[Biojava-l] Distributions and collections

[Schreiber, Mark]

> -----Original Message-----
> From: Matthew Pocock [mailto:mrp@sanger.ac.uk]
> Sent: Thursday, March 08, 2001 12:59 AM
> To: Schreiber, Mark
> Cc: 'biojava-l@biojava.org'
> Subject: Re: [Biojava-l] Distributions and collections
> 
> 
> Hi Mark,
> 
> I think that Distribution is closest in apperance to Map. Because it 
> represents a probability distribution, it places certain 
> restrictions on 
> both the keys (symbols) and the values (doubles). Every 
> Distribution has 
> an associated Alphabet, which has size and iterator methods. 
> An Alphabet 
> most closely resembles a Set. What functionality from 
> Collections would 
> you see it usefull to access?

Mostly I wanted a way to sort the distribution although this could be done
by using the associated alphabet as a list of sorted keys, perhaps with
alphabet index. Could people see a use for a binary search type behaivour eg
find the symbol which has a probability distribution closest to 0.5?

Mostly I was thinking that distributions are so close to a map why don't we
implement them. At some point its gotta be useful to pass your distribution
to reallyUsefulMethod(Collection c).

> 
> What would be the behavior of a Sequence comparator? When would it be 
> used? Java makes it easy enough to define comparators as little inner 
> class closure thingies, but if you can define how a sensible 
> catch-all 
> sequence comparator should work, and you have a use for it, 
> check it in.

Mostly just daydreaming about how it may be useful to sort/compare symbols
by property ie purine/pyrimidine and a way to intellegently sort redundant
sequences (do R's go before or after Y's). Would anybody use anything like
this?

Just my 0.02

Mark


> 
> Matthew
> 
> Schreiber, Mark wrote:
> 
> > Hi,
> > 
> > Do people think it would be a good idea if Distributions 
> implemented the
> > Collection interface?? This could conceivabley give access to the
> > functionality in the Collections class. Also would a 
> Sequence comparator be
> > a good idea or is this functionality present elsewhere in Biojava?
> > 
> > Just some rambling ideas, what do people think?
> > 
> > Mark
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> 
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
>