private void updateReferences(IUsingFormula usingFormula, string moleculeName, string compoundName, Simulation simulation,
IContainer processParameterContainer, InteractionKineticModifications kineticModification)
{
if (!_kineticModifications.Is(kineticModification))
{
return;
}
var formula = usingFormula.Formula;
var kiAliasBase = kiAliasFrom(kineticModification);
var kiParameter = kiParameterFrom(kineticModification);
doOverAllInteractions(moleculeName, compoundName, simulation, kiAliasBase, (interactionProcess, inhibitorAlias, kiAlias, kwaterAlias) =>
{
var inhibitor = interactionProcess.ParentCompound;
if (formula.FormulaUsablePathBy(inhibitorAlias) == null)
{
formula.AddObjectPath(inhiborConcentrationPath(inhibitor, inhibitorAlias, processParameterContainer));
}
if (formula.FormulaUsablePathBy(kwaterAlias) == null)
{
formula.AddObjectPath(kwaterPath(inhibitor, kwaterAlias, processParameterContainer));
}
if (formula.FormulaUsablePathBy(kiAlias) == null)
{
formula.AddObjectPath(kiPath(kiParameter, inhibitor, interactionProcess, kiAlias));
}
});
}
protected InteractionKineticUpdaterSpecificationBase(IObjectPathFactory objectPathFactory, IDimensionRepository dimensionRepository, IInteractionTask interactionTask, InteractionType interactionType,
string kiNumeratorParameter, string kiDenominatorParameter, string kiNumeratorAlias, string kiDenominatorAlias, string inhibitorAlias)
{
_objectPathFactory = objectPathFactory;
_dimensionRepository = dimensionRepository;
_interactionTask = interactionTask;
_interactionType = interactionType;
_kineticModifications = modificationsFrom(interactionType);
_kiNumeratorParameter = kiNumeratorParameter;
_kiDenominatorParameter = kiDenominatorParameter;
_kiNumeratorAlias = kiNumeratorAlias;
_kiDenominatorAlias = kiDenominatorAlias;
_inhibitorAlias = inhibitorAlias;
}
private Tuple <string, string> kiInfoFrom(InteractionKineticModifications kineticModification)
{
switch (kineticModification)
{
case InteractionKineticModifications.KmDenominator:
case InteractionKineticModifications.KcatDenominator:
return(new Tuple <string, string>(_kiDenominatorAlias, _kiDenominatorParameter));
case InteractionKineticModifications.KmNumerator:
case InteractionKineticModifications.CLSpecDenominator:
return(new Tuple <string, string>(_kiNumeratorAlias, _kiNumeratorParameter));
default:
throw new ArgumentOutOfRangeException("kineticModification");
}
}
private (string kiAlias, string kiParameter) kiInfoFrom(InteractionKineticModifications kineticModification)
{
switch (kineticModification)
{
case InteractionKineticModifications.KmDenominator:
case InteractionKineticModifications.KcatDenominator:
return(_kiDenominatorAlias, _kiDenominatorParameter);
case InteractionKineticModifications.KmNumerator:
case InteractionKineticModifications.CLSpecDenominator:
return(_kiNumeratorAlias, _kiNumeratorParameter);
default:
throw new ArgumentOutOfRangeException(nameof(kineticModification));
}
}
public static bool Is(this InteractionKineticModifications modifications, InteractionKineticModifications typeToCompare)
{
return((modifications & typeToCompare) != 0);
}
private string inhibitionTermsFor(string moleculeName, string compoundName, Simulation simulation, InteractionKineticModifications kineticModification)
{
if (!_kineticModifications.Is(kineticModification))
{
return(string.Empty);
}
var kiAliasBase = kiAliasFrom(kineticModification);
var inibitionTerms = new List <string>();
doOverAllInteractions(moleculeName, compoundName, simulation, kiAliasBase,
(interactionProcess, inhibitorAlias, kiAlias, kwaterAlias) => inibitionTerms.Add($"{kwaterAlias}*{inhibitorAlias}/{kiAlias}"));
return(inibitionTerms.ToString(" + "));
}
private string kiParameterFrom(InteractionKineticModifications kineticModification)
{
return(kiInfoFrom(kineticModification).Item2);
}
private string kiAliasFrom(InteractionKineticModifications kineticModification)
{
return(kiInfoFrom(kineticModification).Item1);
}