cytoscape.giny
Class FingCyNetwork

java.lang.Object
  fing.model.FingExtensibleGraphPerspective
      cytoscape.giny.FingCyNetwork

All Implemented Interfaces:

CyNetwork, FixedGraph, GraphPerspective

public class FingCyNetwork
extends FingExtensibleGraphPerspective
implements CyNetwork, GraphPerspective

FinhCyNetwork provides an implementation of the CyNetwork interface, as well as the GraphPerspective inteface, and also provides the functionality formally provided by GraphObjAttributes. The Network will notify listeners when nodes/edges are added/removed and when relavant data changes.

Field Summary

protected Map	clientData The ClientData map
protected Set	listeners The Network Listeners Set
protected SelectFilter	selectFilter The default object to set the selected state of nodes and edges
protected String	title

Fields inherited from interface cytoscape.graph.fixed.FixedGraph

DIRECTED_EDGE, UNDIRECTED_EDGE

Constructor Summary

FingCyNetwork(FingExtensibleRootGraph root, IntIterator rootGraphNodeInx, IntIterator rootGraphEdgeInx)
rootGraphNodeInx need not contain all endpoint nodes corresponding to edges in rootGraphEdgeInx - this is calculated automatically by this constructor.

Method Summary

void	addCyNetworkListener(CyNetworkListener listener) Registers the argument as a listener to this object.
CyEdge	addEdge(Edge cytoscape_edge) Add a edge to this Network that already exists in Cytoscape
int	addEdge(int cytoscape_edge) Add a edge to this Network that already exists in Cytoscape
int	addEdge(String attribute, Object value) Adds a edge to this Network, by looking it up via the given attribute and value
void	addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener) DOCUMENT ME!
int	addNode(int cytoscape_node) Add a node to this Network that already exists in Cytoscape
CyNode	addNode(Node cytoscape_node) Add a node to this Network that already exists in Cytoscape
int	addNode(String attribute, Object value) Adds a node to this Network, by looking it up via the given attribute and value
void	addSelectEventListener(SelectEventListener listener) Adds a listener for SelectEvents to this CyNetwork
void	appendNetwork(CyNetwork network) Appends all of the nodes and edges in teh given Network to this Network
Object	clone() DOCUMENT ME!
boolean	containsEdge(Edge edge) DOCUMENT ME!
boolean	containsEdge(Edge edge, boolean recurse) DOCUMENT ME!
boolean	containsNode(Node node) DOCUMENT ME!
boolean	containsNode(Node node, boolean recurse) DOCUMENT ME!
int	createEdge(int source, int target, boolean directed) This method will create a new edge.
GraphPerspective	createGraphPerspective(Filter filter) DOCUMENT ME!
GraphPerspective	createGraphPerspective(int[] nodeInx) DOCUMENT ME!
GraphPerspective	createGraphPerspective(int[] rootGraphNodeInx, int[] rootGraphEdgeInx) DOCUMENT ME!
GraphPerspective	createGraphPerspective(Node[] nodes, Edge[] edges) DOCUMENT ME!
int	createNode() This method will create a new node.
void	deleteEdgeAttribute(String attribute) Deletes the attribute with the given name from edge attributes
void	deleteNodeAttribute(String attribute) Deletes the attribute with the given name from node attributes
boolean	edgeExists(int fromNodeInx, int toNodeInx) DOCUMENT ME!
boolean	edgeExists(Node from, Node to) DOCUMENT ME!
List	edgeMetaChildrenList(int parentNodeInx) DOCUMENT ME!
List	edgeMetaChildrenList(Node node) DOCUMENT ME!
List	edgeMetaParentsList(int edgeInx) DOCUMENT ME!
IntEnumerator	edges() DOCUMENT ME!
IntEnumerator	edgesAdjacent(int node, boolean outgoing, boolean incoming, boolean undirected) DOCUMENT ME!
IntIterator	edgesConnecting(int node0, int node1, boolean outgoing, boolean incoming, boolean undirected) DOCUMENT ME!
Iterator	edgesIterator() DOCUMENT ME!
List	edgesList() DOCUMENT ME!
List	edgesList(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges) DOCUMENT ME!
List	edgesList(Node from, Node to) DOCUMENT ME!
int	edgeSource(int edge) DOCUMENT ME!
int	edgeTarget(int edge) DOCUMENT ME!
byte	edgeType(int edge) DOCUMENT ME!
void	finalize() DOCUMENT ME!
protected void	fireEvent(int type) Fires an event to all listeners registered with this object.
int[]	getAdjacentEdgeIndicesArray(int nodeInx, boolean undirected, boolean incomingDirected, boolean outgoingDirected) DOCUMENT ME!
List	getAdjacentEdgesList(Node node, boolean undirected, boolean incoming, boolean outgoing) DOCUMENT ME!
Object	getClientData(String data_name) Deprecated. Get Some client data
Collection	getClientDataNames() Deprecated. Get a list of all currently available ClientData objects
int[]	getConnectingEdgeIndicesArray(int[] nodeInx) DOCUMENT ME!
List	getConnectingEdges(List nodes) DOCUMENT ME!
int[]	getConnectingNodeIndicesArray(int[] edgeInx) DOCUMENT ME!
Set	getCyNetworkListeners() Returns the set of listeners registered with this object.
int	getDegree(int nodeInx) DOCUMENT ME!
int	getDegree(Node node) DOCUMENT ME!
Edge	getEdge(int rootGraphEdgeInx) DOCUMENT ME!
String[]	getEdgeAttributesList() Return all availble Attributes for the Edges in this CyNetwork
Object	getEdgeAttributeValue(Edge edge, String attribute) Return the requested Attribute for the given Edge
Object	getEdgeAttributeValue(int edge, String attribute) Return the requested Attribute for the given Edge
int	getEdgeCount() DOCUMENT ME!
int	getEdgeCount(int fromNodeInx, int toNodeInx, boolean countUndirectedEdges) DOCUMENT ME!
int	getEdgeCount(Node from, Node to, boolean countUndirectedEdges) DOCUMENT ME!
int	getEdgeIndex(int rootGraphEdgeInx) DOCUMENT ME!
int[]	getEdgeIndicesArray() DOCUMENT ME!
int[]	getEdgeIndicesArray(int fromNodeInx, int toNodeInx, boolean includeUndirectedEdges) DOCUMENT ME!
int[]	getEdgeIndicesArray(int rootGraphFromNodeInx, int rootGraphToNodeInx, boolean undirectedEdges, boolean bothDirections) DOCUMENT ME!
int[]	getEdgeMetaChildIndicesArray(int parentNodeInx) DOCUMENT ME!
int[]	getEdgeMetaParentIndicesArray(int edgeInx) DOCUMENT ME!
int	getEdgeSourceIndex(int edgeInx) DOCUMENT ME!
int	getEdgeTargetIndex(int edgeInx) DOCUMENT ME!
String	getIdentifier() DOCUMENT ME!
int	getInDegree(int nodeInx) DOCUMENT ME!
