protected override void Context()
{
base.Context();
_enzyme1 = new IndividualEnzyme {
Name = "CYP3A4"
};
_enzyme2 = new IndividualEnzyme {
Name = "CYP2D6"
};
_partialProcess1Enzyme1 = new SimulationPartialProcess {
CompoundProcess = new EnzymaticProcess {
MetaboliteName = "Met1"
}, IndividualMolecule = _enzyme1
};
_partialProcess1Enzyme2 = new SimulationPartialProcess {
CompoundProcess = new EnzymaticProcess {
MetaboliteName = "Metabolite"
}, IndividualMolecule = _enzyme2
};
_partialProcesses.Add(_partialProcess1Enzyme1);
_partialProcesses.Add(_partialProcess1Enzyme2);
A.CallTo(() => _view.BindToPartialProcesses(A <IReadOnlyCollection <SimulationEnzymaticProcessSelectionDTO> > ._))
.Invokes(x => _allPartialProcessDTO = x.GetArgument <IReadOnlyCollection <SimulationEnzymaticProcessSelectionDTO> >(0).ToList());
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Comp", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Metabolite", PKSimBuildingBlockType.Compound)
{
BuildingBlock = new Compound().WithName("Metabolite")
});
}
protected override void Context()
{
base.Context();
_sourceMolecule = new IndividualEnzyme {
Ontogeny = new DatabaseOntogeny()
};
}
public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
_cloneManager = IoC.Resolve <ICloneManager>();
_enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
_transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
_modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>();
_modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = _enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP");
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo;
_individual.AddMolecule(_enzyme);
_hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value;
_metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameter.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
public override void GlobalContext()
{
base.GlobalContext();
//add the molecule in global context otherwise it will be added twice
_undefined = sut.AddUndefinedLiverTo(_individual);
}
protected override void Context()
{
base.Context();
A.CallTo(() => _executionContext.Resolve <IParameterTask>()).Returns(sut);
_relativeExpressionParameter = new Parameter
{
BuildingBlockType = PKSimBuildingBlockType.Individual,
Formula = new ConstantFormula(0.0),
GroupName = CoreConstants.Groups.RELATIVE_EXPRESSION,
Name = CoreConstants.Parameters.REL_EXP
};
_relativeExpressionParameterNorm = new Parameter
{
BuildingBlockType = PKSimBuildingBlockType.Individual,
Formula = new ConstantFormula(0.0),
GroupName = CoreConstants.Groups.RELATIVE_EXPRESSION,
Name = CoreConstants.Parameters.REL_EXP_NORM
};
var expressionContainer = new MoleculeExpressionContainer {
Name = "Plasma"
};
expressionContainer.Add(_relativeExpressionParameter);
expressionContainer.Add(_relativeExpressionParameterNorm);
var molecule = new IndividualEnzyme {
expressionContainer
};
}
protected override void Context()
{
base.Context();
_enzyme1 = new IndividualEnzyme {
Name = "CYP3A4"
};
_enzyme2 = new IndividualEnzyme {
Name = "CYP2D6"
};
_partialProcess1Enzyme1 = new SimulationPartialProcess {
CompoundProcess = new EnzymaticProcess(), IndividualMolecule = _enzyme1
};
_partialProcess1Enzyme2 = new SimulationPartialProcess {
CompoundProcess = new EnzymaticProcess(), IndividualMolecule = _enzyme2
};
_partialProcess1Enzyme3 = new SimulationPartialProcess {
CompoundProcess = new EnzymaticProcess(), IndividualMolecule = _enzyme2
};
_partialProcesses.Add(_partialProcess1Enzyme1);
_partialProcesses.Add(_partialProcess1Enzyme2);
_partialProcesses.Add(_partialProcess1Enzyme3);
A.CallTo(() => _view.BindToPartialProcesses(A <IReadOnlyCollection <SimulationEnzymaticProcessSelectionDTO> > ._))
.Invokes(x => _allPartialProcessDTO = x.GetArgument <IReadOnlyCollection <SimulationEnzymaticProcessSelectionDTO> >(0).ToList());
sut.EditProcessesIn(_simulation, _compoundProperties);
