cytoscape.giny
Class FingCyNetwork

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

All Implemented Interfaces:

CyNetwork, cytoscape.graph.fixed.FixedGraph, giny.model.GraphPerspective

public class FingCyNetwork
extends fing.model.FingExtensibleGraphPerspective
implements CyNetwork, giny.model.GraphPerspective

ColtCyNetwork extends the GraphPerspective implementation found in the coltginy pacakge of the GINY distribution. ColtCyNetwork 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 FlagFilter	flagger The default object for flagging graph objects This will be removed for 2.4
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

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(giny.model.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	addFlagEventListener(FlagEventListener listener) Deprecated. As of 2.3, replaced by addSelectEventListener(SelectEventListener)
void	addGraphPerspectiveChangeListener(giny.model.GraphPerspectiveChangeListener arg0)
int	addNode(int cytoscape_node) Add a node to this Network that already exists in Cytoscape
CyNode	addNode(giny.model.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
void	beginActivity(String callerID) Deprecated. This method should be called before reading or changing the data held in this network object. A CyNetworkEvent of type CyNetworkEvent.BEGIN will be fired to all listeners attached to this object, *only* if this is the first begin of a nested stack of begin/end methods. No event will be fired if a previous beginActivity call hasn't been closed by a matching endActivity call. The argument is simply a String that is useful for identifying the caller of this method. This is provided for debugging purposes, in case an algorithm forgets to provide a matching end method for each begin.
Object	clone()
boolean	containsEdge(giny.model.Edge arg0)
boolean	containsEdge(giny.model.Edge arg0, boolean arg1)
boolean	containsNode(giny.model.Node arg0)
boolean	containsNode(giny.model.Node arg0, boolean arg1)
int	createEdge(int source, int target, boolean directed) This method will create a new edge.
giny.model.GraphPerspective	createGraphPerspective(giny.filter.Filter arg0)
giny.model.GraphPerspective	createGraphPerspective(int[] arg0)
giny.model.GraphPerspective	createGraphPerspective(int[] arg0, int[] arg1)
giny.model.GraphPerspective	createGraphPerspective(giny.model.Node[] arg0, giny.model.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(giny.model.Node arg0, giny.model.Node arg1)
List	edgeMetaChildrenList(int arg0)
List	edgeMetaChildrenList(giny.model.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(giny.model.Node arg0, giny.model.Node arg1)
int	edgeSource(int arg0)
int	edgeTarget(int arg0)
byte	edgeType(int arg0)
void	endActivity(String callerID) Deprecated. This method should be called when an algorithm is finished reading or changing the data held in this network object. A CyNetworkEvent of type CyNetworkEvent.END will be fired to listeners attached to this object, *only* if this is the last end in a nested block of begin/end calls. The argument is a String for identifying the caller of this method.
void	finalize()
protected void	fireEvent(int type) Fires an event to all listeners registered with this object.
void	flagAllEdges() Deprecated. As of 2.3, replaced by selectAllEdges()
void	flagAllNodes() Deprecated. As of 2.3, replaced by selectAllNodes()
void	forceClear(String callerID) Deprecated. This method is provided as a failsafe in case an algorithm fails to close its beginActivity calls without matching endActivity calls. If the current state is not clear, this method resets this object to the state of no activity and fires a CyNetworkEvent of type CyNetworkEvent.END to all registered listeners. If the current state is clear (i.e., there are no calls to beginActivity without matching endActivity calls), then this method does nothing. The argument is a String for identifying the caller of this method.
int[]	getAdjacentEdgeIndicesArray(int arg0, boolean arg1, boolean arg2, boolean arg3)
List	getAdjacentEdgesList(giny.model.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(giny.model.Node arg0)
giny.model.Edge	getEdge(int arg0)
GraphObjAttributes	getEdgeAttributes() Deprecated. Use Cytoscape.getEdgeAttributes() instead. This method will be removed in September, 2006.
String[]	getEdgeAttributesList() Return all availble Attributes for the Edges in this CyNetwork
Object	getEdgeAttributeValue(giny.model.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(giny.model.Node arg0, giny.model.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)
ExpressionData	getExpressionData() Deprecated. @see{getNetworkData} Returns the expression data object associated with this network.
int[]	getFlaggedEdgeIndicesArray() Deprecated. As of 2.3, replaced by getSelectedEdges()
Set	getFlaggedEdges() Deprecated. As of 2.3, replaced by getSelectedEdges()
int[]	getFlaggedNodeIndicesArray() Deprecated. As of 2.3, replaced by getSelectedNodes()
Set	getFlaggedNodes() Deprecated. As of 2.3, replaced by getSelectedNodes()
FlagFilter	getFlagger() Deprecated. As of 2.3, replaced by getSelectFilter()
giny.model.GraphPerspective	getGraphPerspective() Deprecated. This is a GraphPerspective now! Therefore treat it as such. This method will not be changed and will simply return itself, recasted as a GraphPerspective
String	getIdentifier() Can't Change
int	getInDegree(int arg0)
int	getInDegree(int arg0, boolean arg1)
