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, line 139
def initialize(name = nil)
  @name = name if name
end

Public Instance Methods

bootstrap=(num) click to toggle source

sets a bootstrap value

# File lib/bio/tree.rb, line 153
def bootstrap=(num)
  @bootstrap_string = (num ? num.to_s : num)
  @bootstrap = num
end
bootstrap_string=(str) click to toggle source

sets a bootstrap value from a string

# File lib/bio/tree.rb, line 159
def bootstrap_string=(str)
  if str.to_s.strip.empty?
    @bootstrap = nil
    @bootstrap_string = str
  else
    i = str.to_i
    f = str.to_f
    @bootstrap = (i == f ? i : f)
    @bootstrap_string = str
  end
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, line 202
def events
  @events ||= []
  @events
end
inspect() click to toggle source

visualization of this object

# File lib/bio/tree.rb, line 172
def inspect
  if @name and !@name.empty? then
    str = "(Node:#{@name.inspect}"
  else
    str = sprintf('(Node:%x', (self.__id__ << 1) & 0xffffffff)
  end
  if defined?(@bootstrap) and @bootstrap then
    str += " bootstrap=#{@bootstrap.inspect}"
  end
  str += ")"
  str
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, line 221
def nhx_parameters
  @nhx_parameters ||= {}
  @nhx_parameters
end
to_s() click to toggle source

string representation of this object

# File lib/bio/tree.rb, line 186
def to_s
  @name.to_s
end