public ParameterFactory(IPKSimObjectBaseFactory objectBaseFactory, IFormulaFactory formulaFactory, IDimensionRepository dimensionRepository, IDisplayUnitRetriever displayUnitRetriever)
{
_objectBaseFactory = objectBaseFactory;
_formulaFactory = formulaFactory;
_dimensionRepository = dimensionRepository;
_displayUnitRetriever = displayUnitRetriever;
}
protected override Task Context()
{
_tableFormulaMapper = A.Fake <TableFormulaMapper>();
_formulaFactory = A.Fake <IFormulaFactory>();
sut = new DistributedTableFormulaMapper(_tableFormulaMapper, _formulaFactory);
_distributedTableFormula = new DistributedTableFormula();
_distributionMetaData1 = new DistributionMetaData
{
Mean = 1,
Deviation = 2,
Distribution = DistributionTypes.LogNormal
};
_distributionMetaData2 = new DistributionMetaData
{
Mean = 3,
Deviation = 4,
Distribution = DistributionTypes.Normal
};
_distributedTableFormula.AddDistributionMetaData(_distributionMetaData1);
_distributedTableFormula.AddDistributionMetaData(_distributionMetaData2);
_distributedTableFormula.Percentile = 0.8;
return(Task.FromResult(true));
}
public ParameterImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, ASTHandler astHandler, IMoBiContext context, IUnitDefinitionImporter unitDefinitionImporter, IFormulaFactory formulaFactory)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_paramList = new List <IEntity>();
_unitDefinitionImporter = unitDefinitionImporter;
_formulaFactory = formulaFactory;
}
public IndividualModelTask(IParameterContainerTask parameterContainerTask, ISpeciesContainerQuery speciesContainerQuery,
IBuildingBlockFinalizer buildingBlockFinalizer, IFormulaFactory formulaFactory)
{
_parameterContainerTask = parameterContainerTask;
_speciesContainerQuery = speciesContainerQuery;
_buildingBlockFinalizer = buildingBlockFinalizer;
_formulaFactory = formulaFactory;
}
public QuantityValuesUpdater(IKeywordReplacerTask keywordReplacerTask, ICloneManagerForModel cloneManagerForModel,
IFormulaFactory formulaFactory, IConcentrationBasedFormulaUpdater concentrationBasedFormulaUpdater)
{
_keywordReplacerTask = keywordReplacerTask;
_cloneManagerForModel = cloneManagerForModel;
_formulaFactory = formulaFactory;
_concentrationBasedFormulaUpdater = concentrationBasedFormulaUpdater;
}
protected override void Context()
{
_dimensionFactory = A.Fake <IDimensionFactory>();
_formulaFactory = A.Fake <IFormulaFactory>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_concentrationBasedFormulaUpdater = A.Fake <IConcentrationBasedFormulaUpdater>();
_displayUnitRetriever = A.Fake <IDisplayUnitRetriever>();
sut = new ParameterFactory(_formulaFactory, _objectBaseFactory, _dimensionFactory, _concentrationBasedFormulaUpdater, _displayUnitRetriever);
}
public ParameterFactory(IFormulaFactory formulaFactory, IObjectBaseFactory objectBaseFactory, IDimensionFactory dimensionFactory,
IConcentrationBasedFormulaUpdater concentrationBasedFormulaUpdater, IDisplayUnitRetriever displayUnitRetriever)
{
_formulaFactory = formulaFactory;
_objectBaseFactory = objectBaseFactory;
_dimensionFactory = dimensionFactory;
_concentrationBasedFormulaUpdater = concentrationBasedFormulaUpdater;
_displayUnitRetriever = displayUnitRetriever;
}
protected override void Context()
{
_context = A.Fake <IExecutionContext>();
_applicationController = A.Fake <IApplicationController>();
_dataImporter = A.Fake <IDataImporter>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
_entityTask = A.Fake <IEntityTask>();
_formulaFactory = A.Fake <IFormulaFactory>();
sut = new IndividualOntogenyTask(_context, _applicationController, _dataImporter, _dimensionRepository, _ontogenyRepository, _entityTask, _formulaFactory);
