/// <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;
}
}
}
}