkExpressionDataVector> dataVectors, QuantitationType quantitationType)
ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment, Collection<CompositeSequence> designElements, QuantitationType quantitationType)
ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)

Method Summary

Modifier and Type	Method	Description
int	columns()	Obtain the total number of columns.
String	get(int row, int column)	Access a single value of the matrix by row and column.
String[][]	get(List<CompositeSequence> designElements, List<BioAssay> bioAssays)	Access a submatrix
String	get(CompositeSequence designElement, BioAssay bioAssay)	Access a single value of the matrix.
String[]	getColumn(int index)	Access a single column of the matrix.
String[]	getColumn(BioAssay bioAssay)	Access a single column of the matrix.
String[][]	getColumns(List<BioAssay> bioAssays)	Access a submatrix slice by columns
String[][]	getRawMatrix()	Access the entire matrix.
String[]	getRow(int index)	Access a single row of the matrix, by index.
String[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
boolean	hasMissingValues()
int	rows()
void	set(int row, int column, String value)	Set a value in the matrix, by index
protected void	vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)

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, toString, wait, wait, wait

Constructor Detail

ExpressionDataStringMatrix

public ExpressionDataStringMatrix(Collection<? extends BulkExpressionDataVector> vectors)

ExpressionDataStringMatrix

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

ExpressionDataStringMatrix

public ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment,
                                  Collection<CompositeSequence> designElements,
                                  QuantitationType quantitationType)

ExpressionDataStringMatrix

public ExpressionDataStringMatrix(ExpressionExperiment expressionExperiment,
                                  QuantitationType quantitationType)

Method Detail

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Obtain the total number of columns.

get

public String 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.

Parameters:

designElement - de

bioAssay - ba

Returns:

T t

get

public String get(int row,
                  int column)

Description copied from interface: ExpressionDataMatrix

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

get

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

Description copied from interface: BulkExpressionDataMatrix

Access a submatrix

Parameters:

designElements - de

bioAssays - bas

Returns:

T[][]

getColumn

public String[] getColumn(BioAssay bioAssay)

Description copied from interface: BulkExpressionDataMatrix

Access a single column of the matrix.

Parameters:

bioAssay - i

Returns:

T[]

getColumn

public String[] getColumn(int index)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Parameters:

index - index

Returns:

T[]

getColumns

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

Description copied from interface: BulkExpressionDataMatrix

Access a submatrix slice by columns

Parameters:

bioAssays - ba

Returns:

t[][]

getRawMatrix

public String[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Returns:

T[][]

getRow

public String[] getRow(CompositeSequence designElement)

Description copied from interface: ExpressionDataMatrix

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

Parameters:

designElement - de

Returns:

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

getRow

public String[] 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[]

hasMissingValues

public boolean hasMissingValues()

Returns:

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

rows

public int rows()

Returns:

int

set

public void set(int row,
                int column,
                String value)

Description copied from interface: BulkExpressionDataMatrix

Set a value in the matrix, by index

Parameters:

row - row

column - col

value - val

vectorsToMatrix

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

Specified by:

vectorsToMatrix in class BaseExpressionDataMatrix<String>