int	getInDegree(int nodeInx, boolean countUndirectedEdges) DOCUMENT ME!
int	getInDegree(Node node) DOCUMENT ME!
int	getInDegree(Node node, boolean countUndirectedEdges) DOCUMENT ME!
int	getIndex(Edge edge) DOCUMENT ME!
int	getIndex(Node node) DOCUMENT ME!
Node	getNode(int rootGraphNodeInx) DOCUMENT ME!
String[]	getNodeAttributesList() Return all availble Attributes for the Nodes in this CyNetwork
String[]	getNodeAttributesList(Edge[] edges) Return all available Attributes for the given Edges
String[]	getNodeAttributesList(Node[] nodes) Return all available Attributes for the given Nodes
Object	getNodeAttributeValue(int node, String attribute) Return the requested Attribute for the given Node
Object	getNodeAttributeValue(Node node, String attribute) Return the requested Attribute for the given Node
int	getNodeCount() DOCUMENT ME!
int	getNodeIndex(int rootGraphNodeInx) DOCUMENT ME!
int[]	getNodeIndicesArray() DOCUMENT ME!
int[]	getNodeMetaChildIndicesArray(int parentInx) DOCUMENT ME!
int[]	getNodeMetaParentIndicesArray(int nodeInx) DOCUMENT ME!
int	getOutDegree(int nodeInx) DOCUMENT ME!
int	getOutDegree(int nodeInx, boolean countUndirectedEdges) DOCUMENT ME!
int	getOutDegree(Node node) DOCUMENT ME!
int	getOutDegree(Node node, boolean countUndirectedEdges) DOCUMENT ME!
RootGraph	getRootGraph() DOCUMENT ME!
int	getRootGraphEdgeIndex(int rootGraphEdgeInx) DOCUMENT ME!
int	getRootGraphNodeIndex(int rootGraphNodeInx) DOCUMENT ME!
Set	getSelectedEdges() Returns the set of selected edges in this CyNetwork
Set	getSelectedNodes() Returns the set of selected nodes in this CyNetwork
SelectFilter	getSelectFilter()
String	getTitle() Can Change
Edge	hideEdge(Edge edge) DOCUMENT ME!
int	hideEdge(int rootGraphEdgeInx) DOCUMENT ME!
int[]	hideEdges(int[] rootGraphEdgeInx) DOCUMENT ME!
List	hideEdges(List edges) DOCUMENT ME!
int	hideNode(int rootGraphNodeInx) DOCUMENT ME!
Node	hideNode(Node node) DOCUMENT ME!
int[]	hideNodes(int[] rootGraphNodeInx) DOCUMENT ME!
List	hideNodes(List nodes) DOCUMENT ME!
protected void	initialize()
boolean	isEdgeDirected(int edgeInx) DOCUMENT ME!
boolean	isEdgeMetaChild(int parentNodeInx, int childEdgeInx) DOCUMENT ME!
boolean	isEdgeMetaParent(int childEdgeInx, int parentNodeInx) DOCUMENT ME!
boolean	isMetaChild(Node parent, Edge child) DOCUMENT ME!
boolean	isMetaChild(Node parent, Node child) DOCUMENT ME!
boolean	isMetaParent(Edge child, Node parent) DOCUMENT ME!
boolean	isMetaParent(Node child, Node parent) DOCUMENT ME!
boolean	isNeighbor(int nodeInxA, int nodeInxB) DOCUMENT ME!
boolean	isNeighbor(Node a, Node b) DOCUMENT ME!
boolean	isNodeMetaChild(int parentNodeInx, int childNodeInx) DOCUMENT ME!
boolean	isNodeMetaParent(int childNodeInx, int parentNodeInx) DOCUMENT ME!
boolean	isSelected(Edge edge) Returns the selected state of the given edge.
boolean	isSelected(Node node) Returns the selected state of the given node.
GraphPerspective	join(GraphPerspective persp) DOCUMENT ME!
List	metaParentsList(Edge edge) DOCUMENT ME!
List	metaParentsList(Node node) DOCUMENT ME!
int[]	neighborsArray(int nodeIndex) DOCUMENT ME!
List	neighborsList(Node node) DOCUMENT ME!
boolean	nodeExists(int node) DOCUMENT ME!
List	nodeMetaChildrenList(int parentInx) DOCUMENT ME!
List	nodeMetaChildrenList(Node node) DOCUMENT ME!
List	nodeMetaParentsList(int nodeInx) DOCUMENT ME!
IntEnumerator	nodes() DOCUMENT ME!
Iterator	nodesIterator() DOCUMENT ME!
List	nodesList() DOCUMENT ME!
void	putClientData(String data_name, Object data) Deprecated. Networks can support client data.
boolean	removeCyNetworkListener(CyNetworkListener listener) Removes the argument from the set of listeners for this object.
boolean	removeEdge(int edge_index, boolean force) This will remove this edge from the Network.
void	removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener) DOCUMENT ME!
boolean	removeNode(int node_index, boolean force) This will remove this node from the Network.
void	removeSelectEventListener(SelectEventListener listener) Removes a listener for SelectEvents from this CyNetwork
Edge	restoreEdge(Edge edge) DOCUMENT ME!
int	restoreEdge(int rootGraphEdgeInx) DOCUMENT ME!
int[]	restoreEdges(int[] rootGraphEdgeInx) DOCUMENT ME!
List	restoreEdges(List edges) DOCUMENT ME!
int	restoreNode(int rootGraphNodeInx) DOCUMENT ME!
Node	restoreNode(Node node) DOCUMENT ME!
int[]	restoreNodes(int[] rootGraphNodeInx) DOCUMENT ME!
int[]	restoreNodes(int[] rootGraphNodeInx, boolean restoreIncidentEdges) DOCUMENT ME!
List	restoreNodes(List nodes) DOCUMENT ME!
List	restoreNodes(List nodes, boolean restoreIncidentEdges) DOCUMENT ME!
void	selectAllEdges() Sets the selected state of all edges in this CyNetwork to true
void	selectAllNodes() Sets the selected state of all nodes in this CyNetwork to true
boolean	setEdgeAttributeValue(Edge edge, String attribute, Object value) Return the requested Attribute for the given Edge
boolean	setEdgeAttributeValue(int edge, String attribute, Object value) Return the requested Attribute for the given Edge
String	setIdentifier(String new_id) DOCUMENT ME!
boolean	setNodeAttributeValue(int node, String attribute, Object value) Return the requested Attribute for the given Node
boolean	setNodeAttributeValue(Node node, String attribute, Object value) Return the requested Attribute for the given Node
void	setSelectedEdgeState(Collection edges, boolean selected_state) Sets the selected state of a collection of edges.
void	setSelectedEdgeState(Edge edge, boolean selected_state) Sets the selected state of an edge.
void	setSelectedNodeState(Collection nodes, boolean selected_state) Sets the selected state of a collection of nodes.
void	setSelectedNodeState(Node node, boolean selected_state) Sets the selected state of a node.
void	setTitle(String new_id) Can Change Throws a PropertyChangeEvent if the title has changed with a CyNetworkTitleChange object that contains the network id and the name.
void	unselectAllEdges() Sets the selected state of all edges in this CyNetwork to false
void	unselectAllNodes() Sets the selected state of all nodes in this CyNetwork to false

