/// <summary>
/// Saves products of a SBML reaction into a dictionary, containing their compartment and SpeciesReference.
/// </summary>
private Dictionary <string, List <SpeciesReference> > ComputeProducts(Reaction sbmlReaction, Model model)
{
var productCompartmentMoleculeDictionary = new Dictionary <string, List <SpeciesReference> >();
for (long i = 0; i < sbmlReaction.getNumProducts(); i++)
{
var product = sbmlReaction.getProduct(i);
var productSpecies = GetSpeciesById(product.getSpecies(), model);
var compartment = productSpecies.getCompartment();
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != productSpecies.getId())))
{
continue;
}
if (!productCompartmentMoleculeDictionary.ContainsKey(compartment))
{
productCompartmentMoleculeDictionary[compartment] = new List <SpeciesReference> {
product
}
}
;
else
{
productCompartmentMoleculeDictionary[compartment].Add(product);
}
}
return(productCompartmentMoleculeDictionary);
}
/// <summary>
/// Creates a multicompartment reaction.
/// </summary>
private void CreateMulticompartmentReaction(Reaction sbmlReaction, Model model)
{
if ((sbmlReaction.getNumReactants() + sbmlReaction.getNumProducts() == 2) && (IsPassiveTransport(sbmlReaction, model)))
{
CreatePassiveTransport(sbmlReaction, model);
}
else
{
CreateGhostReaction(sbmlReaction, model);
}
}
/// <summary>
/// Creates the Products of the MoBi reaction.
/// </summary>
private void CreateProducts(Reaction sbmlReaction, IReactionBuilder reactionBuilder, Model model)
{
for (long i = 0; i < sbmlReaction.getNumProducts(); i++)
{
var product = CreateReactionPartner(sbmlReaction.getProduct(i), model);
if (product != null)
{
reactionBuilder.AddProduct(product);
}
}
}
public void test_Reaction_addProduct1()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(2,2);
SpeciesReference p1 = new SpeciesReference(2,2);
p1.setSpecies( "k");
p1.setId( "k1");
int i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
p.setSpecies( "k");
p.setId( "k1");
i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumProducts() == 1 );
i = m.addProduct(p1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumProducts() == 1 );
p = null;
p1 = null;
m = null;
}
/// <summary>
/// Checks if all reaction partners are in the same compartment.
/// </summary>
private bool IsMultiCompartmentReaction(Reaction sbmlReaction, Model model)
{
var compartment = String.Empty;
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var x = sbmlReaction.getReactant(i).getSpecies();
var species = GetSpeciesById(x, model);
if (compartment == String.Empty)
{
compartment = species.getCompartment();
}
else
{
if (compartment != species.getCompartment())
{
return(true);
}
}
}
for (long i = 0; i < sbmlReaction.getNumProducts(); i++)
{
var x = sbmlReaction.getProduct(i).getSpecies();
var species = GetSpeciesById(x, model);
if (compartment == String.Empty)
{
compartment = species.getCompartment();
}
else
{
if (compartment != species.getCompartment())
{
return(true);
}
}
}
return(false);
}
public void test_Reaction_addProduct3()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(1,2);
p.setSpecies( "k");
int i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumProducts() == 0 );
p = null;
m = null;
}
public void test_Reaction_createProduct()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = m.createProduct();
assertTrue( m.getNumProducts() == 1 );
assertTrue( (p).getLevel() == 2 );
assertTrue( (p).getVersion() == 2 );
m = null;
}
public void test_Reaction_addProduct4()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = null;
int i = m.addProduct(p);
assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED );
assertTrue( m.getNumProducts() == 0 );
m = null;
}