ojava-l (E-mail)
> Subject: Re: [Biojava-l] Subtle bug in SimpleDistribution
>
>
> Hi Mark,
>
> What are the symptoms of your bug? The handling of ambiguous counts
> should be implemented by:
>
> DistributionTrainerContext.addCount(
>Distribution dist,
>Sym
Hi Mark,
What are the symptoms of your bug? The handling of ambiguous counts
should be implemented by:
DistributionTrainerContext.addCount(
Distribution dist,
Symbol sym,
double times)
This passes the count on to:
DistributionTrainer.addCount(
AtomicSymbol aSym,
double times)
Well maybe not a bug but a potential danger.
SimpleDistribution.Trainer will accept counts from ambiguity symbols (N)
and the Gap symbol however when it comes to train it uses the
AlphabetIndexer for DNA which does not include indices for these symbols
and this leads to some very odd results.
A
