[Bioperl-l] PAML nssites model result object

[Edward Chuong]

Hi all,

I'm trying to parse PAML results, and running into some trouble. I'm
using branch specific omega model, and I want to get the branch
specific ka/ks values out.
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Tools/Phylo/PAML.pm?rev=HEAD&cvsroot=bioperl&content-type=text/vnd.viewcvs-markup
says that $node->param('omega') should work, but Data::Dumper shows
that this value isn't stored in the node (only branch lengths and seq
IDs appear to be stored).

I'm assuming that I can get these values out of the
get_NSSite_result() Bio::Tools::Phylo::PAML::ModelResult object, but
I'm not sure how to call it. The current synopsis uses
"get_model_params" but it seems to be out of date because it's not in
the current souce. The docs at
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/Tools/Phylo/PAML/Result.pm?rev=HEAD&cvsroot=bioperl&content-type=text/vnd.viewcvs-markup
say to use my 
@results = @{$self->get_NSSite_results};
--that looks like a mistake, and I've tried 
@result = $result->get_NSSite_results but that doesn't work either
(just get undefined objs).

Am I doing something wrong, or is this functionality still being
worked on? I've tried using both 1.4 and the LIVE versions. Any help
is appreciated, thanks!

-Ed