Class: Bio::NeXML::IntTree

Inherits:

Tree

• Object
• Tree
• Tree
• Bio::NeXML::IntTree

show all

Defined in:

lib/bio/db/nexml/trees.rb

Overview

Instance Attribute Summary

Attributes inherited from Tree

#id, #label, #rootedge

Instance Method Summary (collapse)

• - (Object) add_edge(edge)
• - (Object) create_edge(options = {})
• - (Object) create_rootedge(options = {})
• - (IntTree) initialize(id = nil, options = {}, &block) constructor

  A new instance of IntTree.

Methods inherited from Tree

#<<, #[], #__add_edge__, #__add_node__, #add_node, #add_rootedge, #ancestors, #children, #create_node, #descendents, #each_edge, #each_edge_with_id, #each_node, #each_node_with_id, #get_edge_by_id, #get_node_by_id, #has_edge?, #has_node?, #include?, #lowest_common_ancestor, #number_of_edges, #number_of_nodes, #parent, #remove_edge, #remove_node, #roots, #to_xml

Methods included from Mapper

#properties

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# File 'lib/bio/db/nexml/trees.rb', line 428

def initialize( id = nil, options = {}, &block )
  super
end

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# File 'lib/bio/db/nexml/trees.rb', line 432

def add_edge( edge )
  edge.length = edge.length.to_i
  super
end

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# File 'lib/bio/db/nexml/trees.rb', line 437

def create_edge( options = {} )
  edge = IntEdge.new( Bio::NeXML.generate_id( IntEdge ), options )
  self << edge
  edge        
end

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# File 'lib/bio/db/nexml/trees.rb', line 443

def create_rootedge( options = {} )
  rootedge = IntRootEdge.new( Bio::NeXML.generate_id( IntRootEdge ), options )
  self << rootedge
  rootedge
end