Version 3.0.0
Version 3.0.0
The umpteenth problem with the students' code led me to replace most
classes related to UPPAAL model generation and analysis (but not Model
itself.. yet) with the latest version from ANIMO 2.57 and re-apply by
hand the latest updates done in ANIMO 3. The problem was due to the
misinterpretation of Scenario 2 interactions, which led any model
containting scenario 2 to strange results. At the end, this was a
problem introduced indeed by the students project, but in Model: they
checked whether the IDs of the two upstream reactants in a Scenario 2
interaction were set before possibly setting them by hand automatically
to the edge's source and target respectively, but unfortunately they
checked the INVERSE of what was needed, ending up ALWAYS setting the
source and target as E1 and E2. Now it is solved, but we still use
Cytoscape 3's SUIDs instead of node/edge names (in Cytoscape 2.x known
as node.getIdentifier(), now known as the CyNetwork.NAME property in the
corresponding table), which results in compatibility issues with models
created in ANIMO 2.x. As the Cytoscape user manual suggests that
node/edge names should be unique for the SIF format networks to properly
work, we could just go back to using those as identifiers. Also the
SUIDs are kept between sessions: if I save a node with SUID 54, the next
time I open the model, that node will still have SUID 54 (that is
guaranteed); but if I import the same network again, the "new" nodes
will have different SUIDs. Probably the advantage coming from SUIDs is
that network copy/merge is made easier because we are ensured that we
always get fresh identifiers. However, I strongly doubt that any
reference to those SUIDs is also updated (indeed, doing so should be our
task because Cytoscape has no way nor right to check all table columns
of type Long or List<Long> to make sure that IDs are mapped correctly.
This means that there is probably no real advantage in using SUIDs also
for ANIMO features, and we can go back to names, gaining
retrocompatibility.