Class Bio::Sequence::DBLink
In: lib/bio/sequence/dblink.rb
Parent: Object

Bio::Sequence::DBLink stores IDs with the database name. Its main purpose is to store database cross-reference information for a sequence entry.

Methods

new   parse_embl_DR_line   parse_uniprot_DR_line  

Attributes

database  [R]  Database name, or namespace identifier (String).
id  [R]  Primary identifier (String)
secondary_ids  [R]  Secondary identifiers (Array of String)

Public Class methods

new(database, primary_id, *secondary_ids)

creates a new DBLink object

[Source]

    # File lib/bio/sequence/dblink.rb, line 19
19:   def initialize(database, primary_id, *secondary_ids)
20:     @database = database
21:     @id = primary_id
22:     @secondary_ids = secondary_ids
23:   end
parse_embl_DR_line(str)

Parses DR line in EMBL entry, and returns a DBLink object.

[Source]

    # File lib/bio/sequence/dblink.rb, line 39
39:   def self.parse_embl_DR_line(str)
40:     str = str.sub(/\.\s*\z/, '')
41:     str.sub!(/\ADR   /, '')
42:     self.new(*(str.split(/\s*\;\s*/, 3)))
43:   end
parse_uniprot_DR_line(str)

Parses DR line in UniProt entry, and returns a DBLink object.

[Source]

    # File lib/bio/sequence/dblink.rb, line 46
46:   def self.parse_uniprot_DR_line(str)
47:     str = str.sub(/\.\s*\z/, '')
48:     str.sub!(/\ADR   /, '')
49:     self.new(*(str.split(/\s*\;\s*/)))
50:   end

[Validate]