public CreateIndividual(
IIndividualRepository individualRepository,
IIndividualFactory individualFactory)
{
_individualRepository = individualRepository;
_individualFactory = individualFactory;
}
protected override void Context()
{
_mapper = A.Fake <IIndividualSettingsDTOToOriginDataMapper>();
_individualFactory = A.Fake <IIndividualFactory>();
_individualSettingsDTO = new IndividualSettingsDTO();
sut = new IndividualSettingsDTOToIndividualMapper(_individualFactory, _mapper);
}
public PopulationSettingsMapper(IOriginDataMapper originDataMapper, IIndividualFactory individualFactory,
IIndividualToPopulationSettingsMapper individualToPopulationSettingsMapper, IGenderRepository genderRepository)
{
_originDataMapper = originDataMapper;
_individualFactory = individualFactory;
_individualToPopulationSettingsMapper = individualToPopulationSettingsMapper;
_genderRepository = genderRepository;
}
internal MatlabIndividualFactory(IOriginDataMapper originDataMapper, IIndividualFactory individualFactory, IIndividualToIndividualPropertiesMapper individualPropertiesMapper, IOntogenyFactorsRetriever ontogenyFactorsRetriever, IEntityPathResolver entityPathResolver)
{
_originDataMapper = originDataMapper;
_individualFactory = individualFactory;
_individualPropertiesMapper = individualPropertiesMapper;
_ontogenyFactorsRetriever = ontogenyFactorsRetriever;
_entityPathResolver = entityPathResolver;
}
public IndividualMapper(IIndividualFactory individualFactory, IOriginDataMapper originDataMapper,
IIndividualMoleculeFactoryResolver moleculeFactoryResolver, IBatchLogger batchLogger)
{
_individualFactory = individualFactory;
_originDataMapper = originDataMapper;
_moleculeFactoryResolver = moleculeFactoryResolver;
_batchLogger = batchLogger;
}
public Population(int size, IIndividualFactory individualFactory, IProblemService problemService)
{
Size = size;
_individualFactory = individualFactory;
_problemService = problemService;
Individuals = new IIndividual[Size];
}
public IndividualDetailsViewService(
IViewModelFactory viewModelFactory,
IIndividualFactory individualFactory,
IIndividualRepository individualRepository)
{
_viewModelFactory = viewModelFactory;
_individualFactory = individualFactory;
_individualRepository = individualRepository;
}
protected override void Context()
{
_speciesRepository = A.Fake <ISpeciesRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_insividualSettingsMapper = A.Fake <IIndividualSettingsDTOToOriginDataMapper>();
_individualDefaultValueRetriever = A.Fake <IIndividualDefaultValueRetriever>();
sut = new DefaultIndividualRetriever(_speciesRepository, _individualFactory, _insividualSettingsMapper, _individualDefaultValueRetriever);
}
public IndividualAppService(
IIndividualRepository individualRepository,
IIndividualFactory individualFactory,
IMapper mapper)
{
_individualRepository = individualRepository;
_individualFactory = individualFactory;
_mapper = mapper;
}
public CreateIndividual(
IConsoleWriter consoleWriter,
IIndividualRepository individualRepo,
IIndividualFactory individualFactory)
{
_consoleWriter = consoleWriter;
_individualRepo = individualRepo;
_individualFactory = individualFactory;
}
public DefaultIndividualRetriever(ISpeciesRepository speciesRepository, IIndividualFactory individualFactory, IIndividualSettingsDTOToOriginDataMapper individualSettingsMapper,
IIndividualDefaultValueRetriever individualDefaultValueRetriever, IPopulationRepository populationRepository)
{
_speciesRepository = speciesRepository;
_individualFactory = individualFactory;
_individualSettingsMapper = individualSettingsMapper;
_individualDefaultValueRetriever = individualDefaultValueRetriever;
_populationRepository = populationRepository;
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_moleculeMapper = A.Fake <MoleculeMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
sut = new IndividualMapper(_parameterMapper, _moleculeMapper, _originDataMapper, _individualFactory);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Liver, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Kidney, "PKidney");
