Java PseudoEnergyCalculator Examples

Example #1

File: PseudoEnergyFitnessAssessor.java Project: bioinformatics-ua/mRNA-Optimiser

  @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());
  }

Example #2

File: PseudoEnergyFitnessAssessor.java Project: bioinformatics-ua/mRNA-Optimiser

 public PseudoEnergyFitnessAssessor() {
   PseudoEnergyCalculator.setBondEnergy(AU, CG, GU); // set energy bonds!
 }