>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"? _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
