Class Bio::Tree::Edge
In: lib/bio/tree.rb
Parent: Object

Edge object of each node. By default, the object doesn‘t contain any node information.

Methods

distance=   distance_string=   inspect   new   nhx_parameters   to_s  

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)

creates a new edge.

[Source]

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

Public Instance methods

distance=(num)

set evolutionary distance value

[Source]

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

set evolutionary distance value from a string

[Source]

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

visualization of this object

[Source]

    # File lib/bio/tree.rb, line 65
65:       def inspect
66:         "<Edge distance=#{@distance.inspect}>"
67:       end
nhx_parameters()

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.

[Source]

    # File lib/bio/tree.rb, line 92
92:       def nhx_parameters
93:         @nhx_parameters ||= {}
94:         @nhx_parameters
95:       end
to_s()

string representation of this object

[Source]

    # File lib/bio/tree.rb, line 70
70:       def to_s
71:         @distance_string.to_s
72:       end

[Validate]