Method: Bio::Tree#remove_nonsense_nodes

Defined in:
lib/bio/tree.rb

#remove_nonsense_nodes ⇒ Object

Removes all nodes that are not branches nor leaves. That is, removes nodes connected with exactly two edges. For each removed node, two adjacent edges are merged and a new edge are created. Returns removed nodes. Note that orphan nodes are still kept unchanged.



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# File 'lib/bio/tree.rb', line 852

def remove_nonsense_nodes
  _clear_cache
  hash = {}
  self.each_node do |node|
    hash[node] = true if @pathway.graph[node].size == 2
  end
  hash.each_key do |node|
    adjs = @pathway.graph[node].keys
    edges = @pathway.graph[node].values
    new_edge = get_edge_merged(edges[0], edges[1])
    @pathway.graph[adjs[0]].delete(node)
    @pathway.graph[adjs[1]].delete(node)
    @pathway.graph.delete(node)
    @pathway.append(Bio::Relation.new(adjs[0], adjs[1], new_edge))
  end
  #@pathway.to_relations
  @pathway.relations.reject! do |rel|
    hash[rel.node[0]] or hash[rel.node[1]]
  end
  return hash.keys
end