/// <summary>
/// Parses an Integer.
/// </summary>
private string parseInteger(ASTNode rootNode)
{
double value = rootNode.getInteger();
if (rootNode.isSetUnits() && _unitDefinitionImporter != null)
{
value = _unitDefinitionImporter.ToMobiBaseUnit(rootNode.getUnits(), value).value;
}
if (value.ToString(CultureInfo.InvariantCulture).Contains("-"))
{
return(SBMLConstants.LBRACE + rootNode.getInteger().ToString(CultureInfo.InvariantCulture) +
SBMLConstants.RBRACE);
}
return(value.ToString(CultureInfo.InvariantCulture));
}
/// <summary>
/// Sets all the autogenerated Molecule Start Values to the right values and updates their
/// "IsPresent" property.
/// </summary>
private void SetMoleculeStartValues(Model model)
{
foreach (var molInfo in _sbmlInformation.MoleculeInformation)
{
foreach (var msv in _moleculeStartValuesBuildingBlock)
{
if (msv.Name != molInfo.GetMoleculeBuilderName())
{
continue;
}
if (molInfo.GetContainer().Any(x => x.Name == msv.ContainerPath.LastOrDefault()))
{
msv.IsPresent = true;
msv.NegativeValuesAllowed = true;
var sbmlSpecies = molInfo.GetSpeciesIfOne();
if (sbmlSpecies == null)
{
return;
}
var sbmlUnit = GetUnit(sbmlSpecies, model);
var amountDimension = _unitDefinitionImporter.DimensionFor(sbmlUnit);
//unit is set by the Unit of SubstanceUnit
if (sbmlSpecies.isSetInitialAmount())
{
msv.StartValue = sbmlSpecies.getInitialAmount();
if (amountDimension != null)
{
msv.Dimension = amountDimension;
molInfo.SetDimension(amountDimension);
}
}
if (!sbmlSpecies.isSetInitialConcentration())
{
continue;
}
//unit is {unit of amount}/{unit of size}
var baseValue = _unitDefinitionImporter.ToMobiBaseUnit(sbmlUnit, sbmlSpecies.getInitialConcentration());
msv.StartValue = baseValue.value;
msv.Formula = _context.Create <ExplicitFormula>($"{msv.Name}_0").WithName($"{msv.Name}_0").WithDimension(amountDimension).WithFormulaString($"{baseValue.value} * {Constants.VOLUME_ALIAS}");
msv.Formula.AddObjectPath(
ObjectPathFactory.CreateFormulaUsablePathFrom(ObjectPath.PARENT_CONTAINER, Constants.Parameters.VOLUME)
.WithAlias(Constants.VOLUME_ALIAS)
.WithDimension(_moBiDimensionFactory.Dimension(Constants.Dimension.VOLUME))
);
_moleculeStartValuesBuildingBlock.AddFormula(msv.Formula);
msv.Dimension = amountDimension;
molInfo.SetDimension(amountDimension);
UseConcentrations = true;
}
else
{
msv.IsPresent = false;
msv.StartValue = 0;
}
}
}
}
/// <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>
/// Creates a Volume Parameter for a MoBi Container.
/// </summary>
private IEntity CreateVolumeParameter(Compartment compartment)
{
var volume = 1.0;
if (compartment.isSetVolume())
{
volume = compartment.getVolume();
}
else if (compartment.isSetSize())
{
volume = compartment.getSize();
}
var unit = compartment.getUnits();
var baseValue = _unitDefinitionImporter.ToMobiBaseUnit(unit, volume);
IFormula formula = _formulaFactory.ConstantFormula(baseValue.value, baseValue.dimension);
var volumeParameter = _objectBaseFactory.Create <IParameter>()
.WithName(SBMLConstants.VOLUME)
.WithDimension(baseValue.dimension)
.WithFormula(formula);
return(volumeParameter);
}