@Override
public double getFitness(EvolvingSolution solution) {
CodonSequenceOptimizationTarget optimizedCodonSequence =
(CodonSequenceOptimizationTarget) solution.getFeatureList().get(0);
/* Calculate pseudo energy. */
return PseudoEnergyCalculator.calculateMFE(
optimizedCodonSequence.getSequence(),
true); // calculateEnergyEstimate(optimizedCodonSequence.getSequence());
}
public PseudoEnergyFitnessAssessor() {
PseudoEnergyCalculator.setBondEnergy(AU, CG, GU); // set energy bonds!
}