cytoscape.giny
Class FingCyNetwork

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

All Implemented Interfaces:

CyNetwork, cytoscape.graph.fixed.FixedGraph, GraphPerspective

public class FingCyNetwork
extends fing.model.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

Fields inherited from interface cytoscape.graph.fixed.FixedGraph

DIRECTED_EDGE, UNDIRECTED_EDGE

Constructor Summary

FingCyNetwork(fing.model.FingExtensibleRootGraph root, cytoscape.util.intr.IntIterator rootGraphNodeInx, cytoscape.util.intr.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 arg0)
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()
boolean	containsEdge(Edge arg0)
boolean	containsEdge(Edge arg0, boolean arg1)
boolean	containsNode(Node arg0)
boolean	containsNode(Node arg0, boolean arg1)
int	createEdge(int source, int target, boolean directed) This method will create a new edge.
GraphPerspective	createGraphPerspective(Filter arg0)
GraphPerspective	createGraphPerspective(int[] arg0)
GraphPerspective	createGraphPerspective(int[] arg0, int[] arg1)
GraphPerspective	createGraphPerspective(Node[] arg0, Edge[] arg1)
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 arg0, int arg1)
boolean	edgeExists(Node arg0, Node arg1)
List	edgeMetaChildrenList(int arg0)
List	edgeMetaChildrenList(Node arg0)
List	edgeMetaParentsList(int arg0)
cytoscape.util.intr.IntEnumerator	edges()
cytoscape.util.intr.IntEnumerator	edgesAdjacent(int arg0, boolean arg1, boolean arg2, boolean arg3)
cytoscape.util.intr.IntIterator	edgesConnecting(int arg0, int arg1, boolean arg2, boolean arg3, boolean arg4)
Iterator	edgesIterator()
List	edgesList()
List	edgesList(int arg0, int arg1, boolean arg2)
List	edgesList(Node arg0, Node arg1)
int	edgeSource(int arg0)
int	edgeTarget(int arg0)
byte	edgeType(int arg0)
void	finalize()
int[]	getAdjacentEdgeIndicesArray(int arg0, boolean arg1, boolean arg2, boolean arg3)
List	getAdjacentEdgesList(Node arg0, boolean arg1, boolean arg2, boolean arg3)
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[] arg0)
List	getConnectingEdges(List arg0)
int[]	getConnectingNodeIndicesArray(int[] arg0)
Set	getCyNetworkListeners() Returns the set of listeners registered with this object.
int	getDegree(int arg0)
int	getDegree(Node arg0)
Edge	getEdge(int arg0)
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()
int	getEdgeCount(int arg0, int arg1, boolean arg2)
int	getEdgeCount(Node arg0, Node arg1, boolean arg2)
int	getEdgeIndex(int arg0)
int[]	getEdgeIndicesArray()
int[]	getEdgeIndicesArray(int arg0, int arg1, boolean arg2)
int[]	getEdgeIndicesArray(int arg0, int arg1, boolean arg2, boolean arg3)
int[]	getEdgeMetaChildIndicesArray(int arg0)
int[]	getEdgeMetaParentIndicesArray(int arg0)
int	getEdgeSourceIndex(int arg0)
int	getEdgeTargetIndex(int arg0)
String	getIdentifier() DOCUMENT ME!
int	getInDegree(int arg0)
int	getInDegree(int arg0, boolean arg1)
int	getInDegree(Node arg0)
int	getInDegree(Node arg0, boolean arg1)
int	getIndex(Edge arg0)
int	getIndex(Node arg0)
Node	getNode(int arg0)
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()
int	getNodeIndex(int arg0)
int[]	getNodeIndicesArray()
int[]	getNodeMetaChildIndicesArray(int arg0)
int[]	getNodeMetaParentIndicesArray(int arg0)
int	getOutDegree(int arg0)
int	getOutDegree(int arg0, boolean arg1)
int	getOutDegree(Node arg0)
int	getOutDegree(Node arg0, boolean arg1)
RootGraph	getRootGraph()
int	getRootGraphEdgeIndex(int arg0)
int	getRootGraphNodeIndex(int arg0)
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 arg0)
int	hideEdge(int arg0)
int[]	hideEdges(int[] arg0)
List	hideEdges(List arg0)
int	hideNode(int arg0)
Node	hideNode(Node arg0)
int[]	hideNodes(int[] arg0)
List	hideNodes(List arg0)
boolean	isEdgeDirected(int arg0)
boolean	isEdgeMetaChild(int arg0, int arg1)
boolean	isEdgeMetaParent(int arg0, int arg1)
boolean	isMetaChild(Node arg0, Edge arg1)
boolean	isMetaChild(Node arg0, Node arg1)
boolean	isMetaParent(Edge arg0, Node arg1)
boolean	isMetaParent(Node arg0, Node arg1)
boolean	isNeighbor(int arg0, int arg1)
boolean	isNeighbor(Node arg0, Node arg1)
boolean	isNodeMetaChild(int arg0, int arg1)
boolean	isNodeMetaParent(int arg0, int arg1)
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 arg0)
List	metaParentsList(Edge arg0)
List	metaParentsList(Node arg0)
int[]	neighborsArray(int arg0)
List	neighborsList(Node arg0)
boolean	nodeExists(int arg0)
List	nodeMetaChildrenList(int arg0)
List	nodeMetaChildrenList(Node arg0)
List	nodeMetaParentsList(int arg0)
cytoscape.util.intr.IntEnumerator	nodes()
Iterator	nodesIterator()
List	nodesList()
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 arg0)
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 arg0)
int	restoreEdge(int arg0)
int[]	restoreEdges(int[] arg0)
List	restoreEdges(List arg0)
int	restoreNode(int arg0)
Node	restoreNode(Node arg0)
int[]	restoreNodes(int[] arg0)
int[]	restoreNodes(int[] arg0, boolean arg1)
List	restoreNodes(List arg0)
List	restoreNodes(List arg0, boolean arg1)
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

Constructor Detail

FingCyNetwork

public FingCyNetwork(fing.model.FingExtensibleRootGraph root,
                     cytoscape.util.intr.IntIterator rootGraphNodeInx,
                     cytoscape.util.intr.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

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: