class Bio::FANTOM::MaXML

Constants

DELIMITER

DTD of MaXML(Mouse annotation XML) fantom.gsc.riken.go.jp/maxml/maxml.dtd

Data_XPath

This class is for {allseq|repseq|allclust}.sep.xml, not for {allseq|repseq|allclust}.xml.

Attributes

elem[R]

Public Class Methods

new(x) click to toggle source
# File lib/bio/db/fantom.rb, line 62
def initialize(x)
  if x.is_a?(REXML::Element) then
    @elem = x
  else
    if x.is_a?(String) then
      x = x.sub(/#{Regexp.escape(DELIMITER)}\z/om, "\n")
    end
    doc = REXML::Document.new(x)
    @elem = doc.elements[self.class::Data_XPath]
    #raise 'element is null' unless @elem
    @elem = REXML::Document.new('') unless @elem
  end
end

Public Instance Methods

entry_id() click to toggle source
# File lib/bio/db/fantom.rb, line 90
def entry_id
  unless defined?(@entry_id)
    @entry_id = @elem.attributes['id']
  end
  @entry_id
end
gsub_entities(str) click to toggle source
# File lib/bio/db/fantom.rb, line 81
def gsub_entities(str)
  # workaround for bug?
  if str then
    str.gsub(/\&\#(\d{1,3})\;/) { sprintf("%c", $1.to_i) }
  else
    str
  end
end
to_s() click to toggle source
# File lib/bio/db/fantom.rb, line 77
def to_s
  @elem.to_s
end