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface giny.model.GraphPerspective

addGraphPerspectiveChangeListener, clone, containsEdge, containsEdge, containsNode, containsNode, createGraphPerspective, createGraphPerspective, createGraphPerspective, createGraphPerspective, edgeExists, edgeExists, edgeMetaChildrenList, edgeMetaChildrenList, edgeMetaParentsList, edgesIterator, edgesList, edgesList, edgesList, getAdjacentEdgeIndicesArray, getAdjacentEdgesList, getConnectingEdgeIndicesArray, getConnectingEdges, getConnectingNodeIndicesArray, getDegree, getDegree, getEdge, getEdgeCount, getEdgeCount, getEdgeCount, getEdgeIndex, getEdgeIndicesArray, getEdgeIndicesArray, getEdgeIndicesArray, getEdgeMetaChildIndicesArray, getEdgeMetaParentIndicesArray, getEdgeSourceIndex, getEdgeTargetIndex, getInDegree, getInDegree, getInDegree, getInDegree, getIndex, getIndex, getNode, getNodeCount, getNodeIndex, getNodeIndicesArray, getNodeMetaChildIndicesArray, getNodeMetaParentIndicesArray, getOutDegree, getOutDegree, getOutDegree, getOutDegree, getRootGraph, getRootGraphEdgeIndex, getRootGraphNodeIndex, hideEdge, hideEdge, hideEdges, hideEdges, hideNode, hideNode, hideNodes, hideNodes, isEdgeDirected, isEdgeMetaChild, isEdgeMetaParent, isMetaChild, isMetaChild, isMetaParent, isMetaParent, isNeighbor, isNeighbor, isNodeMetaChild, isNodeMetaParent, join, metaParentsList, metaParentsList, neighborsArray, neighborsList, nodeMetaChildrenList, nodeMetaChildrenList, nodeMetaParentsList, nodesIterator, nodesList, removeGraphPerspectiveChangeListener, restoreEdge, restoreEdge, restoreEdges, restoreEdges, restoreNode, restoreNode, restoreNodes, restoreNodes, restoreNodes, restoreNodes

Field Detail

title

protected String title

listeners

protected Set listeners

The Network Listeners Set

clientData

protected Map clientData

The ClientData map

selectFilter

protected final SelectFilter selectFilter

The default object to set the selected state of nodes and edges

Constructor Detail

FingCyNetwork

public FingCyNetwork(FingExtensibleRootGraph root,
                     IntIterator rootGraphNodeInx,
                     IntIterator rootGraphEdgeInx)

rootGraphNodeInx need not contain all endpoint nodes corresponding to edges in rootGraphEdgeInx - this is calculated automatically by this constructor. If any index does not correspond to an existing node or edge, an IllegalArgumentException is thrown. The indices lists need not be non-repeating - the logic in this constructor handles duplicate filtering.

Method Detail

initialize

protected void initialize()

getTitle

public String getTitle()

Can Change

Specified by:

getTitle in interface CyNetwork

setTitle

public void setTitle(String new_id)

Can Change Throws a PropertyChangeEvent if the title has changed with a CyNetworkTitleChange object that contains the network id and the name.

Specified by:

setTitle in interface CyNetwork

getIdentifier

public String getIdentifier()

DOCUMENT ME!

Specified by:

getIdentifier in interface CyNetwork

Returns:

DOCUMENT ME!

setIdentifier

public String setIdentifier(String new_id)

DOCUMENT ME!

Specified by:

setIdentifier in interface CyNetwork

Parameters:

new_id - DOCUMENT ME!

Returns:

DOCUMENT ME!

putClientData

public void putClientData(String data_name,
                          Object data)

Deprecated. Networks can support client data.

Description copied from interface: CyNetwork

Networks can support client data.

