Class: GO::Annotation

Inherits:
HashTable show all
Extended by:
GermDefault
Defined in:
lib/go.rb

Defined Under Namespace

Classes: AnnotationLine

Constant Summary

Constants included from GermDefault

GermDefault::CACHE

Instance Attribute Summary

Attributes inherited from HashTable

#header, #types

Instance Method Summary collapse

Methods included from GermDefault

cache, cache_load, default, has_default, method_missing

Methods inherited from HashTable

#<<, #[], #concat, #each, #formatted_header, header_off, header_on, #idx, #idx_keys, #inspect, line_class, line_type, #output, #preamble, #sample, #select!, #sort_by!, #sum, #update_index, #use_header?, use_header?, #wrap

Methods included from HashTableAux

#load_file

Methods included from Printer

#print, #write

Constructor Details

#initialize(file = nil, opts = {}) ⇒ Annotation

Returns a new instance of Annotation.



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# File 'lib/go.rb', line 136

def initialize file=nil, opts={}
  opts = opts.merge :header => [ :db, :db_object_id, :db_object_symbol,
                           :qualifier, :go_id, :db_reference,
                           :evidence_code, :with, :aspect, :db_object_name,
                           :synonym, :db_object_type, :taxon, :date,
                           :assigned_by, :annotation_extension,
                           :gene_product_form_id ],
              :skip_header => true,
              :comment => "!",
              :ontology => GO::Ontology.default
  super file, opts
  @annos = {}
end

Instance Method Details

#gene_annotations(gene) ⇒ Object 



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# File 'lib/go.rb', line 157

def gene_annotations gene
  @annos[gene] ||= select do |g|
    g.db_object_symbol == gene
  end
end

#ontology ⇒ Object 



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# File 'lib/go.rb', line 149

def ontology
  @ontology ||= @opts[:ontology]
end