}
protected override void Context()
{
base.Context();
_enzyme1 = new IndividualOtherProtein().WithName("_enzyme1");
_enzyme2 = new IndividualEnzyme().WithName("_enzyme2");
sut.AddMolecule(_enzyme1);
sut.AddMolecule(_enzyme2);
}
public static IndividualMolecule DefaultIndividualMolecule()
{
var molecule = new IndividualEnzyme();
molecule.Add(ConstantParameterWithValue(10).WithName(CoreConstants.Parameter.REFERENCE_CONCENTRATION));
molecule.Add(ConstantParameterWithValue(20).WithName(CoreConstants.Parameter.HALF_LIFE_LIVER));
molecule.Add(ConstantParameterWithValue(30).WithName(CoreConstants.Parameter.HALF_LIFE_INTESTINE));
return(molecule);
}
protected override void Context()
{
_context = A.Fake <IExecutionContext>();
_enzyme = A.Fake <IndividualEnzyme>();
_value = 5;
_parameterExpression = DomainHelperForSpecs.ConstantParameterWithValue(2);
A.CallTo(() => _context.BuildingBlockContaining(_parameterExpression)).Returns(A.Fake <IPKSimBuildingBlock>());
sut = new SetRelativeExpressionCommand(_parameterExpression, _value);
}
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);
}
protected override void Context()
{
base.Context();
_protein = A.Fake <IndividualProtein>();
_enzyme = A.Fake <IndividualEnzyme>();
_moleculeList.AddRange(new[] { _protein, _enzyme });
_enzymeList.Add(_enzyme);
_enzymeNode = A.Fake <ITreeNode <IndividualEnzyme> >();
A.CallTo(() => _treeNodeFactory.CreateFor(_enzyme)).Returns(_enzymeNode);
}
protected override void Context()
{
base.Context();
_enzyme = A.Fake <IndividualEnzyme>();
A.CallTo(() => _enzyme.Rules).Returns(A.Fake <IBusinessRuleSet>());
_enzyme.Name = "CYP";
_container1 = new MoleculeExpressionContainer();
_container2 = new MoleculeExpressionContainer();
A.CallTo(() => _enzyme.GetChildren <IMoleculeExpressionContainer>()).Returns(new[] { _container1, _container2 });
}
protected override void Context()
{
base.Context();
_enzyme = new IndividualEnzyme {
Name = "CYP"
};
_container1 = new MoleculeExpressionContainer().WithName("EXP1");
_container2 = new MoleculeExpressionContainer().WithName("EXP2");
_enzyme.AddChildren(_container1, _container2);
}
protected override void Context()
{
base.Context();
_cloneManager = A.Fake <ICloneManager>();
_sourceMolecule = new IndividualEnzyme {
Ontogeny = new UserDefinedOntogeny()
};
_clonedOntogeny = new UserDefinedOntogeny();
A.CallTo(() => _cloneManager.Clone(_sourceMolecule.Ontogeny)).Returns(_clonedOntogeny);
}
protected override void Context()
{
_moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>();
sut = new MoleculeParameterTask(_moleculeParameterRepository);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER));
_molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE));
}
protected EnzymaticProcess AddEnzymaticProcess(Compound compound, IndividualEnzyme enzyme)
{
var compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
var cloneManager = IoC.Resolve <ICloneManager>();
var enzymaticProcess = cloneManager.Clone(compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <EnzymaticProcess>());
enzymaticProcess.Name = "My Partial Process " + enzyme.Name;
enzymaticProcess.MoleculeName = enzyme.Name;
enzymaticProcess.Parameter(ConverterConstants.Parameters.CLspec).Value = 10;
compound.AddProcess(enzymaticProcess);
return(enzymaticProcess);
}
public override void GlobalContext()
{
base.GlobalContext();
_compound = DomainFactoryForSpecs.CreateStandardCompound().WithName("Parent");
_metabolite = DomainFactoryForSpecs.CreateStandardCompound().WithName("Metabolite");
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_cyp3A4 = AddEnzymeTo(_individual, "CYP3A4");
_parentMetabolizationCYP3A4 = AddEnzymaticProcess(_compound, _cyp3A4);
_cyp2D6 = AddEnzymeTo(_individual, "CYP2D6");
_parentMetabolizationCYP2D6 = AddEnzymaticProcess(_compound, _cyp2D6);
}
public override void GlobalContext()
{
