org.cytoscape.group
Interface CyGroup

public interface CyGroup

An object that represents a group of nodes and edges. A CyGroup is an object that encapsulates a CyNode that represents a collection of CyNodes and connecting CyEdges stored as a CyNetwork. In addition a CyGroup maintains information about the links between the nodes in the group and nodes external to the group. Groups may be collapsed or expanded. A collapsed group is represented in a network as the CyNode representing the group and a series of "meta" edges that represent the edges between nodes within the group and external nodes. Like any other node, the group node can also have edges connecting to other nodes.

Cytoscape Backwards Compatibility (API Interface): We expect that this interface will be used but not implemented by developers using this interface. As such, we reserve the right to add methods to the interface as part of minor version upgrades. We will not remove methods for any changes other than major version upgrades.

Method Summary

void	addEdges(List<CyEdge> edges) Add a list of edges to a group.
void	addGroupToNetwork(CyNetwork network) Add a group to an additional network.
void	addNodes(List<CyNode> nodes) Add a list of nodes and their edges
void	collapse(CyNetwork network) Collapse this group in the designated network.
void	expand(CyNetwork network) Expand this group in the designated network.
Set<CyEdge>	getExternalEdgeList() Returns the list of exterior edges connected to the nodes within this group.
CyNetwork	getGroupNetwork() Returns the network referenced by this group.
CyNode	getGroupNode() Return the CyNode that represents this group in the network.
List<CyEdge>	getInternalEdgeList() Returns the list of edges contained within this group.
Set<CyNetwork>	getNetworkSet() Return the list of CyNetworks this group is in.
List<CyNode>	getNodeList() Returns the list of nodes contained within this group.
CyRootNetwork	getRootNetwork() Return the root network for this group.
boolean	isCollapsed(CyNetwork network) Return whether this group is expanded or collapsed in the designated network.
boolean	isInNetwork(CyNetwork network) Check to see if this group is defined in a particular network.
void	removeEdges(List<CyEdge> edges) Remove a set of edges from a group.
void	removeGroupFromNetwork(CyNetwork network) Remove a group from a network.
void	removeNodes(List<CyNode> nodes) Remove a set of nodes and their edges from a group

Method Detail

getGroupNode

CyNode getGroupNode()

Return the CyNode that represents this group in the network.

Returns:

the CyNode for this group

getNodeList

List<CyNode> getNodeList()

Returns the list of nodes contained within this group.

Returns:

A list of CyNodes returns null otherwise.

getInternalEdgeList

List<CyEdge> getInternalEdgeList()

Returns the list of edges contained within this group.

Returns:

A list of CyEdges

getExternalEdgeList

Set<CyEdge> getExternalEdgeList()

Returns the list of exterior edges connected to the nodes within this group.

Returns:

A list of CyEdges

getGroupNetwork

CyNetwork getGroupNetwork()

Returns the network referenced by this group. All groups will point to a network, although the network might not have any nodes or edges. This is the internal network representation of the group, not the networks that the group is a member of.

Returns:

A reference to a CyNetwork

addNodes

void addNodes(List<CyNode> nodes)

Add a list of nodes and their edges

Parameters:

nodes - the list of nodes to add

addEdges

void addEdges(List<CyEdge> edges)

Add a list of edges to a group. The edges will be added either to the internal edges or external edges lists. Note that unlike addNodes(java.util.List) either the source node or target node for the edge must be in the group.

Parameters:

edges - the list of edges to add

removeNodes

void removeNodes(List<CyNode> nodes)

Remove a set of nodes and their edges from a group

Parameters:

nodes - the nodes to remove

removeEdges

void removeEdges(List<CyEdge> edges)

Remove a set of edges from a group. Edges can be either internal edges or external edges.

Parameters:

edges - the edges to remove

getRootNetwork

CyRootNetwork getRootNetwork()

Return the root network for this group. A group can only exist within one root network, and all nodes and edges that are part of the group must exist within that root network also.

Returns:

the root network for this group

addGroupToNetwork

void addGroupToNetwork(CyNetwork network)

Add a group to an additional network. When groups are created, they are created in a particular network. The can also be shown in other networks, as long as all of the networks are in the same CyRootNetwork

Parameters:

network - the CyNetwork to add the group to

removeGroupFromNetwork

void removeGroupFromNetwork(CyNetwork network)

Remove a group from a network.

Parameters:

network - the CyNetwork to remove the group from

getNetworkSet

Set<CyNetwork> getNetworkSet()

Return the list of CyNetworks this group is in.

Returns:

the set of CyNetworks that contain this group

isInNetwork

boolean isInNetwork(CyNetwork network)

Check to see if this group is defined in a particular network.

Parameters:

network - the CyNetwork to test

Returns:

true if the group is in that network

collapse

void collapse(CyNetwork network)

Collapse this group in the designated network. Note that this is a "model-level" collapse, which removes all of the member nodes and edges and replaces them with the node that represents the group in the network. This does not imply a specific visual representation.

Parameters:

network - the CyNetwork that this group should be collapsed in

expand

void expand(CyNetwork network)

Expand this group in the designated network. Note that this is a "model-level" expansion, which removes the node that represents the group from the network and adds all of the member nodes and edges. This does not imply a specific visual representation.

Parameters:

network - the CyNetwork that this group should be expanded in

isCollapsed

boolean isCollapsed(CyNetwork network)

Return whether this group is expanded or collapsed in the designated network.

Parameters:

network - the CyNetwork we're interested in

Returns:

true if the group is collapsed in that network.