}
public CompartmentImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory,
IMoBiSpatialStructureFactory spatialStructureFactory, IMoBiDimensionFactory moBiDimensionFactory,
ASTHandler astHandler, IMoBiContext context, IFormulaFactory formulaFactory, IUnitDefinitionImporter unitDefinitionImporter)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_objectBaseFactory = objectBaseFactory;
_spatialStructureFactory = spatialStructureFactory;
_dimensionFactory = moBiDimensionFactory;
_formulaFactory = formulaFactory;
_unitDefinitionImporter = unitDefinitionImporter;
}
public OntogenyTask(IExecutionContext executionContext, IApplicationController applicationController, IDataImporter dataImporter,
IDimensionRepository dimensionRepository, IOntogenyRepository ontogenyRepository, IEntityTask entityTask, IFormulaFactory formulaFactory)
{
_executionContext = executionContext;
_applicationController = applicationController;
_dataImporter = dataImporter;
_dimensionRepository = dimensionRepository;
_ontogenyRepository = ontogenyRepository;
_entityTask = entityTask;
_formulaFactory = formulaFactory;
}
protected override void Context()
{
_concentrationBasedFormulaUpdater = A.Fake <IConcentrationBasedFormulaUpdater>();
_keywordReplacerTask = A.Fake <IKeywordReplacerTask>();
_cloneManagerForModel = A.Fake <ICloneManagerForModel>();
_formulaFactory = A.Fake <IFormulaFactory>();
sut = new QuantityValuesUpdater(_keywordReplacerTask, _cloneManagerForModel, _formulaFactory, _concentrationBasedFormulaUpdater);
_model = A.Fake <IModel>();
_buildConfiguration = A.Fake <IBuildConfiguration>();
}
protected override void Context()
{
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_formulaMapper = A.Fake <IFormulaBuilderToFormulaMapper>();
_parameterMapper = A.Fake <IParameterBuilderCollectionToParameterCollectionMapper>();
_keywordReplacerTask = A.Fake <IKeywordReplacerTask>();
_formulaFactory = A.Fake <IFormulaFactory>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_parameterFactory = A.Fake <IParameterFactory>();
sut = new MoleculeBuilderToMoleculeAmountMapper(_objectBaseFactory, _formulaMapper, _parameterMapper, _dimensionFactory,
_keywordReplacerTask, _formulaFactory, _parameterFactory);
}
public override void GlobalContext()
{
_speciesContainerQuery = A.Fake <ISpeciesContainerQuery>();
_parameterContainerTask = A.Fake <IParameterContainerTask>();
_buildingBlockFinalizer = A.Fake <IBuildingBlockFinalizer>();
_formulaFactory = A.Fake <IFormulaFactory>();
_compartment = new Compartment().WithName("compartment");
_organ = new Organ().WithName("organ");
_organ.Name = "organ";
_organism = new Organism().WithName("organism");
sut = new IndividualModelTask(_parameterContainerTask, _speciesContainerQuery, _buildingBlockFinalizer, _formulaFactory);
}
public PKSimMoleculeStartValuesCreator(
IMoleculeStartValuesCreator moleculeStartValuesCreator,
IMoleculeStartFormulaRepository moleculeStartFormulaRepository,
IFormulaFactory formulaFactory,
IModelContainerMoleculeRepository modelContainerMoleculeRepository,
IEntityPathResolver entityPathResolver)
{
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_moleculeStartFormulaRepository = moleculeStartFormulaRepository;
_formulaFactory = formulaFactory;
_modelContainerMoleculeRepository = modelContainerMoleculeRepository;
_entityPathResolver = entityPathResolver;
}
public PKSimMoleculeStartValuesCreator(IMoleculeStartValuesCreator moleculeStartValuesCreator,
IObjectPathFactory objectPathFactory,
IExpressionContainersRetriever expressionContainersRetriever,
IMoleculeStartFormulaRepository moleculeStartFormulaRepository,
