private void processRule(ReactionRule r) throws SaveFailedException {
if (!iteratorsMatched(r.getRedex().getRoots().iterator(), r.getReactum().getRoots().iterator()))
throw new SaveFailedException("Same number of roots required in redex and reactum");
if (namedRules) write("%rule r_" + (i++) + " "); /* XXX FIXME */
processBigraph(r.getRedex(), false);
write(" -> ");
processBigraph(r.getReactum(), false);
write(";\n");
}
private void processSignature(SimulationSpec ss) throws SaveFailedException {
write("# Controls\n");
if (recProcessSignature(new ArrayList<String>(), ss.getSignature())) {
recHandleParams(ss.getModel());
for (ReactionRule r : ss.getRules()) {
recHandleParams(r.getRedex());
recHandleParams(r.getReactum());
}
}
write("\n");
}
private void processNames(SimulationSpec s) throws SaveFailedException {
ArrayList<String> names = new ArrayList<String>();
String name;
for (ReactionRule r : s.getRules()) {
for (IInnerName i : r.getRedex().getInnerNames()) {
name = "%innername " + normaliseName(i.getName());
if (!validateSameName(names, name)) {
names.add(name);
}
}
for (IOuterName o : r.getRedex().getOuterNames()) {
name = "%outername " + normaliseName(o.getName());
if (!validateSameName(names, name)) {
names.add(name);
}
}
for (IInnerName i : r.getReactum().getInnerNames()) {
name = "%innername " + normaliseName(i.getName());
if (!validateSameName(names, name)) {
names.add(name);
}
}
for (IOuterName o : r.getReactum().getOuterNames()) {
name = "%outername " + normaliseName(o.getName());
if (!validateSameName(names, name)) {
names.add(name);
}
}
}
for (IInnerName i : s.getModel().getInnerNames()) {
name = "%innername " + normaliseName(i.getName());
if (!validateSameName(names, name)) {
names.add(name);
}
}
for (IOuterName o : s.getModel().getOuterNames()) {
name = "%outername " + normaliseName(o.getName());
if (!validateSameName(names, name)) {
names.add(name);
}
}
Collections.sort(names);
if (names.size() == 0) return;
write("# Names\n");
for (String n : names) write(n + ";\n");
write("\n");
}