Class: Bio::KEGG::Keggtab::DB

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/kegg/keggtab.rb

Overview

Bio::KEGG::Keggtab::DB

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(db_name, db_type, db_path, db_abbrev) ⇒ DB

Create a container object for database definitions.



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# File 'lib/bio/db/kegg/keggtab.rb', line 73

def initialize(db_name, db_type, db_path, db_abbrev)
  @name = db_name
  @type = db_type
  @path = db_path
  @abbrev = db_abbrev
  @aliases = Array.new
end

Instance Attribute Details

#abbrevObject (readonly) Also known as: korg, keggorg

Short name for the database. (e.g. 'ec', 'hsa', 'eco', …) korg and keggorg are alias for abbrev method.



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# File 'lib/bio/db/kegg/keggtab.rb', line 88

def abbrev
  @abbrev
end

#aliasesObject (readonly)

Array containing all alias names for the database. (e.g. [“H.sapiens”, “hsa”], [“E.coli”, “eco”], …)



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# File 'lib/bio/db/kegg/keggtab.rb', line 91

def aliases
  @aliases
end

#nameObject (readonly)

Database name. (e.g. 'enzyme', 'h.sapies', 'e.coli', …)



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# File 'lib/bio/db/kegg/keggtab.rb', line 81

def name
  @name
end

#pathObject (readonly)

Database flat file path. (e.g. '$BIOROOT/db/kegg/genes', …)



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# File 'lib/bio/db/kegg/keggtab.rb', line 85

def path
  @path
end

#typeObject (readonly)

Definition type. (e.g. 'enzyme', 'alias', 'genes', …)



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# File 'lib/bio/db/kegg/keggtab.rb', line 83

def type
  @type
end