public static Lst <Polynomize.PolyODE> PositivizeODEs(Lst <Polynomize.PolyODE> odes, Lst <Subst> substs, Style style)
{
//const int annihilationOrder = 1; // generation of annihilation reactions has been moved to Hungarize, otherwise two reactions are generated instead of one from the annihilation monomial
if (odes is Cons <Polynomize.PolyODE> cons)
{
Lst <Polynomize.PolyODE> tail = PositivizeODEs(cons.tail, substs, style);
Polynomize.PolyODE ode = cons.head;
Polynomial poly = Substitute(ode.poly, substs, style);
Subst subst = Lookup(ode.var, substs);
if (subst == null) // we do not split this ODE
{
return(new Cons <Polynomize.PolyODE>(new Polynomize.PolyODE(ode.var, poly, split: Polynomize.Split.No), tail));
}
else // we split this ODE
{
(Lst <Monomial> positive, Lst <Monomial> negative) = Separate(poly.monomials, style);
return(new Cons <Polynomize.PolyODE>(new Polynomize.PolyODE(subst.plus, positive, split: Polynomize.Split.Pos),
new Cons <Polynomize.PolyODE>(new Polynomize.PolyODE(subst.minus, negative, split: Polynomize.Split.Neg),
tail)));
//Monomial damp = new Monomial(Flow.minusOne, Factor.Cons(new Factor(subst.plus, annihilationOrder), Factor.Singleton(new Factor(subst.minus, annihilationOrder))), style); // annihilation monomial
//return new Cons<Polynomize.PolyODE>(new Polynomize.PolyODE(subst.plus, Monomial.Cons(damp, positive), split:Polynomize.Split.Pos),
// new Cons<Polynomize.PolyODE>(new Polynomize.PolyODE(subst.minus, Monomial.Cons(damp, negative), split:Polynomize.Split.Neg),
// tail));
}
}
else
{
return(Polynomize.PolyODE.nil);
}
}
// substitute x with (x+ - x-) in a flow that is already in polynomial form as a result of Polynomize
public static Lst <Polynomize.PolyODE> Substitute(Lst <Polynomize.PolyODE> odes, Lst <Subst> substs, Style style)
{
if (odes is Cons <Polynomize.PolyODE> cons)
{
Polynomize.PolyODE ode = cons.head;
Subst subst = Lookup(ode.var, substs);
if (subst == null)
{
return(new Cons <Polynomize.PolyODE>(new Polynomize.PolyODE(ode.var, Substitute(ode.poly, substs, style), ode.split),
Substitute(cons.tail, substs, style)));
}
else // this should never happen because we split ODEs in PositivizeODEs
{
throw new Error("Polynomize.Substitute");
//return
// new Cons<Polynomize.PolyODE>(new Polynomize.PolyODE(subst.plus, Substitute(ode.poly, substs, style)),
// new Cons<Polynomize.PolyODE>(new Polynomize.PolyODE(subst.minus, Substitute(ode.poly, substs, style)),
// Substitute(cons.tail, substs, style)));
}
}
else
{
return(Polynomize.PolyODE.nil);
}
}
public static Polynomize.PolyODE Rename(Dictionary <Symbol, SpeciesFlow> dict, Polynomize.PolyODE ode, Style style)
{
return(new Polynomize.PolyODE(
dict.ContainsKey(ode.var.species) ? dict[ode.var.species] : ode.var,
new Polynomial(Rename(dict, ode.poly.monomials, style)), ode.split));
}