Class: Bio::NeXML::Edge

Inherits:

Tree::Edge

• Object
• Tree::Edge
• Bio::NeXML::Edge

show all

Includes:

Mapper

Defined in:

lib/bio/db/nexml/trees.rb

Overview

Constant Summary

@@writer =

Bio::NeXML::Writer.new

Instance Attribute Summary (collapse)

• - (Object) id

  A file level unique identifier.

• - (Object) label

  A human readable description.

• - (Object) source

  Source of the edge.

• - (Object) target

  Target of the edge.

Instance Method Summary (collapse)

• - (Edge) initialize(id, options = {}) constructor

  Create a new edge.

• - (Object) length

  Return the length of an edge.

• - (Object) length=(length)

  Set the length of an edge.

• - (Object) to_xml

Methods included from Mapper

#properties

edge = Bio::NeXML::Edge.new( 'edge1' )
edge = Bio::NeXML::Edge.new( 'edge1', :source => node1, :target => node2 )
edge = Bio::NeXML::Edge.new( 'edge1', :source => node1, :target => node2, :length => 1 )

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# File 'lib/bio/db/nexml/trees.rb', line 84

def initialize( id, options = {} )
  super( length )
  @id = id
  properties( options ) unless options.empty?
  block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
end

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# File 'lib/bio/db/nexml/trees.rb', line 66

def id
  @id
end

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# File 'lib/bio/db/nexml/trees.rb', line 75

def label
  @label
end

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# File 'lib/bio/db/nexml/trees.rb', line 69

def source
  @source
end

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# File 'lib/bio/db/nexml/trees.rb', line 72

def target
  @target
end

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# File 'lib/bio/db/nexml/trees.rb', line 92

def length
  distance
end

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# File 'lib/bio/db/nexml/trees.rb', line 97

def length=( length )
  self.distance = length
end

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# File 'lib/bio/db/nexml/trees.rb', line 61

def to_xml
  @@writer.create_node( "edge", @@writer.attributes( self, :id, :source, :target, :length, :label ) )
end