Class: Obo::Ontology

Inherits:

Object

• Object
• Obo::Ontology

show all

Defined in:

lib/obo/ontology.rb

Constant Summary

DIR =

File.expand_path(File.dirname(__FILE__) + '/../../obo')

Instance Attribute Summary (collapse)

• - (Object) elements

  Returns the value of attribute elements.

• - (Object) header

  Returns the value of attribute header.

Instance Method Summary (collapse)

• - (Object) id_to_cast
• - (Object) id_to_element
• - (Object) id_to_name

  returns an id to name Hash.

• - (Ontology) initialize(file_or_io) constructor

  A new instance of Ontology.

• - (Object) name_to_id

  returns a name to id Hash.

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# File 'lib/obo/ontology.rb', line 39

def initialize(file_or_io)
  obo = Obo::Parser.new(file_or_io)
  @elements = obo.elements.to_a
  @header = elements.shift
end

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# File 'lib/obo/ontology.rb', line 37

def elements
  @elements
end

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# File 'lib/obo/ontology.rb', line 36

def header
  @header
end

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# File 'lib/obo/ontology.rb', line 50

def id_to_cast
  @id_to_cast ||= Hash[ id_to_element.map {|id,el| [id, el.cast_method] } ]
end

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# File 'lib/obo/ontology.rb', line 59

def id_to_element
  @id_to_element ||= build_hash('id', nil)
end

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# File 'lib/obo/ontology.rb', line 46

def id_to_name
  @id_to_name ||= build_hash('id', 'name')
end

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# File 'lib/obo/ontology.rb', line 55

def name_to_id
  @name_to_id ||= build_hash('name', 'id')
end