Class | Bio::Tree::Node |
In: |
lib/bio/tree.rb
|
Parent: | Object |
Node object.
bootstrap | [R] | bootstrap value |
bootstrap_string | [R] | bootstrap value as a string |
ec_number | [RW] | EC number (EC_number in PhyloXML, or :E in NHX) |
name | [RW] | name of the node |
order_number | [RW] | the order of the node (lower value, high priority) |
scientific_name | [RW] | scientific name (scientific_name in PhyloXML, or :S in NHX) |
taxonomy_id | [RW] | taxonomy identifier (taxonomy_identifier in PhyloXML, or :T in NHX) |
sets a bootstrap value
# File lib/bio/tree.rb, line 154 154: def bootstrap=(num) 155: @bootstrap_string = (num ? num.to_s : num) 156: @bootstrap = num 157: end
sets a bootstrap value from a string
# File lib/bio/tree.rb, line 160 160: def bootstrap_string=(str) 161: if str.to_s.strip.empty? 162: @bootstrap = nil 163: @bootstrap_string = str 164: else 165: i = str.to_i 166: f = str.to_f 167: @bootstrap = (i == f ? i : f) 168: @bootstrap_string = str 169: end 170: end
visualization of this object
# File lib/bio/tree.rb, line 173 173: def inspect 174: if @name and !@name.empty? then 175: str = "(Node:#{@name.inspect}" 176: else 177: str = sprintf('(Node:%x', (self.__id__ << 1) & 0xffffffff) 178: end 179: if defined?(@bootstrap) and @bootstrap then 180: str += " bootstrap=#{@bootstrap.inspect}" 181: end 182: str += ")" 183: str 184: end
Other NHX parameters. Returns a Hash. Note that :D, :E, :S, and :T 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.
# File lib/bio/tree.rb, line 222 222: def nhx_parameters 223: @nhx_parameters ||= {} 224: @nhx_parameters 225: end