cytoscape
Interface CyNetwork

All Superinterfaces:

GraphPerspective

public interface CyNetwork

extends GraphPerspective

CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork firt need to be created in Cytoscape.

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list.

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.

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
void	addFlagEventListener(cytoscape.data.FlagEventListener listener)
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
void	appendNetwork(CyNetwork network) Appends all of the nodes and edges in the given Network to this Network
void	beginActivity(String callerID) Deprecated.
void	deleteEdgeAttribute(String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
void	deleteNodeAttribute(String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
void	endActivity(String callerID) Deprecated.
void	flagAllEdges()
void	flagAllNodes()
void	forceClear(String callerID) Deprecated.
Object	getClientData(String data_name) Get Some client data
Collection	getClientDataNames() Get a list of all currently available ClientData objects
Set	getCyNetworkListeners() Returns the set of listeners registered with this object.
cytoscape.data.GraphObjAttributes	getEdgeAttributes() Deprecated. Use Cytoscape.getEdgeAttributes() instead. This method will be removed in September, 2006.
String[]	getEdgeAttributesList() Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
Object	getEdgeAttributeValue(Edge edge, String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
Object	getEdgeAttributeValue(int edge, String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
ExpressionData	getExpressionData() Deprecated. @see{getNetworkData} Returns the expression data object associated with this network.
int[]	getFlaggedEdgeIndicesArray()
Set	getFlaggedEdges()
int[]	getFlaggedNodeIndicesArray()
Set	getFlaggedNodes()
cytoscape.data.FlagFilter	getFlagger()
GraphPerspective	getGraphPerspective() Deprecated.
String	getIdentifier() Can't Change
cytoscape.data.GraphObjAttributes	getNodeAttributes() Deprecated. Use Cytoscape.getNodeAttributes() instead. This method will be removed in September, 2006.
String[]	getNodeAttributesList() Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
String[]	getNodeAttributesList(Edge[] edges) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
String[]	getNodeAttributesList(Node[] nodes) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
Object	getNodeAttributeValue(int node, String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
Object	getNodeAttributeValue(Node node, String attribute) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
String	getTitle() Can Change
boolean	isFlagged(Edge edge)
boolean	isFlagged(Node node)
boolean	isStateClear() Deprecated.
void	putClientData(String data_name, Object data) 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 set_remove) This will remove this edge from the Network.
void	removeFlagEventListener(cytoscape.data.FlagEventListener listener)
boolean	removeNode(int node_index, boolean set_remove) This will remove this node from the Network.
boolean	setEdgeAttributeValue(Edge edge, String attribute, Object value) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
boolean	setEdgeAttributeValue(int edge, String attribute, Object value) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
void	setExpressionData(ExpressionData newData) Deprecated. Sets the expression data object associated with this network.
void	setFlagged(Edge edge, boolean state) Flags a edge
void	setFlagged(Node node, boolean state) Flags a node
void	setFlaggedEdges(Collection edges, boolean state) Flag a group of edge
void	setFlaggedEdges(int[] edges, boolean state) Flag a group of edges using their indices
void	setFlaggedNodes(Collection nodes, boolean state) Flag a group of node
void	setFlaggedNodes(int[] nodes, boolean state) Flag a group of nodes using their indices
String	setIdentifier(String new_id) Can't Change
void	setNewGraphFrom(CyNetwork newNetwork, boolean replaceAttributes) Deprecated.
boolean	setNodeAttributeValue(int node, String attribute, Object value) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
boolean	setNodeAttributeValue(Node node, String attribute, Object value) Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.
void	setTitle(String new_id) Can Change
void	unFlagAllEdges()
void	unFlagAllNodes()

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

Method Detail

getTitle

public String getTitle()

Can Change

setTitle

public void setTitle(String new_id)

Can Change

getIdentifier

public String getIdentifier()

Can't Change

setIdentifier

public String setIdentifier(String new_id)

Can't Change

appendNetwork

public void appendNetwork(CyNetwork network)

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

setNewGraphFrom

public void setNewGraphFrom(CyNetwork newNetwork,
                            boolean replaceAttributes)

Deprecated.

A new Network should be made instead.

