[BioRuby] [GSoC][NeXML and RDF API] Code Review.

Rutger Vos rutgeraldo at gmail.com
Sat Jul 10 14:58:00 UTC 2010


sorry for the even later response on my end...

The BioRuby Matrix class is not a suitable superclass for character state
matrices, which are essentially the generalized form of multiple sequence
alignments (but then also allowing for other types of homologyzed data). I
am tempted to suggest you make at least some (and maybe all) nexml character
state matrices either inherit from an alignment class or easily convertible
to it: if people parse a nexml file with a dna alignment there's a good
chance they'll want to be able to use that as an alignment object elsewhere
in their code.

As an aside, I have no problem with using CharacterStateMatrix as a class
name. I don't see people having to type it that frequently so it's not a big
deal, right? Maybe I think this because my java work is starting to get to
me, though :)


On Wed, Jul 7, 2010 at 11:40 PM, Naohisa Goto
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi Anurag,
> > I think they are called character state matrices in the phylo
> terminology.
> > But something like CharactersStateMatrices would be two long. What about
> > CharacterMatrices or StateMatrices? Perhaps Rutger can help me here.
> It is generally bad thing to abbreviate only because it is too long.
> Modifying the upstream original names might be a source of confusion.
> In this case, using CharactersStateMatrices as is is the best. If the
> name is expected to be frequently used by library users, short name
> could also be added.
> However, as Pjotr already mentioned, the class might not be needed,
> depending on the design of classes.
> Sorry for late response.
> --
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ngoto at bioruby.org
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Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
United Kingdom
Tel: +44 (0) 118 378 7535

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