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_enzyme = new IndividualEnzyme
{
Name = "Enz",
};
_individual.AddMolecule(_enzyme);
_transporter = new IndividualTransporter
{
Name = "Trans",
};
_individual.AddMolecule(_transporter);
_enzymeSnapshot = new Molecule {
Type = QuantityType.Enzyme
};
_transporterSnapshot = new Molecule {
Type = QuantityType.Transporter
};
A.CallTo(() => _moleculeMapper.MapToSnapshot(_enzyme)).Returns(_enzymeSnapshot);
A.CallTo(() => _moleculeMapper.MapToSnapshot(_transporter)).Returns(_transporterSnapshot);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > .That.Contains(_parameterKidney))).Returns(new[] { _localizedParameterKidney });
return(_completed);
}
public DefaultIndividualRetriever(
ISpeciesRepository speciesRepository,
IIndividualFactory individualFactory,
OriginDataMapper originDataMapper
)
{
_speciesRepository = speciesRepository;
_individualFactory = individualFactory;
_originDataMapper = originDataMapper;
}
protected override void Context()
{
_orginDataMapper = A.Fake <IOriginDataMapper>();
_individualFactory = A.Fake <IIndividualFactory>();
_popSettingsMapper = A.Fake <IIndividualToPopulationSettingsMapper>();
_genderRepository = A.Fake <IGenderRepository>();
_female = new Gender();
_male = new Gender();
A.CallTo(() => _genderRepository.Female).Returns(_female);
A.CallTo(() => _genderRepository.Male).Returns(_male);
sut = new PopulationSettingsMapper(_orginDataMapper, _individualFactory, _popSettingsMapper, _genderRepository);
}
public StarterRelativeExpressionPresenter(
IStarterRelativeExpressionView view,
OriginDataMapper originDataMapper,
IIndividualFactory individualFactory,
IIndividualEnzymeFactory individualEnzymeFactory, IIndividualEnzymeExpressionsPresenter <Individual> individualEnzymeExpressionsPresenter) : base(view)
{
_originDataMapper = originDataMapper;
_individualFactory = individualFactory;
_individualEnzymeFactory = individualEnzymeFactory;
_individualEnzymeExpressionsPresenter = individualEnzymeExpressionsPresenter;
AddSubPresenters(individualEnzymeExpressionsPresenter);
InitializeWith(new PKSimMacroCommand());
}
protected ProtocolItemPresenter(
TView view,
IProtocolTask protocolTask,
IParameterTask parameterTask,
IIndividualFactory individualFactory,
IRepresentationInfoRepository representationInfoRepository)
: base(view)
{
_protocolTask = protocolTask;
_parameterTask = parameterTask;
_representationInfoRepository = representationInfoRepository;
_defaultIndividual = individualFactory.CreateParameterLessIndividual();
}
public IndividualMapper(
ParameterMapper parameterMapper,
MoleculeMapper moleculeMapper,
OriginDataMapper originDataMapper,
IIndividualFactory individualFactory
)
{
_parameterMapper = parameterMapper;
_moleculeMapper = moleculeMapper;
_individualFactory = individualFactory;
_originDataMapper = originDataMapper;
_originDataMapper = originDataMapper;
}
public SimpleProtocolPresenter(ISimpleProtocolView view,
IMultiParameterEditPresenter dynamicParameterPresenter,
ISimpleProtocolToSimpleProtocolDTOMapper simpleProtocolDTOMapper,
IProtocolTask protocolTask, IParameterTask parameterTask,
IIndividualFactory individualFactory, IRepresentationInfoRepository representationInfoRepository)
: base(view, protocolTask, parameterTask)
{
_simpleProtocolDTOMapper = simpleProtocolDTOMapper;
_representationInfoRepository = representationInfoRepository;
_dynamicParameterPresenter = dynamicParameterPresenter;
_dynamicParameterPresenter.IsSimpleEditor = true;
_view.AddDynamicParameterView(_dynamicParameterPresenter.View);
_defaultIndivdual = individualFactory.CreateParameterLessIndividual();
}
public IndividualMapper(
ParameterMapper parameterMapper,
ExpressionProfileMapper expressionProfileMapper,
OriginDataMapper originDataMapper,
IIndividualFactory individualFactory,
IMoleculeExpressionTask <ModelIndividual> moleculeExpressionTask
)
{
_parameterMapper = parameterMapper;
