private void addReactionToBuildingBlock(IReactionBuilder reaction, Compound compound)
{
_parameterIdUpdater.UpdateBuildingBlockId(reaction.Parameters, compound);
_reactionBuildingBlock.Add(reaction);
}
private bool conversionRequired(IReactionBuilder reaction)
{
return(conversionRequired(reaction, Constants.Dimension.AMOUNT_PER_TIME));
}
public void Visit(IReactionBuilder reactionBuilder)
{
Convert(reactionBuilder, new FormulaCache());
}
public void UpdateReaction(IReactionBuilder reaction, string enzymeName, string compoundName, Simulation simulation, IFormulaCache formulaCache)
{
updateProcess(reaction, enzymeName, compoundName, simulation, formulaCache);
}
public RemoveReactionPartnerFromProductCollection(IReactionBuilder reactionBuilder, IReactionPartnerBuilder reactionPartnerBuilder, IMoBiReactionBuildingBlock reactionBuildingBlock)
: base(reactionBuilder, reactionPartnerBuilder, reactionBuildingBlock, x => x.RemoveProduct)
{
ObjectType = ObjectTypes.Product;
}
public EditReactionPartnerStoichiometricCoefficientCommand(double newCoefficient, IReactionBuilder reaction, IReactionPartnerBuilder reactionPartner, IMoBiReactionBuildingBlock buildingBlock) : base(reaction, reactionPartner, buildingBlock)
{
_newCoefficient = newCoefficient;
_oldCoefficient = reactionPartner.StoichiometricCoefficient;
_moleculeName = reactionPartner.MoleculeName;
Description = AppConstants.Commands.EditStochiometricCoefficient(newCoefficient, _reactionPartner.StoichiometricCoefficient, _reaction.Name, _moleculeName, _isEduct ? ObjectTypes.Educt : ObjectTypes.Product);
}
public void Visit(IReactionBuilder objToVisit)
{
addNamesToHash(_nameHashForVisitor, For(objToVisit));
}
public AddReactionPartnerToProductCollection(IMoBiReactionBuildingBlock reactionBuildingBlock, IReactionPartnerBuilder reactionPartnerBuilder, IReactionBuilder reactionBuilder) :
base(reactionBuildingBlock, reactionPartnerBuilder, reactionBuilder, x => x.AddProduct)
{
ObjectType = ObjectTypes.Product;
}
public AddItemToModifierCollectionCommand(IMoBiReactionBuildingBlock reactionBuildingBlock, string modifier, IReactionBuilder reactionBuilder) :
base(reactionBuildingBlock, modifier, reactionBuilder, x => x.AddModifier)
{
ObjectType = ObjectTypes.Modifier;
}
public override void RestoreExecutionData(IMoBiContext context)
{
base.RestoreExecutionData(context);
_reaction = context.Get <IReactionBuilder>(_parentId);
}
protected RemovePartnerFromReactionCommand(IReactionBuilder reactionBuilder, IReactionPartnerBuilder itemToRemove, IMoBiReactionBuildingBlock reactionBuildingBlock, Func <IReactionBuilder, Action <IReactionPartnerBuilder> > removeMethod) : base(reactionBuilder, itemToRemove, reactionBuildingBlock, removeMethod)
{
}
protected override void ClearReferences()
{
base.ClearReferences();
_reaction = null;
}
protected RemoveItemFromReactionCommand(IReactionBuilder reactionBuilder, T itemToRemove, IMoBiReactionBuildingBlock reactionBuildingBlock, Func <IReactionBuilder, Action <T> > removeMethod) : base(reactionBuilder, itemToRemove, reactionBuildingBlock)
{
_removeMethod = removeMethod;
_reaction = reactionBuilder;
_moleculeName = MoleculeNameFrom(itemToRemove);
}
public RemoveItemFromModifierCollectionCommand(IReactionBuilder reactionBuilder, string modififer, IMoBiReactionBuildingBlock reactionBuildingBlock)
: base(reactionBuilder, modififer, reactionBuildingBlock, x => x.RemoveModifier)
{
ObjectType = ObjectTypes.Modifier;
}
private IReactionBuilder createReactionFromProcess(IReactionBuilder templateReactionBuilder, IReadOnlyCollection <string> forbiddenNames)
{
return(createReactionFromProcess(templateReactionBuilder, templateReactionBuilder, templateReactionBuilder.Name, forbiddenNames));
}
public AddedReactionModifierEvent(IReactionBuilder reaction, string modifierName)
{
Reaction = reaction;
ModifierName = modifierName;
}
private IReactionBuilder createReactionFromProcess(IContainer reactionParameterContainer, IReactionBuilder templateReactionBuilder,
string newReactionName, IReadOnlyCollection <string> forbiddenNames)
{
//retrieve process for the simulation and create a clone
var reaction = _cloner.Clone(templateReactionBuilder).WithName(newReactionName);
while (forbiddenNames.Contains(reaction.Name))
{
reaction.Name = $"@{reaction.Name}";
}
_parameterSetUpdater.UpdateValuesByName(reactionParameterContainer.AllParameters(), reaction.Parameters);
return(reaction);
}
protected AddItemToReactionCommand(IMoBiReactionBuildingBlock reactionBuildingBlock, T itemToAdd, IReactionBuilder reactionBuilder, Func <IReactionBuilder, Action <T> > addMethod)
: base(reactionBuilder, itemToAdd, reactionBuildingBlock)
{
_addMethod = addMethod;
_moleculeName = MoleculeNameFrom(_itemToAdd);
}
public void Edit(IReactionBuilder reactionBuilder)
{
Edit(reactionBuilder, Enumerable.Empty <IObjectBase>());
}
protected AddPartnerToReactionCommand(IMoBiReactionBuildingBlock reactionBuildingBlock, T reactionPartnerBuilder, IReactionBuilder reactionBuilder, Func <IReactionBuilder, Action <T> > addMethod) :
base(reactionBuildingBlock, reactionPartnerBuilder, reactionBuilder, addMethod)
{
}
protected override void Context()
{
base.Context();
_reaction = new ReactionBuilder();
_reaction.AddModifier(_compound1.Name);
}
public RemoveReactionBuilderUICommand <TBuilder> Initialize(TBuilder partnerBuilder, IReactionBuilder builder)
{
_partnerBuilder = partnerBuilder;
_builder = builder;
return(this);
}
public EditReactionPartnerMoleculeNameCommand(string newMoleculeName, IReactionBuilder reaction, IReactionPartnerBuilder reactionPartner, IMoBiReactionBuildingBlock buildingBlock) :
base(reaction, reactionPartner, buildingBlock)
{
_newMoleculeName = newMoleculeName;
Description = AppConstants.Commands.EditDescription(ObjectType, _isEduct ? ObjectTypes.Educt : ObjectTypes.Product, _reactionPartner.MoleculeName, newMoleculeName, _reaction.Name);
}
public ReactionBuilderDTO(IReactionBuilder reactionBuilder)
{
ReactionBuilder = reactionBuilder;
}