private void createNonApplicationEvents()
{
// group events by the event-building block they are using
var eventBuildingBlockInfos = (from eventMapping in _simulation.EventProperties.EventMappings
let usedBuildingBlock = _simulation.UsedBuildingBlockByTemplateId(eventMapping.TemplateEventId)
let eventBuildingBlock = usedBuildingBlock.BuildingBlock.DowncastTo <PKSimEvent>()
select new { eventBuildingBlock.Id, eventBuildingBlock.TemplateName, eventBuildingBlock.Name })
.Distinct();
// create event groups for each used event-building block
foreach (var eventBuildingBlockInfo in eventBuildingBlockInfos)
{
// get event group template
var templateEventGroup = _eventGroupRepository.FindByName(eventBuildingBlockInfo.TemplateName);
// create new event group
var eventGroup = _cloneManagerForBuildingBlock.Clone(templateEventGroup);
eventGroup.Name = eventBuildingBlockInfo.Name;
eventGroup.RemoveChild(eventGroup.MainSubContainer());
// get building block and eventgroup-template to be used
var eventBuildingBlock = _simulation.UsedBuildingBlockById(eventBuildingBlockInfo.Id);
var eventTemplate = eventBuildingBlock.BuildingBlock.DowncastTo <PKSimEvent>();
// set event group parameter
_parameterSetUpdater.UpdateValuesByName(eventTemplate, eventGroup);
// create subcontainers (event groups) for all events of the same type
int eventIndex = 0; //used for naming of event subcontainers only
foreach (var eventMapping in _simulation.EventProperties.EventMappings.OrderBy(em => em.StartTime.Value))
{
if (!eventMapping.TemplateEventId.Equals(eventBuildingBlock.TemplateId))
{
continue; //event from different template
}
// clone main event subcontainer and set its start time
var mainSubContainer = _cloneManagerForBuildingBlock.Clone(templateEventGroup.MainSubContainer());
eventIndex += 1;
mainSubContainer.Name = $"{eventBuildingBlockInfo.Name}_{eventIndex}";
_parameterSetUpdater.UpdateValue(eventMapping.StartTime, mainSubContainer.StartTime());
eventGroup.Add(mainSubContainer);
}
// update building block ids
_parameterIdUpdater.UpdateBuildingBlockId(eventGroup, eventTemplate);
_eventGroupBuildingBlock.Add(eventGroup);
}
}
private void updateParameterFromIndividual(ISpatialStructure spatialStructure, Individual individual)
{
//Update parameter values for parameter that have been changed in individual
var allIndividualParameter = new PathCache <IParameter>(_entityPathResolver).For(individual.GetAllChildren <IParameter>());
var allContainerParameters = new PathCache <IParameter>(_entityPathResolver).For(spatialStructure.TopContainers.SelectMany(x => x.GetAllChildren <IParameter>()));
var allNeighborhoodParameters = new PathCache <IParameter>(_entityPathResolver).For(spatialStructure.Neighborhoods.SelectMany(x => x.GetAllChildren <IParameter>()));
_parameterSetUpdater.UpdateValues(allIndividualParameter, allContainerParameters);
_parameterSetUpdater.UpdateValues(allIndividualParameter, allNeighborhoodParameters);
_parameterIdUpdater.UpdateBuildingBlockId(allContainerParameters, individual);
_parameterIdUpdater.UpdateBuildingBlockId(allNeighborhoodParameters, individual);
}
private void addMolecule(IndividualMolecule individualMolecule)
{
var molecule = _moleculeBuilderFactory.Create(individualMolecule.MoleculeType, _moleculeBuildingBlock.FormulaCache)
.WithName(individualMolecule.Name)
.WithIcon(individualMolecule.Icon);
addMoleculeToBuildingBlock(molecule, null);
//Update protein builder parameters with the parameter ids
_parameterSetUpdater.UpdateValuesByName(individualMolecule, molecule.Parameters);
//Update the building block ids
_parameterIdUpdater.UpdateBuildingBlockId(molecule.Parameters, _individual);
}
private void updateParameterOrginInSimulation(Simulation simulation)
{
var allParameters = simulation.Model.Root.GetAllChildren <IParameter>()
.Where(x => !string.IsNullOrEmpty(x.Origin.BuilingBlockId)).ToList();
var allParametersGroupByBuildingBlockId = allParameters.GroupBy(x => x.Origin.BuilingBlockId);
foreach (var parametersByBuildingBlockId in allParametersGroupByBuildingBlockId)
{
var usedBuildingBlock = _usedBuildingBlockCache[parametersByBuildingBlockId.Key];
if (usedBuildingBlock != null)
{
_parameterIdUpdater.UpdateBuildingBlockId(parametersByBuildingBlockId, usedBuildingBlock.BuildingBlock);
}
else
{
_parameterIdUpdater.ResetParameterOrigin(parametersByBuildingBlockId);
}
}
allParameters.Where(p => !string.IsNullOrEmpty(p.Origin.ParameterId))
.Each(updateParameterOrigin);
_parameterIdUpdater.UpdateSimulationId(simulation);
}
public IMoleculeBuilder Create(Compound compound, CompoundProperties compoundProperties, InteractionProperties interactionProperties, IFormulaCache formulaCache)
{
var drug = Create(QuantityType.Drug, formulaCache).WithName(compound.Name);
//first update all parameters defined in the molecule that are also in the compound and that DO NOT belong in one alternative
_parameterSetUpdater.UpdateValuesByName(allSimpleParametersFrom(compound), drug.AllParameters());
//once simple parameters have been set, set the alternative parameters
updateAlternativeParameters(compound, compoundProperties, drug, formulaCache);
//add interaction parameters
addInteractionParameters(compound, drug, interactionProperties);
_parameterIdUpdater.UpdateBuildingBlockId(drug.GetAllChildren <IParameter>(), compound);
return(drug);
}