Following up my own post, but anyway... I've made the MotifTools test pass again. However in trying to eliminate the gap character (which I'm still not sure I should be doing) I tried to test for the gap symbol in DNA using mySymbol == AlphabetManager.getGapSymbol() but this didn't work (didn't return true for the DNA gap).
Stringifying the DNA gap object I get org.biojava.bio.symbol.SimpleBasisSymbol: [] Can someone clarify the circumstances under which the various gap Symbol(s) are equal (or ==) to each other? ta, Keith -- - Keith James <[EMAIL PROTECTED]> bioinformatics programming support - - Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK - _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
