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 153 153: def bootstrap=(num) 154: @bootstrap_string = (num ? num.to_s : num) 155: @bootstrap = num 156: end
sets a bootstrap value from a string
# File lib/bio/tree.rb, line 159 159: def bootstrap_string=(str) 160: if str.to_s.strip.empty? 161: @bootstrap = nil 162: @bootstrap_string = str 163: else 164: i = str.to_i 165: f = str.to_f 166: @bootstrap = (i == f ? i : f) 167: @bootstrap_string = str 168: end 169: end
visualization of this object
# File lib/bio/tree.rb, line 172 172: def inspect 173: if @name and !@name.empty? then 174: str = "(Node:#{@name.inspect}" 175: else 176: str = sprintf('(Node:%x', (self.__id__ << 1) & 0xffffffff) 177: end 178: if defined?(@bootstrap) and @bootstrap then 179: str += " bootstrap=#{@bootstrap.inspect}" 180: end 181: str += ")" 182: str 183: 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 221 221: def nhx_parameters 222: @nhx_parameters ||= {} 223: @nhx_parameters 224: end