Re: [Treebase-devel] Are "matrixtypes" ignored?

[Rutger V. <rut...@gm...>]

I don't think I would have expected T or N matrices: I've certainly
never seen a continuous matrix or a distance matrix. But obviously
very many (probably the majority) should be Q matrices.

On Thu, Mar 4, 2010 at 4:13 PM, Vladimir Gapeyev
<vla...@du...> wrote:
>
> On Mar 3, 2010, at 11:21 PM, William Piel wrote:
>
> I'm confused by the meaning of standard vs character matrices. In NEXUS
> vernacular, a standard matrix is one that uses discrete characters where the
> symbols are arbitrary -- i.e. no assumptions about the meaning of symbols
> (by contrast, a nucleotide matrix is one where A, C, G, T, N, and IUPAC are
> the assumed symbols).
>
> For me, the most logical way to divide up types of matrices is the
> following:
>
> 1. distance (= taxa x taxa) vs character (= taxa x character)
> 2. and of the character ones: continuous (= floating point) vs discrete (=
> integers)
> 3. and of the discrete ones: standard (= arbitrary symbols) vs nucleotide (=
> a, c, g, t + N and IUPAC) vs amino acid (= 20 letters + X)
>
> ... but evidently that not happening here. I don't understand the
> distinction between character matrix and standard matrix -- sounds like they
> are synonymous.
>
> I agree with you that it certainly sounds like SetMatrixNChar functions to
> count the number of characters in a matrix. An UPDATE SQL statement should
> be able to do this too -- just a matter of counting the number of
> matrixcolumn records for each matrix_id. But that's just a guess -- I would
> think that nchar would be passed to the database from headless Mesquite to
> the database anyway...
>
> Regardless of the original issue with running the SetMatrixNChar step (which
> I do put aside for now), this sounds to me as a possible issues with
> representing matrices in the database. I am not going to probe into this
> further now, but here is what I see, which makes me feel odd.
> There is a class hierarchy of matrix objects in Java, all of which are
> persisted in the same table Matrix, whose field matrixtype is used to
> discriminate between the classes.   Here are the matrixtype's discriminator
> values and the corresponding class hierarchy:
>
>      Matrix (abstract)
> 'T'      DistanceMatrix
> 'C'      CharacterMatrix (abstract)
> 'N'          ContinuousMatrix
> 'D'          DiscreteMatrix
> 'Q'              SequenceMatrix
> 'S'              StandardMatrix
>
> Despite this elaborateness, all matrices in the database are marked with 'S'
> only, both in the pre-migration instance and after I uploaded new matrices
> and study metadata.  From what Bill says, I would have expected to see some
> matrices marked with T, N, and Q as well.
> --VG
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-- 
Dr. Rutger A. Vos
School of Biological Sciences
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