示例#1
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        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>();
        }
示例#2
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 public ParameterSetUpdater(IEntityPathResolver entityPathResolver, IParameterUpdater parameterUpdater, IParameterIdUpdater parameterIdUpdater, IParameterTask parameterTask)
 {
     _entityPathResolver = entityPathResolver;
     _parameterUpdater   = parameterUpdater;
     _parameterIdUpdater = parameterIdUpdater;
     _parameterTask      = parameterTask;
 }
示例#3
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 protected override void Context()
 {
     _entityPathResolver = A.Fake <IEntityPathResolver>();
     _parameterUpdater   = A.Fake <IParameterUpdater>();
     _parameterIdUpdater = A.Fake <IParameterIdUpdater>();
     sut = new ParameterSetUpdater(_entityPathResolver, _parameterUpdater, _parameterIdUpdater);
 }
示例#4
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 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;
 }
示例#5
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 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);
 }
示例#7
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 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;
 }
示例#8
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        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;
 }
示例#10
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 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;
 }
示例#11
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 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;
 }