Class Bio::DB
In: lib/bio/db.rb
Parent: Object

Methods

entry_id   exists?   fetch   get   open   tags  

Public Class methods

open(filename, *mode, &block)

[Source]

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

Public Instance methods

entry_id()

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

[Source]

     # File lib/bio/db.rb, line 162
162:   def entry_id
163:     raise NotImplementedError
164:   end
exists?(tag)

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

[Source]

     # File lib/bio/db.rb, line 173
173:   def exists?(tag)
174:     @orig.include?(tag)
175:   end
fetch(tag, skip = 0)

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

[Source]

     # File lib/bio/db.rb, line 184
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)

Returns an intact field of the tag as a String.

[Source]

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

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

[Source]

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

[Validate]