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, ExpressionDataMatrix<String>

public class ExpressionDataStringMatrix
extends BaseExpressionDataMatrix<String>

Author:

pavlidis

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
ExpressionDataStringMatrix(Collection<? extends DesignElementDataVector> vectors)
ExpressionDataStringMatrix(Collection<? extends DesignElementDataVector> 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()	Total number of columns.
String	get(int row, int column)	Access a single value of the matrix.
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(Integer 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(Integer index)	Access a single row of the matrix, by index.
String[]	getRow(CompositeSequence designElement)	Return a row that 'came from' the given design element.
String[][]	getRows(List<CompositeSequence> designElements)	Access a submatrix
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 DesignElementDataVector> vectors)

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

columns, getBestBioAssayDimension, getBioAssayDimension, getBioAssaysForColumn, getBioMaterialForColumn, getColumnIndex, getDesignElementForRow, getDesignElements, getExpressionExperiment, getQuantitationTypes, getRowElement, getRowElements, getRowIndex

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 DesignElementDataVector> vectors)

ExpressionDataStringMatrix

public ExpressionDataStringMatrix(Collection<? extends DesignElementDataVector> 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

Total number of columns.

Returns:

int

get

public String get(CompositeSequence designElement,
                  BioAssay bioAssay)

Description copied from interface: ExpressionDataMatrix

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. This is generally the easiest way to do it.

Parameters:

row - row

column - col

Returns:

t

get

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

Description copied from interface: ExpressionDataMatrix

Access a submatrix

Parameters:

designElements - de

bioAssays - bas

Returns:

T[][]

getColumn

public String[] getColumn(BioAssay bioAssay)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Parameters:

bioAssay - i

Returns:

T[]

getColumn

public String[] getColumn(Integer 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: ExpressionDataMatrix

Access a submatrix slice by columns

Parameters:

bioAssays - ba

Returns:

t[][]

getRawMatrix

public String[][] getRawMatrix()

Description copied from interface: ExpressionDataMatrix

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:

t

getRow

public String[] getRow(Integer 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[]

getRows

public String[][] getRows(List<CompositeSequence> designElements)

Description copied from interface: ExpressionDataMatrix

Access a submatrix

Parameters:

designElements - de

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: ExpressionDataMatrix

Set a value in the matrix, by index

Parameters:

row - row

column - col

value - val

vectorsToMatrix

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

Specified by:

vectorsToMatrix in class BaseExpressionDataMatrix<String>