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

Naohisa GOTO ngoto at gen-info.osaka-u.ac.jp
Sat Jul 3 10:40:22 UTC 2010

Hi Anurag,

On Fri, 2 Jul 2010 19:45:12 +0530
Anurag Priyam <anurag08priyam at gmail.com> wrote:

> Is it advisable to use Ruby's Matrix class as the base class of
> Bio::NeXML::Matrix? I can define methods to make it mutable. What I do not
> like about the matrix class is its use of Vectors in many places. I would
> like to redefine those methods to work with Arrays.

It seems it isn't.

The Ruby's Matrix class is implemented as the mathematical matrix.
It has many useful mathematical matrix operations, but all elements
should be Numeric values. However, it seems that NeXML matrix stores
not only numeric values but also sequences or characters.

In addition, the use of the name Matrix might be a source of confusion
or conflicts with Ruby standard Matrix, even if in the separate name
space. It may be good to rename Bio::NeXML::Matrix to another name
if it isn't hard to keep consistency with the specification of NeXML.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

More information about the BioRuby mailing list