public MembraneLocation MembraneLocationToUse(ITransporterExpressionContainer transporterContainer, TransportType newTransportType)
{
if (!transporterContainer.HasPolarizedMembrane)
{
return(transporterContainer.MembraneLocation);
}
//Brain always plasma
if (transporterContainer.IsNamed(CoreConstants.Organ.Brain))
{
return(MembraneLocation.BloodBrainBarrier);
}
//intestine always apical
if (transporterContainer.GroupName == CoreConstants.Groups.GI_MUCOSA)
{
return(MembraneLocation.Apical);
}
//pgp and efflux always apical
if (newTransportType == TransportType.PgpLike || newTransportType == TransportType.Efflux)
{
return(MembraneLocation.Apical);
}
//not brain and intestine=>Influx is always basolateral
if (newTransportType == TransportType.Influx)
{
return(MembraneLocation.Basolateral);
}
return(transporterContainer.MembraneLocation);
}
protected override void Context()
{
base.Context();
_transporterContainer = A.Fake<ITransporterExpressionContainer>();
A.CallTo(() => _transporterContainer.Name).Returns(_liver);
_species = "human";
A.CallTo(() => _repository.TransportersFor(_species, _liver)).Returns(_allTransporters);
_membrane = MembraneLocation.Apical;
_transportType = TransportType.Efflux;
_transporterContainerTemplate = new TransporterContainerTemplate {MembraneLocation = _membrane, TransportType = _transportType};
_allTransporters.Add(_transporterContainerTemplate);
}
public SetMembraneTypeCommand(ITransporterExpressionContainer transporterContainer, TransportType transportType, MembraneLocation newMembraneLocation, IExecutionContext context)
{
_transporterContainer = transporterContainer;
_transportType = transportType;
_transporterContainerId = _transporterContainer.Id;
_newMembraneLocation = newMembraneLocation;
_individual = context.BuildingBlockContaining(_transporterContainer).DowncastTo <Individual>();
BuildingBlockId = _individual.Id;
_oldMembraneLocation = _transporterContainer.MembraneLocation;
ObjectType = PKSimConstants.ObjectTypes.Transporter;
CommandType = PKSimConstants.Command.CommandTypeEdit;
context.UpdateBuildinBlockProperties(this, _individual);
}
protected override void Context()
{
sut = new IndividualTransporter().WithName("T");
_transpoterExpressionLiver = new TransporterExpressionContainer().WithName("Liver");
_transpoterExpressionLiver.AddProcessName("P1");
_transpoterExpressionKidney = new TransporterExpressionContainer().WithName("Kidney");
_transpoterExpressionKidney.AddProcessName("P2");
_transpoterExpressionBrain = new TransporterExpressionContainer().WithName("Brain");
_transpoterExpressionBrain.AddProcessName("P1");
sut.Add(_transpoterExpressionLiver);
sut.Add(_transpoterExpressionKidney);
sut.Add(_transpoterExpressionBrain);
}
public SetTransportTypeCommand(ITransporterExpressionContainer transporterContainer, TransportType oldTransportType, TransportType newTransportType, MembraneLocation membraneLocationToUse, IExecutionContext context)
{
_transporterContainer = transporterContainer;
_membraneLocationToUse = membraneLocationToUse;
_transporterContainerId = _transporterContainer.Id;
_individual = context.BuildingBlockContaining(transporterContainer).DowncastTo <Individual>();
BuildingBlockId = _individual.Id;
_newTransportType = newTransportType;
_oldTransportType = oldTransportType;
ObjectType = PKSimConstants.ObjectTypes.Transporter;
CommandType = PKSimConstants.Command.CommandTypeEdit;
context.UpdateBuildinBlockProperties(this, _individual);
Visible = false;
}
public void UpdateTransporterFromTemplate(ITransporterExpressionContainer transporterContainer, string species, MembraneLocation membraneLocation, TransportType transportType)
{
//we need to retrieve the process name for the given MembraneTupe/Process Type combo
var templateToUse = _transporterContainerTemplateRepository.TransportersFor(species, transporterContainer.Name)
