[Biojava-l] A question about NexusFile and NewickTreeString

[Tiago Antão]

Hi,

2009/12/15 Hilmar Lapp <hlapp at drycafe.net>:
> Actually no. Ancestor1 is the node label of the ancestor node of A, C, and
> E. Node labels follow after a parenthesis without a comma.


I think I've found the cause for this mistake: I was following
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php/Phylogenetics:_NEXUS_Format
which happens not to discuss newick trees in sufficient detail. I
should have used a more detailed spec.
I've found this:
http://en.wikipedia.org/wiki/Newick_format
Question:
I am assuming that the name string is a string in the usual sense, ie,
something starting with an alpha (not numeric) and ending in the first
whitespace.
Given your experience with the format (and considering that sometimes
de facto implementations are somewhat liberal), do you think this
notion of string is good enough?

If so, the change seems trivial and should be ready today.

Tiago
-- 
“Pessimism of the Intellect; Optimism of the Will” -Antonio Gramsci