/// <summary>
/// Saves educts of a SBML reaction into a dictionary, containing their compartment and SpeciesReference.
/// </summary>
private Dictionary <string, List <SpeciesReference> > ComputeEducts(Reaction sbmlReaction, Model model)
{
var eductCompartmentMoleculeDictionary = new Dictionary <string, List <SpeciesReference> >();
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var reactant = sbmlReaction.getReactant(i);
var reactantSpecies = GetSpeciesById(reactant.getSpecies(), model);
var compartment = reactantSpecies.getCompartment();
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != reactantSpecies.getId())))
{
continue;
}
if (!eductCompartmentMoleculeDictionary.ContainsKey(compartment))
{
eductCompartmentMoleculeDictionary[compartment] = new List <SpeciesReference> {
reactant
}
}
;
else
{
eductCompartmentMoleculeDictionary[compartment].Add(reactant);
}
}
return(eductCompartmentMoleculeDictionary);
}
/// <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 Educts of the MoBi reaction.
/// </summary>
private void CreateEducts(Reaction sbmlReaction, IReactionBuilder reactionBuilder, Model model)
{
for (long i = 0; i < sbmlReaction.getNumReactants(); i++)
{
var educt = CreateReactionPartner(sbmlReaction.getReactant(i), model);
if (educt != null)
{
reactionBuilder.AddEduct(educt);
}
}
}
/// <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_createReactant()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = m.createReactant();
assertTrue( m.getNumReactants() == 1 );
assertTrue( (p).getLevel() == 2 );
assertTrue( (p).getVersion() == 2 );
m = null;
}
public void test_Reaction_addReactant4()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = null;
int i = m.addReactant(p);
assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED );
assertTrue( m.getNumReactants() == 0 );
m = null;
}
public void test_Reaction_addReactant3()
{
Reaction m = new Reaction(2,2);
SpeciesReference p = new SpeciesReference(1,2);
p.setSpecies( "k");
int i = m.addReactant(p);
assertTrue( i == libsbml.LIBSBML_LEVEL_MISMATCH );
assertTrue( m.getNumReactants() == 0 );
p = null;
m = null;
}
public void test_Reaction_addReactant1()
{
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.addReactant(p);
assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT );
p.setSpecies( "k");
p.setId( "k1");
i = m.addReactant(p);
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
assertTrue( m.getNumReactants() == 1 );
i = m.addReactant(p1);
assertTrue( i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID );
assertTrue( m.getNumReactants() == 1 );
p1 = null;
p = null;
m = null;
}