no, the scores are not normalized by default. If you want to normalize them by yourself, you could do it in the CountTable::getBestSequence() method:
//Filling a sequence with the best |count| items
Sequence seq = new Sequence(-1);
sd.normalize();// Implement this method in the ScoreDistribution class
List<Integer> bestItems = sd.getBest(1.002);
However the scores do not represent real proportions, because of the multiplication of the individual subscores in the CountTable::push() method.
You would have to rewrite the score system if you are interested in real proportional probabilities.
Disclaimer: I am just a student who worked with this algorithm for half a year, so I can not guarantee correctness