class Bio::Tree::Node

Node object.

Attributes

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)

Public Class Methods

new(name = nil) click to toggle source

Creates a new node.

    # File lib/bio/tree.rb
139 def initialize(name = nil)
140   @name = name if name
141 end

Public Instance Methods

bootstrap=(num) click to toggle source

sets a bootstrap value

    # File lib/bio/tree.rb
153 def bootstrap=(num)
154   @bootstrap_string = (num ? num.to_s : num)
155   @bootstrap = num
156 end

bootstrap_string=(str) click to toggle source

sets a bootstrap value from a string

    # 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

events() click to toggle source

Phylogenetic events. Returns an Array of one (or more?) of the following symbols

:gene_duplication
:speciation

    # File lib/bio/tree.rb
202 def events
203   @events ||= []
204   @events
205 end

inspect() click to toggle source

visualization of this object

    # 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

nhx_parameters() click to toggle source

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
221 def nhx_parameters
222   @nhx_parameters ||= {}
223   @nhx_parameters
224 end

to_s() click to toggle source

string representation of this object

    # File lib/bio/tree.rb
186 def to_s
187   @name.to_s
188 end