[Biojava-l] DNA letters are lowercase???

[Schreiber, Mark]

> (Someone who knows): does the default tokenization for DNA 
> use upper or 
> lower case? I don't care either way.
>

The default is lower case. I think this is some kind of not very often
observed convention where DNA/RNA symbols are lower case and Amino Acids
are upper case.
 
> Ryan: To maintain the upper/lower case info in cromatograph files we 
> would need to do a little trickery. If you send a file (mixed 
> case) and 
> a couple of use-cases, we can probably sort this out quickly 
> enough. If 
> the case is important to you (e.g. you need to know where the 
> uncertain 
> calls are), we can do this, and if you want to discard this 
> information 
> then we can also do that trivialy. I'm thinking thoughts like 
> alighment 
> of DNA against booleans (or 0/1) where A,1 would be A and supported 
> (upper case), and T,0 would be T and not well supported (lower case).
> 
> Has this already been done?
> 
> Matthew
> 

There is not currently a Boolean or Binary alphabet in biojava, however
you could fake it by making a SubInteger Alphabet (from 0 to 1) using
the static method from IntegerAlphabet. This would be more binary than
boolean but should do the same thing.

- Mark
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