IFormulaFactory formulaFactory,
IModelContainerMoleculeRepository modelContainerMoleculeRepository)
{
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_objectPathFactory = objectPathFactory;
_expressionContainersRetriever = expressionContainersRetriever;
_moleculeStartFormulaRepository = moleculeStartFormulaRepository;
_formulaFactory = formulaFactory;
_modelContainerMoleculeRepository = modelContainerMoleculeRepository;
}
public MoleculeBuilderToMoleculeAmountMapper(IObjectBaseFactory objectBaseFactory,
IFormulaBuilderToFormulaMapper formulaMapper,
IParameterBuilderToParameterMapper parameterMapper,
IDimensionFactory dimensionFactory, IKeywordReplacerTask keywordReplacerTask, IFormulaFactory formulaFactory,
IParameterFactory parameterFactory)
{
_objectBaseFactory = objectBaseFactory;
_formulaMapper = formulaMapper;
_parameterMapper = parameterMapper;
_keywordReplacerTask = keywordReplacerTask;
_formulaFactory = formulaFactory;
_parameterFactory = parameterFactory;
_amountDimension = dimensionFactory.Dimension(Constants.Dimension.MOLAR_AMOUNT);
}
public ParameterAlternativeFactory(
IObjectBaseFactory objectBaseFactory,
ICloner cloner,
ISpeciesRepository speciesRepository,
ICoreUserSettings userSettings,
IFormulaFactory formulaFactory
)
{
_objectBaseFactory = objectBaseFactory;
_cloner = cloner;
_speciesRepository = speciesRepository;
_userSettings = userSettings;
_formulaFactory = formulaFactory;
}
public AmountToConcentrationConverter(IReactionDimensionRetriever reactionDimensionRetriever,
IDimensionFactory dimensionFactory, IAmoutToConcentrationFormulaMapper amoutToConcentrationFormulaMapper,
IObjectBaseFactory objectBaseFactory, IFormulaTask formulaTask, IDisplayUnitRetriever displayUnitRetriever,
IObjectTypeResolver objectTypeResolver, IFormulaFactory formulaFactory)
{
_reactionDimensionRetriever = reactionDimensionRetriever;
_amoutToConcentrationFormulaMapper = amoutToConcentrationFormulaMapper;
_objectBaseFactory = objectBaseFactory;
_formulaTask = formulaTask;
_displayUnitRetriever = displayUnitRetriever;
_objectTypeResolver = objectTypeResolver;
_formulaFactory = formulaFactory;
_concentrationDimension = dimensionFactory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION);
_concentrationPerTimeDimension = dimensionFactory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION_PER_TIME);
}
public ApplicationFactory(IApplicationRepository applicationRepository, IObjectBaseFactory objectBaseFactory,
IObjectPathFactory objectPathFactory, IParameterSetUpdater parameterSetUpdater,
IDimensionRepository dimensionRepository, IParameterContainerTask parameterContainerTask,
IParticleApplicationCreator particleApplicationCreator, ICloneManagerForBuildingBlock cloneManagerForBuildingBlock, IFormulaFactory formulaFactory)
{
_applicationRepository = applicationRepository;
_objectBaseFactory = objectBaseFactory;
_objectPathFactory = objectPathFactory;
_parameterSetUpdater = parameterSetUpdater;
_dimensionRepository = dimensionRepository;
_parameterContainerTask = parameterContainerTask;
_particleApplicationCreator = particleApplicationCreator;
_cloneManagerForBuildingBlock = cloneManagerForBuildingBlock;
_formulaFactory = formulaFactory;
}
protected override void Context()
{
_reactionDimensionRetriever = A.Fake <IReactionDimensionRetriever>();
_dimensionFactory = A.Fake <IDimensionFactory>();
_amoutToConcentrationFormulaMapper = A.Fake <IAmoutToConcentrationFormulaMapper>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_formulaTask = A.Fake <IFormulaTask>();
_displayUnitRetriever = A.Fake <IDisplayUnitRetriever>();