base.GlobalContext();
var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
var templateIndividual = DomainFactoryForSpecs.CreateStandardIndividual();
var compound = DomainFactoryForSpecs.CreateStandardCompound();
var protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = enzymeFactory.CreateFor(templateIndividual).DowncastTo <IndividualEnzyme>().WithName("CYP");
templateIndividual.AddMolecule(_enzyme);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(templateIndividual, compound, protocol).DowncastTo <IndividualSimulation>();
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public override void GlobalContext()
{
base.GlobalContext();
_withIdRepository = IoC.Resolve <IWithIdRepository>();
_simulation = new IndividualSimulation().WithId("Sim");
_simulation.IsLoaded = true;
_withIdRepository.Register(_simulation);
_simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Ind", PKSimBuildingBlockType.Individual)
{
BuildingBlock = DomainHelperForSpecs.CreateIndividual()
});
_transporter = new IndividualTransporter().WithName("Trans");
_enzyme = new IndividualEnzyme().WithName("Enz");
_simulation.Individual.AddMolecule(_transporter);
_simulation.Individual.AddMolecule(_enzyme);
}
protected override void Context()
{
base.Context();
_pp1 = A.Fake <EnzymaticProcess>().WithName("pp1");
_pp1.MoleculeName = "enzyme1";
_pp2 = A.Fake <EnzymaticProcess>().WithName("pp2");
_pp2.MoleculeName = "enzyme1";
_pp3 = A.Fake <EnzymaticProcess>().WithName("pp3");
_pp3.MoleculeName = "enzyme3";
_pp4 = A.Fake <EnzymaticProcess>().WithName("pp4");
_pp4.MoleculeName = "enzyme4";
_pp5 = A.Fake <EnzymaticProcess>().WithName("pp5");
_pp5.MoleculeName = "enzyme5";
_unknowProteinName = "unknow";
_moleculeName = "TITI";
_compound.AddProcess(_pp1);
_compound.AddProcess(_pp2);
_compound.AddProcess(_pp3);
_compound.AddProcess(_pp4);
_compound.AddProcess(_pp5);
_enzyme = A.Fake <IndividualEnzyme>().WithName(_pp3.MoleculeName);
_anotherProtein = A.Fake <IndividualEnzyme>().WithName(_moleculeName);
_notMappedProtein = A.Fake <IndividualEnzyme>().WithName("not mapped");
_individual.AddMolecule(_enzyme);
_individual.AddMolecule(_anotherProtein);
_individual.AddMolecule(_notMappedProtein);
_availableProcesses = new List <ProcessSelection>
{
new ProcessSelection {
ProcessName = _pp3.Name, MoleculeName = _notMappedProtein.Name, CompoundName = "DOES NOT EXIST"
},
new ProcessSelection {
ProcessName = _pp4.Name, MoleculeName = _moleculeName, CompoundName = _compound.Name
},
new ProcessSelection {
ProcessName = _pp5.Name, MoleculeName = _unknowProteinName, CompoundName = _compound.Name
}
};
}
public override void GlobalContext()
{
base.GlobalContext();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_moleculeExpressionTask = IoC.Resolve <IMoleculeExpressionTask <Individual> >();
_ontogenyRepository = IoC.Resolve <IOntogenyRepository>();
_expressionProfileForEnzyme = DomainFactoryForSpecs.CreateExpressionProfile <IndividualEnzyme>();
_moleculeExpressionTask.AddExpressionProfile(_individual, _expressionProfileForEnzyme);
_individualEnzyme = _individual.MoleculeByName <IndividualEnzyme>(_expressionProfileForEnzyme.MoleculeName);
_expressionProfileEnzyme = _expressionProfileForEnzyme.Molecule.DowncastTo <IndividualEnzyme>();
_expressionProfileForTransporter = DomainFactoryForSpecs.CreateExpressionProfile <IndividualTransporter>(moleculeName: "TRANS");
_moleculeExpressionTask.AddExpressionProfile(_individual, _expressionProfileForTransporter);
_individualTransporter = _individual.MoleculeByName <IndividualTransporter>(_expressionProfileForTransporter.MoleculeName);
_expressionProfileTransporter = _expressionProfileForTransporter.Molecule.DowncastTo <IndividualTransporter>();
}
protected override void Context()
{
_interactionProcessRetriever = A.Fake <IInteractionProcessRetriever>();
_view = A.Fake <ISimulationCompoundInteractionSelectionView>();