See Also:

appendNetwork(cytoscape.CyNetwork)

beginActivity

public void beginActivity(String callerID)

Deprecated.

endActivity

public void endActivity(String callerID)

Deprecated.

isStateClear

public boolean isStateClear()

Deprecated.

forceClear

public void forceClear(String callerID)

Deprecated.

addCyNetworkListener

public void addCyNetworkListener(CyNetworkListener listener)

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

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.

getCyNetworkListeners

public Set getCyNetworkListeners()

Returns the set of listeners registered with this object.

getExpressionData

public ExpressionData getExpressionData()

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

setExpressionData

public void setExpressionData(ExpressionData newData)

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

getNodeAttributes

public cytoscape.data.GraphObjAttributes getNodeAttributes()

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

Gets Global Node Attributes: GraphObjAttributes.

getEdgeAttributes

public cytoscape.data.GraphObjAttributes getEdgeAttributes()

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

Gets Global Edge Attributes: GraphObjAttributes.

getGraphPerspective

public GraphPerspective getGraphPerspective()

Deprecated.

flagAllNodes

public void flagAllNodes()

flagAllEdges

public void flagAllEdges()

unFlagAllNodes

public void unFlagAllNodes()

unFlagAllEdges

public void unFlagAllEdges()

setFlagged

public void setFlagged(Node node,
                       boolean state)

Flags a node

setFlaggedNodes

public void setFlaggedNodes(Collection nodes,
                            boolean state)

Flag a group of node

setFlaggedNodes

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

Flag a group of nodes using their indices

setFlagged

public void setFlagged(Edge edge,
                       boolean state)

Flags a edge

setFlaggedEdges

public void setFlaggedEdges(Collection edges,
                            boolean state)

Flag a group of edge

setFlaggedEdges

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

Flag a group of edges using their indices

isFlagged

public boolean isFlagged(Node node)

isFlagged

public boolean isFlagged(Edge edge)

getFlaggedNodes

public Set getFlaggedNodes()

getFlaggedEdges

public Set getFlaggedEdges()

getFlaggedNodeIndicesArray

public int[] getFlaggedNodeIndicesArray()

getFlaggedEdgeIndicesArray

public int[] getFlaggedEdgeIndicesArray()

addFlagEventListener

public void addFlagEventListener(cytoscape.data.FlagEventListener listener)

removeFlagEventListener

public void removeFlagEventListener(cytoscape.data.FlagEventListener listener)

getFlagger

public cytoscape.data.FlagFilter getFlagger()

getNodeAttributeValue

public Object getNodeAttributeValue(Node node,
                                    String attribute)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

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)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return the requested Attribute for the given Node

getEdgeAttributeValue

public Object getEdgeAttributeValue(Edge edge,
                                    String attribute)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return the requested Attribute for the given Edge

getEdgeAttributeValue

public Object getEdgeAttributeValue(int edge,
                                    String attribute)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return the requested Attribute for the given Edge

getNodeAttributesList

public String[] getNodeAttributesList()

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all availble Attributes for the Nodes in this CyNetwork

getNodeAttributesList

public String[] getNodeAttributesList(Node[] nodes)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all available Attributes for the given Nodes

getEdgeAttributesList

public String[] getEdgeAttributesList()

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all availble Attributes for the Edges in this CyNetwork

getNodeAttributesList

public String[] getNodeAttributesList(Edge[] edges)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return all available Attributes for the given Edges

setNodeAttributeValue

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

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

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)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return the requested Attribute for the given Node

setEdgeAttributeValue

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

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return the requested Attribute for the given Edge

setEdgeAttributeValue

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

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Return the requested Attribute for the given Edge

deleteNodeAttribute

public void deleteNodeAttribute(String attribute)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Deletes the attribute with the given name from node attributes

deleteEdgeAttribute

public void deleteEdgeAttribute(String attribute)

Deprecated. Use CyAttributes directly. This method will be removed in September, 2006.

Deleted the attribute with the given name from edge attributes

putClientData

public void putClientData(String data_name,
                          Object data)

Networks can support client data.

Parameters:

data_name - the name of this client data

getClientDataNames

public Collection getClientDataNames()

Get a list of all currently available ClientData objects

getClientData

public Object getClientData(String data_name)

Get Some client data

Parameters:

data_name - the data to get

addNode

public int addNode(int cytoscape_node)

Add a node to this Network that already exists in Cytoscape

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

Returns:

the Network Index of this node

removeNode

public boolean removeNode(int node_index,
                          boolean set_remove)

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.

Parameters:

set_remove - true removes this node from all of Cytoscape, false lets it be used by other CyNetworks

Returns:

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

addEdge

public int addEdge(int cytoscape_edge)

Add a edge to this Network that already exists in Cytoscape

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

Returns:

the Network Index of this edge

removeEdge

public boolean removeEdge(int edge_index,
                          boolean set_remove)

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.

Parameters:

set_remove - true removes this edge from all of Cytoscape, false lets it be used by other CyNetworks

Returns:

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