[Biojava-l] Alphabets with ambiguity symbols included

[Schreiber, Mark]

Probably the best way (currently) to get a Distribution to emmit an
ambiguity is to emit two symbols and merge them together. The
getWeight(Symbol s) methods also work where s is an ambiguity (should
return the summed weight of each). Could possibly put a method in
DistributionTools but I'm not sure how you would parameterize the
frequency of ambiguity.

Another possiblity would be to look at the phred sequence classes in
org.biojava.bio.programs.phred, Sequences over this alphabet contain the
concept of ambiguity. You could randomly generate symbols from this
alphabet and then convert them to DNA using some quality threshold to
decide when to use an ambiguity Symbol.

The getToken method is obsolete, the SymbolTokenization is now used
instead.

- Mark

> -----Original Message-----
> From: David Huen [mailto:david.huen@ntlworld.com] 
> Sent: Tuesday, 29 October 2002 11:29 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Alphabets with ambiguity symbols included
> 
> 
> How do I get an Alphabet that has all the ambiguity symbols 
> too?  Do we have 
> one canned?
> 
> I'm trying to get a Distribution to generate an almighty brew 
> of random 
> symbols to torture test the SymbolList implementations with a jUnit.
> 
> Incidentally, in the Symbol interface blurb, it mentions a 
> getToken method 
> that doesn't seem to be there.  Is that obsolete or has the 
> method been 
> inadvertently omitted?
> 
> Regards,
> David Huen
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
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