_expressionProfileMapper = expressionProfileMapper;
_individualFactory = individualFactory;
_moleculeExpressionTask = moleculeExpressionTask;
_originDataMapper = originDataMapper;
}
public ExpressionProfileFactory(
ISpeciesRepository speciesRepository,
IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver,
IPKSimObjectBaseFactory objectBaseFactory,
IIndividualFactory individualFactory,
IUsedExpressionProfileCategoryRepository usedExpressionProfileCategoryRepository
)
{
_speciesRepository = speciesRepository;
_individualMoleculeFactoryResolver = individualMoleculeFactoryResolver;
_objectBaseFactory = objectBaseFactory;
_individualFactory = individualFactory;
_usedExpressionProfileCategoryRepository = usedExpressionProfileCategoryRepository;
}
public SimpleProtocolPresenter(ISimpleProtocolView view,
IMultiParameterEditPresenter dynamicParameterPresenter,
ISimpleProtocolToSimpleProtocolDTOMapper simpleProtocolDTOMapper,
IProtocolTask protocolTask, IParameterTask parameterTask,
IIndividualFactory individualFactory, IRepresentationInfoRepository representationInfoRepository)
: base(view, protocolTask, parameterTask, individualFactory, representationInfoRepository)
{
_simpleProtocolDTOMapper = simpleProtocolDTOMapper;
_dynamicParameterPresenter = dynamicParameterPresenter;
_dynamicParameterPresenter.IsSimpleEditor = true;
_dynamicParameterPresenter.ValueOriginVisible = false;
_dynamicParameterPresenter.HeaderVisible = false;
_view.AddDynamicParameterView(_dynamicParameterPresenter.View);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionProfileMapper = A.Fake <ExpressionProfileMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <ModelIndividual> >();
sut = new IndividualMapper(_parameterMapper, _expressionProfileMapper, _originDataMapper, _individualFactory, _moleculeExpressionTask);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
var kidney = _individual.EntityAt <IContainer>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY);
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.LIVER, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY, "PKidney");
_parameterKidneyRelExp = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.REL_EXP);
_parameterKidneyRelExp.DefaultValue = 10;
kidney.Add(_parameterKidneyRelExp);
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_parameterKidneyRelExp.Value = 50;
_parameterKidneyRelExp.ValueDiffersFromDefault().ShouldBeTrue();
_expressionProfile1 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(moleculeName: "Enz");
_expressionProfile2 = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>(moleculeName: "Trans");
_individual.AddExpressionProfile(_expressionProfile1);
_individual.AddExpressionProfile(_expressionProfile2);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > ._))
.Invokes(x => _mappedParameters = x.GetArgument <IEnumerable <IParameter> >(0).ToList())
.Returns(new[] { _localizedParameterKidney });
return(_completed);
}
public CKDDiseaseStateImplementation(
IValueOriginRepository valueOriginRepository,
IDimensionRepository dimensionRepository,
IFormulaFactory formulaFactory,
IIndividualFactory individualFactory,
IContainerTask containerTask,
IParameterSetUpdater parameterSetUpdater)
{
_valueOriginRepository = valueOriginRepository;
_formulaFactory = formulaFactory;
_individualFactory = individualFactory;
_containerTask = containerTask;
_parameterSetUpdater = parameterSetUpdater;
_dimensionForGFR = dimensionRepository.DimensionForUnit(GFR_UNIT);
_ageDimension = dimensionRepository.AgeInYears;
}
protected override void Context()
{
_view = A.Fake <ISimpleProtocolView>();
_schemaDTOMapper = A.Fake <ISchemaToSchemaDTOMapper>();
_protocolTask = A.Fake <IProtocolTask>();
_parameterTask = A.Fake <IParameterTask>();
_individualFactory = A.Fake <IIndividualFactory>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
_dynamicParameterPresenter = A.Fake <IMultiParameterEditPresenter>();
_simpleProtocolToSimpleProtocolDTOMapper = A.Fake <ISimpleProtocolToSimpleProtocolDTOMapper>();
