Class Bio::Tree::Node
In: lib/bio/tree.rb
Parent: Object

Node object.

Methods

bootstrap=   bootstrap_string=   events   inspect   new   nhx_parameters   to_s  

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)

Creates a new node.

[Source]

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

Public Instance methods

bootstrap=(num)

sets a bootstrap value

[Source]

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

sets a bootstrap value from a string

[Source]

     # File lib/bio/tree.rb, line 160
160:       def bootstrap_string=(str)
161:         if str.to_s.strip.empty?
162:           @bootstrap = nil
163:           @bootstrap_string = str
164:         else
165:           i = str.to_i
166:           f = str.to_f
167:           @bootstrap = (i == f ? i : f)
168:           @bootstrap_string = str
169:         end
170:       end
events()

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

  :gene_duplication
  :speciation

[Source]

     # File lib/bio/tree.rb, line 203
203:       def events
204:         @events ||= []
205:         @events
206:       end
inspect()

visualization of this object

[Source]

     # File lib/bio/tree.rb, line 173
173:       def inspect
174:         if @name and !@name.empty? then
175:           str = "(Node:#{@name.inspect}"
176:         else
177:           str = sprintf('(Node:%x', (self.__id__ << 1) & 0xffffffff)
178:         end
179:         if defined?(@bootstrap) and @bootstrap then
180:           str += " bootstrap=#{@bootstrap.inspect}"
181:         end
182:         str += ")"
183:         str
184:       end
nhx_parameters()

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, line 222
222:       def nhx_parameters
223:         @nhx_parameters ||= {}
224:         @nhx_parameters
225:       end
to_s()

string representation of this object

[Source]

     # File lib/bio/tree.rb, line 187
187:       def to_s
188:         @name.to_s
189:       end

[Validate]