protected override void PerformExecuteWith(IExecutionContext context)
{
//Retrieve building block id in execute only since molecule might have been added in a macro command and bbid was not available in constructor
BuildingBlockId = context.BuildingBlockIdContaining(_molecule);
var allRelExpressionContainer = _molecule.AllExpressionsContainers().ToList();
var max = allRelExpressionContainer.Select(x => x.RelativeExpression).Max();
allRelExpressionContainer.Each(relExp => relExp.RelativeExpressionNorm = max == 0 ? 0 : relExp.RelativeExpression / max);
}
private void updateAllParametersFor(Simulation simulation, Individual individual, IList <IContainer> allOrganismContainers, IndividualMolecule molecule, PathCache <IMoleculeAmount> moleculeAmountPath)
{
var globalMoleculeContainer = simulation.Model.Root
.GetSingleChildByName <IContainer>(molecule.Name);
globalMoleculeContainer.Parameter(CoreConstants.Parameter.ONTOGENY_FACTOR_GI).Visible = false;
globalMoleculeContainer.Parameter(CoreConstants.Parameter.ONTOGENY_FACTOR).Visible = false;
hideGlobalParametersForUndefinedMolecule(globalMoleculeContainer);
foreach (var expressionContainer in molecule.AllExpressionsContainers())
{
var relExpNorm = expressionContainer.RelativeExpressionNormParameter;
var relExp = expressionContainer.RelativeExpressionParameter;
if (expressionContainer.IsSurrogate())
{
string relExpName;
if (expressionContainer.IsBloodCell())
{
relExpName = CoreConstants.Parameter.RelExpBloodCell;
}
else if (expressionContainer.IsPlasma())
{
relExpName = CoreConstants.Parameter.RelExpPlasma;
}
else if (expressionContainer.IsVascularEndothelium())
{
relExpName = CoreConstants.Parameter.RelExpVascEndo;
}
else
{
continue;
}
string relExpNormName = CoreConstants.Parameter.NormParameterFor(relExpName);
updateFromIndividualParameter(globalMoleculeContainer.Parameter(relExpName), relExp, individual, molecule);
updateFromIndividualParameter(globalMoleculeContainer.Parameter(relExpNormName), relExpNorm, individual, molecule);
}
else
{
//not a global parameter simply update the norm parameters
var allContainers = _expressionContainersRetriever.AllContainersFor(individual.Organism, allOrganismContainers, molecule, expressionContainer);
foreach (var container in allContainers)
{
var amount = moleculeAmountPath[_entityPathResolver.ObjectPathFor(container).AndAdd(molecule.Name).ToString()];
if (amount == null)
{
continue;
}
updateFromIndividualParameter(amount.Parameter(CoreConstants.Parameter.RelExpNorm), relExpNorm, individual, molecule);
updateFromIndividualParameter(amount.Parameter(CoreConstants.Parameter.RelExp), relExp, individual, molecule);
}
}
}
}
public IEnumerable <IContainer> AllContainersFor(Organism organism, IndividualMolecule molecule)
{
var allContainers = AllOrganismContainers(organism).ToList();
var allContainersForProtein = new List <IContainer>();
foreach (var expressionContainer in molecule.AllExpressionsContainers())
{
allContainersForProtein.AddRange(allContainersFor(organism, molecule, allContainers, expressionContainer));
}
return(allContainersForProtein.Distinct());
}
protected override void Context()
{
base.Context();
_clonedProtein = A.Fake <IndividualMolecule>();
A.CallTo(() => _clonedProtein.AllExpressionsContainers()).Returns(_molecule.AllExpressionsContainers());
_individual.AddMolecule(_molecule);
_querySettings = A.Fake <QueryExpressionSettings>();
_queryResults = A.Fake <QueryExpressionResults>();
A.CallTo(() => _executionContext.Clone(_molecule)).Returns(_clonedProtein);
A.CallTo(() => _querySettingsMapper.MapFrom(_molecule)).Returns(_querySettings);
A.CallTo(() => _proteinExpressionPresenter.Start()).Returns(true);
A.CallTo(() => _proteinExpressionPresenter.GetQueryResults()).Returns(_queryResults);
}
private void updateAllParametersFor(Simulation simulation, Individual individual, IList <IContainer> allOrganismContainers, IndividualMolecule molecule, PathCache <IMoleculeAmount> moleculeAmountPath)
{
var globalMoleculeContainer = simulation.Model.Root
.GetSingleChildByName <IContainer>(molecule.Name);
hideGlobalParametersForUndefinedMolecule(globalMoleculeContainer);
hideInterstialParametersForIntracellularLocalizationInTissue(individual, molecule, allOrganismContainers, moleculeAmountPath);
foreach (var expressionContainer in molecule.AllExpressionsContainers())
{
if (expressionContainer.IsSurrogate())
{
updateReferenceToIndividualParametersForSurrogateContainer(individual, molecule, expressionContainer, globalMoleculeContainer);
}
else
{
updateReferenceToIndividualParametersForStandardContainer(individual, molecule, expressionContainer, allOrganismContainers, moleculeAmountPath);
}
}
}
private void updateOntogeny(IndividualMolecule molecule)
{
var liver = molecule.ExpressionContainer(CoreConstants.Organ.Liver);
if (liver == null)
{
return;
}
var ontogenyFactorLiver = liver.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR);
if (ontogenyFactorLiver != null)
{
molecule.Add(ontogenyFactorLiver);
}
IParameter ontogenyFactorDuodenum = null;
var duodenum = molecule.ExpressionContainer(CoreConstants.Compartment.Duodenum);
if (duodenum != null)
{
ontogenyFactorDuodenum = duodenum.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR);
}
//remove old ontogeny factor parameter in container
foreach (var expressionContainer in molecule.AllExpressionsContainers())
{
var ontogenyFactor = expressionContainer.Parameter(CoreConstants.Parameters.ONTOGENY_FACTOR);
if (ontogenyFactor != null)
{
expressionContainer.RemoveChild(ontogenyFactor);
}
}
if (ontogenyFactorDuodenum != null)
{
ontogenyFactorDuodenum.Name = CoreConstants.Parameters.ONTOGENY_FACTOR_GI;
molecule.Add(ontogenyFactorDuodenum);
}
}
public QueryExpressionSettings MapFrom(IndividualMolecule molecule)
{
var expressionContainer = new List <ExpressionContainerInfo>(molecule.AllExpressionsContainers().MapAllUsing(_expressionContainerInfoMapper));
return(new QueryExpressionSettings(expressionContainer, molecule.QueryConfiguration));
}
