Class: Bio::Tree::Node

Inherits:
Object show all
Defined in:
lib/bio/tree.rb

Overview

Node object.

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(name = nil) ⇒ Node

Creates a new node.



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# File 'lib/bio/tree.rb', line 139

def initialize(name = nil)
  @name = name if name
end

Instance Attribute Details

#bootstrap ⇒ Object

bootstrap value



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# File 'lib/bio/tree.rb', line 147

def bootstrap
  @bootstrap
end

#bootstrap_string ⇒ Object

bootstrap value as a string



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# File 'lib/bio/tree.rb', line 150

def bootstrap_string
  @bootstrap_string
end

#ec_number ⇒ Object

EC number (EC_number in PhyloXML, or :E in NHX)



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# File 'lib/bio/tree.rb', line 208

def ec_number
  @ec_number
end

#name ⇒ Object

name of the node



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# File 'lib/bio/tree.rb', line 144

def name
  @name
end

#order_number ⇒ Object

the order of the node (lower value, high priority)



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# File 'lib/bio/tree.rb', line 192

def order_number
  @order_number
end

#scientific_name ⇒ Object

scientific name (scientific_name in PhyloXML, or :S in NHX)



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# File 'lib/bio/tree.rb', line 211

def scientific_name
  @scientific_name
end

#taxonomy_id ⇒ Object

taxonomy identifier (taxonomy_identifier in PhyloXML, or :T in NHX)



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# File 'lib/bio/tree.rb', line 214

def taxonomy_id
  @taxonomy_id
end

Instance Method Details

#events ⇒ Object

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

:gene_duplication
:speciation



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# File 'lib/bio/tree.rb', line 202

def events
  @events ||= []
  @events
end

#inspect ⇒ Object

visualization of this object



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# 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 ⇒ Object

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.



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# File 'lib/bio/tree.rb', line 221

def nhx_parameters
  @nhx_parameters ||= {}
  @nhx_parameters
end

#to_s ⇒ Object

string representation of this object



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# File 'lib/bio/tree.rb', line 186

def to_s
  @name.to_s
end