public ExpressionModule(ExpressionModule m)
{
_name = m._name;
_bioBricks = new LinkedList<BioBrick>();
foreach (BioBrick b in m.getBioBricks())
_bioBricks.AddLast(b);
}
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);
}
//copy constructor
public ExpressionModule(ExpressionModule m)
{
Logger.Log("ExpressionModule::ExpressionModule(" + m + ")", Logger.Level.DEBUG);
_name = m._name;
_bioBricks = new LinkedList <BioBrick>();
foreach (BioBrick b in m.getBioBricks())
{
_bioBricks.AddLast(b.copy());
}
}
//copy constructor
public ExpressionModule(ExpressionModule m)
{
Logger.Log("ExpressionModule::ExpressionModule("+m+")", Logger.Level.DEBUG);
_name = m._name;
_bioBricks = new LinkedList<BioBrick>();
foreach (BioBrick b in m.getBioBricks())
{
_bioBricks.AddLast(b.copy());
}
}
public PromoterProprieties getPromoterReaction(ExpressionModule em, int id)
{
PromoterProprieties prom = new PromoterProprieties();
LinkedList<BioBrick> bricks = em.getBioBricks();
prom.name = _name + 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();
prom.energyCost = getSize();
return prom;
}
private static bool checkModuleValidity(ExpressionModule module)
{
if (module == null)
return false;
LinkedList<BioBrick> bricks = new LinkedList<BioBrick>(module.getBioBricks());
if (bricks == null)
return false;
if (bricks.Count == 0 || bricks.First.Value == null)
return false;
if (checkPromoter(bricks.First.Value) == false)
return false;
bricks.RemoveFirst();
if (checkOperon(bricks) == false)
return false;
if (bricks.Count == 0 || bricks.First.Value != null || checkTerminator(bricks.First.Value) == false)
return false;
bricks.RemoveFirst();
if (bricks.Count != 0)
return false;
return true;
}
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;
}