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.
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) |
set evolutionary distance value
# File lib/bio/tree.rb, line 48 48: def distance=(num) 49: @distance = num 50: @distance_string = (num ? num.to_s : num) 51: end
set evolutionary distance value from a string
# 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
visualization of this object
# File lib/bio/tree.rb, line 65 65: def inspect 66: "<Edge distance=#{@distance.inspect}>" 67: 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 92 92: def nhx_parameters 93: @nhx_parameters ||= {} 94: @nhx_parameters 95: end