Counter counter = new SplitCounter();
calculatorList.add(new PoissonDistributionCalculator(counter, alignmentList));
calculatorList.add(new TranslationCalculator(bestAlignmentList));
Calculator calculator = new CompositeCalculator(calculatorList);
HmmAlignAlgorithmFactory algorithmFactory =
new ForwardBackwardAlgorithmFactory();
AlignAlgorithm algorithm =