edu.ucsf.groups.data
Interface GroupAttributesHandler

public interface GroupAttributesHandler

An interface for classes that handle the node and edge attributes of groups. Since there are many different ways of transfering node and edge attributes from children nodes and edges to their parent nodes, we need an interface that then can be implemented by classes so that they can handle this operation as they desire.

Field Summary

static String

DEFAULT_NODE_LABEL_ATTRIBUTE 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

Method Summary

String	assignName(CyNetwork cy_net, CyNode node) Creates a unique name for the CyNode and registers this name and node into Cytoscape
String	getDefaultNodeLabelAttribute() Returns the current default node label attribute.
String	getNodeLabelAttribute() 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
boolean	removeFromAttributes(CyNetwork cy_network, CyNode group_node, List meta_edge_list) Removes all attributes created for the given group node
boolean	removeMetaEdgesFromAttributes(CyNetwork cy_network, CyNode group_node, List meta_edge_list) Remove attributes for the given meta-edges in CyNetwork, but leave the attributes for the group node as they are.
boolean	setAttributes(CyNetwork cy_network, CyNode group_node, List members, cern.colt.map.AbstractIntIntMap meta_edge_to_child_edge) Sets the node and edge attributes of the meta-node
boolean	setEdgeAttributes(CyNetwork cy_network, CyNode group_node, cern.colt.map.AbstractIntIntMap meta_edge_to_child_edge) Sets the edge attributes of the group node
boolean	setNodeAttributes(CyNetwork cy_network, CyNode group_node, List children) Sets the node attributes of the group node
void	setNodeLabelAttribute(String attribute_name) 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

Field Detail

DEFAULT_NODE_LABEL_ATTRIBUTE

static final String DEFAULT_NODE_LABEL_ATTRIBUTE

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

See Also:

Constant Field Values

Method Detail

getDefaultNodeLabelAttribute

String getDefaultNodeLabelAttribute()

Returns the current default node label attribute.

Returns:

the String representing the default node label.

setNodeLabelAttribute

void setNodeLabelAttribute(String attribute_name)

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

Parameters:

attribute_name - the name of a node attribute of type String

getNodeLabelAttribute

String getNodeLabelAttribute()

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

Returns:

a String representing the name of the node attribute

assignName

String assignName(CyNetwork cy_net,
                  CyNode node)

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

Parameters:

cy_net - the CyNetwork where the node is contained

node - the node

Returns:

the name, or null if something went wrong

setAttributes

boolean setAttributes(CyNetwork cy_network,
                      CyNode group_node,
                      List members,
                      cern.colt.map.AbstractIntIntMap meta_edge_to_child_edge)

Sets the node and edge attributes of the meta-node

Parameters:

cy_network - the CyNetwork that contains the member nodes of the group

group_node - the group node

members - an array of CyNodes that are the member nodes of "node"

meta_edge_to_child_edge - maps a meta-edge (edge connected to the group_node) to a child edge (edge that connects a member of the group node to another node) so that classes implementing this interface know which child edge corresponds to which meta-edge

Returns:

true if all went well, false if there was an error

setNodeAttributes

boolean setNodeAttributes(CyNetwork cy_network,
                          CyNode group_node,
                          List children)

Sets the node attributes of the group node

Parameters:

cy_network - the CyNetwork that contains the member nodes of "node"

group_node - the group node for which node attributes will be set

children - an List of CyNodes that are members of the given node

Returns:

true if all went well, false if there was an error

setEdgeAttributes

boolean setEdgeAttributes(CyNetwork cy_network,
                          CyNode group_node,
                          cern.colt.map.AbstractIntIntMap meta_edge_to_child_edge)

Sets the edge attributes of the group node

Parameters:

cy_network - the CyNetwork that contains the member nodes of "node"

group_node - the group node for which edge attributes will be set

meta_edge_to_child_edge - maps a meta-edge (edge connected to the group node) to a child edge (edge that connects a child of the group node to another node) so that classes implementing this interface know which child edge corresponds to which meta-edge

Returns:

true if all went well, false if there was an error

removeFromAttributes

boolean removeFromAttributes(CyNetwork cy_network,
                             CyNode group_node,
                             List meta_edge_list)

Removes all attributes created for the given group node

Parameters:

cy_network - were the members for the group live

group_node - the group node

meta_edge_list - the edges connected to the group node whose attributes should alse be removed

Returns:

true if all went well, false otherwise

removeMetaEdgesFromAttributes

boolean removeMetaEdgesFromAttributes(CyNetwork cy_network,
                                      CyNode group_node,
                                      List meta_edge_list)

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

Parameters:

cy_network - the CyNetwork where the meta-edges are

group_node - the group node

meta_edge_list - a list of CyEdges for which the attributes should be removed

Returns:

true if all went well, false otherwise