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) { }