/*!
* \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);
}
private PromoterProperties getPromoterReaction(ExpressionModule em, int id)
{
Logger.Log("Device::getPromoterReaction(" + em.ToString() + ", " + id + ")", Logger.Level.TRACE);
PromoterProperties prom = new PromoterProperties();
prom.energyCost = _energyPerBasePair * em.getSize();
//promoter only
//prom.energyCost = _energyPerBasePair*em.getBioBricks().First.Value.getSize();
LinkedList <BioBrick> bricks = em.getBioBricks();
//TODO fix this: create good properties' name
prom.name = _internalName + id;
PromoterBrick p = bricks.First.Value as PromoterBrick;
prom.formula = p.getFormula();
prom.beta = p.getBeta();
bricks.RemoveFirst();
prom.products = getProductsFromBiobricks(bricks);
TerminatorBrick tb = bricks.First.Value as TerminatorBrick;
prom.terminatorFactor = tb.getTerminatorFactor();
bricks.RemoveFirst();
if (bricks.Count != 0)
{
Logger.Log("Device::getPromoterReaction Warning: bricks.Count =" + bricks.Count, Logger.Level.TRACE);
}
return(prom);
}
private PromoterProperties getPromoterReaction(ExpressionModule em, int id)
{
Logger.Log("Device::getPromoterReaction("+em.ToString()+", "+id+")", Logger.Level.TRACE);
PromoterProperties prom = new PromoterProperties();
prom.energyCost = _energyPerBasePair*em.getSize();
//promoter only
//prom.energyCost = _energyPerBasePair*em.getBioBricks().First.Value.getSize();
LinkedList<BioBrick> bricks = em.getBioBricks();
//TODO fix this: create good properties' name
prom.name = _internalName + id;
PromoterBrick p = bricks.First.Value as PromoterBrick;
prom.formula = p.getFormula();
prom.beta = p.getBeta();
bricks.RemoveFirst();
prom.products = getProductsFromBiobricks(bricks);
TerminatorBrick tb = bricks.First.Value as TerminatorBrick;
prom.terminatorFactor = tb.getTerminatorFactor();
bricks.RemoveFirst();
if(bricks.Count != 0) {
Logger.Log("Device::getPromoterReaction Warning: bricks.Count ="+bricks.Count, Logger.Level.TRACE);
}
return prom;
}
/*!
\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;
}
