class Bio::DB

Public Class Methods

open(filename, *mode, &block) click to toggle source

    # File lib/bio/db.rb
156 def self.open(filename, *mode, &block)
157   Bio::FlatFile.open(self, filename, *mode, &block)
158 end

Public Instance Methods

entry_id() click to toggle source

Returns an entry identifier as a String. This method must be implemented in every database classes by overriding this method.

    # File lib/bio/db.rb
162 def entry_id
163   raise NotImplementedError
164 end

exists?(tag) click to toggle source

Returns true or false - wether the entry contains the field of the given tag name.

    # File lib/bio/db.rb
173 def exists?(tag)
174   @orig.include?(tag)
175 end

fetch(tag, skip = 0) click to toggle source

Similar to the get method, however, fetch returns the content of the field without its tag and any extra white spaces stripped.

    # File lib/bio/db.rb
184 def fetch(tag, skip = 0)
185   field = @orig[tag].split(/\n/, skip + 1).last.to_s
186   truncate(field.gsub(/^.{0,#{@tagsize}}/,''))
187 end

get(tag) click to toggle source

Returns an intact field of the tag as a String.

    # File lib/bio/db.rb
178 def get(tag)
179   @orig[tag]
180 end

tags() click to toggle source

Returns a list of the top level tags of the entry as an Array of String.

    # File lib/bio/db.rb
167 def tags
168   @orig.keys
169 end