---------------------- 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" <[EMAIL PROTECTED]> cc: "Russell Smithies" <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> on 12/03/2002 09:48:26 PM To: [EMAIL PROTECTED] 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 _________________________________________________________________ Tired of spam? Get advanced junk mail protection with MSN 8. http://join.msn.com/?page=features/junkmail _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
