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);
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick("PromY2", 75f, "[0.01,2]Y");
RBSBrick rbs = new RBSBrick("RBS3", 3.0f);
GeneBrick gene = new GeneBrick("MOV", "MOV");
TerminatorBrick term = new TerminatorBrick("T1", 1.0f);
LinkedList<BioBrick> bricks = new LinkedList<BioBrick>(new List<BioBrick>(){prom, rbs, gene, term});
ExpressionModule module = new ExpressionModule("expr", bricks);
return Device.buildDevice("DEV", new LinkedList<ExpressionModule>(new List<ExpressionModule>(){module}));
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick(promoterName, promoterBeta, promoterFormula);
RBSBrick rbs = new RBSBrick(rbsName, rbsFactor);
GeneBrick gene = new GeneBrick(geneName, geneProteinName);
TerminatorBrick term = new TerminatorBrick(terminatorName, terminatorFactor);
LinkedList<BioBrick> bricks = new LinkedList<BioBrick>(new List<BioBrick>(){prom, rbs, gene, term});
ExpressionModule module = new ExpressionModule(expressionModuleName, bricks);
Device result = Device.buildDevice(deviceName, new LinkedList<ExpressionModule>(new List<ExpressionModule>(){module}));
return result;
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick("PromY2", 75f, "[0.01,2]Y");
RBSBrick rbs = new RBSBrick("RBS3", 3.0f);
GeneBrick gene = new GeneBrick("MOV", "MOV");
TerminatorBrick term = new TerminatorBrick("T1", 1.0f);
LinkedList <BioBrick> bricks = new LinkedList <BioBrick>(new List <BioBrick>()
{
prom, rbs, gene, term
});
ExpressionModule module = new ExpressionModule("expr", bricks);
return(Device.buildDevice("DEV", new LinkedList <ExpressionModule>(new List <ExpressionModule>()
{
module
})));
}
protected override DNABit produceDNABit()
{
PromoterBrick prom = new PromoterBrick(promoterName, promoterBeta, promoterFormula);
RBSBrick rbs = new RBSBrick(rbsName, rbsFactor);
GeneBrick gene = new GeneBrick(geneName, geneProteinName);
TerminatorBrick term = new TerminatorBrick(terminatorName, terminatorFactor);
LinkedList <BioBrick> bricks = new LinkedList <BioBrick>(new List <BioBrick>()
{
prom, rbs, gene, term
});
ExpressionModule module = new ExpressionModule(expressionModuleName, bricks);
Device result = Device.buildDevice(deviceName, new LinkedList <ExpressionModule>(new List <ExpressionModule>()
{
module
}));
return(result);
}
public PromoterBrick(PromoterBrick p) : this(p._name, p._beta, p._formula)
{
}
public override bool Equals(System.Object obj)
{
PromoterBrick pb = obj as PromoterBrick;
return(base.Equals(obj) && (_beta == pb._beta) && (_formula == pb._formula));
}
public PromoterBrick(PromoterBrick p) : this(p._name, p._beta, p._formula)
{
}
