1. Lack of knowledge of root node
The Newick tree string is read as-is and is not parsed. It only gets
parsed at the point of conversion to a Undirected or WeightedGraph
inside the TreeBlocks.java source code (inside the two types of get-As-
JGraphT methods). It's at this point the string is parsed and it's
here that root note determination should take place. It's already
known whether &R or &U have been specified here, which should help the
code work out what to do.
2. The p* stuff.
Exactly the same part of the code as described above. Wherever it
pushes values to the stack but prepends them with 'p' first, you'll
need to change the 'p' to some instance variable and provide a getter/
setter to change it, with 'p' being the default setting.
cheers,
Richard
Tiago
2009/11/3 Richard Holland <[email protected]>:
Agreed that there is a bug. Now all we need is someone to go in and
fix it!
:)
cheers,
Richard
On 3 Nov 2009, at 18:16, Tiago Antão wrote:
2009/11/3 Thasso Griebel <[email protected]>:
There is a way to uniquely get a root from a newick string.
Usually a
rooted newick is surrounded with brackets, which indicates the
root as
the
highest node in the tree. For example:
(A, (B,C))
Agree, it is quite easy to get the root of the tree from the newick
representation. But it should be done on parsing and returned in
some
way by the parsing system. If the user has to do it again, it means
that the user has to parse it again just to know the root node.
I would also suggest to generally parse trees as rooted trees
(maybe jsut
for th initial internal model). Creating an unrooted tree from a
rooted
one
is easy, remove the root and forget about directions. The other
way might
be
hard and ambiguous.
100% agree.
The newick _representation_ always has a root by virtue of the way
it
is done. If that root has meaning or not depends. Doing as you
suggest
seems the most reasonable idea.
I would add that even if it is an unrooted tree, the topology
might be
of interest. In my case I am doing a comparative visualizer and it
might be nice for the user to be able to visualize the topology as
specified. It has no biological meaning, but in practice, for many
users, it helps.
I note that PhyloXML (even by virtue of being a XML format) always
represents the phylogenies as trees (not weigthed DAGs). There an
attribute rooted which can be true or false.
But, anyway. Even assuming a very conservative view on this, the
current parser, for rooted trees, does not allow to determine
where is
the root. I think that there would be a consensus that that is a
bug?
Tiago
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
--
"The hottest places in hell are reserved for those who, in times of
moral crisis, maintain a neutrality." - Dante
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
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