Changed all the + "E1" with _E1, so we do have two constants
specifically to refer to the ID of the first upstream reactant and to
refer to its being active or inactive when for the interaction to have
an effect. Same thing with E2 as the second upstream reactant.
- Tried to set the node/edge IDs so that we can still accept and use
properly old ANIMO 2.x models (and possibly even save them so that they
can be re-opened with old ANIMO 2.x), while using (mostly) Cytoscape 3's
SUIDs. Also old simulations should be opened correctly, but the vice
versa is not true.
- Removed the node border width mapping, and just set border
transparency to 0 for disabled nodes. This allows us to mostly avoid
problems arising when both node color and border width mappings are
present. Also, removed the call to the "timed" network view update when
we move the slider
- Probably need to be tested more