[Biojava-l] Re: [Biojava-dev] Tutorial 1 and ambiguous symbols

[andy hammer]

Those are very helpful ideas.  I will give them a try.

Thank you.

Andy

----- Original Message ----- 
From: "Matthew Pocock" <matthew_pocock@yahoo.co.uk>
To: "andy hammer" <ahammer@genetics.utah.edu>; <biojava-l@biojava.org>
Sent: Monday, October 21, 2002 10:05 AM
Subject: Re: [Biojava-dev] Tutorial 1 and ambiguous symbols


> Hi Andy,
> 
> You can check if a Symbol is non-ambiguous by seeing
> if it is an instance of AtomicSymbol. If not, you can
> use the getMatches() method to get back an alphabet
> over all the AtomicSymbol instances it could match. So
> something like this:
> 
> Symbol sym = ...;
> 
> if(sym instanceof AtomicSymbol) {
>   // add counts as normal
> } else {
>   Finite Alphabet matches = (FiniteAlphabet)
> sym.getMatches();
>   for(Iterator si = matches.iterator(); si.hasNext();
> ) {
>     AtomicSymbol as = (AtomicSymbol) si.next();
>     // do stuff with this potential match
>   }
> }
> 
> Alternatively, you could replace the == in the demo
> with an Alphabet.contains() where you make one
> ambiguity symbol from the pair (G,C) and one from
> (A,T) using the method getSymbol(Set) method, and
> extract getMatches() from them.
> 
> You could try both and compare the relative speed of
> each. Also, what should you be doing in the case where
> the ambiguity matches both symbols in (A,T) and (G,C)?
> Do you want to add whole counts to both pots, or part
> counts?
> 
> Matthew
> 
>  --- andy hammer <ahammer@genetics.utah.edu> wrote:
> > Hello!
> > 
> > I just discovered biojava a few days ago and am very
> > excited to start using
> > it in my code.
> > The tutorials and demos are very helpful.
> > I still have a question on how to handle ambibuous
> > symbols.
> > The last sentence in Tutorial 1 suggests modifing
> > GCContent.java to ignore
> > any ambiguous symbols.
> > When I run GCContent it already ignores any
> > ambiguous symbols.
> > I am interesting in counting the ambiguous symbols.
> > Any ideas on how I can include ambiguous symbols in
> > the count?
> > Is there a demo or something I could look at?
> > 
> > Andy Hammer
> > University of Utah
> > Human Genetics
> > 
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-dev 
> 
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