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>();
}
public ParameterSetUpdater(IEntityPathResolver entityPathResolver, IParameterUpdater parameterUpdater, IParameterIdUpdater parameterIdUpdater, IParameterTask parameterTask)
{
_entityPathResolver = entityPathResolver;
_parameterUpdater = parameterUpdater;
_parameterIdUpdater = parameterIdUpdater;
_parameterTask = parameterTask;
}
protected override void Context()
{
_entityPathResolver = A.Fake <IEntityPathResolver>();
_parameterUpdater = A.Fake <IParameterUpdater>();
_parameterIdUpdater = A.Fake <IParameterIdUpdater>();
sut = new ParameterSetUpdater(_entityPathResolver, _parameterUpdater, _parameterIdUpdater);
}
public ConfigureSimulationTask(IBuildingBlockTask buildingBlockTask, IActiveSubjectRetriever activeSubjectRetriever,
ISimulationSettingsRetriever simulationSettingsRetriever, IApplicationController applicationController, IExecutionContext executionContext,
IParameterIdUpdater parameterIdUpdater, ISimulationResultsTask simulationResultsTask)
{
_buildingBlockTask = buildingBlockTask;
_activeSubjectRetriever = activeSubjectRetriever;
_simulationSettingsRetriever = simulationSettingsRetriever;
_applicationController = applicationController;
_executionContext = executionContext;
_parameterIdUpdater = parameterIdUpdater;
_simulationResultsTask = simulationResultsTask;
}
public SimulationModelCreator(IBuildConfigurationTask buildConfigurationTask, IModelConstructor modelConstructor, IParameterIdUpdater parameterIdUpdater,
IEntityPathResolver entityPathResolver, IExpressionContainersRetriever expressionContainersRetriever,
ISimulationSettingsFactory simulationSettingsFactory, ISimulationPersistableUpdater simulationPersistableUpdater)
{
_buildConfigurationTask = buildConfigurationTask;
_modelConstructor = modelConstructor;
_parameterIdUpdater = parameterIdUpdater;
_entityPathResolver = entityPathResolver;
_expressionContainersRetriever = expressionContainersRetriever;
_simulationSettingsFactory = simulationSettingsFactory;
_simulationPersistableUpdater = simulationPersistableUpdater;
}
protected override void Context()
{
_executionContext = A.Fake <IExecutionContext>();
_buildingBlockTask = A.Fake <IBuildingBlockTask>();
_applicationController = A.Fake <IApplicationController>();
_activeSubjectRetriever = A.Fake <IActiveSubjectRetriever>();
_simulationSettingsRetriever = A.Fake <ISimulationSettingsRetriever>();
_parameterIdUpdater = A.Fake <IParameterIdUpdater>();
_simulationResultsTask = A.Fake <ISimulationResultsTask>();
_parameterIdentificationTask = A.Fake <IParameterIdentificationTask>();
sut = new ConfigureSimulationTask(_buildingBlockTask, _activeSubjectRetriever, _simulationSettingsRetriever, _applicationController,
_executionContext, _parameterIdUpdater, _simulationResultsTask);
}
public MoleculeBuilderFactory(IParameterFactory parameterFactory, IParameterSetUpdater parameterSetUpdater,
IObjectBaseFactory objectBaseFactory, IParameterIdUpdater parameterIdUpdater,
IFlatMoleculeRepository flatMoleculeRepository, IParameterContainerTask parameterContainerTask,
IFlatMoleculeToMoleculeBuilderMapper moleculeMapper, IDimensionRepository dimensionRepository)
{
_parameterFactory = parameterFactory;
_parameterSetUpdater = parameterSetUpdater;
_objectBaseFactory = objectBaseFactory;
_parameterIdUpdater = parameterIdUpdater;
_flatMoleculeRepository = flatMoleculeRepository;
_parameterContainerTask = parameterContainerTask;
_moleculeMapper = moleculeMapper;
_dimensionRepository = dimensionRepository;
}
public PKSimSpatialStructureFactory(IObjectBaseFactory objectBaseFactory, IParameterContainerTask parameterContainerTask,
IModelContainerQuery modelContainerQuery, IModelNeighborhoodQuery modelNeighborhoodQuery,
IParameterSetUpdater parameterSetUpdater, IParameterIdUpdater parameterIdUpdater,
INeighborhoodFinalizer neighborhoodFinalizer, IEntityPathResolver entityPathResolver) : base(objectBaseFactory)
{
_objectBaseFactory = objectBaseFactory;
_parameterContainerTask = parameterContainerTask;
_modelContainerQuery = modelContainerQuery;
_modelNeighborhoodQuery = modelNeighborhoodQuery;
_parameterSetUpdater = parameterSetUpdater;
_parameterIdUpdater = parameterIdUpdater;
_neighborhoodFinalizer = neighborhoodFinalizer;
_entityPathResolver = entityPathResolver;
}
public EventBuildingBlockCreator(IObjectBaseFactory objectBaseFactory,
IProtocolToSchemaItemsMapper schemaItemsMapper,
IApplicationFactory applicationFactory,
IFormulationFromMappingRetriever formulationFromMappingRetriever,
ICloneManagerForBuildingBlock cloneManagerForBuildingBlock,
IParameterIdUpdater parameterIdUpdater,
IParameterSetUpdater parameterSetUpdater,
IEventGroupRepository eventGroupRepository)
{
_objectBaseFactory = objectBaseFactory;
_schemaItemsMapper = schemaItemsMapper;
_applicationFactory = applicationFactory;
_formulationFromMappingRetriever = formulationFromMappingRetriever;
_cloneManagerForBuildingBlock = cloneManagerForBuildingBlock;
_parameterIdUpdater = parameterIdUpdater;
_parameterSetUpdater = parameterSetUpdater;
_eventGroupRepository = eventGroupRepository;
}
public ExpressionProfileUpdater(
IParameterSetUpdater parameterSetUpdater,
IContainerTask containerTask,
IOntogenyTask ontogenyTask,
ICloner cloner,
IPKSimProjectRetriever projectRetriever,
ILazyLoadTask lazyLoadTask,
IParameterIdUpdater parameterIdUpdater,
IExecutionContext executionContext,
IDiseaseStateImplementationFactory diseaseStateImplementationFactory)
{
_parameterSetUpdater = parameterSetUpdater;
_containerTask = containerTask;
_ontogenyTask = ontogenyTask;
_cloner = cloner;
_projectRetriever = projectRetriever;
_lazyLoadTask = lazyLoadTask;
_parameterIdUpdater = parameterIdUpdater;
_executionContext = executionContext;
_diseaseStateImplementationFactory = diseaseStateImplementationFactory;
}
public ObjectIdResetter(IIdGenerator idGenerator, IParameterIdUpdater parameterIdUpdater) : base(idGenerator)
{
_parameterIdUpdater = parameterIdUpdater;
}
protected override void Context()
{
_parameterIdUpdater = A.Fake <IParameterIdUpdater>();
_referenceResolver = A.Fake <IReferencesResolver>();
sut = new SimulationUpdaterAfterDeserialization(_parameterIdUpdater, _referenceResolver);
}
public SimulationUpdaterAfterDeserialization(IParameterIdUpdater parameterIdUpdater, IReferencesResolver referencesResolver)
{
_parameterIdUpdater = parameterIdUpdater;
_referencesResolver = referencesResolver;
}