[Dynamite] new test xml: protein-smith-waterman.xml

[Guy Slater]

I've started telegraph coding in earnest, but I won't be checking
stuff in until I have automake/autoconf working properly
(probably monday).  Automake/autoconf are a pain to get working
well across platforms, but I think in the long run it will help
portability and save a lot of hassle.

Anyway, I've just checked in an initial attempt for another
test telegraph model: protein-smith-waterman.xml

You can see it on cvs web in the test directory:

http://dev.ensembl.org/cgi-bin/cvsweb_telegraph/cvsweb.cgi/telegraph/Telegraph/test/xml/

I'm pretty unsure about a lot of this, so if you
could both have a look over this it would be good.

Some questions and comments:
---------------------------

    o (telegraph == Moore) && (dynamite == Mealey) ??
      (or vice-versa - I can't remember)
      The advance and param tags are with the transitions,
      but they way I've put them, they repeat on a per-state basis,
      which seems pretty pointless and verbose.
      How should this bit be done properly ?
      What are the pros and cons of moore vs mealey ?
      (I thought we'd discussed this but couldn't find it in the archive)

    o Is the way I've done gap_open and gap_extend correct ?
      Why are these vectors not scalars ?  It looks really silly.

    o I still don't like the tag name "scores" being used in the
      parameter assignments.  It only marginally less vague than
      using "numbers" or "data".  Alternatives ?  "populate" ?

    o Similarly, I don't like the use of char and chars.
      Are we limiting alphabet sizes to 256 ?
      Maybe 'character' or 'symbol' ?

(disclaimer: ian - I know we discusses most of these when you
             were over here, but if they're still bothering me,
             they *must* be wrong ;)

Anyway, looking forward to hearing how I *should* have written this,

Guy.

--
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