[Biojava-dev] RE: FASTA

[Matthew Pocock]

Hi Ted,

I think the closest thing to what you want would be a SymbolTokenization 
object. Alphabets are used to represent things like DNA, RNA, Protein 
symbols and then SymbolTokenizations make these symbols into text. So, 
you can have one tokenization that is upper or lower case single 
letters, another that is human-readable names and another that prints 
out gaps as ~ instead of -, or n as x. Grab an alphabet instance - call 
DNATools.getDNA() - and then call getTokenization("token") and 
interogate the object you get back.

Happy playing,

Matthew

Ted Quon wrote:
> Hi,
> 
> I was wondering if you guys have written a class in BioJava for file
> formats (i.e. fasta) that returns an iterator of all allowable symbols for
> sequences from these formats?  Thanks!
> 
> 
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