_individual = DomainHelperForSpecs.CreateIndividual();
A.CallTo(() => _individualFactory.CreateParameterLessIndividual()).Returns(_individual);
sut = new SimpleProtocolPresenter(_view, _dynamicParameterPresenter, _simpleProtocolToSimpleProtocolDTOMapper,
_protocolTask, _parameterTask, _individualFactory, _representationInfoRepository);
sut.InitializeWith(A.Fake <ICommandCollector>());
}
public AdvancedProtocolPresenter(
IAdvancedProtocolView view,
ISchemaItemToSchemaItemDTOMapper schemaItemDTOMapper,
ISchemaToSchemaDTOMapper schemaDTOMapper,
IParameterToParameterDTOMapper parameterDTOMapper,
IProtocolTask protocolTask,
IParameterTask parameterTask,
IDimensionRepository dimensionRepository,
IIndividualFactory individualFactory,
IRepresentationInfoRepository representationInfoRepository)
: base(view, protocolTask, parameterTask, individualFactory, representationInfoRepository)
{
_schemaItemDTOMapper = schemaItemDTOMapper;
_schemaDTOMapper = schemaDTOMapper;
_parameterDTOMapper = parameterDTOMapper;
_dimensionRepository = dimensionRepository;
}
protected override void Context()
{
_advancedProtocol = A.Fake <AdvancedProtocol>();
_allSchemas = new List <Schema>();
A.CallTo(() => _advancedProtocol.AllSchemas).Returns(_allSchemas);
_schemaDTOMapper = A.Fake <ISchemaToSchemaDTOMapper>();
_schemaItemDTOMapper = A.Fake <ISchemaItemToSchemaItemDTOMapper>();
_parameterDTOMapper = A.Fake <IParameterToParameterDTOMapper>();
_protocolTask = A.Fake <IProtocolTask>();
_parameterTask = A.Fake <IParameterTask>();
_view = A.Fake <IAdvancedProtocolView>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
sut = new AdvancedProtocolPresenter(_view, _schemaItemDTOMapper, _schemaDTOMapper, _parameterDTOMapper, _protocolTask, _parameterTask, _dimensionRepository, _individualFactory, _representationInfoRepository);
sut.InitializeWith(A.Fake <ICommandCollector>());
}
public Converter552To561(ICompoundCalculationMethodCategoryRepository compoundCalculationMethodCategoryRepository, IIndividualFactory individualFactory,
ICloner cloner, INeighborhoodFinalizer neighborhoodFinalizer, IContainerTask containerTask,
IPKSimXmlSerializerRepository serializerRepository, IReactionBuildingBlockCreator reactionBuildingBlockCreator,
IDiagramModelFactory diagramModelFactory, ICompoundProcessRepository compoundProcessRepository, IParameterSetUpdater parameterSetUpdater, IDialogCreator dialogCreator,
IRenalAgingCalculationMethodUpdater renalAgingCalculationMethodUpdater,
IIndividualUpdater individualUpdater)
{
_compoundCalculationMethodCategoryRepository = compoundCalculationMethodCategoryRepository;
_individualFactory = individualFactory;
_cloner = cloner;
_neighborhoodFinalizer = neighborhoodFinalizer;
_containerTask = containerTask;
_serializerRepository = serializerRepository;
_reactionBuildingBlockCreator = reactionBuildingBlockCreator;
_diagramModelFactory = diagramModelFactory;
_compoundProcessRepository = compoundProcessRepository;
_parameterSetUpdater = parameterSetUpdater;
_dialogCreator = dialogCreator;
_renalAgingCalculationMethodUpdater = renalAgingCalculationMethodUpdater;
_individualUpdater = individualUpdater;
}
public UpdateStreet(IIndividualRepository individualRepository, IIndividualFactory individualFactory)
{
_individualRepository = individualRepository;
_individualFactory = individualFactory;
}
public IndividualDataModelAdapter(IIndividualFactory individualFactory, IMapper mapper) : base(mapper)
{
_individualFactory = individualFactory;
}
public IndividualDtoAdapter(IMapper mapper, IIndividualFactory individualFactory) : base(mapper)
{
_individualFactory = individualFactory;
}
/// <summary>
/// Initializes a new instance of the <see cref="GeneticAlgorithm"/> class.
/// </summary>
/// <param name="individualFactory">The individual settings to use during this run.</param>
public GeneticAlgorithm(IIndividualFactory individualFactory)
{
this.randomGenerator = new Random();
this.individualFactory = individualFactory;
}
