# File lib/bio/io/registry.rb, line 99 def initialize(file = nil) @spec_version = nil @databases = Array.new read_local(file) if file env_path = ENV['OBDA_SEARCH_PATH'] if env_path and env_path.size > 0 read_env(env_path) else read_local("#{ENV['HOME']}/.bioinformatics/seqdatabase.ini") read_local("/etc/bioinformatics/seqdatabase.ini") if @databases.empty? read_remote("http://www.open-bio.org/registry/seqdatabase.ini") end end end
Returns a dababase handle (Bio::SQL, Bio::Fetch etc.) or nil if not found (case insensitive). The handles should have get_by_id method.
# File lib/bio/io/registry.rb, line 124 def get_database(dbname) @databases.each do |db| if db.database == dbname.downcase case db.protocol when 'biofetch' return serv_biofetch(db) when 'biosql' return serv_biosql(db) when 'flat', 'index-flat', 'index-berkeleydb' return serv_flat(db) when 'bsane-corba', 'biocorba' raise NotImplementedError when 'xembl' raise NotImplementedError end end end return nil end
Returns a Registry::DB object corresponding to the first dbname entry in the registry records (case insensitive).
# File lib/bio/io/registry.rb, line 147 def query(dbname) @databases.each do |db| return db if db.database == dbname.downcase end end
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