[Biojava-l] CrossProductSymbols & stuff

[Matthew Pocock]

Hi.

It is that time again when I am looking at the symbol and alphabet
indexes. All in all, they are working very well. The one rinkle for me
at the moment is the Cross Product stuff. Pre 1.0 I changed Symbol so
that all symbols were ambiguous, but AttomicSymbol is a sub-interface
that guarantees that the only symbol it matches is itself. I am
proposing to do the similar flip with CrossProduct symbol - all symbols
are thought of as being cross products of other symbols, but a special
sub-set are prime - can only be represented by raising themselves to the
power 1, not by multiplying any other symbols together.

This flip should not in practice change the day-to-day use of BioJava
one jot. It will, however, clean up some of the internals for handeling
alignments and probability distributions. The gap symbol should also
become lest skitzoid (i hope for embarasement's sake that none of you
have given the gap symbol a good poke arround). I hope that we can get
things to be prety much binary compatible when seen from the outside. It
will certainly have settled down by the time we get arround to a 1.1
release.

This all came to light because I am trying to write strand-reversible
2nd order HMMs for modeling chromosomes, and the current scheim makes
life painfull. All those with objections speak now & loudly, or next
time you check out from CVS, this will all have been silently changed.

Matthew