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 47 47: def distance=(num) 48: @distance = num 49: @distance_string = (num ? num.to_s : num) 50: end
set evolutionary distance value from a string
# File lib/bio/tree.rb, line 53 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
visualization of this object
# File lib/bio/tree.rb, line 64 64: def inspect 65: "<Edge distance=#{@distance.inspect}>" 66: 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 91: def nhx_parameters 92: @nhx_parameters ||= {} 93: @nhx_parameters 94: end