/*!
* \brief This reaction build a PromoterReaction reaction from a PromoterProperties class
* \param props The PromoterProperties which will serve to create the reaction
* \return Return the new reaction or null if it fail.
*/
public static IReaction buildPromoterFromProps(PromoterProperties props)
{
if (props == null)
{
return(null);
}
PromoterParser parser = new PromoterParser();
PromoterReaction reaction = new PromoterReaction();
reaction.setName(props.name);
reaction.setBeta(props.beta);
reaction.setTerminatorFactor(props.terminatorFactor);
reaction.setEnergyCost(props.energyCost);
TreeNode <PromoterNodeData> formula = parser.Parse(props.formula);
reaction.setFormula(formula);
Product newProd;
foreach (Product p in props.products)
{
newProd = new Product(p);
reaction.addProduct(newProd);
}
return(reaction);
}
public LinkedList <IReaction> getReactions()
{
Logger.Log("Device::getReactions(); device=" + this, Logger.Level.TRACE);
LinkedList <IReaction> reactions = new LinkedList <IReaction>();
LinkedList <PromoterProperties> props = new LinkedList <PromoterProperties>(getPromoterReactions());
foreach (PromoterProperties promoterProps in props)
{
Logger.Log("Device::getReactions() adding prop " + promoterProps, Logger.Level.TRACE);
reactions.AddLast(PromoterReaction.buildPromoterFromProps(promoterProps));
}
Logger.Log("Device::getReactions() with device=" + this + " returns " + Logger.ToString <IReaction>(reactions), Logger.Level.INFO);
return(reactions);
}
/* !
* \brief Checks that two reactions have the same PromoterReaction field values.
* \param reaction The reaction that will be compared to 'this'.
*/
protected override bool PartialEquals(IReaction reaction)
{
PromoterReaction promoter = reaction as PromoterReaction;
bool bnullProm = (promoter != null);
bool btermFac = (_terminatorFactor == promoter._terminatorFactor);
bool bformula = formulaEquals(_formula, promoter._formula);
bool bbeta = (_beta == promoter._beta);
Logger.Log("PromoterReaction::PartialEquals"
+ ", bnullProm=" + bnullProm
+ ", btermFac=" + btermFac
+ ", bformula=" + bformula
+ ", bbeta=" + bbeta
, Logger.Level.DEBUG);
return((promoter != null) &&
base.PartialEquals(reaction) &&
(_terminatorFactor == promoter._terminatorFactor)
//&& _formula.Equals(promoter._formula)
&& formulaEquals(_formula, promoter._formula) &&
(_beta == promoter._beta));
}
//! Copy constructor
public PromoterReaction(PromoterReaction r) : base(r)
{
_terminatorFactor = r._terminatorFactor;
_formula = r._formula;
_beta = r._beta;
}
/*!
* \brief Execute everything about simulation into the Medium
*/
public void Update()
{
if (enableShufflingReactionOrder)
{
LinkedListExtensions.Shuffle <IReaction>(_reactions);
}
foreach (IReaction reaction in _reactions)
{
if (Logger.isLevel(Logger.Level.TRACE))
{
PromoterReaction promoter = reaction as PromoterReaction;
if (promoter != null)
{
Logger.Log("Medium::Update reaction.react(" + _molecules + ") with reaction=" + reaction, Logger.Level.TRACE);
}
}
reaction.react(_molecules);
}
applyVariation();
if (_enableNoise)
{
float noise;
foreach (Molecule m in _molecules)
{
noise = _numberGenerator.getNumber();
if (_enableSequential)
{
m.addConcentration(noise);
}
else
{
m.addNewConcentration(noise);
}
}
}
//TODO improve check that it's the medium of the hero bacterium Cellia
//TODO refactor interactions out of medium
if (_name == "Cellia")
{
manageMoleculeConcentrationWithKey("AMPI");
if (GameStateController.isAdminMode)
{
//TODO manage this differently
manageMoleculeConcentrationWithKey("AMPR");
manageMoleculeConcentrationWithKey("ATC");
manageMoleculeConcentrationWithKey("FLUO1");
manageMoleculeConcentrationWithKey("FLUO2");
manageMoleculeConcentrationWithKey("IPTG");
manageMoleculeConcentrationWithKey("MOV");
manageMoleculeConcentrationWithKey("REPR1");
manageMoleculeConcentrationWithKey("REPR2");
manageMoleculeConcentrationWithKey("REPR3");
manageMoleculeConcentrationWithKey("REPR4");
}
}
}
/*!
\brief This reaction build a PromoterReaction reaction from a PromoterProperties class
\param props The PromoterProperties which will serve to create the reaction
\return Return the new reaction or null if it fail.
*/
public static IReaction buildPromoterFromProps(PromoterProperties props)
{
if (props == null)
return null;
PromoterParser parser = new PromoterParser();
PromoterReaction reaction = new PromoterReaction();
reaction.setName(props.name);
reaction.setBeta(props.beta);
reaction.setTerminatorFactor(props.terminatorFactor);
reaction.setEnergyCost(props.energyCost);
TreeNode<PromoterNodeData> formula = parser.Parse(props.formula);
reaction.setFormula(formula);
Product newProd;
foreach (Product p in props.products)
{
newProd = new Product(p);
reaction.addProduct(newProd);
}
return reaction;
}
//! Copy constructor
public PromoterReaction(PromoterReaction r) : base(r)
{
_terminatorFactor = r._terminatorFactor;
_formula = r._formula;
_beta = r._beta;
}
