private async Task <ParameterRange[]> snapshotDiseaseStateParameters(Model.Individual individual, RandomPopulationSettings randomPopulationSettings)
{
var diseaseStateParameterRanges = individual.OriginData?.DiseaseStateParameters
.Select(x => randomPopulationSettings.ParameterRange(x.Name))
.ToList();
if (diseaseStateParameterRanges == null)
{
return(null);
}
if (!diseaseStateParameterRanges.Any())
{
return(null);
}
var snapshotParameterRanges = new List <ParameterRange>();
foreach (var parameterRange in diseaseStateParameterRanges)
{
var snapshot = await _parameterRangeMapper.MapToSnapshot(parameterRange);
snapshot.Name = parameterRange.ParameterName;
snapshotParameterRanges.Add(snapshot);
}
return(snapshotParameterRanges.ToArray());
}
public ModelProperties MapFrom(SimulationConfiguration configuration, Model.Individual individual)
{
var modelProperties = _modelPropertiesTask.DefaultFor(individual.OriginData, configuration.Model);
_batchLogger.AddDebug($"Using model method '{configuration.Model}'");
return(modelProperties);
}
private TMolecule addMoleculeTo <TMolecule>(Model.Individual individual, Molecule molecule) where TMolecule : IndividualMolecule
{
var proteinFactory = _moleculeFactoryResolver.FactoryFor <TMolecule>();
var newMolecule = proteinFactory.CreateFor(individual);
newMolecule.ReferenceConcentration.Value = molecule.ReferenceConcentration;
newMolecule.HalfLifeLiver.Value = molecule.HalfLifeLiver;
newMolecule.HalfLifeIntestine.Value = molecule.HalfLifeIntestine;
newMolecule.Name = molecule.Name;
individual.AddMolecule(newMolecule);
foreach (var expression in molecule.Expressions)
{
var expressionParameter = newMolecule.GetRelativeExpressionNormParameterFor(expression.Key);
if (expressionParameter == null)
{
_batchLogger.AddWarning($"Relative Expression container '{expression.Key}' not found for '{molecule.Name}'");
continue;
}
expressionParameter.Value = expression.Value;
_batchLogger.AddDebug($"Relative Expression norm for container '{expression.Key}' set to {expression.Value}");
}
return(newMolecule.DowncastTo <TMolecule>());
}
private void addPartialProcesses <TPartialProcess, TIndividualMolecule, TProcessSelection>(Model.Compound compound, Model.Individual individual, ProcessSelectionGroup processSelectionGroup)
where TPartialProcess : Model.PartialProcess
where TIndividualMolecule : IndividualMolecule
where TProcessSelection : ProcessSelection, new()
{
//default mapping with processes: Mapping done only by name
foreach (var process in compound.AllProcesses <TPartialProcess>())
{
var molecule = individual.MoleculeByName <TIndividualMolecule>(process.MoleculeName);
//enzyme not found in individual
if (molecule == null)
{
_batchLogger.AddDebug($"Molecule '{process.MoleculeName}' not found in individual but is defined in compound for process '{process.Name}'");
continue;
}
_batchLogger.AddDebug($"Adding process {process.Name} for molecule {molecule.Name}");
processSelectionGroup.AddPartialProcessSelection(new TProcessSelection {
ProcessName = process.Name, MoleculeName = molecule.Name, CompoundName = compound.Name
});
}
}
