Package ubic.gemma.core.datastructure.matrix

Class ExpressionDataStringMatrix

java.lang.Object

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

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

ubic.gemma.core.datastructure.matrix.ExpressionDataStringMatrix

All Implemented Interfaces:

BulkExpressionDataMatrix<String>, ExpressionDataMatrix<String>, MultiAssayBulkExpressionDataMatrix<String>

public class ExpressionDataStringMatrix
extends AbstractMultiAssayExpressionDataMatrix<String>

Author:

pavlidis

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
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.
protected String	format(int row, int column)	Format the value at the provided indices of the matrix.
String	get(int row, int column)	Access a single value of the matrix by row and column.
String[]	getColumn(int index)	Access a single column of the matrix.
String[][]	getRawMatrix()	Access the entire matrix.
String[]	getRow(int index)	Access a single row of the matrix, by index.
boolean	hasMissingValues()
int	rows()
ExpressionDataMatrix<String>	sliceRows(List<CompositeSequence> designElements)
protected void	vectorsToMatrix(Collection<? extends BulkExpressionDataVector> vectors)

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

Constructor Details

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 Details

columns

public int columns()

Description copied from interface: ExpressionDataMatrix

Obtain the total number of columns.

get

public String get(int row,
 int column)

Description copied from interface: ExpressionDataMatrix

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

getColumn

public String[] getColumn(int index)

Description copied from interface: ExpressionDataMatrix

Access a single column of the matrix.

Parameters:

index - index

Returns:

T[]

getRawMatrix

public String[][] getRawMatrix()

Description copied from interface: BulkExpressionDataMatrix

Access the entire matrix.

Returns:

T[][]

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[]

sliceRows

public ExpressionDataMatrix<String> sliceRows(List<CompositeSequence> designElements)

hasMissingValues

public boolean hasMissingValues()

Returns:

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

rows

public int rows()

Returns:

int

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<String>

vectorsToMatrix

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

Specified by:

vectorsToMatrix in class AbstractMultiAssayExpressionDataMatrix<String>