protected void computeReferenceBiomassValue(SteadyStateSimulationResult simResult) {
IntegratedSimulationResult intResult = (IntegratedSimulationResult) simResult;
ISteadyStateModel model = simResult.getModel();
String IntsimulationMethod = "";
String metabolimethodtype = "";
String regulatorysimmethodtype = "";
if (intResult.getMethod().equals(IntegratedSimulationMethods.SRFBA))
IntsimulationMethod = IntegratedSimulationMethods.SRFBA;
else {
IntsimulationMethod = IntegratedSimulationMethods.INTEGRATED_BRN;
metabolimethodtype = intResult.getMetSimulMethod();
regulatorysimmethodtype = RegulatoryNetworkSimulationMethods.BRNV;
}
EnvironmentalConditions env = simResult.getEnvironmentalConditions();
VariablesContainer varcont = intResult.getInitialUsedVariablesContainer();
HashSet<String> falsenodes = null;
falsenodes = intResult.getInitialusedfalsenodes();
IntegratedSimulationControlCenter simulationControlCenter =
new IntegratedSimulationControlCenter(
env,
null,
model,
IntsimulationMethod,
metabolimethodtype,
regulatorysimmethodtype,
varcont,
falsenodes,
true,
solver);
// SteadyStateSimulationResult solution = null;
IntegratedSimulationResult solution = null;
try {
solution = (IntegratedSimulationResult) simulationControlCenter.simulate();
} catch (Exception e) {
System.err.println(
"YieldMinimumBiomassObjectiveFunction: could not compute reference biomass value");
e.printStackTrace();
}
if (solution != null) {
double biomass = solution.getFluxValues().getValue(biomassId);
minimumBiomassValue = biomass * minimumBiomassPercentage;
}
biomassComputed = true;
}
public double evaluate(SteadyStateSimulationResult simResult) {
if (!biomassComputed) computeReferenceBiomassValue(simResult);
FluxValueMap fluxValues = simResult.getFluxValues();
double biomassValue = fluxValues.getValue(biomassId);
double desiredFlux = fluxValues.getValue(desiredFluxId);
double fitness = 0.0;
if (biomassValue >= (minimumBiomassPercentage * minimumBiomassValue)) {
fitness = desiredFlux;
}
return fitness;
}