void toNormalizedNEXUS(ifstream & inf, ostream *os)
{
NxsTaxaBlock taxa;
NxsTreesBlock trees(&taxa);
NxsAssumptionsBlock assumptions(&taxa);
NxsCharactersBlock character(&taxa, &assumptions);
NxsDataBlock data(&taxa, &assumptions);
NxsDistancesBlock distances(&taxa);
NxsUnalignedBlock unaligned(&taxa, &assumptions);
NormalizingReader nexus(os);
nexus.Add(&taxa);
nexus.Add(&trees);
nexus.Add(&assumptions);
nexus.Add(&character);
nexus.Add(&data);
nexus.Add(&distances);
nexus.Add(&unaligned);
if (os)
{
*os << "#NEXUS\n";
}
NormalizingToken token(inf, os);
nexus.Execute(token);
}
z3::check_result Z3AssumptionSolverImpl::check(const Query &query) {
std::list<ConditionNodeRef> cur_constraints;
for (ConditionNodeRef node = query.constraints.head(),
root = query.constraints.root();
node != root; node = node->parent()) {
cur_constraints.push_front(node);
}
z3::expr_vector assumptions(context_);
for (std::list<ConditionNodeRef>::iterator it = cur_constraints.begin(),
ie = cur_constraints.end(); it != ie; ++it) {
assumptions.push_back(getAssumption((*it)->expr()));
}
assumptions.push_back(getAssumption(Expr::createIsZero(query.expr)));
return solver_.check(assumptions);
}
