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 85

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 77

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 83

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 75

def taxonomy_id
  @taxonomy_id
end

#uri ⇒ Object

Uri object



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 79

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 91

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

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


  return taxonomy
end