private void convertIndividualTransporter(IndividualMolecule moleculeToConvert, IndividualMolecule newMolecule, Individual individual)
{
var transporterToConvert = moleculeToConvert as IndividualTransporter;
var newTransporter = newMolecule as IndividualTransporter;
if (transporterToConvert == null || newTransporter == null)
{
return;
}
newTransporter.TransportType = transporterToConvert.TransportType;
var allTransporterExpressionContainers = individual.AllMoleculeContainersFor <TransporterExpressionContainer>(newTransporter)
.Where(x => x.TransportDirection != TransportDirectionId.None).ToList();
//Ensure we update the default direction based on the selected transporter type
allTransporterExpressionContainers.Each(x => x.TransportDirection = TransportDirections.DefaultDirectionFor(newTransporter.TransportType, x));
moleculeToConvert.GetAllChildren <TransporterExpressionContainer>().Each(x => convertTransportContainer(x, allTransporterExpressionContainers));
}
private ICommand removeAdvancedParametersForMolecule(IndividualMolecule molecule, Population population)
{
var macroCommand = new PKSimMacroCommand
{
CommandType = PKSimConstants.Command.CommandTypeDelete,
Description = PKSimConstants.Command.RemoveAdvancedParametersForMoleculeInPopulation(molecule.Name, population.Name)
};
foreach (var parameter in molecule.GetAllChildren <IParameter>())
{
var advancedParameter = population.AdvancedParameterFor(_entityPathResolver, parameter);
if (advancedParameter != null)
{
macroCommand.AddCommand(new RemoveAdvancedParameterFromContainerCommand(advancedParameter, population, _executionContext).Run(_executionContext));
}
}
_executionContext.UpdateBuildingBlockPropertiesInCommand(macroCommand, population);
return(macroCommand);
}
private void convertMolecule(IndividualMolecule moleculeToConvert, Individual individual)
{
//Complete reorganization of molecules in the new version. We need to update value of relative expression.
//We know that localization was already updated during xml conversion
var factory = _individualMoleculeFactoryResolver.FactoryFor(moleculeToConvert);
//Remove from individual so that we can add it again.
individual.RemoveMolecule(moleculeToConvert);
//New molecules is added. We need to update all global parameters as well as relative expression parameters
var newMolecule = factory.AddMoleculeTo(individual, moleculeToConvert.Name);
if (newMolecule == null)
{
return;
}
newMolecule.Ontogeny = moleculeToConvert.Ontogeny;
var allExpressionParameters = individual.AllExpressionParametersFor(newMolecule);
moleculeToConvert.GetAllChildren <MoleculeExpressionContainer>().Each(x => { convertParameter(x.RelativeExpressionParameter, allExpressionParameters[x.Name]); });
moleculeToConvert.AllParameters().Each(p => convertParameter(p, newMolecule.Parameter(p.Name)));
//Perform normalization
NormalizeRelativeExpressionCommand.NormalizeExpressions(individual, newMolecule);
//Do reset default value that may be set to 0
allExpressionParameters.Each(x => x.DefaultValue = null);
//molecule specific conversion
convertIndividualProtein(moleculeToConvert, newMolecule, individual);
convertIndividualTransporter(moleculeToConvert, newMolecule, individual);
}
