Cytoscape Wiki|
← Revision 1 as of 2006-03-03 16:46:45 →
Size: 756
Comment:
|
Size: 2514
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| * GaryBader - What is the definition of a group in Cytoscape? Is it just a set? If so, what things can be in the set? Is this correct? "A group is a set of one or more nodes (CyNode) and zero or more edges (CyEdge) that connect nodes in the group. A group can be treated as a node (CyNode) itself by being the source or target of an edge." | * GaryBader - What is the definition of a group in Cytoscape? Is it just a set? If so, what things can be in the set? Is this correct? "A group is a set of one or more nodes (CyNode) and zero or more edges (CyEdge) that connect nodes in the group. A group can be treated as a node (CyNode) itself by being the source or target of an edge." |
| Line 6: | Line 6: |
|
* IlianaAvila - In the interfaces I created, the word {{{group}}} is always closely tied to the relationship between a subnetwork and its containing network: * {{{GroupManager.addGroupToNetwork(network, subnetwork)}}}: record the fact that {{{subnetwork}}} is a group in {{{network}}} * {{{GroupingStrategy.group(network, subnetwork)}}}: depict {{{subnetwork}}} as a group in {{{network}}} The reason why I don't simply call a {{{group}}} a {{{subnetwork}}} or a {{{network}}} is because the word {{{group}}} suggests that the nodes and edges contained in it are held together by a special relationship that other subnetworks in the containing network don't have. So, the word {{{group}}} could also be seen as an adjective for {{{subnetwork}}}: a {{{grouped subnetwork}}} is a subnetwork that has been deemed to be a special subnetwork (because its nodes and/or edges are related to each other in some special way) in the containing network. Does that make sense? I hope so...would the interface make more sense if the methods looked like this?: * {{{GroupManager.markSubnetworkAsGroup(network,subnetwork)}}} * {{{GroupingStrategy.groupSubnetwork(network, subnetwork)}}} * GaryBader - Can a group be used as a CyNode? Can I create a CyEdge that has a group as a source or target? * IlianaAvila - You should be able to. To depict a group as a {{{CyNode}}} you use the {{{COLLAPSING_STRATEGY}}}. Then, there needs to be a way of the user obtaining the {{{CyNode}}} that represents the group. This could be done in a number of ways. One of them could be changing the returned object of the {{{GroupingStrategy.group(network,subnetwork)}}} method from a boolean to an {{{Object}}} that the user should cast to the appropriate type. |
GaryBader - What is the definition of a group in Cytoscape? Is it just a set? If so, what things can be in the set? Is this correct? "A group is a set of one or more nodes (CyNode) and zero or more edges (CyEdge) that connect nodes in the group. A group can be treated as a node (CyNode) itself by being the source or target of an edge."
I said one or more nodes because I assume it doesn't make sense for a group to have zero nodes - is that true? Maybe there is a case for a group to have zero nodes.
This is different than the hyperedge, which is a set of two or more nodes. The hyperedge cannot contain other edges and cannot be treated as a node itself. (I'm assuming that it doesn't make sense to create a hyperedge with 0 or 1 nodes).
IlianaAvila - In the interfaces I created, the word group is always closely tied to the relationship between a subnetwork and its containing network:
GroupManager.addGroupToNetwork(network, subnetwork): record the fact that subnetwork is a group in network
GroupingStrategy.group(network, subnetwork): depict subnetwork as a group in network
The reason why I don't simply call a group a subnetwork or a network is because the word group suggests that the nodes and edges contained in it are held together by a special relationship that other subnetworks in the containing network don't have. So, the word group could also be seen as an adjective for subnetwork: a grouped subnetwork is a subnetwork that has been deemed to be a special subnetwork (because its nodes and/or edges are related to each other in some special way) in the containing network. Does that make sense? I hope so...would the interface make more sense if the methods looked like this?:
GroupManager.markSubnetworkAsGroup(network,subnetwork)
GroupingStrategy.groupSubnetwork(network, subnetwork)
GaryBader - Can a group be used as a CyNode? Can I create a CyEdge that has a group as a source or target?
IlianaAvila - You should be able to. To depict a group as a CyNode you use the COLLAPSING_STRATEGY. Then, there needs to be a way of the user obtaining the CyNode that represents the group. This could be done in a number of ways. One of them could be changing the returned object of the GroupingStrategy.group(network,subnetwork) method from a boolean to an Object that the user should cast to the appropriate type.