Specified by:

putClientData in interface CyNetwork

Parameters:

data_name - the name of this client data

getClientDataNames

public Collection getClientDataNames()

Deprecated. Get a list of all currently available ClientData objects

Description copied from interface: CyNetwork

Get a list of all currently available ClientData objects

Specified by:

getClientDataNames in interface CyNetwork

getClientData

public Object getClientData(String data_name)

Deprecated. Get Some client data

Description copied from interface: CyNetwork

Get Some client data

Specified by:

getClientData in interface CyNetwork

Parameters:

data_name - the data to get

appendNetwork

public void appendNetwork(CyNetwork network)

Appends all of the nodes and edges in teh given Network to this Network

Specified by:

appendNetwork in interface CyNetwork

selectAllNodes

public void selectAllNodes()

Sets the selected state of all nodes in this CyNetwork to true

Specified by:

selectAllNodes in interface CyNetwork

selectAllEdges

public void selectAllEdges()

Sets the selected state of all edges in this CyNetwork to true

Specified by:

selectAllEdges in interface CyNetwork

unselectAllNodes

public void unselectAllNodes()

Sets the selected state of all nodes in this CyNetwork to false

Specified by:

unselectAllNodes in interface CyNetwork

unselectAllEdges

public void unselectAllEdges()

Sets the selected state of all edges in this CyNetwork to false

Specified by:

unselectAllEdges in interface CyNetwork

setSelectedNodeState

public void setSelectedNodeState(Collection nodes,
                                 boolean selected_state)

Sets the selected state of a collection of nodes.

Specified by:

setSelectedNodeState in interface CyNetwork

Parameters:

nodes - a Collection of Nodes

selected_state - the desired selection state for the nodes

setSelectedNodeState

public void setSelectedNodeState(Node node,
                                 boolean selected_state)

Sets the selected state of a node.

Specified by:

setSelectedNodeState in interface CyNetwork

Parameters:

nodes - a Node

selected_state - the desired selection state for the node

setSelectedEdgeState

public void setSelectedEdgeState(Collection edges,
                                 boolean selected_state)

Sets the selected state of a collection of edges.

Specified by:

setSelectedEdgeState in interface CyNetwork

Parameters:

edges - a Collection of Edges

selected_state - the desired selection state for the edges

setSelectedEdgeState

public void setSelectedEdgeState(Edge edge,
                                 boolean selected_state)

Sets the selected state of an edge.

Specified by:

setSelectedEdgeState in interface CyNetwork

Parameters:

edges - an Edge

selected_state - the desired selection state for the edge

isSelected

public boolean isSelected(Node node)

Returns the selected state of the given node.

Specified by:

isSelected in interface CyNetwork

Parameters:

node - the node

Returns:

true if selected, false otherwise

isSelected

public boolean isSelected(Edge edge)

Returns the selected state of the given edge.

Specified by:

isSelected in interface CyNetwork

Parameters:

edge - the edge

Returns:

true if selected, false otherwise

getSelectedNodes

public Set getSelectedNodes()

Returns the set of selected nodes in this CyNetwork

Specified by:

getSelectedNodes in interface CyNetwork

Returns:

a Set of selected nodes

getSelectedEdges

public Set getSelectedEdges()

Returns the set of selected edges in this CyNetwork

Specified by:

getSelectedEdges in interface CyNetwork

Returns:

a Set of selected edges

addSelectEventListener

public void addSelectEventListener(SelectEventListener listener)

Adds a listener for SelectEvents to this CyNetwork

Specified by:

addSelectEventListener in interface CyNetwork

Parameters:

listener -

removeSelectEventListener

public void removeSelectEventListener(SelectEventListener listener)

Removes a listener for SelectEvents from this CyNetwork

Specified by:

removeSelectEventListener in interface CyNetwork

Parameters:

listener -

getSelectFilter

public SelectFilter getSelectFilter()

Specified by:

getSelectFilter in interface CyNetwork

Returns:

SelectFilter

getNodeAttributeValue

public Object getNodeAttributeValue(Node node,
                                    String attribute)

Return the requested Attribute for the given Node

Parameters:

node - the given CyNode

attribute - the name of the requested attribute

Returns:

the value for the give node, for the given attribute

getNodeAttributeValue

public Object getNodeAttributeValue(int node,
                                    String attribute)

Return the requested Attribute for the given Node

getEdgeAttributeValue

public Object getEdgeAttributeValue(Edge edge,
                                    String attribute)

Return the requested Attribute for the given Edge

getEdgeAttributeValue

public Object getEdgeAttributeValue(int edge,
                                    String attribute)

Return the requested Attribute for the given Edge

getNodeAttributesList

public String[] getNodeAttributesList()

Return all availble Attributes for the Nodes in this CyNetwork

getNodeAttributesList

public String[] getNodeAttributesList(Node[] nodes)

Return all available Attributes for the given Nodes

getEdgeAttributesList

public String[] getEdgeAttributesList()

Return all availble Attributes for the Edges in this CyNetwork

getNodeAttributesList

public String[] getNodeAttributesList(Edge[] edges)

Return all available Attributes for the given Edges

setNodeAttributeValue

public boolean setNodeAttributeValue(Node node,
                                     String attribute,
                                     Object value)

Return the requested Attribute for the given Node

Parameters:

node - the given CyNode

attribute - the name of the requested attribute

value - the value to be set

Returns:

if it overwrites a previous value

setNodeAttributeValue

public boolean setNodeAttributeValue(int node,
                                     String attribute,
                                     Object value)

Return the requested Attribute for the given Node

setEdgeAttributeValue

public boolean setEdgeAttributeValue(Edge edge,
                                     String attribute,
                                     Object value)

Return the requested Attribute for the given Edge

setEdgeAttributeValue

public boolean setEdgeAttributeValue(int edge,
                                     String attribute,
                                     Object value)

Return the requested Attribute for the given Edge

deleteNodeAttribute

public void deleteNodeAttribute(String attribute)

Deletes the attribute with the given name from node attributes

deleteEdgeAttribute

public void deleteEdgeAttribute(String attribute)

Deletes the attribute with the given name from edge attributes

addCyNetworkListener

public void addCyNetworkListener(CyNetworkListener listener)

Registers the argument as a listener to this object. Does nothing if the argument is already a listener.

