Re: [jgrapht-users] Getting all connected sets of a graph as graphs

[Tim J. <ts...@rc...>]

 Hi,

 On Mon, 25 Apr 2011 22:26:13 -0700, John Sichi <js...@gm...> 
 wrote:

> Does your ProteinGraph add anything interesting?  If not, you might
> consider discarding it and just using the out-of-the-box classes
> directly.

 Yes, it adds some functions that are specific for protein graphs, e.g. 
 determining the N-terminus and T-terminus of the protein chain and 
 returning different linear notations for protein graphs. I also plan to 
 add functions that draw the graph and write them to an image file.

 But I think my current way of implementing the ProteinGraph class is 
 far from perfect. I'll start a new thread for this though.

> If you need it for some reason, then either do what you said at the
> end to make copies of the subgraphs (using Graphs.addGraph), or else
> make ProteinGraph an interface and create subclasses for extending
> SimpleGraph and UndirectedSubgraph.

 Thanks a lot for, I didn't know about Graphs.addGraph() and it does 
 exactly what I wanted. Here's what I do now:

 List<Set<SSE>> conVertSets = ci.connectedSets();
 
 // Create graphs out of the connected sets
 for(Integer j = 0; j < conVertSets.size(); j++) {

             UndirectedSubgraph<SSE, LabeledEdge> sg = new 
 UndirectedSubgraph<SSE, LabeledEdge>(g, conVertSets.get(j), null);
             ProteinGraph<SSE, LabeledEdge> psg = new ProteinGraph<SSE, 
 LabeledEdge>(new ClassBasedEdgeFactory<SSE, 
 LabeledEdge>(LabeledEdge.class));
             Graphs.addGraph(psg, sg);
 }

 This works. :)


-- 
 Tim