/// <summary>
/// This is for the special Species Assignment in a RateRule.
/// </summary>
private void DoSpeciesAssignment(Rule rule)
{
var formula = _astHandler.Parse(rule.getMath(), rule.getVariable(), true, _sbmlProject, _sbmlInformation);
if (formula == null)
{
return;
}
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(SBMLConstants.RATE_RULE + rule.getMetaId())
.WithFormula(formula);
var product = CreateProduct(rule.getVariable());
reactionBuilder.AddProduct(product);
var rbb = GetMainReactionBuildingBlock();
if (rbb == null)
{
rbb = _reactionBuildingBlockFactory.Create()
.WithName(SBMLConstants.SBML_REACTION_BB);
_context.AddToHistory(new AddBuildingBlockCommand <IMoBiReactionBuildingBlock>(rbb));
}
rbb.FormulaCache.Add(formula);
rbb.Add(reactionBuilder);
}
public ReactionImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoBiDimensionFactory moBiDimensionFactory, ASTHandler astHandler, IMoBiContext context, IReactionBuildingBlockFactory reactionBuildingBlockFactory)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_dimensionFactory = moBiDimensionFactory;
ReactionBuilderList = new List <IReactionBuilder>();
_passiveTransportList = new List <ITransportBuilder>();
_reactionBuildingBlock = reactionBuildingBlockFactory.Create().WithName(SBMLConstants.SBML_REACTION_BB);
_passiveTransportBuildingBlock = ObjectBaseFactory.Create <IPassiveTransportBuildingBlock>()
.WithName(SBMLConstants.SBML_PASSIVETRANSPORTS_BB);
}
private void generateDefaultsInCurrentProject()
{
addDefault <IMoleculeBuildingBlock>(AppConstants.DefaultNames.MoleculeBuildingBlock);
addDefault(AppConstants.DefaultNames.ReactionBuildingBlock, () => _reactionBuildingBlockFactory.Create());
addDefault(AppConstants.DefaultNames.SpatialStructure, () => _spatialStructureFactory.CreateDefault(AppConstants.DefaultNames.SpatialStructure));
addDefault <IPassiveTransportBuildingBlock>(AppConstants.DefaultNames.PassiveTransportBuildingBlock);
addDefault <IEventGroupBuildingBlock>(AppConstants.DefaultNames.EventBuildingBlock);
addDefault <IObserverBuildingBlock>(AppConstants.DefaultNames.ObserverBuildingBlock);
addDefault(AppConstants.DefaultNames.SimulationSettings, _simulationSettingsFactory.CreateDefault);
}
public override IMoBiReactionBuildingBlock CreateNewEntity(IMoBiProject parent)
{
return(_reactionBuildingBlockFactory.Create());
}