[Biojava-l] DNA alphabet token

[noah.a.clements@gsk.com]

>I have a simple silly question:  Is there any reason that the DNA tokens 
as
>specified in AlphabetManager.xml  are lowercase rather than uppercase? 
All
>of the sources we see use uppercase by default. 
> 
>
Have you tried replacing the lower case letters with upper case in the 
AlphabetManager.xml?  I don't see why this would cause a problem.

I have.  It works as you would expect but breaks the AGAVE-XML test (which 
tests a lower case input).  I was thinking of duplicating the symbolrefs 
so that what goes in comes back out (including mixed case, for those apps 
that use it) and having the token be case sensitive.  I was wondering if 
that might break RNA translation though.  Is this something I should check 
in? 

>This can be easily worked around, but not without a cost in terms of 
string
>generation and memory usage.
>
How so?  What do you mean by "string generation"? 


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