org.systemsbiology.gaggle.core.datatypes
Class DataMatrix

java.lang.Object
  org.systemsbiology.gaggle.core.datatypes.DataMatrix

All Implemented Interfaces:

java.io.Serializable, GaggleData

Direct Known Subclasses:

LensedDataMatrix

public class DataMatrix
extends java.lang.Object
implements GaggleData

See Also:

Serialized Form

Field Summary

protected java.lang.String[]	columnTitles
protected double[][]	data
protected java.lang.String	dataTypeBriefName
protected java.lang.String	fileExtension
protected java.lang.String	fullName
protected Tuple	metadata
protected java.lang.String	name
protected java.lang.String[]	rowTitles
protected java.lang.String	rowTitlesTitle
protected java.lang.String	shortName
protected java.lang.String	species
protected java.lang.String	uri

Constructor Summary

DataMatrix()

DataMatrix(java.lang.String uri)

Method Summary

void	addRow(java.lang.String rowName, double[] values)
protected java.lang.String	calculateFileExtension()
protected java.lang.String	calculateShortName()
boolean	equals(DataMatrix other)
double[][]	get()
double[]	get(int row)
double	get(int row, int column)
double[]	get(java.lang.String rowName)
double[]	getColumn(int columnNumber)
double[]	getColumn(java.lang.String columnName)
int	getColumnCount()
int	getColumnNumber(java.lang.String columnName)
java.lang.String[]	getColumnTitles()
java.lang.String	getDataTypeBriefName() the 'data type brief name' is often the file extension of the uri from which the data has been read, eg, 'ratio' or 'lambda'.
java.lang.String	getFileExtension()
java.lang.String	getFullName()
Tuple	getMetadata() Every GaggleData object contains a Tuple which can contain optional metadata.
java.lang.String	getName() Returns the name of this GaggleData object
int	getRowCount()
int	getRowNumber(java.lang.String rowName)
java.lang.String[]	getRowTitles()
java.lang.String	getRowTitlesTitle()
java.lang.String	getShortName()
java.lang.String	getSpecies() Returns the species of this GaggleData object
static DataMatrix	readObject(java.lang.String uri)
void	set(double[][] d)
void	set(int row, double[] values)
void	set(int row, int column, double value)
void	setColumnTitles(java.lang.String[] newValues)
void	setDataTypeBriefName(java.lang.String newValue)
void	setDefault(double value)
void	setFullName(java.lang.String newValue)
void	setMetadata(Tuple metadata)
void	setName(java.lang.String name)
void	setRowTitles(java.lang.String[] newValues)
void	setRowTitlesTitle(java.lang.String newValue)
void	setShortName(java.lang.String newValue)
void	setSize(int rows, int columns)
void	setSpecies(java.lang.String newValue)
void	sortByRowName()
java.lang.String	toString()
void	writeObject(java.lang.String uri)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

name

protected java.lang.String name

metadata

protected Tuple metadata

rowTitlesTitle

protected java.lang.String rowTitlesTitle

columnTitles

protected java.lang.String[] columnTitles

rowTitles

protected java.lang.String[] rowTitles

data

protected double[][] data

uri

protected java.lang.String uri

fullName

protected java.lang.String fullName

shortName

protected java.lang.String shortName

fileExtension

protected java.lang.String fileExtension

dataTypeBriefName

protected java.lang.String dataTypeBriefName

species

protected java.lang.String species

Constructor Detail

DataMatrix

public DataMatrix()

DataMatrix

public DataMatrix(java.lang.String uri)

Method Detail

setShortName

public void setShortName(java.lang.String newValue)

getShortName

public java.lang.String getShortName()

setSpecies

public void setSpecies(java.lang.String newValue)

getSpecies

public java.lang.String getSpecies()

Description copied from interface: GaggleData

Returns the species of this GaggleData object

Specified by:

getSpecies in interface GaggleData

Returns:

the species of this GaggleData object

calculateShortName

protected java.lang.String calculateShortName()

calculateFileExtension

protected java.lang.String calculateFileExtension()

getFileExtension

public java.lang.String getFileExtension()

getDataTypeBriefName

public java.lang.String getDataTypeBriefName()

the 'data type brief name' is often the file extension of the uri from which the data has been read, eg, 'ratio' or 'lambda'. indeed, that file extension is the value of this variable by default. but it may be reset here.

Returns:

brief name of data type

setDataTypeBriefName

public void setDataTypeBriefName(java.lang.String newValue)

setFullName

public void setFullName(java.lang.String newValue)

getFullName

public java.lang.String getFullName()

setSize

public void setSize(int rows,
                    int columns)

setDefault

public void setDefault(double value)

set

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

set

public void set(int row,
                double[] values)

addRow

public void addRow(java.lang.String rowName,
                   double[] values)
            throws java.lang.IllegalArgumentException

Throws:

java.lang.IllegalArgumentException

setColumnTitles

public void setColumnTitles(java.lang.String[] newValues)

setRowTitles

public void setRowTitles(java.lang.String[] newValues)

setRowTitlesTitle

public void setRowTitlesTitle(java.lang.String newValue)

getRowCount

public int getRowCount()

getColumnCount

public int getColumnCount()

get

public double get(int row,
                  int column)

get

public double[] get(int row)

get

public double[] get(java.lang.String rowName)

getRowTitles

public java.lang.String[] getRowTitles()

set

public void set(double[][] d)

get

public double[][] get()

getColumnNumber

public int getColumnNumber(java.lang.String columnName)

getRowNumber

public int getRowNumber(java.lang.String rowName)

getColumn

public double[] getColumn(java.lang.String columnName)

getColumn

public double[] getColumn(int columnNumber)

getRowTitlesTitle

public java.lang.String getRowTitlesTitle()

getColumnTitles

public java.lang.String[] getColumnTitles()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

sortByRowName

public void sortByRowName()

equals

public boolean equals(DataMatrix other)

writeObject

public void writeObject(java.lang.String uri)
                 throws java.io.IOException

Throws:

java.io.IOException

readObject

public static DataMatrix readObject(java.lang.String uri)
                             throws java.io.IOException,
                                    java.lang.ClassNotFoundException

Throws:

java.io.IOException

java.lang.ClassNotFoundException

getName

public java.lang.String getName()

Description copied from interface: GaggleData

Returns the name of this GaggleData object

Specified by:

getName in interface GaggleData

Returns:

the name of this GaggleData object

setName

public void setName(java.lang.String name)

getMetadata

public Tuple getMetadata()

Description copied from interface: GaggleData

Every GaggleData object contains a Tuple which can contain optional metadata. The Tuple is a general-purpose object which can hold data in many ways; it is up to the sending and receiving goose to put together and parse out the metadata from the Tuple.

Specified by:

getMetadata in interface GaggleData

Returns:

a Tuple containing optional metadata

setMetadata

public void setMetadata(Tuple metadata)