sut = new SimulationCompoundInteractionSelectionPresenter(_view, _interactionProcessRetriever);
_interactionProperties = new InteractionProperties();
_allSimulationInteractionProcesses = new List <SimulationPartialProcess>();
_simulation = A.Fake <Simulation>();
var individual = new Individual().WithName("Enzyme");
_molecule1 = new IndividualEnzyme().WithName("CYP3A4");
_undefinedLiver = new IndividualEnzyme().WithName(CoreConstants.Molecule.UndefinedLiver);
individual.AddMolecule(_molecule1);
individual.AddMolecule(_undefinedLiver);
_interactionProcess1 = new InhibitionProcess().WithName("INTERACTION1");
_interactionProcess2 = new InhibitionProcess().WithName("INTERACTION2");
_interactionProcess3 = new InhibitionProcess().WithName("INTERACTION3");
var comp1 = new Compound();
comp1.AddProcess(_interactionProcess1);
var comp2 = new Compound();
comp2.AddProcess(_interactionProcess2);
comp2.AddProcess(_interactionProcess3);
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess1, IndividualMolecule = _molecule1
});
_allSimulationInteractionProcesses.Add(new SimulationPartialProcess {
CompoundProcess = _interactionProcess2, IndividualMolecule = _molecule1
});
A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties);
A.CallTo(() => _simulation.Individual).Returns(individual);
A.CallTo(() => _simulation.Compounds).Returns(new[] { comp1, comp2 });
A.CallTo(_interactionProcessRetriever).WithReturnType <IReadOnlyList <SimulationPartialProcess> >()
.Invokes(x => _useDefaultMap = x.GetArgument <bool>(2))
.Returns(_allSimulationInteractionProcesses);
A.CallTo(() => _view.BindTo(A <IEnumerable <SimulationInteractionProcessSelectionDTO> > ._))
.Invokes(x => _allSimulationInteractionProcessSelectionDTO = x.GetArgument <IEnumerable <SimulationInteractionProcessSelectionDTO> >(0));
}
protected override void Context()
{
base.Context();
_moleculeMappable = new IndividualEnzyme().WithName("MoleculeMapped");
_moleculeAlreadySelected = new IndividualEnzyme().WithName("MoleculeAlreadySelected");
_moleculeNotMapped = new IndividualEnzyme().WithName("MoleculeNotMapped");
_inhibitionProcess1 = new InhibitionProcess().WithName("InhibitionProcess1");
_inhibitionProcess2 = new InhibitionProcess().WithName("InhibitionProcess2");
_inductionProcess1 = new InductionProcess().WithName("InductionProcess1");
_inhibitionProcess3 = new InhibitionProcess().WithName("InhibitionProcess3");
_individual.AddMolecule(_moleculeNotMapped);
_individual.AddMolecule(_moleculeMappable);
_individual.AddMolecule(_moleculeAlreadySelected);
_compound.AddProcess(_inhibitionProcess1);
_compound2 = new Compound().WithName("Comp2");
_compound2.AddProcess(_inhibitionProcess2);
_inhibitionProcess2.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inhibitionProcess3);
_inhibitionProcess3.MoleculeName = _moleculeMappable.Name;
_compound2.AddProcess(_inductionProcess1);
_inductionProcess1.MoleculeName = _moleculeMappable.Name;
var interactionProperties = new InteractionProperties();
interactionProperties.AddInteraction(new InteractionSelection {
MoleculeName = _moleculeAlreadySelected.Name, ProcessName = _inhibitionProcess1.Name, CompoundName = _compound.Name
});
A.CallTo(() => _simulation.InteractionProperties).Returns(interactionProperties);
A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound, _compound2 });
}
protected override void Context()
{
_view = A.Fake <IIndividualProteinExpressionsView>();
_individualProteinMapper = A.Fake <IIndividualProteinToIndividualProteinDTOMapper>();
_moleculesPropertiesPresenter = A.Fake <IIndividualMoleculePropertiesPresenter <Individual> >();
_expressionLocalizationPresenter = A.Fake <IExpressionLocalizationPresenter <Individual> >();
_expressionParametersPresenter = A.Fake <IExpressionParametersPresenter>();
sut = new IndividualEnzymeExpressionsPresenter <Individual>(
_view, _individualProteinMapper,
