private void addLiverZoneCompartmentObserver(IObserverBuilder observerBuilder, string compartment, IObserverBuildingBlock observerBuildingBlock, Compound compound)
{
var observerName = CoreConstants.CompositeNameFor(observerBuilder.Name, CoreConstants.Organ.Liver, compartment);
if (observerBuildingBlock.ExistsByName(observerName))
{
return;
}
var observer = _objectBaseFactory.Create <IContainerObserverBuilder>()
.WithName(observerName)
.WithDimension(_dimensionRepository.Fraction);
observer.ForAll = false;
observerBuilder.MoleculeNames().Each(observer.AddMoleculeName);
observer.ContainerCriteria = Create.Criteria(x => x.With(CoreConstants.Organ.Liver)
.And.With(compartment)
.And.Not(CoreConstants.Compartment.Pericentral)
.And.Not(CoreConstants.Compartment.Periportal));
var formula = _objectBaseFactory.Create <ExplicitFormula>()
.WithName(observerName)
.WithFormulaString("(M_periportal + M_pericentral)/" + TOTAL_DRUG_MASS_ALIAS)
.WithDimension(_dimensionRepository.Fraction);
formula.AddObjectPath(createZoneAmoutPath(compartment, CoreConstants.Compartment.Periportal, "M_periportal"));
formula.AddObjectPath(createZoneAmoutPath(compartment, CoreConstants.Compartment.Pericentral, "M_pericentral"));
formula.AddObjectPath(createTotalDrugMassObjectPath(compound.Name));
observer.Formula = formula;
observerBuildingBlock.Add(observer);
observerBuildingBlock.AddFormula(formula);
}
protected override void Context()
{
base.Context();
_observer = new ObserverBuilder().WithName("NNNNNN");
_observer.ContainerCriteria.Add(new MatchTagCondition(_changedName));
_observerBuildingBlock = new ObserverBuildingBlock().WithName("Observer").WithId("Observer");
_observerBuildingBlock.Add(_observer);
}
private IContainerObserverBuilder createContainerFractionObserver(string observerName, IObserverBuildingBlock observerBuildingBlock, Func <IFormula> getFormula)
{
var observer = _objectBaseFactory.Create <IContainerObserverBuilder>()
.WithName(observerName)
.WithDimension(_dimensionRepository.Fraction)
.WithFormula(getFormula());
observerBuildingBlock.Add(observer);
return(observer);
}
private void addStandardObserversTo(Simulation simulation, IObserverBuildingBlock observerBuildingBlock, IMoleculeBuildingBlock moleculeBuildingBlock)
{
var allMoleculesNeedingConcentrationObservers = moleculeBuildingBlock.Where(concentrationIsNeeded).Select(x => x.Name).ToList();
var compoundNames = simulation.CompoundNames;
foreach (var observerTemplate in _observerBuilderRepository.AllFor(simulation.ModelProperties))
{
if (isDrugFcRnObserver(observerTemplate))
{
//special case: protein model observer for drug and its FcRn complex.
//Observer must be created separately for every drug because complexname can not be referenced in generic way by now
//E.g.: for drug C1, Observer is f("C1", "C1-FcRn_Complex"))
foreach (var compoundName in compoundNames)
{
var observer = _cloneManager.Clone(observerTemplate.ObserverBuilder, observerBuildingBlock.FormulaCache);
observer.Name = CoreConstants.Observer.ObserverNameFrom(observer.Name, compoundName);
observer.Formula.ReplaceKeywordsInObjectPaths(
new[] { CoreConstants.Molecule.DrugFcRnComplexTemplate },
new[] { CoreConstants.Molecule.DrugFcRnComplexName(compoundName) }
);
observer.AddMoleculeName(compoundName);
observerBuildingBlock.Add(observer);
}
}
else
{
var observer = _cloneManager.Clone(observerTemplate.ObserverBuilder, observerBuildingBlock.FormulaCache);
compoundNames.Each(observer.AddMoleculeName);
if (observer.IsConcentration())
{
allMoleculesNeedingConcentrationObservers.Each(observer.AddMoleculeName);
}
observerBuildingBlock.Add(observer);
}
}
}
protected override void Context()
{
base.Context();
var monitor = new ExplicitFormula("TotalDrugMass");
var observer = new ContainerObserverBuilder().WithName("Tralala").WithFormula(monitor);
_totalDrugMassReference = new FormulaUsablePath(new[] { "Applications", "TotalDrugMass" }).WithAlias("TotalDrugMass");
monitor.AddObjectPath(_totalDrugMassReference);
_observerBuildingBlock = new ObserverBuildingBlock();
_observerBuildingBlock.Add(observer);
}
private IAmountObserverBuilder createFractionObserver(string observerName, IObserverBuildingBlock observerBuildingBlock, Func <IFormula> getFormula)
{
var observer = _objectBaseFactory.Create <IAmountObserverBuilder>()
.WithName(observerName)
.WithDimension(_dimensionRepository.Fraction)
.WithFormula(getFormula());
observer.ContainerCriteria.Add(new MatchAllCondition());
observerBuildingBlock.Add(observer);
return(observer);
}