int	getInDegree(giny.model.Node arg0)
int	getInDegree(giny.model.Node arg0, boolean arg1)
int	getIndex(giny.model.Edge arg0)
int	getIndex(giny.model.Node arg0)
boolean	getNeedsLayout() Deprecated.
giny.model.Node	getNode(int arg0)
GraphObjAttributes	getNodeAttributes() Deprecated. Use Cytoscape.getNodeAttributes() instead. This method will be removed in September, 2006.
String[]	getNodeAttributesList() Return all availble Attributes for the Nodes in this CyNetwork
String[]	getNodeAttributesList(giny.model.Edge[] edges) Return all available Attributes for the given Edges
String[]	getNodeAttributesList(giny.model.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(giny.model.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(giny.model.Node arg0)
int	getOutDegree(giny.model.Node arg0, boolean arg1)
giny.model.RootGraph	getRootGraph() Deprecated. use @link{Cytoscape.getRootGraph()} instead
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
giny.model.Edge	hideEdge(giny.model.Edge arg0)
int	hideEdge(int arg0)
int[]	hideEdges(int[] arg0)
List	hideEdges(List arg0)
int	hideNode(int arg0)
giny.model.Node	hideNode(giny.model.Node arg0)
int[]	hideNodes(int[] arg0)
List	hideNodes(List arg0)
protected void	initialize()
boolean	isEdgeDirected(int arg0)
boolean	isEdgeMetaChild(int arg0, int arg1)
boolean	isEdgeMetaParent(int arg0, int arg1)
boolean	isFlagged(giny.model.Edge edge) Deprecated. As of 2.3, replaced by isSelected(Edge)
boolean	isFlagged(giny.model.Node node) Deprecated. As of 2.3, replaced by isSelected(Node)
boolean	isMetaChild(giny.model.Node arg0, giny.model.Edge arg1)
boolean	isMetaChild(giny.model.Node arg0, giny.model.Node arg1)
boolean	isMetaParent(giny.model.Edge arg0, giny.model.Node arg1)
boolean	isMetaParent(giny.model.Node arg0, giny.model.Node arg1)
boolean	isNeighbor(int arg0, int arg1)
boolean	isNeighbor(giny.model.Node arg0, giny.model.Node arg1)
boolean	isNodeMetaChild(int arg0, int arg1)
boolean	isNodeMetaParent(int arg0, int arg1)
boolean	isSelected(giny.model.Edge edge) Returns the selected state of the given edge.
boolean	isSelected(giny.model.Node node) Returns the selected state of the given node.
boolean	isStateClear() Deprecated. This method returns true if the current state of this object is clear; that is, if every beginActivity call has been followed by a matching endActivity call, so that one can reasonably assume that no one is currently working with the network.
giny.model.GraphPerspective	join(giny.model.GraphPerspective arg0)
List	metaParentsList(giny.model.Edge arg0)
List	metaParentsList(giny.model.Node arg0)
int[]	neighborsArray(int arg0)
List	neighborsList(giny.model.Node arg0)
boolean	nodeExists(int arg0)
List	nodeMetaChildrenList(int arg0)
List	nodeMetaChildrenList(giny.model.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	removeFlagEventListener(FlagEventListener listener) Deprecated. As of 2.3, replaced by removeSelectEventListener(SelectEventListener)
void	removeGraphPerspectiveChangeListener(giny.model.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
giny.model.Edge	restoreEdge(giny.model.Edge arg0)
int	restoreEdge(int arg0)
int[]	restoreEdges(int[] arg0)
List	restoreEdges(List arg0)
int	restoreNode(int arg0)
giny.model.Node	restoreNode(giny.model.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
void	setEdgeAttributes(GraphObjAttributes newEdgeAttributes) Deprecated. This method will be removed in September, 2006.
boolean	setEdgeAttributeValue(giny.model.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
void	setExpressionData(ExpressionData newData) Deprecated. Sets the expression data object associated with this network.
void	setFlagged(giny.model.Edge edge, boolean state) Deprecated. As of 2.3, replaced by setSelectedEdgeState(Collection,boolean)
void	setFlagged(giny.model.Node node, boolean state) Deprecated. As of 2.3, replaced by setSelectedNodeState(Collection,boolean)
void	setFlaggedEdges(Collection edges, boolean state) Deprecated. As of 2.3, replaced by setSelectedEdgeState(Collection,boolean)
void	setFlaggedEdges(int[] edges, boolean state) Deprecated. As of 2.3, replaced by setSelectedEdgeState(Collection,boolean)
void	setFlaggedNodes(Collection nodes, boolean state) Deprecated. As of 2.3, replaced by setSelectedNodeState(Collection,boolean)
void	setFlaggedNodes(int[] nodes, boolean state) Deprecated. As of 2.3, replaced by setSelectedNodeState(Collection,boolean)
void	setGraphPerspective(giny.model.GraphPerspective perspective) Deprecated.
String	setIdentifier(String new_id) Can't Change
void	setNeedsLayout(boolean needsLayout) Deprecated.
void	setNewGraphFrom(CyNetwork newNetwork, boolean replaceAttributes) Deprecated.
void	setNodeAttributes(GraphObjAttributes newNodeAttributes) Deprecated. This method will be removed in September, 2006.
boolean	setNodeAttributeValue(int node, String attribute, Object value) Return the requested Attribute for the given Node
boolean	setNodeAttributeValue(giny.model.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	setSelectedNodeState(Collection nodes, boolean selected_state) Sets the selected state of a collection of nodes.
void	setTitle(String new_id) Can Change
void	unFlagAllEdges() Deprecated. As of 2.3, replaced by unselectAllEdges()
void	unFlagAllNodes() Deprecated. As of 2.3, replaced by unselectAllNodes()
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, 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

