private void hideInterstialParametersForIntracellularLocalizationInTissue(Individual individual, IndividualMolecule molecule, IList <IContainer> allOrganismContainers, PathCache <IMoleculeAmount> moleculeAmountPath)
{
var protein = molecule as IndividualProtein;
if (protein?.TissueLocation != TissueLocation.Intracellular || protein.IntracellularVascularEndoLocation != IntracellularVascularEndoLocation.Interstitial)
{
return;
}
var vascularEndothelium = protein.ExpressionContainer(CoreConstants.Compartment.VascularEndothelium);
if (vascularEndothelium == null)
{
return;
}
var allInterstitialContainer = _expressionContainersRetriever.AllContainersFor(individual.Organism, allOrganismContainers, protein, vascularEndothelium);
foreach (var interstitial in allInterstitialContainer)
{
var amount = amountFor(interstitial, molecule, moleculeAmountPath);
if (amount == null)
{
continue;
}
hideParameter(amount.Parameter(CoreConstants.Parameters.REL_EXP));
hideParameter(amount.Parameter(CoreConstants.Parameters.REL_EXP_NORM));
}
}
private void updateProteinParametersValues(IndividualProtein protein)
{
setGlobalParameterValue(protein, CoreConstants.Parameter.REL_EXP_BLOOD_CELL, CoreConstants.Compartment.BloodCells);
setGlobalParameterValue(protein, CoreConstants.Parameter.REL_EXP_PLASMA, CoreConstants.Compartment.Plasma);
setGlobalParameterValue(protein, CoreConstants.Parameter.REL_EXP_VASC_ENDO, CoreConstants.Compartment.VascularEndothelium);
foreach (var expressionContainer in _expressionContainersRetriever.AllContainersFor(_spatialStructure, protein))
{
if (expressionContainer.IsBloodCell())
{
setParameterValuesForBloodCells(protein, expressionContainer);
}
else if (expressionContainer.IsPlasma())
{
setParameterValuesForPlasma(protein, expressionContainer);
}
else if (expressionContainer.IsInterstitial())
{
setParameterValuesForInterstitial(protein, expressionContainer);
}
else if (expressionContainer.IsEndosome())
{
setParameterValuesForEndosome(protein, expressionContainer);
}
else
{
setParameterValuesForStandardContainer(protein, expressionContainer);
}
}
}
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);
}
}
}
}
private IEnumerable <IObjectPath> moleculesInvolvedInExpression(ISpatialStructure spatialStructure, IndividualMolecule molecule,
IReadOnlyList <CompoundProperties> compoundPropertiesList)
{
foreach (var expressionContainer in _expressionContainersRetriever.AllContainersFor(spatialStructure, molecule))
{
var containerPath = _objectPathFactory.CreateAbsoluteObjectPath(expressionContainer);
foreach (var compoundProperties in compoundPropertiesList)
{
foreach (var moleculeName in compoundProperties.Processes.AllInducedMoleculeNames(molecule))
{
yield return(containerPath.Clone <IObjectPath>().AndAdd(moleculeName));
}
}
}
}
