Class: Bio::Taxonomy

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

Overview

This is general Taxonomy class.

Direct Known Subclasses

PhyloXML::Taxonomy

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Constructor Details

- (Taxonomy) initialize

Returns a new instance of Taxonomy



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 64

def initialize
  @common_names = []
  @synonyms = []
end

Instance Attribute Details

- (Object) authority

is used to keep the authority, such as 'J. G. Cooper, 1863', associated with the 'scientific_name'.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 58

def authority
  @authority
end

- (Object) code

pattern = [a-zA-Z0-9_]2,10 Can refer to any code/abbreviation/mnemonic, such as Bsu for Bacillus subtilis.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 40

def code
  @code
end

- (Object) common_names

An array of strings



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 45

def common_names
  @common_names
end

- (Object) rank

value comes from list: domain kingdom, subkingdom, branch, infrakingdom, superphylum, phylum, subphylum, infraphylum, microphylum, superdivision, division, subdivision, infradivision, superclass, class, subclass, infraclass, superlegion, legion, sublegion, infralegion, supercohort, cohort, subcohort, infracohort, superorder, order, suborder, superfamily, family, subfamily, supertribe, tribe, subtribe, infratribe, genus, subgenus, superspecies, species, subspecies, variety, subvariety, form, subform, cultivar, unknown, other



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 55

def rank
  @rank
end

- (Object) scientific_name

String.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 43

def scientific_name
  @scientific_name
end

- (Object) synonyms

An array of strings. Holds synonyms for scientific names or common names.



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 61

def synonyms
  @synonyms
end