flagger

protected FlagFilter flagger

The default object for flagging graph objects This will be removed for 2.4

selectFilter

protected SelectFilter selectFilter

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

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

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

Specified by:

setTitle in interface CyNetwork

getIdentifier

public String getIdentifier()

Description copied from interface: CyNetwork

Can't Change

Specified by:

getIdentifier in interface CyNetwork

setIdentifier

public String setIdentifier(String new_id)

Description copied from interface: CyNetwork

Can't Change

Specified by:

setIdentifier in interface CyNetwork

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

beginActivity

public void beginActivity(String callerID)

Deprecated. This method should be called before reading or changing the data held in this network object. A CyNetworkEvent of type CyNetworkEvent.BEGIN will be fired to all listeners attached to this object, *only* if this is the first begin of a nested stack of begin/end methods. No event will be fired if a previous beginActivity call hasn't been closed by a matching endActivity call.

The argument is simply a String that is useful for identifying the caller of this method. This is provided for debugging purposes, in case an algorithm forgets to provide a matching end method for each begin.

Specified by:

beginActivity in interface CyNetwork

endActivity

public void endActivity(String callerID)

Deprecated. This method should be called when an algorithm is finished reading or changing the data held in this network object. A CyNetworkEvent of type CyNetworkEvent.END will be fired to listeners attached to this object, *only* if this is the last end in a nested block of begin/end calls.

The argument is a String for identifying the caller of this method.

Specified by:

endActivity in interface CyNetwork

isStateClear

public boolean isStateClear()

Deprecated. This method returns true if the current state of this object is clear; that is, if every beginActivity call has been followed by a matching endActivity call, so that one can reasonably assume that no one is currently working with the network.

Specified by:

isStateClear in interface CyNetwork

forceClear

public void forceClear(String callerID)

Deprecated. This method is provided as a failsafe in case an algorithm fails to close its beginActivity calls without matching endActivity calls. If the current state is not clear, this method resets this object to the state of no activity and fires a CyNetworkEvent of type CyNetworkEvent.END to all registered listeners.

If the current state is clear (i.e., there are no calls to beginActivity without matching endActivity calls), then this method does nothing.

The argument is a String for identifying the caller of this method.

Specified by:

forceClear in interface CyNetwork

getRootGraph

public giny.model.RootGraph getRootGraph()

Deprecated. use @link{Cytoscape.getRootGraph()} instead

Specified by:

getRootGraph in interface giny.model.GraphPerspective

getGraphPerspective

public giny.model.GraphPerspective getGraphPerspective()

Deprecated. This is a GraphPerspective now! Therefore treat it as such. This method will not be changed and will simply return itself, recasted as a GraphPerspective

Specified by:

getGraphPerspective in interface CyNetwork

setGraphPerspective

public void setGraphPerspective(giny.model.GraphPerspective perspective)

Deprecated.

A new Network should be made instead.

See Also:

appendNetwork(cytoscape.CyNetwork)

setNewGraphFrom

public void setNewGraphFrom(CyNetwork newNetwork,
                            boolean replaceAttributes)

Deprecated.

A new Network should be made instead.

Specified by:

setNewGraphFrom in interface CyNetwork

See Also:

appendNetwork(cytoscape.CyNetwork)

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

getNeedsLayout

public boolean getNeedsLayout()

Deprecated.

setNeedsLayout

public void setNeedsLayout(boolean needsLayout)

Deprecated.

getNodeAttributes

public GraphObjAttributes getNodeAttributes()

Deprecated. Use Cytoscape.getNodeAttributes() instead. This method will be removed in September, 2006.

Returns the node attributes data object for this network.

Specified by:

getNodeAttributes in interface CyNetwork

setNodeAttributes

public void setNodeAttributes(GraphObjAttributes newNodeAttributes)

Deprecated. This method will be removed in September, 2006.

does nothing, all attributes are shared right now

getEdgeAttributes

public GraphObjAttributes getEdgeAttributes()

Deprecated. Use Cytoscape.getEdgeAttributes() instead. This method will be removed in September, 2006.

Returns the edge attributes data object for this network.

