[Biojava-l] Re: DBSR

[Patrick McConnell]

---------------------- Forwarded by Patrick McConnell/CanCtr/mc/Duke on
12/04/2002 02:48 PM ---------------------------


Patrick McConnell
12/04/2002 02:45 PM

To:    Biojava-L<Biojava-L@Biojava. Org" <biojava-l@biojava.org>
cc:    "Russell Smithies" <russell_smithies@hotmail.com>

Subject:    Re: DBSR  (Document link: Patrick McConnell)

We have not produced any documentation because the library is primarily for
internal use.

We do have some code for building and manipulating GO trees, but it is
unlikely to be flexible and robust enough for use in BioJava.

In our system:

Every term is an object that extends from DefaultMutableTreeNode and
includes fields for the term id, accession, name, and description.  Where
one term has multiple parents, multiple nodes are created with the same
information.

Our viewer extends JTree and provides methods for marking nodes with custom
counts (used primarily for # of gene's annotated at that term, etc.),
tooltips, colors, etc.  We also provide methods to hide unmarked nodes and
the such.

We build our trees from the GO database using SQL (I think a MySQL driver
is hard-coded right now).  This is a slow process, so we first try to build
the tree via Java serialization from a File (our GO nodes are
serializable).

I would gladly donate the source "as is" if anyone is interested, but I do
not think I have the time to alter and maintain it for BioJava.

-Patrick




"Russell Smithies" <russell_smithies@hotmail.com> on 12/03/2002 09:48:26 PM

To:    mccon012@mc.duke.edu
cc:

Subject:    DBSR

Hi Patrick,

I was hunting about for a java BLAST parsers (I usually use BioJava) and
found your library on Duke's site.
I downloaded the .jar of DBSR but there's no documentation or javadoc.
Have I missed something or is it availible elsewhere?

thanx

Russell Smithies
University of Otago,
Dunedin
New Zealand





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