Specified by:

addCyNetworkListener in interface CyNetwork

removeCyNetworkListener

public boolean removeCyNetworkListener(CyNetworkListener listener)

Removes the argument from the set of listeners for this object. Returns true if the argument was a listener before this call, false otherwise.

Specified by:

removeCyNetworkListener in interface CyNetwork

getCyNetworkListeners

public Set getCyNetworkListeners()

Returns the set of listeners registered with this object.

Specified by:

getCyNetworkListeners in interface CyNetwork

fireEvent

protected void fireEvent(int type)

Fires an event to all listeners registered with this object. The argument should be a constant from the CyNetworkEvent class identifying the type of the event.

createNode

public int createNode()

This method will create a new node.

Returns:

the Cytoscape index of the created node

addNode

public int addNode(int cytoscape_node)

Add a node to this Network that already exists in Cytoscape

Specified by:

addNode in interface CyNetwork

Returns:

the Network Index of this node

addNode

public CyNode addNode(Node cytoscape_node)

Add a node to this Network that already exists in Cytoscape

Specified by:

addNode in interface CyNetwork

Returns:

the Network Index of this node

addNode

public int addNode(String attribute,
                   Object value)

Adds a node to this Network, by looking it up via the given attribute and value

Returns:

the Network Index of this node

removeNode

public boolean removeNode(int node_index,
                          boolean force)

This will remove this node from the Network. However, unless forced, it will remain in Cytoscape to be possibly resused by another Network in the future.

Specified by:

removeNode in interface CyNetwork

Parameters:

force - force this node to be removed from all Networks

Returns:

true if the node is still present in Cytoscape ( i.e. in another Network )

createEdge

public int createEdge(int source,
                      int target,
                      boolean directed)

This method will create a new edge.

Parameters:

source - the source node

target - the target node

directed - weather the edge should be directed

Returns:

the Cytoscape index of the created edge

addEdge

public int addEdge(int cytoscape_edge)

Add a edge to this Network that already exists in Cytoscape

Specified by:

addEdge in interface CyNetwork

Returns:

the Network Index of this edge

addEdge

public CyEdge addEdge(Edge cytoscape_edge)

Add a edge to this Network that already exists in Cytoscape

Specified by:

addEdge in interface CyNetwork

Returns:

the Network Index of this edge

addEdge

public int addEdge(String attribute,
                   Object value)

Adds a edge to this Network, by looking it up via the given attribute and value

Returns:

the Network Index of this edge

removeEdge

public boolean removeEdge(int edge_index,
                          boolean force)

This will remove this edge from the Network. However, unless forced, it will remain in Cytoscape to be possibly resused by another Network in the future.

Specified by:

removeEdge in interface CyNetwork

Parameters:

force - force this edge to be removed from all Networks

Returns:

true if the edge is still present in Cytoscape ( i.e. in another Network )

nodes

public IntEnumerator nodes()

DOCUMENT ME!

Specified by:

nodes in interface FixedGraph

Returns:

DOCUMENT ME!

edges

public IntEnumerator edges()

DOCUMENT ME!

Specified by:

edges in interface FixedGraph

Returns:

DOCUMENT ME!

nodeExists

public boolean nodeExists(int node)

DOCUMENT ME!

Specified by:

nodeExists in interface FixedGraph

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeType

public byte edgeType(int edge)

DOCUMENT ME!

Specified by:

edgeType in interface FixedGraph

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeSource

public int edgeSource(int edge)

DOCUMENT ME!

Specified by:

edgeSource in interface FixedGraph

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeTarget

public int edgeTarget(int edge)

DOCUMENT ME!

Specified by:

edgeTarget in interface FixedGraph

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgesAdjacent

public IntEnumerator edgesAdjacent(int node,
                                   boolean outgoing,
                                   boolean incoming,
                                   boolean undirected)

DOCUMENT ME!

Specified by:

edgesAdjacent in interface FixedGraph

Parameters:

node - DOCUMENT ME!

outgoing - DOCUMENT ME!

incoming - DOCUMENT ME!

undirected - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgesConnecting

public IntIterator edgesConnecting(int node0,
                                   int node1,
                                   boolean outgoing,
                                   boolean incoming,
                                   boolean undirected)

DOCUMENT ME!

Specified by:

edgesConnecting in interface FixedGraph

Parameters:

node0 - DOCUMENT ME!

node1 - DOCUMENT ME!

outgoing - DOCUMENT ME!

incoming - DOCUMENT ME!

undirected - DOCUMENT ME!

Returns:

DOCUMENT ME!

addGraphPerspectiveChangeListener

public void addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)

DOCUMENT ME!

Specified by:

addGraphPerspectiveChangeListener in interface GraphPerspective

Parameters:

listener - DOCUMENT ME!

removeGraphPerspectiveChangeListener

public void removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)

DOCUMENT ME!

Specified by:

removeGraphPerspectiveChangeListener in interface GraphPerspective

Parameters:

listener - DOCUMENT ME!

clone

public Object clone()

DOCUMENT ME!

Specified by:

clone in interface GraphPerspective

Overrides:

clone in class Object

Returns:

DOCUMENT ME!

getRootGraph

public RootGraph getRootGraph()

DOCUMENT ME!

Specified by:

getRootGraph in interface GraphPerspective

Returns:

DOCUMENT ME!

getNodeCount

public int getNodeCount()

DOCUMENT ME!

Specified by:

getNodeCount in interface GraphPerspective

Returns:

DOCUMENT ME!

getEdgeCount

public int getEdgeCount()

DOCUMENT ME!

Specified by:

getEdgeCount in interface GraphPerspective

Returns:

DOCUMENT ME!

nodesIterator

public Iterator nodesIterator()

DOCUMENT ME!

Specified by:

nodesIterator in interface GraphPerspective

Returns:

DOCUMENT ME!

nodesList

public List nodesList()

DOCUMENT ME!

