[Treebase-devel] Are "matrixtypes" ignored?

[Vladimir G. <vla...@du...>]

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