Class: Bio::NeXML::Otus

Inherits:
Object
  • Object
show all
Includes:
Mapper, Enumerable
Defined in:
lib/bio/db/nexml/taxa.rb

Overview

DESCRIPTION

Otus is a container for Otu objects; an implementation of the Taxa[http://nexml.org/nexml/html/doc/schema-1/taxa/taxa/#Taxa] type. An Otus must have an ‘id’ and may take an optional ‘label’. Adding two or more Otu objects with the same ‘id’ to an Otus is not allowed. Doing so will overwrite the previous Otu object with the same the same ‘id’.

taxa1 = Bio::NeXML::Otus.new( 'taxa1', :label => 'Label for taxa1' )
taxa1.id       #=> 'taxa1'
taxa1.label    #=> 'Label for taxa1'

taxon1 = Bio::NeXML::Otu.new( 'taxon1' )
taxon2 = Bio::NeXML::Otu.new( 'taxon2' )

taxa1 << taxon1 << taxon2
taxa1.count                      #=> 2
taxa1.each { |otu| puts otu.id }
taxon2.otus                      #=> taxa1
taxa1.include?( taxon1 )         #=> true
taxa1.delete( taxon2 )           #=> taxon2

Constant Summary collapse

@@writer = 
Bio::NeXML::Writer.new

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods included from Mapper

#properties

Constructor Details

#initialize(id, options = {}, &block) ⇒ Otus

Returns a new instance of Otus.



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# File 'lib/bio/db/nexml/taxa.rb', line 80

def initialize( id, options = {}, &block )
  @id = id
  properties( options ) unless options.empty?
  block.arity < 1 ? instance_eval( &block ) : block.call( self ) if block_given?
end

Instance Attribute Details

#id ⇒ Object

A file level unique identifier.



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# File 'lib/bio/db/nexml/taxa.rb', line 69

def id
  @id
end

#label ⇒ Object

A human readable description.



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# File 'lib/bio/db/nexml/taxa.rb', line 72

def label
  @label
end

Instance Method Details

#<<(otu) ⇒ Object

Takes an otu object and appends it to self.



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# File 'lib/bio/db/nexml/taxa.rb', line 92

def <<( otu )
  add_otu( otu )
  self
end

#[](id) ⇒ Object

Returns the otu object with the given id; nil if an otu with the given id is not contained in self.



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# File 'lib/bio/db/nexml/taxa.rb', line 116

def []( id )
  get_otu_by_id( id )
end

#create_otu(options = {}) ⇒ Object

Creates and returns an otu after appending it to self



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# File 'lib/bio/db/nexml/taxa.rb', line 98

def create_otu( options = {} )
  otu = Otu.new( Bio::NeXML.generate_id( Otu ), options )
  self << otu
  otu
end

#delete(otu) ⇒ Object

Takes an otu or its id and deletes it. Returns the object deleted or nil.



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# File 'lib/bio/db/nexml/taxa.rb', line 105

def delete( otu )
  delete_otu( otu )
end

#each(&block) ⇒ Object

Iterate over each otu in self passing it to the block given. If no block is provided, it returns an Enumerator.



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# File 'lib/bio/db/nexml/taxa.rb', line 122

def each( &block )
  @otus.each( &block )
end

#each_with_id(&block) ⇒ Object

Iterate over each otu in self passing the otu and its id to the block given. If no block is provided, it returns an Enumerator.



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# File 'lib/bio/db/nexml/taxa.rb', line 128

def each_with_id( &block )
  @otus.each_with_id( &block )
end

#include?(object) ⇒ Boolean

Takes an otu or its id and returns true if it is contained in self.

Returns:

  • (Boolean) 


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# File 'lib/bio/db/nexml/taxa.rb', line 110

def include?( object )
  has_otu?( object )
end

#length ⇒ Object

Return the number of otu in self.



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# File 'lib/bio/db/nexml/taxa.rb', line 133

def length
  number_of_otus
end

#otus ⇒ Object

Returns an array of otu contained in self.



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# File 'lib/bio/db/nexml/taxa.rb', line 87

def otus;  end

#to_xml ⇒ Object 



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# File 'lib/bio/db/nexml/taxa.rb', line 137

def to_xml
  node = @@writer.create_node( "otus", @@writer.attributes( self, :id, :label ) )
  self.each do |otu|
    node << otu.to_xml
  end
  node        
end