Class: Bio::PhyloXML::Taxonomy

Inherits:
Taxonomy show all
Defined in:
lib/bio/db/phyloxml/phyloxml_elements.rb

Overview

Taxonomy class

Instance Attribute Summary collapse

Attributes inherited from Taxonomy

#authority, #code, #common_names, #rank, #scientific_name, #synonyms

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Taxonomy

Returns a new instance of Taxonomy.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 86

def initialize
  super
  @other = []
end

Instance Attribute Details

#id_source ⇒ Object

Used to link other elements to a taxonomy (on the xml-level)



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 78

def id_source
  @id_source
end

#other ⇒ Object

Array of Other objects. Used to save additional information from other than PhyloXML namspace.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 84

def other
  @other
end

#taxonomy_id ⇒ Object

String. Unique identifier of a taxon.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 76

def taxonomy_id
  @taxonomy_id
end

#uri ⇒ Object

Uri object



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 80

def uri
  @uri
end

Instance Method Details

#to_xml ⇒ Object

Converts elements to xml representation. Called by PhyloXML::Writer class.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 92

def to_xml
  taxonomy = LibXML::XML::Node.new('taxonomy')
  taxonomy["type"] = @type if @type != nil
  taxonomy["id_source"] = @id_source if @id_source != nil

  PhyloXML::Writer.generate_xml(taxonomy, self, [[:complex, 'id', @taxonomy_id],
    [:pattern, 'code', @code, Regexp.new("^[a-zA-Z0-9_]{2,10}$")],
    [:simple, 'scientific_name', @scientific_name],
    [:simple, 'authority', @authority],
    [:simplearr, 'common_name', @common_names],
    [:simplearr, 'synonym', @synonyms],
    [:simple, 'rank', @rank],
    [:complex, 'uri',@uri]])
    #@todo anything else


  return taxonomy
end