On Jul 24, 2009, at 10:42 AM, Kenny Daily wrote:
>
> I guess what I mean then is how are the edges assigned in the graph?
> When you do something like:
>
>>>> G[exon1][exon2] = some_edge
>
> what is 'some_edge'? Is it an index? Is it an object created from the
> database?
Ordinarily, just like exon1 and exon2, it is an object from a
database, in this case from edgeDB. Alternatively, in the
modification that you and I were discussing, it became simply an int,
that would be stored directly.
>
> How does the Graph object know that there is an edge between exon1 and
> exon2, just by creating Graph(sourceDB=exonDB, targetDB=exonDB,
> edgeDB=spliceDB)?
Instantiating a Graph object creates an *empty* graph, to which you
then add nodes via
graph += node
and add edges via
graph[node1][node2] = edge
When you instantiate the Graph object, you are just telling it your
*schema* ("I want to create a graph that maps source nodes from
sourceDB to target nodes from targetDB, with edge information from
edgeDB").
-- Chris
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