Specified by:

getEdgeAttributes in interface CyNetwork

setEdgeAttributes

public void setEdgeAttributes(GraphObjAttributes newEdgeAttributes)

Deprecated. This method will be removed in September, 2006.

does nothing, all attributes are shared right now

getExpressionData

public ExpressionData getExpressionData()

Deprecated. @see{getNetworkData} Returns the expression data object associated with this network.

Specified by:

getExpressionData in interface CyNetwork

setExpressionData

public void setExpressionData(ExpressionData newData)

Deprecated. Sets the expression data object associated with this network.

Specified by:

setExpressionData 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

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

isSelected

public boolean isSelected(giny.model.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(giny.model.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

getFlagger

public FlagFilter getFlagger()

Deprecated. As of 2.3, replaced by getSelectFilter()

Returns the default object for flagging graph objects.

Specified by:

getFlagger in interface CyNetwork

Returns:

FlagFilter

flagAllNodes

public void flagAllNodes()

Deprecated. As of 2.3, replaced by selectAllNodes()

Description copied from interface: CyNetwork

Flags all nodes in this CyNetwork

Specified by:

flagAllNodes in interface CyNetwork

flagAllEdges

public void flagAllEdges()

Deprecated. As of 2.3, replaced by selectAllEdges()

Description copied from interface: CyNetwork

Flags all edges in this network

Specified by:

flagAllEdges in interface CyNetwork

unFlagAllNodes

public void unFlagAllNodes()

Deprecated. As of 2.3, replaced by unselectAllNodes()

Description copied from interface: CyNetwork

Unflags all nodes in this CyNetwork

Specified by:

unFlagAllNodes in interface CyNetwork

unFlagAllEdges

public void unFlagAllEdges()

Deprecated. As of 2.3, replaced by unselectAllEdges()

Description copied from interface: CyNetwork

Unflags all edges in this CyNetwork

Specified by:

unFlagAllEdges in interface CyNetwork

setFlagged

public void setFlagged(giny.model.Node node,
                       boolean state)

Deprecated. As of 2.3, replaced by setSelectedNodeState(Collection,boolean)

Flags a node

Specified by:

setFlagged in interface CyNetwork

setFlaggedNodes

public void setFlaggedNodes(Collection nodes,
                            boolean state)

Deprecated. As of 2.3, replaced by setSelectedNodeState(Collection,boolean)

Flag a group of node

Specified by:

setFlaggedNodes in interface CyNetwork

setFlaggedNodes

public void setFlaggedNodes(int[] nodes,
                            boolean state)

Deprecated. As of 2.3, replaced by setSelectedNodeState(Collection,boolean)

Flag a group of nodes using their indices

Specified by:

setFlaggedNodes in interface CyNetwork

setFlagged

public void setFlagged(giny.model.Edge edge,
                       boolean state)

Deprecated. As of 2.3, replaced by setSelectedEdgeState(Collection,boolean)

Flags a edge

Specified by:

setFlagged in interface CyNetwork

setFlaggedEdges

public void setFlaggedEdges(Collection edges,
                            boolean state)

Deprecated. As of 2.3, replaced by setSelectedEdgeState(Collection,boolean)

Flag a group of edge

Specified by:

setFlaggedEdges in interface CyNetwork

setFlaggedEdges

public void setFlaggedEdges(int[] edges,
                            boolean state)

Deprecated. As of 2.3, replaced by setSelectedEdgeState(Collection,boolean)

Flag a group of edges using their indices

Specified by:

setFlaggedEdges in interface CyNetwork

isFlagged

public boolean isFlagged(giny.model.Node node)

Deprecated. As of 2.3, replaced by isSelected(Node)

Description copied from interface: CyNetwork

Whether or not the given node is flagged in this CyNetwork

Specified by:

isFlagged in interface CyNetwork

Returns:

whether or not the node has been flagged

isFlagged

public boolean isFlagged(giny.model.Edge edge)

Deprecated. As of 2.3, replaced by isSelected(Edge)

Description copied from interface: CyNetwork

Whether or not the given edges is flagged in this CyNetwork

Specified by:

isFlagged in interface CyNetwork

Returns:

whether or not the edge has been flagged

getFlaggedNodes

public Set getFlaggedNodes()

Deprecated. As of 2.3, replaced by getSelectedNodes()

Description copied from interface: CyNetwork

Returns the set of flagged nodes in this CyNetwork

Specified by:

getFlaggedNodes in interface CyNetwork

Returns:

a Set of flagged nodes

getFlaggedEdges

public Set getFlaggedEdges()

Deprecated. As of 2.3, replaced by getSelectedEdges()

Description copied from interface: CyNetwork

Returns the set of flagged edges in this CyNetwork

Specified by:

getFlaggedEdges in interface CyNetwork

Returns:

a Set of flagged edges

getFlaggedNodeIndicesArray

public int[] getFlaggedNodeIndicesArray()

Deprecated. As of 2.3, replaced by getSelectedNodes()

