module Bio::BioAlignment::Tree
The Tree
module turns a tree into a traversable object, by wrapping BioRuby's basic tree objects. The Bio::Tree
object can always be fetched using to_bioruby_tree.
Public Class Methods
init(tree, alignment)
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Make all nodes in the Bio::Tree
aware of the tree object, and the alignment, so get a more intuitive API
# File lib/bio-alignment/tree.rb, line 16 def Tree::init tree, alignment if tree.kind_of?(Bio::Tree) # walk all nodes and infect the tree info tree.each_node do | node | node.inject_tree(tree, alignment) end # tree.root.set_tree(tree) else raise "BioAlignment::Tree does not understand tree type "+tree.class.to_s end return tree end
Public Instance Methods
root()
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# File lib/bio-alignment/tree.rb, line 29 def root @tree.root end