public MoleculesAndReactionsCreator(IObjectBaseFactory objectBaseFactory,
IMoleculeBuilderFactory moleculeBuilderFactory,
IParameterIdUpdater parameterIdUpdater,
IProcessToProcessBuilderMapper processBuilderMapper,
IParameterSetUpdater parameterSetUpdater,
IIndividualEnzymeFactory individualEnzymeFactory,
IIndividualTransporterFactory individualTransporterFactory,
IModelContainerMoleculeRepository modelContainerMoleculeRepo,
IStaticReactionRepository staticReactionRepository,
IMoleculeCalculationRetriever moleculeCalculationRetriever,
IInteractionKineticUpdater interactionKineticUpdater,
IInteractionTask interactionTask
)
{
_objectBaseFactory = objectBaseFactory;
_moleculeBuilderFactory = moleculeBuilderFactory;
_parameterIdUpdater = parameterIdUpdater;
_processBuilderMapper = processBuilderMapper;
_parameterSetUpdater = parameterSetUpdater;
_individualEnzymeFactory = individualEnzymeFactory;
_individualTransporterFactory = individualTransporterFactory;
_modelContainerMoleculeRepo = modelContainerMoleculeRepo;
_staticReactionRepository = staticReactionRepository;
_moleculeCalculationRetriever = moleculeCalculationRetriever;
_interactionKineticUpdater = interactionKineticUpdater;
_interactionTask = interactionTask;
_allMoleculeNames = new List <string>();
_moleculeWithTurnoverReactions = new List <IMoleculeBuilder>();
}
protected override void Context()
{
_spatialStructureFactory = A.Fake <IPKSimSpatialStructureFactory>();
_modelObserverQuery = A.Fake <IModelObserverQuery>();
_modelPassiveTransportQuery = A.Fake <IModelPassiveTransportQuery>();
_parameterStartValueCreator = A.Fake <IPKSimParameterStartValuesCreator>();
_moleculesAndReactionsCreator = A.Fake <IMoleculesAndReactionsCreator>();
_eventBuildingBlockCreator = A.Fake <IEventBuildingBlockCreator>();
_moleculeStartValueCreator = A.Fake <IPKSimMoleculeStartValuesCreator>();
_moleculeCalculationRetriever = A.Fake <IMoleculeCalculationRetriever>();
_distributedTableConverter = A.Fake <IDistributedParameterToTableParameterConverter>();
_parameterDefaultStateUpdater = A.Fake <IParameterDefaultStateUpdater>();
_cm1 = new CoreCalculationMethod();
_cm2 = new CoreCalculationMethod();
_simulation = new IndividualSimulation {
Properties = new SimulationProperties()
};
_simulation.SimulationSettings = new SimulationSettings();
_simulation.ModelConfiguration = new ModelConfiguration();
_individual = new Individual().WithName("MyIndividuyal");
_compound = A.Fake <Compound>().WithName("MyCompound");
_protocol = new SimpleProtocol().WithName("MyProtocol");
_spatialStructure = A.Fake <ISpatialStructure>();
_passiveTransportBuilingBlock = A.Fake <IPassiveTransportBuildingBlock>();
_observerBuildingBlock = A.Fake <IObserverBuildingBlock>();
_eventBuildingBlock = A.Fake <IEventGroupBuildingBlock>();
_parameterValuesBuildingBlock = A.Fake <IParameterStartValuesBuildingBlock>();
_moleculeStartValueBuildingBlock = A.Fake <IMoleculeStartValuesBuildingBlock>();
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Individual", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Compound", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Protocol", PKSimBuildingBlockType.Protocol)
{
BuildingBlock = _protocol
});
A.CallTo(() => _moleculeCalculationRetriever.AllMoleculeCalculationMethodsUsedBy(_simulation)).Returns(new[] { _cm1, _cm2 });
A.CallTo(() => _spatialStructureFactory.CreateFor(_individual, _simulation)).Returns(_spatialStructure);
A.CallTo(() => _modelPassiveTransportQuery.AllPassiveTransportsFor(_simulation)).Returns(_passiveTransportBuilingBlock);
A.CallTo(() => _modelObserverQuery.AllObserversFor(A <IMoleculeBuildingBlock> .Ignored, _simulation)).Returns(_observerBuildingBlock);
A.CallTo(() => _eventBuildingBlockCreator.CreateFor(_simulation)).Returns(_eventBuildingBlock);
A.CallTo(() => _parameterStartValueCreator.CreateFor(A <IBuildConfiguration> .Ignored, A <Simulation> .Ignored)).Returns(_parameterValuesBuildingBlock);
A.CallTo(() => _moleculeStartValueCreator.CreateFor(A <IBuildConfiguration> .Ignored, A <Simulation> .Ignored)).Returns(_moleculeStartValueBuildingBlock);
sut = new BuildConfigurationTask(_spatialStructureFactory, _modelObserverQuery, _modelPassiveTransportQuery, _parameterStartValueCreator,
_moleculesAndReactionsCreator, _eventBuildingBlockCreator, _moleculeStartValueCreator, _moleculeCalculationRetriever,
_distributedTableConverter, _parameterDefaultStateUpdater);
}
public BuildConfigurationTask(IPKSimSpatialStructureFactory spatialStructureFactory, IModelObserverQuery modelObserverQuery,
IModelPassiveTransportQuery modelPassiveTransportQuery, IPKSimParameterStartValuesCreator parameterStartValuesCreator,
IMoleculesAndReactionsCreator moleculesAndReactionsCreator, IEventBuildingBlockCreator eventBuildingBlockCreator,
IPKSimMoleculeStartValuesCreator moleculeStartValuesCreator, IMoleculeCalculationRetriever moleculeCalculationRetriever,
IDistributedParameterToTableParameterConverter distributedParameterToTableParameterConverter)
{
_moleculeCalculationRetriever = moleculeCalculationRetriever;
_distributedParameterToTableParameterConverter = distributedParameterToTableParameterConverter;
_spatialStructureFactory = spatialStructureFactory;
_modelObserverQuery = modelObserverQuery;
_modelPassiveTransportQuery = modelPassiveTransportQuery;
_parameterStartValuesCreator = parameterStartValuesCreator;
_moleculesAndReactionsCreator = moleculesAndReactionsCreator;
_eventBuildingBlockCreator = eventBuildingBlockCreator;
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_moleculeCalculationRetriever = moleculeCalculationRetriever;
}
