[Biojava-l] DNA alphabet token

[Dave Keller]

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>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.  
>  
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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.

>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"?