org.systemsbiology.gaggle.core.datatypes
Class Network

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

All Implemented Interfaces:

java.io.Serializable, GaggleData

public class Network
extends java.lang.Object
implements GaggleData

See Also:

Serialized Form

Constructor Summary

Network()

Method Summary

void	add(Interaction interaction)
void	add(Interaction[] interactions)
void	add(java.lang.String nodeName)
void	addEdgeAttribute(java.lang.String edgeName, java.lang.String attributeName, java.lang.Object value)
void	addNodeAttribute(java.lang.String nodeName, java.lang.String attributeName, java.lang.Object value)
int	edgeCount()
java.util.HashSet<java.lang.String>	getConnectedNodes()
java.lang.String[]	getEdgeAttributeNames()
java.util.HashMap	getEdgeAttributes(java.lang.String attributeName)
Interaction[]	getInteractions()
Tuple	getMetadata() Every GaggleData object contains a Tuple which can contain optional metadata.
java.lang.String	getName() Returns the name of this GaggleData object
java.lang.String[]	getNodeAttributeNames()
java.util.HashMap	getNodeAttributes(java.lang.String attributeName)
java.lang.String[]	getNodes()
int	getOrphanNodeCount()
java.lang.String[]	getOrphanNodes()
java.lang.String	getSpecies() Returns the species of this GaggleData object
int	nodeCount()
void	setMetadata(Tuple metadata)
void	setName(java.lang.String name)
void	setSpecies(java.lang.String newValue)
java.lang.String	toString()
protected void	validateObjectType(java.lang.Object value)

Methods inherited from class java.lang.Object

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

Constructor Detail

Network

public Network()

Method Detail

add

public void add(Interaction interaction)

add

public void add(java.lang.String nodeName)

add

public void add(Interaction[] interactions)

getInteractions

public Interaction[] getInteractions()

nodeCount

public int nodeCount()

getNodes

public java.lang.String[] getNodes()

getConnectedNodes

public java.util.HashSet<java.lang.String> getConnectedNodes()

getOrphanNodes

public java.lang.String[] getOrphanNodes()

getOrphanNodeCount

public int getOrphanNodeCount()

edgeCount

public int edgeCount()

validateObjectType

protected void validateObjectType(java.lang.Object value)

addEdgeAttribute

public void addEdgeAttribute(java.lang.String edgeName,
                             java.lang.String attributeName,
                             java.lang.Object value)

addNodeAttribute

public void addNodeAttribute(java.lang.String nodeName,
                             java.lang.String attributeName,
                             java.lang.Object value)

getNodeAttributeNames

public java.lang.String[] getNodeAttributeNames()

getEdgeAttributeNames

public java.lang.String[] getEdgeAttributeNames()

getEdgeAttributes

public java.util.HashMap getEdgeAttributes(java.lang.String attributeName)

getNodeAttributes

public java.util.HashMap getNodeAttributes(java.lang.String attributeName)

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

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)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object