class Bio::Tree::Node
Node object.
Attributes
bootstrap value
bootstrap value as a string
EC number (EC_number in PhyloXML, or :E in NHX)
name of the node
the order of the node (lower value, high priority)
scientific name (scientific_name in PhyloXML, or :S in NHX)
taxonomy identifier (taxonomy_identifier in PhyloXML, or :T in NHX)
Public Class Methods
Source
# File lib/bio/tree.rb 139 def initialize(name = nil) 140 @name = name if name 141 end
Creates a new node.
Public Instance Methods
Source
# File lib/bio/tree.rb 153 def bootstrap=(num) 154 @bootstrap_string = (num ? num.to_s : num) 155 @bootstrap = num 156 end
sets a bootstrap value
Source
# File lib/bio/tree.rb 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
sets a bootstrap value from a string
Source
# File lib/bio/tree.rb 202 def events 203 @events ||= [] 204 @events 205 end
Phylogenetic events. Returns an Array of one (or more?) of the following symbols
:gene_duplication :speciation
Source
# File lib/bio/tree.rb 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
visualization of this object
Source
# File lib/bio/tree.rb 221 def nhx_parameters 222 @nhx_parameters ||= {} 223 @nhx_parameters 224 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.
Source
# File lib/bio/tree.rb 186 def to_s 187 @name.to_s 188 end
string representation of this object