On Sep 13, 2011, at 1:30 AM, Jim Procter wrote:
Hi David.
On 12/09/2011 19:05, David M. Goodstein wrote:
It would be nice to have NHX capabilities, so we can annotate the
various nodes and work with arbitrary length names.
Jalview's tree viewer doesn't support any NHX annotations, but the
parser does support quoted node names and preserves all node
comments within the tree datamodel, so they are there if you want to
parse them out.
Unfortunately, when I was working on it, I didn't have a
comprehensive set of NHX files to test the parser with, and instead
left in checks that will raise a warning dialog if the tree file
contains NHX annotations to warn the user that there may be
problems. If you know (and trust) the source of the file, however,
then it should be possible to safely squash that error within the
JABAWS phylogeny service web service client.
What NHX annotations are you interested in using ? It's of course
possible to extend Jalview to cope with anything, but we should
seriously consider if it will be more efficient to incorporate
Archeopteryx, if you need full NHX capabilities.
If we can support long names, bootstraps, and the ability to provide
URLs to crown nodes with the current Jalview version of newick, there
probably isn't any need to go to NHX.
-David
Jim.
ps. Everyone on this thread is now subscribed to the jalview-dev
list, so we should move further discussion there.
pps. arbitrary length node names are only important if you are
importing trees from outside of Jalview. Normally, any sequences
sent to a service have an autogenerated ID string, and jalview
replaces the ID with the displayed sequence name when the results
are retrieved.
David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley
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