[BioRuby] BioRuby Phyloxml update
Tomoaki NISHIYAMA
tomoakin at kenroku.kanazawa-u.ac.jp
Wed Nov 18 00:24:34 UTC 2009
Hi,
One point seems that tree can be unrooted or rooted.
Perhaps, Goto-san's Bio::Tree represents unrooted tree (not
distinguishing parents and childrenn),
while Diana's class is for rooted trees (having distinction of
parents and children).
If, this is the point, Bio::RootedTree is better name than
Bio::FamilyTree.
In general, rooted tree should be easily converted to unrooted tree,
while
conversion of an unrooted tree to rooted tree requires specification
of the root.
For text representation like NEWICK there is anyway a root while
the tree can be interpreted either as rooted or unrooted.
It could be good to have distinct interface for rooted and unrooted
trees,
to let the user's be aware of the conceptual difference.
--
Tomoaki NISHIYAMA
Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan
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