_formulaFactory = A.Fake <IFormulaFactory>();
_constantZeroFormula = new ConstantFormula(0);
_formulaCache = new FormulaCache();
_objectTypeResolver = new ObjectTypeResolver();
A.CallTo(() => _formulaTask.AddParentVolumeReferenceToFormula(A <IFormula> ._)).Returns(Constants.VOLUME_ALIAS);
A.CallTo(() => _dimensionFactory.Dimension(Constants.Dimension.AMOUNT)).Returns(DomainHelperForSpecs.AmountDimension);
A.CallTo(() => _dimensionFactory.Dimension(Constants.Dimension.AMOUNT_PER_TIME)).Returns(DomainHelperForSpecs.AmountPerTimeDimension);
A.CallTo(() => _dimensionFactory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION)).Returns(DomainHelperForSpecs.ConcentrationDimension);
A.CallTo(() => _dimensionFactory.Dimension(Constants.Dimension.MOLAR_CONCENTRATION_PER_TIME)).Returns(DomainHelperForSpecs.ConcentrationPerTimeDimension);
A.CallTo(() => _objectBaseFactory.Create <ExplicitFormula>()).Returns(new ExplicitFormula());
A.CallTo(() => _formulaFactory.ConstantFormula(0, DomainHelperForSpecs.ConcentrationDimension)).Returns(_constantZeroFormula);
sut = new AmountToConcentrationConverter(_reactionDimensionRetriever, _dimensionFactory, _amoutToConcentrationFormulaMapper,
_objectBaseFactory, _formulaTask, _displayUnitRetriever, _objectTypeResolver, _formulaFactory);
}
public FirstOrderValuesRetriever(IFormulaFactory formulaFactory) : base(formulaFactory)
{
}
public SpeciesImporter(IObjectPathFactory objectPathFactory, IObjectBaseFactory objectBaseFactory, IMoleculeBuilderFactory moleculeBuilderFactory, IMoleculeStartValuesCreator moleculeStartValuesCreator, IMoBiDimensionFactory moBiDimensionFactory, ASTHandler astHandler, IMoBiContext context, IUnitDefinitionImporter unitDefinitionImporter, IFormulaFactory formulaFactory)
: base(objectPathFactory, objectBaseFactory, astHandler, context)
{
_moleculeBuilderFactory = moleculeBuilderFactory;
_moleculeStartValuesCreator = moleculeStartValuesCreator;
_moBiDimensionFactory = moBiDimensionFactory;
_counter = 1;
_dimensionDictionary = new Dictionary <string, Dimension>();
_unitDefinitionImporter = unitDefinitionImporter;
}
public ConversionService(IFormulaFactory formulaFactory)
{
FormulaFactory = formulaFactory;
}
public WeibullValuesRetriever(IFormulaFactory formulaFactory) : base(formulaFactory)
{
}
public DissolvedValuesRetriever(IFormulaFactory formulaFactory) : base(formulaFactory)
{
}
public DistributedTableFormulaMapper(TableFormulaMapper tableFormulaMapper, IFormulaFactory formulaFactory)
{
_tableFormulaMapper = tableFormulaMapper;
_formulaFactory = formulaFactory;
}
public TableSolubilityParameterPresenter(ITableParameterView view, IParameterTask parameterTask, IFormulaFactory formulaFactory, ICloner cloner, ICompoundAlternativeTask compoundAlternativeTask) :
base(view, parameterTask, formulaFactory, cloner, compoundAlternativeTask.ImportSolubilityTableFormula)
{
}
public IndividualOntogenyTask(IExecutionContext executionContext, IApplicationController applicationController, IDataImporter dataImporter, IDimensionRepository dimensionRepository, IOntogenyRepository ontogenyRepository, IEntityTask entityTask, IFormulaFactory formulaFactory) : base(executionContext, applicationController, dataImporter, dimensionRepository, ontogenyRepository, entityTask, formulaFactory)
{
}
public TableFormulationParameterPresenter(ITableParameterView view, IParameterTask parameterTask, IFormulaFactory formulaFactory, ICloner cloner, IFormulationTask formulationTask) :
base(view, parameterTask, formulaFactory, cloner, formulationTask.ImportTableFormula)
{
}
public Lint80ValuesRetriever(IFormulaFactory formulaFactory) : base(formulaFactory)
{
}
