public void Visit(Individual individual)
{
_currentSpecies = individual.Species;
convertTransitTimeFor(individual);
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
_converted = true;
}
private void convertIndividual(Individual individual)
{
if (individual == null)
{
return;
}
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
if (!individual.IsHuman)
{
return;
}
if (individual.Organism.Parameter(CoreConstants.Parameter.BSA) != null)
{
return;
}
var defaultHuman = _defaultIndividualRetriever.DefaultHuman();
var bsa = defaultHuman.Organism.Parameter(CoreConstants.Parameter.BSA);
individual.Organism.Add(_cloner.Clone(bsa));
}
private void convertIndividual(Individual individual)
{
if (individual == null)
{
return;
}
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
}
private void convertIndividual(Individual individual)
{
if (individual == null)
{
return;
}
// create hidden Renal Aging factor-parameter and set it to 1
var kidney = individual.Organism.Organ(CoreConstants.Organ.Kidney);
var renalAgingParameter = _parameterFactory.CreateFor(ConverterConstants.Parameter.RenalAgingScaleFactor, 1.0, PKSimBuildingBlockType.Individual);
renalAgingParameter.CanBeVaried = false;
renalAgingParameter.CanBeVariedInPopulation = false;
renalAgingParameter.Editable = false;
renalAgingParameter.Visible = false;
kidney.Add(renalAgingParameter);
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
}
public void Visit(Individual individual)
{
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
performCommonConversion(individual);
Visit(individual.OriginData);
foreach (var transporter in individual.AllMolecules <IndividualTransporter>().SelectMany(x => x.AllExpressionsContainers()))
{
var oldProcessNames = transporter.ProcessNames.ToList();
transporter.ClearProcessNames();
foreach (var processName in oldProcessNames)
{
transporter.AddProcessName(processName.Replace("_MM", ""));
}
}
//change container type for molecules
foreach (var molecule in individual.AllMolecules())
{
molecule.ContainerType = ContainerType.Molecule;
updateOntogeny(molecule);
}
//special parameters that need conversion by hand
convertIndividualParameters(individual.Organism);
convertIndividualForTwoPore(individual);
var human = _defaultIndividualRetriever.DefaultHuman();
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.ONTOGENY_FACTOR_ALBUMIN));
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.ONTOGENY_FACTOR_AGP));
individual.Organism.Add(clone(human.Organism, CoreConstants.Parameters.PLASMA_PROTEIN_SCALE_FACTOR));
if (!individual.IsHuman)
{
individual.OriginData.AddCalculationMethod(_calculationMethodRepository.FindByName("MucosaVolume_Animals"));
}
else
{
individual.OriginData.AddCalculationMethod(_calculationMethodRepository.FindByName("MucosaVolume_Human"));
individual.OriginData.GestationalAge = CoreConstants.NOT_PRETERM_GESTATIONAL_AGE_IN_WEEKS;
individual.OriginData.GestationalAgeUnit = CoreConstants.Units.Weeks;
var gestationalAge = human.Organism.Parameter(Constants.Parameters.GESTATIONAL_AGE);
if (!individual.Organism.ContainsName(Constants.Parameters.GESTATIONAL_AGE))
{
individual.Organism.Add(_cloner.Clone(gestationalAge));
}
}
}
private void convertIndividual(Individual individual)
{
if (individual == null)
{
return;
}
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
individual.AllMolecules().SelectMany(m => m.AllExpressionsContainers())
.Select(c => c.RelativeExpressionParameter)
.Each(p => p.Dimension = Constants.Dimension.NO_DIMENSION);
}
public void Visit(Individual individual)
{
if (individual == null)
{
return;
}
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
_individualUpdater.AddScalingExponentForFluidFlowTo(individual);
addSurfaceAreaParametersTo(individual);
updateSurfaceAreaIntCellMucosa(individual);
_converted = true;
}
private void convertIndividual(Individual individual)
{
//possible for imported simulation where individual is not defined
if (individual == null)
{
return;
}
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
_individualUpdater.AddScalingExponentForFluidFlowTo(individual);
updateLiverStructure(individual);
updateIsLiverZonatedValue(individual);
updateLiverExpressions(individual);
updateOntogenyFactorVisibility(individual);
removeVolumePlasmaParameter(individual.Organism);
_neighborhoodFinalizer.SetNeighborsIn(individual);
}
public void Visit(Individual individual)
{
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
updateVariableInPopulationFlag(individual);
_converted = true;
}
public void Visit(Individual individual)
{
_individualCalculationMethodsUpdater.AddMissingCalculationMethodsTo(individual);
addIndividualParameters(individual, individual.Species);
_converted = true;
}