class Bio::Tree::Edge

Edge object of each node. By default, the object doesn’t contain any node information.

Attributes

distance[R]

evolutionary distance

distance_string[R]

evolutionary distance represented as a string

log_likelihood[RW]

log likelihood value (:L in NHX)

width[RW]

width of the edge (<branch width=“w”> of PhyloXML, or :W=“w” in NHX)

Public Class Methods

new(distance = nil) click to toggle source

creates a new edge.

   # File lib/bio/tree.rb
32 def initialize(distance = nil)
33   if distance.kind_of?(Numeric)
34     self.distance = distance
35   elsif distance
36     self.distance_string = distance
37   end
38 end

Public Instance Methods

distance=(num) click to toggle source

set evolutionary distance value

   # File lib/bio/tree.rb
47 def distance=(num)
48   @distance = num
49   @distance_string = (num ? num.to_s : num)
50 end

distance_string=(str) click to toggle source

set evolutionary distance value from a string

   # File lib/bio/tree.rb
53 def distance_string=(str)
54   if str.to_s.strip.empty?
55     @distance = nil
56     @distance_string = str
57   else
58     @distance = str.to_f
59     @distance_string = str
60   end
61 end

inspect() click to toggle source

visualization of this object

   # File lib/bio/tree.rb
64 def inspect
65   "<Edge distance=#{@distance.inspect}>"
66 end

nhx_parameters() click to toggle source

Other NHX parameters. Returns a Hash. Note that :L and :W are not stored here but stored in the proper attributes in this class. However, if you force to set these parameters in this hash, the parameters in this hash are preferred when generating NHX. In addition, If the same parameters are defined at Node object, the parameters in the node are preferred.

   # File lib/bio/tree.rb
91 def nhx_parameters
92   @nhx_parameters ||= {}
93   @nhx_parameters
94 end

to_s() click to toggle source

string representation of this object

   # File lib/bio/tree.rb
69 def to_s
70   @distance_string.to_s
71 end