/// <summary>
/// Sets the Parameter Start Value of a given Parameter to the given Math Formula.
/// </summary>
protected internal void SetPSV(ASTNode math, IParameter parameter, string containerName)
{
if (parameter == null)
{
CreateErrorMsg();
return;
}
var formula = _astHandler.Parse(math, parameter.Name, false, _sbmlProject, _sbmlInformation);
if (formula == null)
{
return;
}
var psvbb = GetMainParameterStartValuesBuildingBlock();
if (psvbb == null)
{
return;
}
psvbb.AddFormula(formula);
foreach (var declaredPSV in psvbb.Where(declaredPSV => declaredPSV.Name == parameter.Name))
{
if (string.IsNullOrEmpty(containerName))
{
declaredPSV.Formula = formula;
return;
}
if (!declaredPSV.Path.Contains(containerName))
{
continue;
}
declaredPSV.Formula = formula;
return;
}
var psv = ObjectBaseFactory.Create <IParameterStartValue>()
.WithName(parameter.Name)
.WithFormula(formula)
.WithDimension(parameter.Dimension);
psvbb.Add(psv);
}
/// <summary>
/// Creates the Kinetic Formula for a passive Transport.
/// </summary>
private void CreateKinetic(Reaction sbmlReaction, ITransportBuilder passiveTransport)
{
_astHandler.NeedAbsolutePath = true;
var formula = sbmlReaction.getKineticLaw() == null
? ObjectBaseFactory.Create <ExplicitFormula>().WithFormulaString(String.Empty)
: _astHandler.Parse(sbmlReaction.getKineticLaw().getMath(), sbmlReaction.getId(), _sbmlProject, _sbmlInformation);
if (formula == null)
{
passiveTransport.Formula = ObjectBaseFactory.Create <ExplicitFormula>()
.WithFormulaString(String.Empty)
.WithName(SBMLConstants.DEFAULT_FORMULA_NAME);
}
else
{
passiveTransport.Formula = formula;
_passiveTransportBuildingBlock.FormulaCache.Add(formula);
}
}
/// <summary>
/// Creates the MoBi Reaction Formula by the given SBML Kinetic Law.
/// </summary>
private void CreateKineticLaw(KineticLaw kineticLaw, IReactionBuilder reactionBuilder, bool needAbsolutePath)
{
if (needAbsolutePath)
{
_astHandler.NeedAbsolutePath = true;
}
var formula = kineticLaw == null?ObjectBaseFactory.Create <ExplicitFormula>().WithFormulaString(String.Empty).WithName(SBMLConstants.DEFAULT_FORMULA_NAME) : _astHandler.Parse(kineticLaw.getMath(), reactionBuilder, _sbmlProject, _sbmlInformation);
if (formula == null)
{
reactionBuilder.Formula = ObjectBaseFactory.Create <ExplicitFormula>()
.WithFormulaString(String.Empty)
.WithName(SBMLConstants.DEFAULT_FORMULA_NAME);
}
else
{
reactionBuilder.Formula = formula;
_reactionBuildingBlock.FormulaCache.Add(formula);
}
}
/// <summary>
/// Creates a MoBi Parameter from a given SBML Parameter.
/// </summary>
public IFormulaUsable CreateParameter(Parameter sbmlParameter)
{
var value = 0.0;
if (sbmlParameter.isSetValue())
{
value = sbmlParameter.getValue();
}
if (!sbmlParameter.isSetUnits())
{
return(ObjectBaseFactory.Create <IParameter>()
.WithName(sbmlParameter.getId())
.WithFormula(ObjectBaseFactory.Create <ConstantFormula>().WithValue(value)));
}
var sbmlUnit = sbmlParameter.getUnits();
var baseValue = _unitDefinitionImporter.ToMobiBaseUnit(sbmlUnit, value);
return(ObjectBaseFactory.Create <IParameter>()
.WithName(sbmlParameter.getId())
.WithFormula(_formulaFactory.ConstantFormula(baseValue.value, baseValue.dimension))
.WithDimension(baseValue.dimension));
}
/// <summary>
/// Imports a SBML Reaction by creating a passive Transport.
