protected override void Context() { base.Context(); _formulaCache = new FormulaCache(); _compoundFactory = IoC.Resolve <ICompoundFactory>(); _parameterAlternativeFactory = IoC.Resolve <IParameterAlternativeFactory>(); _compound = _compoundFactory.Create().WithName("Comp"); _compound.Parameter(Constants.Parameters.MOL_WEIGHT).Value = 250; //Two simple parameters without alternatives //one parameter defined as a constant for which an alternative was also specififed var lipoGroup = _compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY); _alternativeLipo1 = _parameterAlternativeFactory.CreateAlternativeFor(lipoGroup).WithName("ALT_LIPO1").WithId("ALT_LIPO1"); _alternativeLipo1.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = 2; _alternativeLipo2 = _parameterAlternativeFactory.CreateAlternativeFor(lipoGroup).WithName("ALT_LIPO2").WithId("ALT_LIPO2"); _alternativeLipo2.Parameter(CoreConstants.Parameters.LIPOPHILICITY).Value = 5; lipoGroup.AddAlternative(_alternativeLipo1); lipoGroup.AddAlternative(_alternativeLipo2); //one parameter defined as a formula with a default calculated alternative var permAlternativeGroup = _compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY); //value cannot be changed by user _alternativePerm1 = _parameterAlternativeFactory.CreateDefaultAlternativeFor(permAlternativeGroup).WithName("ALT_PERM1").WithId("ALT_PERM1"); _alternativePerm2 = _parameterAlternativeFactory.CreateAlternativeFor(permAlternativeGroup).WithName("ALT_PERM2").WithId("ALT_PERM2"); _alternativePerm2.Parameter(CoreConstants.Parameters.PERMEABILITY).Value = 10; permAlternativeGroup.AddAlternative(_alternativePerm1); permAlternativeGroup.AddAlternative(_alternativePerm2); }
public Converter740To80( ICompoundFactory compoundFactory, ICloner cloner) { _templateCompound = new Lazy <Compound>(compoundFactory.Create); _cloner = cloner; }
public ObservedDataToCompoundMappingPresenter(IObservedDataToCompoundMappingView view, ICompoundFactory compoundFactory) : base(view) { _compoundFactory = compoundFactory; _undefinedCompound = _compoundFactory.Create().WithName(PKSimConstants.UI.Undefined); _allAvailableCompounds = new List <PKSim.Core.Model.Compound> { _undefinedCompound }; view.CancelVisible = false; }
public CreateCompoundPresenter(ICreateCompoundView view, ISubPresenterItemManager <ICompoundItemPresenter> subPresenterItemManager, IDialogCreator dialogCreator, ICompoundFactory compoundFactory, IObjectBaseDTOFactory objectBaseDTOFactory, IBuildingBlockPropertiesMapper propertiesMapper) : base(view, subPresenterItemManager, CompoundItems.All, dialogCreator) { _compoundFactory = compoundFactory; _objectBaseDTOFactory = objectBaseDTOFactory; _propertiesMapper = propertiesMapper; AllowQuickFinish = true; }
public CompoundMapper( ParameterMapper parameterMapper, AlternativeMapper alternativeMapper, CalculationMethodCacheMapper calculationMethodCacheMapper, CompoundProcessMapper processMapper, ICompoundFactory compoundFactory) : base(parameterMapper) { _alternativeMapper = alternativeMapper; _calculationMethodCacheMapper = calculationMethodCacheMapper; _processMapper = processMapper; _compoundFactory = compoundFactory; }
protected override void Context() { _parameterAlternativeFactory = A.Fake <IParameterAlternativeFactory>(); _applicationController = A.Fake <IApplicationController>(); _executionContext = A.Fake <IExecutionContext>(); _entityTask = A.Fake <IEntityTask>(); _formulaFactory = A.Fake <IFormulaFactory>(); _parameterTask = A.Fake <IParameterTask>(); _buildingBlockRepository = A.Fake <IBuildingBlockRepository>(); _compoundFactory = new CompoundFactoryForSpecs(); sut = new CompoundAlternativeTask(_parameterAlternativeFactory, _applicationController, _executionContext, _compoundFactory, _entityTask, _formulaFactory, _parameterTask, _buildingBlockRepository); }
public CompoundAlternativeTask(IParameterAlternativeFactory parameterAlternativeFactory, IApplicationController applicationController, IExecutionContext executionContext, ICompoundFactory compoundFactory, IEntityTask entityTask, IFormulaFactory formulaFactory, IParameterTask parameterTask, IBuildingBlockRepository buildingBlockRepository) { _parameterAlternativeFactory = parameterAlternativeFactory; _applicationController = applicationController; _executionContext = executionContext; _compoundFactory = compoundFactory; _entityTask = entityTask; _formulaFactory = formulaFactory; _parameterTask = parameterTask; _buildingBlockRepository = buildingBlockRepository; }