Description copied from interface: CyNetwork

Returns an array of the indices of flagged nodes in this CyNetwork

Specified by:

getFlaggedNodeIndicesArray in interface CyNetwork

Returns:

an array of indices

getFlaggedEdgeIndicesArray

public int[] getFlaggedEdgeIndicesArray()

Deprecated. As of 2.3, replaced by getSelectedEdges()

Description copied from interface: CyNetwork

Returns an array of the indices of flagged edges in this CyNetwork

Specified by:

getFlaggedEdgeIndicesArray in interface CyNetwork

Returns:

an array of indices

addFlagEventListener

public void addFlagEventListener(FlagEventListener listener)

Deprecated. As of 2.3, replaced by addSelectEventListener(SelectEventListener)

Description copied from interface: CyNetwork

Adds a listener for FlagEvents to this CyNetwork

Specified by:

addFlagEventListener in interface CyNetwork

removeFlagEventListener

public void removeFlagEventListener(FlagEventListener listener)

Deprecated. As of 2.3, replaced by removeSelectEventListener(SelectEventListener)

Description copied from interface: CyNetwork

Removes a listener fro FlagEvents from this CyNetwork

Specified by:

removeFlagEventListener in interface CyNetwork

getNodeAttributeValue

public Object getNodeAttributeValue(giny.model.Node node,
                                    String attribute)

Return the requested Attribute for the given Node

Specified by:

getNodeAttributeValue in interface CyNetwork

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

Specified by:

getNodeAttributeValue in interface CyNetwork

getEdgeAttributeValue

public Object getEdgeAttributeValue(giny.model.Edge edge,
                                    String attribute)

Return the requested Attribute for the given Edge

Specified by:

getEdgeAttributeValue in interface CyNetwork

getEdgeAttributeValue

public Object getEdgeAttributeValue(int edge,
                                    String attribute)

Return the requested Attribute for the given Edge

Specified by:

getEdgeAttributeValue in interface CyNetwork

getNodeAttributesList

public String[] getNodeAttributesList()

Return all availble Attributes for the Nodes in this CyNetwork

Specified by:

getNodeAttributesList in interface CyNetwork

getNodeAttributesList

public String[] getNodeAttributesList(giny.model.Node[] nodes)

Return all available Attributes for the given Nodes

Specified by:

getNodeAttributesList in interface CyNetwork

getEdgeAttributesList

public String[] getEdgeAttributesList()

Return all availble Attributes for the Edges in this CyNetwork

Specified by:

getEdgeAttributesList in interface CyNetwork

getNodeAttributesList

public String[] getNodeAttributesList(giny.model.Edge[] edges)

Return all available Attributes for the given Edges

Specified by:

getNodeAttributesList in interface CyNetwork

setNodeAttributeValue

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

Return the requested Attribute for the given Node

Specified by:

setNodeAttributeValue in interface CyNetwork

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

Specified by:

setNodeAttributeValue in interface CyNetwork

setEdgeAttributeValue

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

Return the requested Attribute for the given Edge

Specified by:

setEdgeAttributeValue in interface CyNetwork

setEdgeAttributeValue

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

Return the requested Attribute for the given Edge

Specified by:

setEdgeAttributeValue in interface CyNetwork

deleteNodeAttribute

public void deleteNodeAttribute(String attribute)

Deletes the attribute with the given name from node attributes

Specified by:

deleteNodeAttribute in interface CyNetwork

deleteEdgeAttribute

public void deleteEdgeAttribute(String attribute)

Deletes the attribute with the given name from edge attributes

Specified by:

deleteEdgeAttribute in interface CyNetwork

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(giny.model.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(giny.model.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 cytoscape.util.intr.IntEnumerator nodes()

Specified by:

nodes in interface cytoscape.graph.fixed.FixedGraph

edges

public cytoscape.util.intr.IntEnumerator edges()

Specified by:

edges in interface cytoscape.graph.fixed.FixedGraph

nodeExists

public boolean nodeExists(int arg0)

Specified by:

nodeExists in interface cytoscape.graph.fixed.FixedGraph

edgeType

public byte edgeType(int arg0)

Specified by:

edgeType in interface cytoscape.graph.fixed.FixedGraph

edgeSource

public int edgeSource(int arg0)

Specified by:

edgeSource in interface cytoscape.graph.fixed.FixedGraph

edgeTarget

public int edgeTarget(int arg0)

Specified by:

edgeTarget in interface cytoscape.graph.fixed.FixedGraph

edgesAdjacent

public cytoscape.util.intr.IntEnumerator edgesAdjacent(int arg0,
                                                       boolean arg1,
                                                       boolean arg2,
                                                       boolean arg3)

Specified by:

edgesAdjacent in interface cytoscape.graph.fixed.FixedGraph

edgesConnecting

public cytoscape.util.intr.IntIterator edgesConnecting(int arg0,
                                                       int arg1,
                                                       boolean arg2,
                                                       boolean arg3,
                                                       boolean arg4)