_moleculesPropertiesPresenter,
_expressionLocalizationPresenter,
_expressionParametersPresenter);
_individual = new Individual();
sut.SimulationSubject = _individual;
_enzyme = new IndividualEnzyme().WithName("CYP3A4");
_enzymeDTO = new IndividualProteinDTO(_enzyme);
_initialConcentration = createParameter(INITIAL_CONCENTRATION);
_relativeExpression = createParameter(REL_EXP);
_relativeExpression2 = createParameter(REL_EXP);
_fraction_exp_bc = createParameter(FRACTION_EXPRESSED_BLOOD_CELLS);
_enzymeDTO.AddExpressionParameter(_initialConcentration);
_enzymeDTO.AddExpressionParameter(_relativeExpression);
_enzymeDTO.AddExpressionParameter(_fraction_exp_bc);
A.CallTo(() => _individualProteinMapper.MapFrom(_enzyme, _individual)).Returns(_enzymeDTO);
A.CallTo(() => _expressionParametersPresenter.Edit(A <IReadOnlyList <ExpressionParameterDTO> > ._))
.Invokes(x => _allParameters = x.GetArgument <IReadOnlyList <ExpressionParameterDTO> >(0).ToList());
sut.ActivateMolecule(_enzyme);
}
protected override void Context()
{
sut = new IndividualEnzyme();
}
protected override async Task Because()
{
_newMolecule = await sut.MapToModel(_snapshot, _individual) as IndividualEnzyme;
}
protected override void Because()
{
_undefined = sut.UndefinedLiverFor(_individual);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionContainerMapper = A.Fake <ExpressionContainerMapper>();
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyMapper = A.Fake <OntogenyMapper>();
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
_individualMoleculeParametersTask = A.Fake <IMoleculeParameterTask>();
sut = new MoleculeMapper(_parameterMapper, _expressionContainerMapper,
_ontogenyMapper, _individualMoleculeFactoryResolver, _executionContext, _ontogenyTask, _individualMoleculeParametersTask);
_ontogeny = new DatabaseOntogeny
{
Name = "Ontogeny"
};
_enzyme = new IndividualEnzyme
{
Name = "Enzyme",
Description = "Help",
Ontogeny = _ontogeny,
};
_transporter = new IndividualTransporter
{
Name = "Transporter",
Description = "Help"
};
_otherProtein = new IndividualOtherProtein
{
Name = "OtherProtein",
Description = "Help"
};
_enzymeGlobalParameter = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: true).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_enzymeGlobalParameterSnapshot = new Parameter();
A.CallTo(() => _parameterMapper.MapToSnapshot(_enzymeGlobalParameter)).Returns(_enzymeGlobalParameterSnapshot);
_expressionContainer1 = new MoleculeExpressionContainer {
Name = "Exp Container1"
};
_expressionContainer2 = new MoleculeExpressionContainer {
Name = "Exp Container2"
};
_enzyme.AddChildren(_expressionContainer1, _expressionContainer2, _enzymeGlobalParameter);
_relativeExpressionParameter1 = DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameters.REL_EXP);
_relativeExpressionParameterNorm1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.REL_EXP_NORM);
_expressionContainer1.Add(_relativeExpressionParameter1);
_expressionContainer1.Add(_relativeExpressionParameterNorm1);
_relativeExpressionParameterNotSet = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP);
_relativeExpressionParameterNotSetNorm = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP_NORM);
_expressionContainer2.Add(_relativeExpressionParameterNotSet);
_expressionContainer2.Add(_relativeExpressionParameterNotSetNorm);
_relativeExpressionContainerSnapshot1 = new ExpressionContainer();
_relativeExpressionContainerSnapshot2 = new ExpressionContainer();
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer1)).Returns(_relativeExpressionContainerSnapshot1);
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer2)).Returns(_relativeExpressionContainerSnapshot2);
_snapshotOntogeny = new Snapshots.Ontogeny();
A.CallTo(() => _ontogenyMapper.MapToSnapshot(_ontogeny)).Returns(_snapshotOntogeny);
_individual = new Individual();
return(_completed);
}
