Class: Bio::Tree::Node

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-alignment/tree.rb

Instance Method Summary collapse

Instance Method Details

#alignment ⇒ Object

Return the alignment attached to the tree



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# File 'lib/bio-alignment/tree.rb', line 109

def alignment
  @alignment
end

#children ⇒ Object

Get the children of this Node



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# File 'lib/bio-alignment/tree.rb', line 54

def children
  @tree.children(self)
end

#descendents ⇒ Object 



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# File 'lib/bio-alignment/tree.rb', line 58

def descendents
  @tree.descendents(self)
end

#distance(other) ⇒ Object

Get the distance to another node



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# File 'lib/bio-alignment/tree.rb', line 84

def distance other
  @tree.distance(self,other)
end

#inject_tree(tree, alignment) ⇒ Object

Add tree information to this node, so it can be queried



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# File 'lib/bio-alignment/tree.rb', line 41

def inject_tree tree, alignment
  @tree = tree
  @tree.freeze
  @alignment = alignment
  self
end

#leaf? ⇒ Boolean

Is this Node a leaf?

Returns:

  • (Boolean) 


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# File 'lib/bio-alignment/tree.rb', line 49

def leaf?
  children.size == 0
end

#leaves ⇒ Object

Return the leaves of this node



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# File 'lib/bio-alignment/tree.rb', line 73

def leaves
  @tree.leaves(self)
end

#nearest ⇒ Object

Find the nearest and dearest, i.e. the leafs attached to the parent node



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# File 'lib/bio-alignment/tree.rb', line 79

def nearest
  @tree.leaves(parent) - [self]
end

#nearest_child ⇒ Object

Get child node with the shortest edge - note that if there are more than one, the first will be picked



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# File 'lib/bio-alignment/tree.rb', line 90

def nearest_child
  c = nil
  children.each do |n|
    c=n if not c or distance(n)<distance(c)
  end
  c
end

#nearest_children ⇒ Object

Get the child nodes with the shortest edge - returns an Array



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# File 'lib/bio-alignment/tree.rb', line 99

def nearest_children
  min_distance = distance(nearest_child)
  cs = []
  children.each do |n|
    cs << n if distance(n) == min_distance
  end
  cs
end

#parent ⇒ Object

Get the parents of this Node



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# File 'lib/bio-alignment/tree.rb', line 63

def parent
  @tree.parent(self)
end

#sequence ⇒ Object 



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# File 'lib/bio-alignment/tree.rb', line 113

def sequence
  @alignment.find(name)
end

#siblings ⇒ Object

Get the direct sibling nodes (i.e. parent.children)



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# File 'lib/bio-alignment/tree.rb', line 68

def siblings
  parent.children - [self]
end