Specified by:

nodesList in interface GraphPerspective

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.nodesIterator()

getNodeIndicesArray

public int[] getNodeIndicesArray()

DOCUMENT ME!

Specified by:

getNodeIndicesArray in interface GraphPerspective

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.nodesIterator(), GraphObject.getRootGraphIndex()

edgesIterator

public Iterator edgesIterator()

DOCUMENT ME!

Specified by:

edgesIterator in interface GraphPerspective

Returns:

DOCUMENT ME!

edgesList

public List edgesList()

DOCUMENT ME!

Specified by:

edgesList in interface GraphPerspective

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.edgesIterator()

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

DOCUMENT ME!

Specified by:

getEdgeIndicesArray in interface GraphPerspective

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.edgesIterator(), GraphObject.getRootGraphIndex()

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int rootGraphFromNodeInx,
                                 int rootGraphToNodeInx,
                                 boolean undirectedEdges,
                                 boolean bothDirections)

DOCUMENT ME!

Specified by:

getEdgeIndicesArray in interface GraphPerspective

Parameters:

rootGraphFromNodeInx - DOCUMENT ME!

rootGraphToNodeInx - DOCUMENT ME!

undirectedEdges - DOCUMENT ME!

bothDirections - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

hideNode

public Node hideNode(Node node)

DOCUMENT ME!

Specified by:

hideNode in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

hideNode

public int hideNode(int rootGraphNodeInx)

DOCUMENT ME!

Specified by:

hideNode in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

hideNodes

public List hideNodes(List nodes)

DOCUMENT ME!

Specified by:

hideNodes in interface GraphPerspective

Parameters:

nodes - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.hideNode(Node), GraphPerspective.hideNodes(int[])

hideNodes

public int[] hideNodes(int[] rootGraphNodeInx)

DOCUMENT ME!

Specified by:

hideNodes in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

restoreNode

public Node restoreNode(Node node)

DOCUMENT ME!

Specified by:

restoreNode in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

restoreNode

public int restoreNode(int rootGraphNodeInx)

DOCUMENT ME!

Specified by:

restoreNode in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

restoreNodes

public List restoreNodes(List nodes)

DOCUMENT ME!

Specified by:

restoreNodes in interface GraphPerspective

Parameters:

nodes - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.restoreNode(Node), GraphPerspective.restoreNodes(int[])

restoreNodes

public List restoreNodes(List nodes,
                         boolean restoreIncidentEdges)

DOCUMENT ME!

Specified by:

restoreNodes in interface GraphPerspective

Parameters:

nodes - DOCUMENT ME!

restoreIncidentEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.restoreNodes(int[]), GraphPerspective.restoreEdges(int[]), RootGraph.getConnectingEdgeIndicesArray(int[])

restoreNodes

public int[] restoreNodes(int[] rootGraphNodeInx,
                          boolean restoreIncidentEdges)

DOCUMENT ME!

Specified by:

restoreNodes in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

restoreIncidentEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.restoreNodes(int[]), GraphPerspective.restoreEdges(int[]), RootGraph.getConnectingEdgeIndicesArray(int[])

restoreNodes

public int[] restoreNodes(int[] rootGraphNodeInx)

DOCUMENT ME!

Specified by:

restoreNodes in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

hideEdge

public Edge hideEdge(Edge edge)

DOCUMENT ME!

Specified by:

hideEdge in interface GraphPerspective

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

hideEdge

public int hideEdge(int rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

hideEdge in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

hideEdges

public List hideEdges(List edges)

DOCUMENT ME!

Specified by:

hideEdges in interface GraphPerspective

Parameters:

edges - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.hideEdge(Edge), GraphPerspective.hideEdges(int[])

hideEdges

public int[] hideEdges(int[] rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

hideEdges in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

restoreEdge

public Edge restoreEdge(Edge edge)

DOCUMENT ME!

Specified by:

restoreEdge in interface GraphPerspective

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

restoreEdge

public int restoreEdge(int rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

restoreEdge in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

restoreEdges

public List restoreEdges(List edges)

DOCUMENT ME!

Specified by:

restoreEdges in interface GraphPerspective

Parameters:

edges - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.restoreEdges(int[])

restoreEdges

public int[] restoreEdges(int[] rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

restoreEdges in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

containsNode

public boolean containsNode(Node node)

DOCUMENT ME!

Specified by:

containsNode in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.containsNode(Node, boolean)

containsNode

public boolean containsNode(Node node,
                            boolean recurse)

DOCUMENT ME!

Specified by:

containsNode in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

recurse - DOCUMENT ME!

Returns:

DOCUMENT ME!

containsEdge

public boolean containsEdge(Edge edge)

DOCUMENT ME!

Specified by:

containsEdge in interface GraphPerspective

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

containsEdge

public boolean containsEdge(Edge edge,
                            boolean recurse)

DOCUMENT ME!

Specified by:

containsEdge in interface GraphPerspective

Parameters:

edge - DOCUMENT ME!

recurse - DOCUMENT ME!

Returns:

DOCUMENT ME!

join

public GraphPerspective join(GraphPerspective persp)

DOCUMENT ME!

Specified by:

join in interface GraphPerspective

Parameters:

persp - DOCUMENT ME!

Returns:

DOCUMENT ME!

createGraphPerspective

public GraphPerspective createGraphPerspective(Node[] nodes,
                                               Edge[] edges)

DOCUMENT ME!

Specified by:

createGraphPerspective in interface GraphPerspective

Parameters:

nodes - DOCUMENT ME!

edges - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

RootGraph.createGraphPerspective(int[], int[])

createGraphPerspective

public GraphPerspective createGraphPerspective(int[] rootGraphNodeInx,
                                               int[] rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

createGraphPerspective in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

RootGraph.createGraphPerspective(int[], int[])

createGraphPerspective

public GraphPerspective createGraphPerspective(Filter filter)

DOCUMENT ME!

Specified by:

createGraphPerspective in interface GraphPerspective

Parameters:

filter - DOCUMENT ME!

