A C D E G I R S U V

A

assignName(CyNetwork, CyNode) - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Creates a unique name for the CyNode and registers this name and node into Cytoscape

C

copyGroup(CyNode, CyNetwork) - Static method in class edu.ucsf.groups.GroupManager

This method copies a group from one network to another.

copyGroup(CyNode, CyNode) - Method in interface edu.ucsf.groups.model.GroupModel

This method is called from the GroupManager API when it copies a group from one network to another.

createGroup(CyNetwork, CyNetwork, GroupAttributesHandler, GroupModel) - Static method in class edu.ucsf.groups.GroupManager

This method creates a group when given two networks: the current network and the new network that will be "contained" within the group.

createGroup(CyNetwork, CyNetwork) - Static method in class edu.ucsf.groups.GroupManager

This method creates a group when given two networks: the current network and the new network that will be "contained" within the group.

createGroup(CyNetwork, CyNode) - Method in interface edu.ucsf.groups.model.GroupModel

This method is called from the GroupManager API upon creation of a new group to allow the group abstraction implementation to perform any initialization required.

D

DEFAULT_NODE_LABEL_ATTRIBUTE - Static variable in interface edu.ucsf.groups.data.GroupAttributesHandler

The default attribute that is used to label nodes, this is not the same as the unique ID of nodes which are internal keys to nodes

E

edu.ucsf.groups - package edu.ucsf.groups

edu.ucsf.groups.data - package edu.ucsf.groups.data

edu.ucsf.groups.model - package edu.ucsf.groups.model

edu.ucsf.groups.view - package edu.ucsf.groups.view

G

getAllGroupNodes(CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method returns the list of groups (as represented by CyNodes) that this CyNode is a member of (reguardless of which network).

getCyNetwork(CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method returns the CyNetwork this group is part of.

getDefaultNodeLabelAttribute() - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Returns the current default node label attribute.

getGroupAttributesHandler(CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method returns the current attributes handler for this group.

getGroupMembers(CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method returns the list of members that are contained within this group.

getGroupModel(CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method returns the current model for this group.

getGroupName() - Method in interface edu.ucsf.groups.model.GroupModel

Return the "name" of this abstraction.

getGroupNodes(CyNetwork, CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method returns the list of groups (as represented by CyNodes) that this CyNode is a member of.

getGroupViewer() - Method in interface edu.ucsf.groups.model.GroupModel

Get the GroupViewer for this group.

getGroupViewerName() - Method in interface edu.ucsf.groups.view.GroupViewer

Returns the name of this viewer.

getNodeLabelAttribute() - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Gets the name of the node attribute to which meta-node names should be assigned to, if not set, it is DEFAULT_NODE_LABEL_ATTRIBUTE

getSubGroups(CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method returns a List of the groups contained within this group

GroupAttributesHandler - Interface in edu.ucsf.groups.data

An interface for classes that handle the node and edge attributes of groups.

GroupManager - Class in edu.ucsf.groups

This is just a container class to provide convenient access to the group methods.

GroupManager() - Constructor for class edu.ucsf.groups.GroupManager

GroupModel - Interface in edu.ucsf.groups.model

An interface for classes that handle the model associated with presentation of grouped nodes.

GroupViewer - Interface in edu.ucsf.groups.view

An interface for classes that handle the actual presentation of groups.

I

isGrouped(CyNode) - Static method in class edu.ucsf.groups.GroupManager

Test to see if a group node is in the "group" or "ungrouped" state.

R

regroupGroup(CyNode, boolean, boolean) - Static method in class edu.ucsf.groups.GroupManager

This method will "regroup" the group, that is, it will present the nodes in an "grouped" state.

regroupGroup(CyNode) - Method in interface edu.ucsf.groups.model.GroupModel

This method is called from the GroupManager API to actually present the group in a 'grouped' state.

removeFromAttributes(CyNetwork, CyNode, List) - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Removes all attributes created for the given group node

removeGroup(CyNode) - Static method in class edu.ucsf.groups.GroupManager

This method will remove a group -- essentially a permanent "ungroup".

removeGroup(CyNode) - Method in interface edu.ucsf.groups.model.GroupModel

This method is called from the GroupManager API upon deletion of a new group to allow the group abstraction implementation to perform any updates in internal data structures.

removeMetaEdgesFromAttributes(CyNetwork, CyNode, List) - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Remove attributes for the given meta-edges in CyNetwork, but leave the attributes for the group node as they are.

S

setAttributes(CyNetwork, CyNode, List, AbstractIntIntMap) - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Sets the node and edge attributes of the meta-node

setEdgeAttributes(CyNetwork, CyNode, AbstractIntIntMap) - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Sets the edge attributes of the group node

setGroupAttributesHandler(CyNode, GroupAttributesHandler) - Static method in class edu.ucsf.groups.GroupManager

This method allows the caller to explicitly set the attributes handler used with this group.

setGroupModel(CyNode, GroupModel) - Static method in class edu.ucsf.groups.GroupManager

This method allows the caller to explicitly set the abstraction model used to represent the group.

setGroupViewer(GroupViewer) - Method in interface edu.ucsf.groups.model.GroupModel

Set the GroupViewer for this group.

setNodeAttributes(CyNetwork, CyNode, List) - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Sets the node attributes of the group node

setNodeLabelAttribute(String) - Method in interface edu.ucsf.groups.data.GroupAttributesHandler

Sets the name of the node attribute to which meta-node names should be assigned to, if not set, it is DEFAULT_NODE_LABEL_ATTRIBUTE

U

ungroupGroup(CyNode, boolean) - Static method in class edu.ucsf.groups.GroupManager

This method will "ungroup" the group, that is, it will present the nodes in an "ungrouped" state.

ungroupGroup(CyNode) - Method in interface edu.ucsf.groups.model.GroupModel

This method is called from the GroupManager API to actually present the group in an 'ungrouped' state.

V

viewGrouped(CyNetworkView, CyNetwork, CyNode, List, List, List) - Method in interface edu.ucsf.groups.view.GroupViewer

Show this group in a grouped state.

viewUngrouped(CyNetworkView, CyNetwork, CyNode, List, List, List) - Method in interface edu.ucsf.groups.view.GroupViewer

Show this group in an ungrouped state.

A C D E G I R S U V