Class Bio::DB
In: lib/bio/db.rb  (CVS)
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
  def self.open(filename, *mode, &block)
    Bio::FlatFile.open(self, filename, *mode, &block)
  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
  def entry_id
    raise NotImplementedError
  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
  def exists?(tag)
    @orig.include?(tag)
  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
  def fetch(tag, skip = 0)
    field = @orig[tag].split(/\n/, skip + 1).last.to_s
    truncate(field.gsub(/^.{0,#{@tagsize}}/,''))
  end
get(tag)

Returns an intact field of the tag as a String.

[Source]

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

[Validate]