Returns:

DOCUMENT ME!

neighborsList

public List neighborsList(Node node)

DOCUMENT ME!

Specified by:

neighborsList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

neighborsArray

public int[] neighborsArray(int nodeIndex)

DOCUMENT ME!

Specified by:

neighborsArray in interface GraphPerspective

Parameters:

nodeIndex - DOCUMENT ME!

Returns:

DOCUMENT ME!

isNeighbor

public boolean isNeighbor(Node a,
                          Node b)

DOCUMENT ME!

Specified by:

isNeighbor in interface GraphPerspective

Parameters:

a - DOCUMENT ME!

b - DOCUMENT ME!

Returns:

DOCUMENT ME!

isNeighbor

public boolean isNeighbor(int nodeInxA,
                          int nodeInxB)

DOCUMENT ME!

Specified by:

isNeighbor in interface GraphPerspective

Parameters:

nodeInxA - DOCUMENT ME!

nodeInxB - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeExists

public boolean edgeExists(Node from,
                          Node to)

DOCUMENT ME!

Specified by:

edgeExists in interface GraphPerspective

Parameters:

from - DOCUMENT ME!

to - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeExists

public boolean edgeExists(int fromNodeInx,
                          int toNodeInx)

DOCUMENT ME!

Specified by:

edgeExists in interface GraphPerspective

Parameters:

fromNodeInx - DOCUMENT ME!

toNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeCount

public int getEdgeCount(Node from,
                        Node to,
                        boolean countUndirectedEdges)

DOCUMENT ME!

Specified by:

getEdgeCount in interface GraphPerspective

Parameters:

from - DOCUMENT ME!

to - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeCount

public int getEdgeCount(int fromNodeInx,
                        int toNodeInx,
                        boolean countUndirectedEdges)

DOCUMENT ME!

Specified by:

getEdgeCount in interface GraphPerspective

Parameters:

fromNodeInx - DOCUMENT ME!

toNodeInx - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgesList

public List edgesList(Node from,
                      Node to)

DOCUMENT ME!

Specified by:

edgesList in interface GraphPerspective

Parameters:

from - DOCUMENT ME!

to - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgesList

public List edgesList(int fromNodeInx,
                      int toNodeInx,
                      boolean includeUndirectedEdges)

DOCUMENT ME!

Specified by:

edgesList in interface GraphPerspective

Parameters:

fromNodeInx - DOCUMENT ME!

toNodeInx - DOCUMENT ME!

includeUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int fromNodeInx,
                                 int toNodeInx,
                                 boolean includeUndirectedEdges)

DOCUMENT ME!

Specified by:

getEdgeIndicesArray in interface GraphPerspective

Parameters:

fromNodeInx - DOCUMENT ME!

toNodeInx - DOCUMENT ME!

includeUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getInDegree

public int getInDegree(Node node)

DOCUMENT ME!

Specified by:

getInDegree in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

getInDegree

public int getInDegree(int nodeInx)

DOCUMENT ME!

Specified by:

getInDegree in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getInDegree

public int getInDegree(Node node,
                       boolean countUndirectedEdges)

DOCUMENT ME!

Specified by:

getInDegree in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

getInDegree

public int getInDegree(int nodeInx,
                       boolean countUndirectedEdges)

DOCUMENT ME!

Specified by:

getInDegree in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

getOutDegree

public int getOutDegree(Node node)

DOCUMENT ME!

Specified by:

getOutDegree in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

getOutDegree

public int getOutDegree(int nodeInx)

DOCUMENT ME!

Specified by:

getOutDegree in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getOutDegree

public int getOutDegree(Node node,
                        boolean countUndirectedEdges)

DOCUMENT ME!

Specified by:

getOutDegree in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

getOutDegree

public int getOutDegree(int nodeInx,
                        boolean countUndirectedEdges)

DOCUMENT ME!

Specified by:

getOutDegree in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

countUndirectedEdges - DOCUMENT ME!

Returns:

DOCUMENT ME!

getDegree

public int getDegree(Node node)

DOCUMENT ME!

Specified by:

getDegree in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

getDegree

public int getDegree(int nodeInx)

DOCUMENT ME!

Specified by:

getDegree in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getIndex

public int getIndex(Node node)

DOCUMENT ME!

Specified by:

getIndex in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeIndex

public int getNodeIndex(int rootGraphNodeInx)

DOCUMENT ME!

Specified by:

getNodeIndex in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.getRootGraphNodeIndex(int)

getRootGraphNodeIndex

public int getRootGraphNodeIndex(int rootGraphNodeInx)

DOCUMENT ME!

Specified by:

getRootGraphNodeIndex in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNode

public Node getNode(int rootGraphNodeInx)

DOCUMENT ME!

Specified by:

getNode in interface GraphPerspective

Parameters:

rootGraphNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getIndex

public int getIndex(Edge edge)

DOCUMENT ME!

Specified by:

getIndex in interface GraphPerspective

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeIndex

public int getEdgeIndex(int rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

getEdgeIndex in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.getRootGraphEdgeIndex(int)

getRootGraphEdgeIndex

public int getRootGraphEdgeIndex(int rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

getRootGraphEdgeIndex in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdge

public Edge getEdge(int rootGraphEdgeInx)

DOCUMENT ME!

Specified by:

getEdge in interface GraphPerspective

Parameters:

rootGraphEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeSourceIndex

public int getEdgeSourceIndex(int edgeInx)

DOCUMENT ME!

Specified by:

getEdgeSourceIndex in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeTargetIndex

public int getEdgeTargetIndex(int edgeInx)

DOCUMENT ME!

Specified by:

getEdgeTargetIndex in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

isEdgeDirected

public boolean isEdgeDirected(int edgeInx)

DOCUMENT ME!

Specified by:

isEdgeDirected in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

isMetaParent

public boolean isMetaParent(Node child,
                            Node parent)

DOCUMENT ME!

Specified by:

isMetaParent in interface GraphPerspective

Parameters:

child - DOCUMENT ME!

parent - DOCUMENT ME!

