private IMoleculeStartValuesBuildingBlock createStartValuesBasedOnUsedTemplates(IMoleculeStartValuesBuildingBlock moleculeStartValues)
{
var molecules = BuildingBlockById <IMoleculeBuildingBlock>(moleculeStartValues.MoleculeBuildingBlockId);
var spatialStructure = BuildingBlockById <ISpatialStructure>(moleculeStartValues.SpatialStructureId);
return(_startValuesCreator.CreateFrom(spatialStructure, molecules));
}
private void CreateMoleculeStartValueBuildingBlock(Model model)
{
_moleculeStartValuesBuildingBlock = _moleculeStartValuesCreator.CreateFrom(GetMainSpatialStructure(model),
MoleculeBuildingBlock)
.WithId(SBMLConstants.SBML_MOLECULESTARTVALUES_BB)
.WithName(SBMLConstants.SBML_MOLECULESTARTVALUES_BB)
.WithDescription(SBMLConstants.SBML_MOLECULESTARTVALUES_DESCRIPTION);
}
public IMoleculeStartValuesBuildingBlock CreateFor(IBuildConfiguration buildConfiguration, Simulation simulation)
{
//default molecule start values matrix
var compounds = simulation.Compounds;
var defaultStartValues = _moleculeStartValuesCreator.CreateFrom(buildConfiguration.SpatialStructure, buildConfiguration.Molecules);
//set available start formulas for molecules
setStartFormulasForStaticMolecules(defaultStartValues, simulation, compounds);
foreach (var protein in simulation.Individual.AllMolecules())
{
var allMoleculesObjectPath = moleculesInvolvedInExpression(buildConfiguration.SpatialStructure, protein, simulation.CompoundPropertiesList);
//path involved expression might not exist in the start values structure=>hence check that they are not null
var allAvailbleStartValues = allMoleculesObjectPath.Select(objectPath => defaultStartValues[objectPath]).Where(msv => msv != null);
//the one found should be set to present
allAvailbleStartValues.Each(msv => msv.IsPresent = true);
}
return(defaultStartValues.WithName(simulation.Name));
}
private IBuildConfiguration createBuildConfiguration()
{
var buildConfiguration = new BuildConfigurationForSpecs();
buildConfiguration.Molecules = getMolecules();
buildConfiguration.Reactions = getReactions();
buildConfiguration.SpatialStructure = getSpatialStructure();
buildConfiguration.PassiveTransports = new PassiveTransportBuildingBlock();
buildConfiguration.Observers = new ObserverBuildingBlock();
buildConfiguration.EventGroups = new EventGroupBuildingBlock();
buildConfiguration.SimulationSettings = createSimulationConfiguration();
buildConfiguration.MoleculeStartValues = _moleculeStartValuesCreator.CreateFrom(buildConfiguration.SpatialStructure, buildConfiguration.Molecules);
var objectPathForContainerThatDoesNotExist = _objectPathFactory.CreateObjectPathFrom("TOTO", "TATA");
buildConfiguration.MoleculeStartValues.Add(_moleculeStartValuesCreator.CreateMoleculeStartValue(objectPathForContainerThatDoesNotExist, "A", _concentrationDimension));
buildConfiguration.ParameterStartValues = _parameterStartValuesCreator.CreateFrom(buildConfiguration.SpatialStructure, buildConfiguration.Molecules);
setMoleculeStartValues(buildConfiguration.MoleculeStartValues);
return(buildConfiguration);
}
protected override IMoleculeStartValuesBuildingBlock CreateStartValuesFromDTO(StartValuesDTO dto)
{
return(_startValuesCreator.CreateFrom(dto.SpatialStructrue, dto.Molecules).WithName(dto.Name));
}