Now SUIDs are always used to identify Cytoscape nodes (and edges) in
ANIMO. If a model is from ANIMO 2.x (where we used String names as IDs),
the conversion is done automatically (when a session is loaded, see in
EventListener) to a 3.x-compatible model (the E1 and E2 references to
nodes are changed from String to Long with the references to the nodes
correctly kept). If that model is saved, it will NOT be usable in a 2.x
version of ANIMO.
If a model is from ANIMO 3.x, we still need to translated the references
to node SUIDs: we do it (also when the session is loaded) by just
translating each reference from its old (Long SUIDs) to its new (Long
SUIDs) value. Also this is only applied to the E1 and E2 references for
edges with a scenario[2].