Specified by:

edgesConnecting in interface cytoscape.graph.fixed.FixedGraph

addGraphPerspectiveChangeListener

public void addGraphPerspectiveChangeListener(giny.model.GraphPerspectiveChangeListener arg0)

Specified by:

addGraphPerspectiveChangeListener in interface giny.model.GraphPerspective

removeGraphPerspectiveChangeListener

public void removeGraphPerspectiveChangeListener(giny.model.GraphPerspectiveChangeListener arg0)

Specified by:

removeGraphPerspectiveChangeListener in interface giny.model.GraphPerspective

clone

public Object clone()

Specified by:

clone in interface giny.model.GraphPerspective

Overrides:

clone in class Object

getNodeCount

public int getNodeCount()

Specified by:

getNodeCount in interface giny.model.GraphPerspective

getEdgeCount

public int getEdgeCount()

Specified by:

getEdgeCount in interface giny.model.GraphPerspective

nodesIterator

public Iterator nodesIterator()

Specified by:

nodesIterator in interface giny.model.GraphPerspective

nodesList

public List nodesList()

Specified by:

nodesList in interface giny.model.GraphPerspective

getNodeIndicesArray

public int[] getNodeIndicesArray()

Specified by:

getNodeIndicesArray in interface giny.model.GraphPerspective

edgesIterator

public Iterator edgesIterator()

Specified by:

edgesIterator in interface giny.model.GraphPerspective

edgesList

public List edgesList()

Specified by:

edgesList in interface giny.model.GraphPerspective

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Specified by:

getEdgeIndicesArray in interface giny.model.GraphPerspective

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int arg0,
                                 int arg1,
                                 boolean arg2,
                                 boolean arg3)

Specified by:

getEdgeIndicesArray in interface giny.model.GraphPerspective

hideNode

public giny.model.Node hideNode(giny.model.Node arg0)

Specified by:

hideNode in interface giny.model.GraphPerspective

hideNode

public int hideNode(int arg0)

Specified by:

hideNode in interface giny.model.GraphPerspective

hideNodes

public List hideNodes(List arg0)

Specified by:

hideNodes in interface giny.model.GraphPerspective

hideNodes

public int[] hideNodes(int[] arg0)

Specified by:

hideNodes in interface giny.model.GraphPerspective

restoreNode

public giny.model.Node restoreNode(giny.model.Node arg0)

Specified by:

restoreNode in interface giny.model.GraphPerspective

restoreNode

public int restoreNode(int arg0)

Specified by:

restoreNode in interface giny.model.GraphPerspective

restoreNodes

public List restoreNodes(List arg0)

Specified by:

restoreNodes in interface giny.model.GraphPerspective

restoreNodes

public List restoreNodes(List arg0,
                         boolean arg1)

Specified by:

restoreNodes in interface giny.model.GraphPerspective

restoreNodes

public int[] restoreNodes(int[] arg0,
                          boolean arg1)

Specified by:

restoreNodes in interface giny.model.GraphPerspective

restoreNodes

public int[] restoreNodes(int[] arg0)

Specified by:

restoreNodes in interface giny.model.GraphPerspective

hideEdge

public giny.model.Edge hideEdge(giny.model.Edge arg0)

Specified by:

hideEdge in interface giny.model.GraphPerspective

hideEdge

public int hideEdge(int arg0)

Specified by:

hideEdge in interface giny.model.GraphPerspective

hideEdges

public List hideEdges(List arg0)

Specified by:

hideEdges in interface giny.model.GraphPerspective

hideEdges

public int[] hideEdges(int[] arg0)

Specified by:

hideEdges in interface giny.model.GraphPerspective

restoreEdge

public giny.model.Edge restoreEdge(giny.model.Edge arg0)

Specified by:

restoreEdge in interface giny.model.GraphPerspective

restoreEdge

public int restoreEdge(int arg0)

Specified by:

restoreEdge in interface giny.model.GraphPerspective

restoreEdges

public List restoreEdges(List arg0)

Specified by:

restoreEdges in interface giny.model.GraphPerspective

restoreEdges

public int[] restoreEdges(int[] arg0)

Specified by:

restoreEdges in interface giny.model.GraphPerspective

containsNode

public boolean containsNode(giny.model.Node arg0)

Specified by:

containsNode in interface giny.model.GraphPerspective

containsNode

public boolean containsNode(giny.model.Node arg0,
                            boolean arg1)

Specified by:

containsNode in interface giny.model.GraphPerspective

containsEdge

public boolean containsEdge(giny.model.Edge arg0)

Specified by:

containsEdge in interface giny.model.GraphPerspective

containsEdge

public boolean containsEdge(giny.model.Edge arg0,
                            boolean arg1)

Specified by:

containsEdge in interface giny.model.GraphPerspective

join

public giny.model.GraphPerspective join(giny.model.GraphPerspective arg0)

Specified by:

join in interface giny.model.GraphPerspective

createGraphPerspective

public giny.model.GraphPerspective createGraphPerspective(giny.model.Node[] arg0,
                                                          giny.model.Edge[] arg1)