Returns:

DOCUMENT ME!

isNodeMetaParent

public boolean isNodeMetaParent(int childNodeInx,
                                int parentNodeInx)

DOCUMENT ME!

Specified by:

isNodeMetaParent in interface GraphPerspective

Parameters:

childNodeInx - DOCUMENT ME!

parentNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

metaParentsList

public List metaParentsList(Node node)

DOCUMENT ME!

Specified by:

metaParentsList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

nodeMetaParentsList

public List nodeMetaParentsList(int nodeInx)

DOCUMENT ME!

Specified by:

nodeMetaParentsList in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeMetaParentIndicesArray

public int[] getNodeMetaParentIndicesArray(int nodeInx)

DOCUMENT ME!

Specified by:

getNodeMetaParentIndicesArray in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

isMetaChild

public boolean isMetaChild(Node parent,
                           Node child)

DOCUMENT ME!

Specified by:

isMetaChild in interface GraphPerspective

Parameters:

parent - DOCUMENT ME!

child - DOCUMENT ME!

Returns:

DOCUMENT ME!

isNodeMetaChild

public boolean isNodeMetaChild(int parentNodeInx,
                               int childNodeInx)

DOCUMENT ME!

Specified by:

isNodeMetaChild in interface GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

childNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

nodeMetaChildrenList

public List nodeMetaChildrenList(Node node)

DOCUMENT ME!

Specified by:

nodeMetaChildrenList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

nodeMetaChildrenList

public List nodeMetaChildrenList(int parentInx)

DOCUMENT ME!

Specified by:

nodeMetaChildrenList in interface GraphPerspective

Parameters:

parentInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int parentInx)

DOCUMENT ME!

Specified by:

getNodeMetaChildIndicesArray in interface GraphPerspective

Parameters:

parentInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

isMetaParent

public boolean isMetaParent(Edge child,
                            Node parent)

DOCUMENT ME!

Specified by:

isMetaParent in interface GraphPerspective

Parameters:

child - DOCUMENT ME!

parent - DOCUMENT ME!

Returns:

DOCUMENT ME!

isEdgeMetaParent

public boolean isEdgeMetaParent(int childEdgeInx,
                                int parentNodeInx)

DOCUMENT ME!

Specified by:

isEdgeMetaParent in interface GraphPerspective

Parameters:

childEdgeInx - DOCUMENT ME!

parentNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

metaParentsList

public List metaParentsList(Edge edge)

DOCUMENT ME!

Specified by:

metaParentsList in interface GraphPerspective

Parameters:

edge - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeMetaParentsList

public List edgeMetaParentsList(int edgeInx)

DOCUMENT ME!

Specified by:

edgeMetaParentsList in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeMetaParentIndicesArray

public int[] getEdgeMetaParentIndicesArray(int edgeInx)

DOCUMENT ME!

Specified by:

getEdgeMetaParentIndicesArray in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

isMetaChild

public boolean isMetaChild(Node parent,
                           Edge child)

DOCUMENT ME!

Specified by:

isMetaChild in interface GraphPerspective

Parameters:

parent - DOCUMENT ME!

child - DOCUMENT ME!

Returns:

DOCUMENT ME!

isEdgeMetaChild

public boolean isEdgeMetaChild(int parentNodeInx,
                               int childEdgeInx)

DOCUMENT ME!

Specified by:

isEdgeMetaChild in interface GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

childEdgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeMetaChildrenList

public List edgeMetaChildrenList(Node node)

DOCUMENT ME!

Specified by:

edgeMetaChildrenList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

Returns:

DOCUMENT ME!

edgeMetaChildrenList

public List edgeMetaChildrenList(int parentNodeInx)

DOCUMENT ME!

Specified by:

edgeMetaChildrenList in interface GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getEdgeMetaChildIndicesArray

public int[] getEdgeMetaChildIndicesArray(int parentNodeInx)

DOCUMENT ME!

Specified by:

getEdgeMetaChildIndicesArray in interface GraphPerspective

Parameters:

parentNodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAdjacentEdgesList

public List getAdjacentEdgesList(Node node,
                                 boolean undirected,
                                 boolean incoming,
                                 boolean outgoing)

DOCUMENT ME!

Specified by:

getAdjacentEdgesList in interface GraphPerspective

Parameters:

node - DOCUMENT ME!

undirected - DOCUMENT ME!

incoming - DOCUMENT ME!

outgoing - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)

getAdjacentEdgeIndicesArray

public int[] getAdjacentEdgeIndicesArray(int nodeInx,
                                         boolean undirected,
                                         boolean incomingDirected,
                                         boolean outgoingDirected)

DOCUMENT ME!

Specified by:

getAdjacentEdgeIndicesArray in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

undirected - DOCUMENT ME!

incomingDirected - DOCUMENT ME!

outgoingDirected - DOCUMENT ME!

Returns:

DOCUMENT ME!

getConnectingEdges

public List getConnectingEdges(List nodes)

DOCUMENT ME!

Specified by:

getConnectingEdges in interface GraphPerspective

Parameters:

nodes - DOCUMENT ME!

Returns:

DOCUMENT ME!

getConnectingEdgeIndicesArray

public int[] getConnectingEdgeIndicesArray(int[] nodeInx)

DOCUMENT ME!

Specified by:

getConnectingEdgeIndicesArray in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

getConnectingNodeIndicesArray

public int[] getConnectingNodeIndicesArray(int[] edgeInx)

DOCUMENT ME!

Specified by:

getConnectingNodeIndicesArray in interface GraphPerspective

Parameters:

edgeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

See Also:

GraphPerspective.getEdgeSourceIndex(int), GraphPerspective.getEdgeTargetIndex(int)

createGraphPerspective

public GraphPerspective createGraphPerspective(int[] nodeInx)

DOCUMENT ME!

Specified by:

createGraphPerspective in interface GraphPerspective

Parameters:

nodeInx - DOCUMENT ME!

Returns:

DOCUMENT ME!

finalize

public void finalize()

DOCUMENT ME!

Overrides:

finalize in class Object