[Biojava-l] DNA alphabet token

noah.a.clements@gsk.com noah.a.clements@gsk.com
Mon, 17 Jun 2002 10:23:22 -0400

"Dave Keller" <dave.c.keller@verizon.net>

Sent by: biojava-l-admin@biojava.org
14-Jun-2002 14:27


        To:     noah.a.clements

        cc:     biojava-l
        Subject:        Re: [Biojava-l] DNA alphabet token

>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 
>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 

I am new to the project and am still trying to familiarize myself with 
the code.  But, I think I see where you are going with this.  If the DNA 
sequence in the XML file is all upper case or a mix of uppercase and 
lower case,  the sequence is parsed from the XML and transformed into 
all lower case.  When the test case compares the sequence generated by 
the Sequence object, the result is, for example "ATGC" != "atgc" so the 
test case fails.  So, in reality, the XML was parsed correctly but fails 
because the cases don't match.  Is this correct?

This is correct.  After trying to change the AlphabetManager.xml file, 
however, DNATools is not initializing correctly.  All tests reliant on 
DNATools then fail.  The problem for me is that other tools depend on