Specified by:

createGraphPerspective in interface giny.model.GraphPerspective

createGraphPerspective

public giny.model.GraphPerspective createGraphPerspective(int[] arg0,
                                                          int[] arg1)

Specified by:

createGraphPerspective in interface giny.model.GraphPerspective

createGraphPerspective

public giny.model.GraphPerspective createGraphPerspective(giny.filter.Filter arg0)

Specified by:

createGraphPerspective in interface giny.model.GraphPerspective

neighborsList

public List neighborsList(giny.model.Node arg0)

Specified by:

neighborsList in interface giny.model.GraphPerspective

neighborsArray

public int[] neighborsArray(int arg0)

Specified by:

neighborsArray in interface giny.model.GraphPerspective

isNeighbor

public boolean isNeighbor(giny.model.Node arg0,
                          giny.model.Node arg1)

Specified by:

isNeighbor in interface giny.model.GraphPerspective

isNeighbor

public boolean isNeighbor(int arg0,
                          int arg1)

Specified by:

isNeighbor in interface giny.model.GraphPerspective

edgeExists

public boolean edgeExists(giny.model.Node arg0,
                          giny.model.Node arg1)

Specified by:

edgeExists in interface giny.model.GraphPerspective

edgeExists

public boolean edgeExists(int arg0,
                          int arg1)

Specified by:

edgeExists in interface giny.model.GraphPerspective

getEdgeCount

public int getEdgeCount(giny.model.Node arg0,
                        giny.model.Node arg1,
                        boolean arg2)

Specified by:

getEdgeCount in interface giny.model.GraphPerspective

getEdgeCount

public int getEdgeCount(int arg0,
                        int arg1,
                        boolean arg2)

Specified by:

getEdgeCount in interface giny.model.GraphPerspective

edgesList

public List edgesList(giny.model.Node arg0,
                      giny.model.Node arg1)

Specified by:

edgesList in interface giny.model.GraphPerspective

edgesList

public List edgesList(int arg0,
                      int arg1,
                      boolean arg2)

Specified by:

edgesList in interface giny.model.GraphPerspective

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int arg0,
                                 int arg1,
                                 boolean arg2)

Specified by:

getEdgeIndicesArray in interface giny.model.GraphPerspective

getInDegree

public int getInDegree(giny.model.Node arg0)

Specified by:

getInDegree in interface giny.model.GraphPerspective

getInDegree

public int getInDegree(int arg0)

Specified by:

getInDegree in interface giny.model.GraphPerspective

getInDegree

public int getInDegree(giny.model.Node arg0,
                       boolean arg1)

Specified by:

getInDegree in interface giny.model.GraphPerspective

getInDegree

public int getInDegree(int arg0,
                       boolean arg1)

Specified by:

getInDegree in interface giny.model.GraphPerspective

getOutDegree

public int getOutDegree(giny.model.Node arg0)

Specified by:

getOutDegree in interface giny.model.GraphPerspective

getOutDegree

public int getOutDegree(int arg0)

Specified by:

getOutDegree in interface giny.model.GraphPerspective

getOutDegree

public int getOutDegree(giny.model.Node arg0,
                        boolean arg1)

Specified by:

getOutDegree in interface giny.model.GraphPerspective

getOutDegree

public int getOutDegree(int arg0,
                        boolean arg1)

Specified by:

getOutDegree in interface giny.model.GraphPerspective

getDegree

public int getDegree(giny.model.Node arg0)

Specified by:

getDegree in interface giny.model.GraphPerspective

getDegree

public int getDegree(int arg0)

Specified by:

getDegree in interface giny.model.GraphPerspective

getIndex

public int getIndex(giny.model.Node arg0)

Specified by:

getIndex in interface giny.model.GraphPerspective

getNodeIndex

public int getNodeIndex(int arg0)

Specified by:

getNodeIndex in interface giny.model.GraphPerspective

getRootGraphNodeIndex

public int getRootGraphNodeIndex(int arg0)

Specified by:

getRootGraphNodeIndex in interface giny.model.GraphPerspective

getNode

public giny.model.Node getNode(int arg0)

Specified by:

getNode in interface giny.model.GraphPerspective

getIndex

public int getIndex(giny.model.Edge arg0)

Specified by:

getIndex in interface giny.model.GraphPerspective

getEdgeIndex

public int getEdgeIndex(int arg0)

Specified by:

getEdgeIndex in interface giny.model.GraphPerspective

getRootGraphEdgeIndex

public int getRootGraphEdgeIndex(int arg0)

Specified by:

getRootGraphEdgeIndex in interface giny.model.GraphPerspective

getEdge

public giny.model.Edge getEdge(int arg0)

Specified by:

getEdge in interface giny.model.GraphPerspective

getEdgeSourceIndex

public int getEdgeSourceIndex(int arg0)

Specified by:

getEdgeSourceIndex in interface giny.model.GraphPerspective

getEdgeTargetIndex

public int getEdgeTargetIndex(int arg0)

