class Bio::Tree::Edge
Edge object of each node. By default, the object doesn't contain any node information.
Attributes
evolutionary distance
evolutionary distance represented as a string
log likelihood value (:L in NHX)
width of the edge (<branch width=“w”> of PhyloXML, or :W=“w” in NHX)
Public Class Methods
creates a new edge.
# File lib/bio/tree.rb, line 32 def initialize(distance = nil) if distance.kind_of?(Numeric) self.distance = distance elsif distance self.distance_string = distance end end
Public Instance Methods
set evolutionary distance value
# File lib/bio/tree.rb, line 47 def distance=(num) @distance = num @distance_string = (num ? num.to_s : num) end
set evolutionary distance value from a string
# File lib/bio/tree.rb, line 53 def distance_string=(str) if str.to_s.strip.empty? @distance = nil @distance_string = str else @distance = str.to_f @distance_string = str end end
visualization of this object
# File lib/bio/tree.rb, line 64 def inspect "<Edge distance=#{@distance.inspect}>" end
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, line 91 def nhx_parameters @nhx_parameters ||= {} @nhx_parameters end
string representation of this object
# File lib/bio/tree.rb, line 69 def to_s @distance_string.to_s end