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