.Where(x => x.MembraneLocation == membraneLocation)
.FirstOrDefault(x => x.TransportType == transportType);
//That should never happen, otherwise we would have a transporter container with an unknown process
if (templateToUse == null)
{
throw new PKSimException(PKSimConstants.Error.CouldNotFindTransporterFor(transporterContainer.Name, membraneLocation.ToString(), transportType.ToString()));
}
transporterContainer.UpdatePropertiesFrom(templateToUse);
}
protected override void Context()
{
base.Context();
_transporter = new IndividualTransporter {TransportType = TransportType.Efflux, Name = "toto"};
_transporterWithTemplate = new TransporterExpressionContainer {MembraneLocation = MembraneLocation.Apical}.WithName(_liver);
_transporterWithoutTemplate = new TransporterExpressionContainer {MembraneLocation = MembraneLocation.Basolateral}.WithName("Kidney");
_transporter.Add(_transporterWithTemplate);
_transporter.Add(_transporterWithoutTemplate);
_transporterContainerTemplate = new TransporterContainerTemplate {MembraneLocation = MembraneLocation.Apical, TransportType = TransportType.Influx};
_defaultTemplate = new TransporterContainerTemplate {MembraneLocation = MembraneLocation.Basolateral, TransportType = TransportType.Influx};
_allTransporterTemplates.Add(_transporterContainerTemplate);
A.CallTo(() => _repository.HasTransporterTemplateFor(_species, _transporter.Name)).Returns(true);
A.CallTo(() => _repository.TransportTypeFor(_species, _transporter.Name)).Returns(TransportType.Influx);
A.CallTo(() => _repository.TransportersFor(_species, _liver, _transporter.Name)).Returns(_allTransporterTemplates);
A.CallTo(() => _repository.TransportersFor(_species, _kidney, _transporter.Name)).Returns(new List<TransporterContainerTemplate>());
A.CallTo(() => _repository.TransportersFor(_species, _kidney)).Returns(new List<TransporterContainerTemplate> {_defaultTemplate});
}
public override void RestoreExecutionData(IExecutionContext context)
{
base.RestoreExecutionData(context);
_individual = context.Get <Individual>(BuildingBlockId);
_transporterContainer = context.Get <ITransporterExpressionContainer>(_transporterContainerId);
}
protected override void ClearReferences()
{
_transporterContainer = null;
_individual = null;
}
private void addContainerExpression(TransporterExpressionDTO proteinExpressionDTO, IndividualTransporter transporter, ITransporterExpressionContainer transporterExpressionContainer)
{
var expressionDTO = new TransporterExpressionContainerDTO(transporterExpressionContainer)
{
MoleculeName = transporter.Name, ContainerName = transporterExpressionContainer.Name
};
_expressionContainerDTOUpdater.UpdateProperties(expressionDTO, transporterExpressionContainer);
proteinExpressionDTO.AddProteinExpression(expressionDTO);
}
public ICommand SetMembraneLocationFor(ITransporterExpressionContainer transporterContainer, TransportType transportType, MembraneLocation membraneLocation)
{
return(new SetMembraneTypeCommand(transporterContainer, transportType, membraneLocation, _executionContext).Run(_executionContext));
}
public TransporterExpressionContainerDTO(ITransporterExpressionContainer transporterContainer)
{
_transporterContainer = transporterContainer;
_transporterContainer.PropertyChanged += raisePropertyChange;
}
public override void ClearReferences()
{
base.ClearReferences();
_transporterContainer.PropertyChanged -= raisePropertyChange;
_transporterContainer = null;
}
private IEnumerable <IContainer> allContainersForTransporter(Organism organism, IndividualTransporter transporter, IEnumerable <IContainer> allContainers, ITransporterExpressionContainer expressionContainer)
{
if (expressionContainer.IsSurrogate())
{
return(allCompartmentsOfNames(allContainers, expressionContainer.Name));
}
return(compartmentFor(organism, expressionContainer, expressionContainer.CompartmentName));
}
