public override void Execute(IExecutionContext context)
{
ObjectType = context.TypeFor(_molecule);
var containerName = string.IsNullOrEmpty(_simulationSubject.Name) ? CoreConstants.ContainerName.NameTemplate : _simulationSubject.Name;
Description = PKSimConstants.Command.AddEntityToContainer(ObjectType, _molecule.Name, context.TypeFor(_simulationSubject), containerName);
//First add the protein expression to the individual so that undo will be available
Add(AddMoleculeToSimulationSubjectCommand(_molecule, _simulationSubject, context));
//Then update the new expression values
foreach (var expressionResult in _queryExpressionResults.ExpressionResults)
{
Add(new SetRelativeExpressionCommand(_molecule.GetRelativeExpressionParameterFor(expressionResult.ContainerName), expressionResult.RelativeExpression));
}
Add(new NormalizeRelativeExpressionCommand(_molecule, context));
//update properties from first command
this.UpdatePropertiesFrom(All().FirstOrDefault());
base.Execute(context);
//clear references
_molecule = null;
_queryExpressionResults = null;
_simulationSubject = null;
}
private void setGlobalParameterValue(IndividualMolecule molecule, string expressionName, string containerName)
{
if (!molecule.HasContainerNamed(containerName))
{
return;
}
trySetValue(moleculeGlobalPathFor(molecule.Name).AndAdd(CoreConstants.Parameter.NormParameterFor(expressionName)), molecule.GetRelativeExpressionNormParameterFor(containerName));
trySetValue(moleculeGlobalPathFor(molecule.Name).AndAdd(expressionName), molecule.GetRelativeExpressionParameterFor(containerName));
}
private void setParameterValuesForStandardContainer(IndividualMolecule molecule, IContainer expressionContainer)
{
var containerName = relativeExpressionContainerNameFrom(molecule, expressionContainer);
var relExpNormPath = relExpNormPathFor(molecule, expressionContainer);
var relExpPath = relExpPathFor(molecule, expressionContainer);
trySetValue(relExpNormPath, molecule.GetRelativeExpressionNormParameterFor(containerName));
trySetValue(relExpPath, molecule.GetRelativeExpressionParameterFor(containerName));
var relExpOut = relExpOutPathFor(molecule, expressionContainer);
trySetFormula(relExpOut, CoreConstants.Rate.RelExpOutFromNorm);
}
public SetRelativeExpressionAndNormalizeCommand(IndividualMolecule molecule, string proteinContainerName, double value)
{
_molecule = molecule;
_relExpParameter = molecule.GetRelativeExpressionParameterFor(proteinContainerName);
_newValue = value;
}
