[Biojava-l] Issues with FlexibleAlignment

[Matthew Pocock]

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

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