/// </summary>
private void CreatePassiveTransport(Reaction sbmlReaction, Model model)
{
var reactant = sbmlReaction.getReactant(0).getSpecies();
var product = sbmlReaction.getProduct(0).getSpecies();
var reactantSpecies = GetSpeciesById(reactant, model);
var productSpecies = GetSpeciesById(product, model);
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != reactant)))
{
return;
}
if (_sbmlInformation.MoleculeInformation.All(info => info.SpeciesIds.TrueForAll(s => s != product)))
{
return;
}
var molInfoReactant = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(reactant));
var molInfoProduct = _sbmlInformation.MoleculeInformation.FirstOrDefault(info => info.SpeciesIds.Contains(product));
if (molInfoProduct == null)
{
return;
}
if (molInfoReactant == null)
{
return;
}
//must be the same Molecule
if (molInfoReactant.GetMoleculeBuilder() != molInfoProduct.GetMoleculeBuilder())
{
CreateErrorMessage();
}
var passiveTransport = ObjectBaseFactory.Create <ITransportBuilder>().WithName(sbmlReaction.getId());
passiveTransport.ForAll = false;
if (molInfoReactant.GetMoleculeBuilderName() == null)
{
return;
}
passiveTransport.MoleculeList.AddMoleculeName(molInfoReactant.GetMoleculeBuilderName());
var reactantCompartment = GetContainerFromCompartment_(molInfoReactant.GetCompartment(reactantSpecies));
var productCompartment = GetContainerFromCompartment_(molInfoProduct.GetCompartment(productSpecies));
if (reactantCompartment != null && productCompartment != null)
{
var reactantMatchTag = new MatchTagCondition(reactantCompartment.Name);
var productMatchTag = new MatchTagCondition(productCompartment.Name);
passiveTransport.SourceCriteria.Add(reactantMatchTag);
passiveTransport.TargetCriteria.Add(productMatchTag);
}
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(passiveTransport.AddParameter);
}
CreateKinetic(sbmlReaction, passiveTransport);
AddNeighbourhood(reactantCompartment, productCompartment, model);
_passiveTransportBuildingBlock.Add(passiveTransport);
}
/// <summary>
/// Creates for each compartment of the SBML Reaction one "Ghostreaction" to import multicompartment reactions.
/// </summary>
private void CreateGhostReactions(Reaction sbmlReaction, Dictionary <string, List <SpeciesReference> > eductCompartmentMoleculeDictionary, Dictionary <string, List <SpeciesReference> > productCompartmentMoleculeDictionary, Model model)
{
var usedProducts = new List <string>();
foreach (var keyValuePair in eductCompartmentMoleculeDictionary)
{
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId() + "_" + keyValuePair.Key + "_ghostReaction")
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, keyValuePair.Key, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, true);
var compartmentName = keyValuePair.Key;
if (!_sbmlInformation.DummyNameContainerDictionary.ContainsValue(compartmentName))
{
return;
}
var dummyMolecule = _sbmlInformation.DummyNameContainerDictionary.FirstOrDefault(x => x.Value == compartmentName).Key;
reactionBuilder.AddModifier(dummyMolecule);
foreach (var species in keyValuePair.Value)
{
var reactionPartner = CreateReactionPartner(species, model);
if (reactionPartner != null)
{
reactionBuilder.AddEduct(reactionPartner);
}
}
if (productCompartmentMoleculeDictionary.ContainsKey(keyValuePair.Key))
{
usedProducts.Add(keyValuePair.Key);
var productsInThisCompartment = productCompartmentMoleculeDictionary[keyValuePair.Key];
foreach (var product in productsInThisCompartment)
{
var reactionPartner = CreateReactionPartner(product, model);
if (reactionPartner != null)
{
reactionBuilder.AddProduct(reactionPartner);
}
}
}
ReactionBuilderList.Add(reactionBuilder);
}
foreach (var keyValuePair in productCompartmentMoleculeDictionary)
{
if (usedProducts.Contains(keyValuePair.Key))
{
continue;
}
var reactionBuilder = ObjectBaseFactory.Create <IReactionBuilder>()
.WithName(sbmlReaction.getId() + "_" + keyValuePair.Key + "_ghostReaction")
.WithDescription(sbmlReaction.getNotesString());
CreateModifiers(sbmlReaction, reactionBuilder, keyValuePair.Key, model);
var parameters = CreateLocalParameters(sbmlReaction);
if (parameters != null)
{
parameters.ForEach(reactionBuilder.AddParameter);
}
CreateKineticLaw(sbmlReaction.getKineticLaw(), reactionBuilder, true);
var compartmentName = keyValuePair.Key;
if (!_sbmlInformation.DummyNameContainerDictionary.ContainsValue(compartmentName))
{
return;
}
var dummyMolecule = _sbmlInformation.DummyNameContainerDictionary.FirstOrDefault(x => x.Value == compartmentName).Key;
reactionBuilder.AddModifier(dummyMolecule);
foreach (var species in keyValuePair.Value)
{
var reactionPartner = CreateReactionPartner(species, model);
if (reactionPartner != null)
{
reactionBuilder.AddProduct(reactionPartner);
}
}
ReactionBuilderList.Add(reactionBuilder);
}
}
/// <summary>
/// Creates the Molecule - and the Molecule Start Values Building Block.
/// </summary>
internal void CreateMoleculeBuildingBlock()
{
MoleculeBuildingBlock = ObjectBaseFactory.Create <IMoleculeBuildingBlock>()
.WithName(SBMLConstants.SBML_SPECIES_BB);
}