public CompoundMapper(ICompoundFactory compoundFactory, ICompoundProcessRepository compoundProcessRepository, IBatchLogger batchLogger, ICloner cloner, ICompoundCalculationMethodCategoryRepository calculationMethodCategoryRepository, ICalculationMethodRepository calculationMethodRepository, ICompoundProcessTask compoundProcessTask, ISpeciesRepository speciesRepository) { _compoundFactory = compoundFactory; _compoundProcessRepository = compoundProcessRepository; _batchLogger = batchLogger; _cloner = cloner; _calculationMethodCategoryRepository = calculationMethodCategoryRepository; _calculationMethodRepository = calculationMethodRepository; _compoundProcessTask = compoundProcessTask; _speciesRepository = speciesRepository; }
protected override void Context() { _parameterAlternativeFactory = A.Fake <IParameterAlternativeFactory>(); _executionContext = A.Fake <IExecutionContext>(); _formulaFactory = A.Fake <IFormulaFactory>(); _parameterTask = A.Fake <IParameterTask>(); _buildingBlockRepository = A.Fake <IBuildingBlockRepository>(); _dimensionRepository = A.Fake <IDimensionRepository>(); _dataImporter = A.Fake <IDataImporter>(); _compoundFactory = new CompoundFactoryForSpecs(); sut = new CompoundAlternativeTask(_parameterAlternativeFactory, _executionContext, _compoundFactory, _formulaFactory, _parameterTask, _buildingBlockRepository, _dimensionRepository, _dataImporter); }
public CompoundAlternativeTask( IParameterAlternativeFactory parameterAlternativeFactory, IExecutionContext executionContext, ICompoundFactory compoundFactory, IFormulaFactory formulaFactory, IParameterTask parameterTask, IBuildingBlockRepository buildingBlockRepository, IDimensionRepository dimensionRepository, IDataImporter dataImporter) { _parameterAlternativeFactory = parameterAlternativeFactory; _executionContext = executionContext; _compoundFactory = compoundFactory; _formulaFactory = formulaFactory; _parameterTask = parameterTask; _buildingBlockRepository = buildingBlockRepository; _dimensionRepository = dimensionRepository; _dataImporter = dataImporter; }
protected override Task Context() { _alternativeMapper = A.Fake <AlternativeMapper>(); _parameterMapper = A.Fake <ParameterMapper>(); _calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>(); _processMapper = A.Fake <CompoundProcessMapper>(); _compoundFactory = A.Fake <ICompoundFactory>(); sut = new CompoundMapper(_parameterMapper, _alternativeMapper, _calculationMethodCacheMapper, _processMapper, _compoundFactory); _compound = new Model.Compound { Name = "Compound", Description = "Description" }; addPkAParameters(_compound, 0, 8, CompoundType.Base); addPkAParameters(_compound, 1, 4, CompoundType.Acid); addPkAParameters(_compound, 2, 7, CompoundType.Neutral); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY)); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND)); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY)); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY)); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY)); _compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.IS_SMALL_MOLECULE)); _compound.Add(DomainHelperForSpecs.ConstantParameterWithValue((int)PlasmaProteinBindingPartner.Glycoprotein).WithName(CoreConstants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER)); _partialProcess = new EnzymaticProcess().WithName("EnzymaticProcess"); _systemicProcess = new SystemicProcess().WithName("SystemicProcess"); _compound.AddProcess(_partialProcess); _compound.AddProcess(_systemicProcess); _calculationMethodCacheSnapshot = new CalculationMethodCache(); A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compound.CalculationMethodCache)).Returns(_calculationMethodCacheSnapshot); _snapshotProcess1 = new CompoundProcess(); _snapshotProcess2 = new CompoundProcess(); A.CallTo(() => _processMapper.MapToSnapshot(_partialProcess)).Returns(_snapshotProcess1); A.CallTo(() => _processMapper.MapToSnapshot(_systemicProcess)).Returns(_snapshotProcess2); return(_completed); }
