On Friday 25 November 2005 14:34, Russ Kepler wrote: > On Friday 25 November 2005 04:39 am, Matthew Pocock wrote: > > This should be returning the symbol AlphabetManager.getGap(), which > > should be the same as EMPTY_ALPHABET.getGap(). Could somebody fix this? > > I wouldn't think that a gap symbol would be appropriate for the areas > outside the sequence to sequence overlap. Something that displays as a > space or something would be a lot more appropriate, but my lack of > experience in the Symbol package prevents me from finding it.
The EMPTY_ALPHABET.getGap() symbol is not the same as the gap symbol used within a sequence. It represents an unocupiable position in the sequence. It is like the ~ symbol you see in multi-fasta at the beginning and end of sequences vs - in the middle of sequences. In an end-user applications, you could choose to render ~ as a space, or an empty box or whatever. Kalle has been fixing the serialization of these guys, and I beleive they get tokenized correctly to/from ascii. Matthew > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