Specified by:

getEdgeTargetIndex in interface giny.model.GraphPerspective

isEdgeDirected

public boolean isEdgeDirected(int arg0)

Specified by:

isEdgeDirected in interface giny.model.GraphPerspective

isMetaParent

public boolean isMetaParent(giny.model.Node arg0,
                            giny.model.Node arg1)

Specified by:

isMetaParent in interface giny.model.GraphPerspective

isNodeMetaParent

public boolean isNodeMetaParent(int arg0,
                                int arg1)

Specified by:

isNodeMetaParent in interface giny.model.GraphPerspective

metaParentsList

public List metaParentsList(giny.model.Node arg0)

Specified by:

metaParentsList in interface giny.model.GraphPerspective

nodeMetaParentsList

public List nodeMetaParentsList(int arg0)

Specified by:

nodeMetaParentsList in interface giny.model.GraphPerspective

getNodeMetaParentIndicesArray

public int[] getNodeMetaParentIndicesArray(int arg0)

Specified by:

getNodeMetaParentIndicesArray in interface giny.model.GraphPerspective

isMetaChild

public boolean isMetaChild(giny.model.Node arg0,
                           giny.model.Node arg1)

Specified by:

isMetaChild in interface giny.model.GraphPerspective

isNodeMetaChild

public boolean isNodeMetaChild(int arg0,
                               int arg1)

Specified by:

isNodeMetaChild in interface giny.model.GraphPerspective

nodeMetaChildrenList

public List nodeMetaChildrenList(giny.model.Node arg0)

Specified by:

nodeMetaChildrenList in interface giny.model.GraphPerspective

nodeMetaChildrenList

public List nodeMetaChildrenList(int arg0)

Specified by:

nodeMetaChildrenList in interface giny.model.GraphPerspective

getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int arg0)

Specified by:

getNodeMetaChildIndicesArray in interface giny.model.GraphPerspective

isMetaParent

public boolean isMetaParent(giny.model.Edge arg0,
                            giny.model.Node arg1)

Specified by:

isMetaParent in interface giny.model.GraphPerspective

isEdgeMetaParent

public boolean isEdgeMetaParent(int arg0,
                                int arg1)

Specified by:

isEdgeMetaParent in interface giny.model.GraphPerspective

metaParentsList

public List metaParentsList(giny.model.Edge arg0)

Specified by:

metaParentsList in interface giny.model.GraphPerspective

edgeMetaParentsList

public List edgeMetaParentsList(int arg0)

Specified by:

edgeMetaParentsList in interface giny.model.GraphPerspective

getEdgeMetaParentIndicesArray

public int[] getEdgeMetaParentIndicesArray(int arg0)

Specified by:

getEdgeMetaParentIndicesArray in interface giny.model.GraphPerspective

isMetaChild

public boolean isMetaChild(giny.model.Node arg0,
                           giny.model.Edge arg1)

Specified by:

isMetaChild in interface giny.model.GraphPerspective

isEdgeMetaChild

public boolean isEdgeMetaChild(int arg0,
                               int arg1)

Specified by:

isEdgeMetaChild in interface giny.model.GraphPerspective

edgeMetaChildrenList

public List edgeMetaChildrenList(giny.model.Node arg0)

Specified by:

edgeMetaChildrenList in interface giny.model.GraphPerspective

edgeMetaChildrenList

public List edgeMetaChildrenList(int arg0)

Specified by:

edgeMetaChildrenList in interface giny.model.GraphPerspective

getEdgeMetaChildIndicesArray

public int[] getEdgeMetaChildIndicesArray(int arg0)

Specified by:

getEdgeMetaChildIndicesArray in interface giny.model.GraphPerspective

getAdjacentEdgesList

public List getAdjacentEdgesList(giny.model.Node arg0,
                                 boolean arg1,
                                 boolean arg2,
                                 boolean arg3)

Specified by:

getAdjacentEdgesList in interface giny.model.GraphPerspective

getAdjacentEdgeIndicesArray

public int[] getAdjacentEdgeIndicesArray(int arg0,
                                         boolean arg1,
                                         boolean arg2,
                                         boolean arg3)

Specified by:

getAdjacentEdgeIndicesArray in interface giny.model.GraphPerspective

getConnectingEdges

public List getConnectingEdges(List arg0)

Specified by:

getConnectingEdges in interface giny.model.GraphPerspective

getConnectingEdgeIndicesArray

public int[] getConnectingEdgeIndicesArray(int[] arg0)

Specified by:

getConnectingEdgeIndicesArray in interface giny.model.GraphPerspective

getConnectingNodeIndicesArray

public int[] getConnectingNodeIndicesArray(int[] arg0)

Specified by:

getConnectingNodeIndicesArray in interface giny.model.GraphPerspective

createGraphPerspective

public giny.model.GraphPerspective createGraphPerspective(int[] arg0)

Specified by:

createGraphPerspective in interface giny.model.GraphPerspective

finalize

public void finalize()

Overrides:

finalize in class Object