Bioperl: Alignment factories

[Ian Holmes]

Matt mentioned alignment factories the other day. I wonder if anyone
(Ewan?) can tell me how these are meant to work. Eg I assume that
$factory->pairwise_alignment($seq1,$seq2) is meant to be a base method of
the AlignmentFactory interface but from the website docs it appears to be
just in the pSW class. There are a couple of other things like this; the
documentation is pretty sparse and yet Matt sounded like he had a firmish
idea of the abstract concept of an AlignmentFactory even though it isn't
really explained on the website.

can anyone enlighten me? I'm currently writing C++ code to handle multiple
alignment in a probabilistic manner and would like to make a perl wrapper
that fits the AlignmentFactory API... if only i can work out what that is.
;->

yam

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