public void testRenaming()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = "species1";
species1.InitialAmount = 4.0d;
species1.InitialConcentration = 7.0d;
species1.xPosition = 2.0f;
// Set some values for species2 that has the same id and same values
species2.ID = "species2";
species2.InitialAmount = 4.0d;
species2.InitialConcentration = 7.0d;
species2.xPosition = 2.0f;
// Add to the model
model.AddId(species1.ID, species1);
model.AddId(species2.ID, species2);
// Rename
species1.ID = "new_species1";
// Check the id in the species object
Assert.AreEqual("new_species1", species1.ID);
Assert.AreEqual("species1", species1.getOldID());
model.updateID(species1);
// Check the ids in the model
Assert.IsTrue(model.idExists("new_species1"));
Assert.IsTrue(model.idExists("species2"));
Assert.IsFalse(model.idExists("species1"));
}
public void testInterrogateModelForIDs()
{
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species3 = new MuCell.Model.SBML.Species();
species1.ID = "species1";
species2.ID = "species2";
species3.ID = "species 3";
model.AddId("species1", species1);
MuCell.Model.SBML.Reaction r1 = new MuCell.Model.SBML.Reaction();
MuCell.Model.SBML.SpeciesReference sp1r = new MuCell.Model.SBML.SpeciesReference();
sp1r.species = species1;
MuCell.Model.SBML.SpeciesReference sp2r = new MuCell.Model.SBML.SpeciesReference();
sp2r.species = species2;
MuCell.Model.SBML.SpeciesReference sp3r = new MuCell.Model.SBML.SpeciesReference();
sp3r.species = species3;
r1.Reactants.Add(sp1r);
r1.Reactants.Add(sp2r);
r1.Products.Add(sp3r);
MuCell.Model.SBML.KineticLaw kl = new MuCell.Model.SBML.KineticLaw(model);
r1.KineticLaw = kl;
MuCell.Model.SBML.Parameter k1 = new MuCell.Model.SBML.Parameter();
k1.ID = "k1";
r1.Parameters.Add(k1);
r1.Formula = "species1*species_3*k1";
model.listOfSpecies.Add(species1);
model.listOfReactions.Add(r1);
// Assert the unknown entities
Assert.AreEqual(2, r1.KineticLaw.UnknownEntitiesFromFormula().Count);
Assert.AreEqual("species_3", r1.KineticLaw.UnknownEntitiesFromFormula().ToArray()[0].ID);
Assert.AreEqual("k1", r1.KineticLaw.UnknownEntitiesFromFormula().ToArray()[1].ID);
// Assert missing items in model
Assert.IsTrue(model.idExists("species1"));
Assert.IsFalse(model.idExists("species2"));
Assert.IsFalse(model.idExists("species 3"));
Assert.IsFalse(model.idExists("k1"));
model.InterrogateModelForMissingIDs();
// redo formula
r1.Formula = "species1*species_3*k1";
// assert no unknown entities
Assert.AreEqual(0, r1.KineticLaw.UnknownEntitiesFromFormula().Count);
// Assert everything is in the model
Assert.IsTrue(model.idExists("species1"));
Assert.IsTrue(model.idExists("species2"));
Assert.IsTrue(model.idExists("species 3"));
Assert.IsTrue(model.idExists("k1"));
}