Hi. While writing the Distribution tutorial for the bootcamp, I noticed that Distribution didn't actualy define a probability dencity funciton because it does some trickery when handling ambiguity symbols. The correct behavior is to sum the probability of each atomic symbol that matches the ambiguity symbol and return that sum. This makes the semantics of getWeight like - give me the probability that we observe one of this set of symbols - rather than - give me the probability that we observe one of this set of symbols given some null model. I think this is a throw-back to the days before null-models realy existed. Anyway, for DP with odds ratios the sum should give the expected result. One up-side to this is that it makes Distribution play much better with infinite sets like doubles - integrating Distribution over a range is exactly what is expected now when handling an ambiguity symbol over doubles that matches an interval (e.g. given the ambiguity symbol [-Infinity, 10.0] we would integrate the associated probability dencity function up to 10.o from -Infinity, wich is the normal meaning of p(10.0) in stats). If anybody disagrees, be vocal. The change is in CVS, but won't be back-ported to 1.1 ever. Matthew _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