public Converter721To730( ICompoundFactory compoundFactory, ICloner cloner, ICreationMetaDataFactory creationMetaDataFactory, IContainerTask containerTask, IFormulationRepository formulationRepository, IEventGroupRepository eventGroupRepository, Converter710To730 coreConverter, ICompoundProcessRepository compoundProcessRepository, ISchemaItemRepository schemaItemRepository ) { _compoundFactory = compoundFactory; _cloner = cloner; _creationMetaDataFactory = creationMetaDataFactory; _containerTask = containerTask; _formulationRepository = formulationRepository; _eventGroupRepository = eventGroupRepository; _coreConverter = coreConverter; _compoundProcessRepository = compoundProcessRepository; _schemaItemRepository = schemaItemRepository; }
protected override Task Context() { _parameterMapper = A.Fake <ParameterMapper>(); _alternativeMapper = A.Fake <AlternativeMapper>(); _calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>(); _processMapper = A.Fake <CompoundProcessMapper>(); _compoundFactory = A.Fake <ICompoundFactory>(); _valueOriginMapper = A.Fake <ValueOriginMapper>(); sut = new CompoundMapper(_parameterMapper, _alternativeMapper, _calculationMethodCacheMapper, _processMapper, _valueOriginMapper, _compoundFactory); _compound = new Model.Compound { Name = "Compound", Description = "Description" }; _pkaValueOrigin = new ValueOrigin { Method = ValueOriginDeterminationMethods.InVitro, Description = "PKA" }; _snapshotValueOrigin = new Snapshots.ValueOrigin { Method = ValueOriginDeterminationMethodId.InVivo, Description = "PKA" }; addPkAParameters(_compound, 0, 8, CompoundType.Base); addPkAParameters(_compound, 1, 4, CompoundType.Acid); addPkAParameters(_compound, 2, 7, CompoundType.Neutral); _compoundIntestinalPermeabilityAlternativeGroup = createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_LIPOPHILICITY)); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_FRACTION_UNBOUND)); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_SOLUBILITY)); _compound.AddParameterAlternativeGroup(createParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_PERMEABILITY)); _compound.AddParameterAlternativeGroup(_compoundIntestinalPermeabilityAlternativeGroup); _compoundIntestinalPermeabilityAlternativeGroup.DefaultAlternative.IsDefault = true; //Calculated alternative will not be the default alternative for intestinal perm _calculatedAlternative = new ParameterAlternative { Name = PKSimConstants.UI.CalculatedAlernative, IsDefault = false }; _compoundIntestinalPermeabilityAlternativeGroup.AddAlternative(_calculatedAlternative); //Mapping of a calculated alternative returns null A.CallTo(() => _alternativeMapper.MapToSnapshot(_calculatedAlternative)).Returns(Task.FromResult <Alternative>(null)); _compound.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.IS_SMALL_MOLECULE)); _compound.Add(DomainHelperForSpecs.ConstantParameterWithValue((int)PlasmaProteinBindingPartner.Glycoprotein).WithName(CoreConstants.Parameters.PLASMA_PROTEIN_BINDING_PARTNER)); _partialProcess = new EnzymaticProcess().WithName("EnzymaticProcess"); _systemicProcess = new SystemicProcess().WithName("SystemicProcess"); _compound.AddProcess(_partialProcess); _compound.AddProcess(_systemicProcess); _calculationMethodCacheSnapshot = new CalculationMethodCache(); A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compound.CalculationMethodCache)).Returns(_calculationMethodCacheSnapshot); _snapshotProcess1 = new CompoundProcess(); _snapshotProcess2 = new CompoundProcess(); A.CallTo(() => _processMapper.MapToSnapshot(_partialProcess)).Returns(_snapshotProcess1); A.CallTo(() => _processMapper.MapToSnapshot(_systemicProcess)).Returns(_snapshotProcess2); _molweightParameter = DomainHelperForSpecs.ConstantParameterWithValue(400).WithName(Constants.Parameters.MOL_WEIGHT); _molweightParameter.ValueOrigin.Method = ValueOriginDeterminationMethods.InVivo; //Do not update F value origin to ensure that it's being synchronized when mapping from snapshot _halogenFParameter = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(Constants.Parameters.F); _compound.Add(_molweightParameter); _compound.Add(_halogenFParameter); return(_completed); }
public CompoundBuilder(ICompoundFactory <TInA, TInB, TResult> factory) => _factory = factory;
public CompoundConverter(ICompoundFactory compoundFactory, ICloner cloner) { _compoundFactory = compoundFactory; _cloner = cloner; }