Class: Bio::FANTOM::MaXML

Inherits:
DB show all
Defined in:
lib/bio/db/fantom.rb

Direct Known Subclasses

Annotation, Annotations, Cluster, Sequence, Sequences

Defined Under Namespace

Classes: Annotation, Annotations, Cluster, Sequence, Sequences

Constant Summary collapse

DELIMITER =

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

RS = "\n--EOF--\n"
Data_XPath =

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

''

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

Constructor Details

#initialize(x) ⇒ MaXML

Returns a new instance of MaXML.



62
63
64
65
66
67
68
69
70
71
72
73
74
 
# 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

Instance Attribute Details

#elem ⇒ Object (readonly)

Returns the value of attribute elem.



75
76
77
 
# File 'lib/bio/db/fantom.rb', line 75

def elem
  @elem
end

Instance Method Details

#entry_id ⇒ Object 



90
91
92
93
94
95
 
# 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) ⇒ Object 



81
82
83
84
85
86
87
88
 
# 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 ⇒ Object 



77
78
79
 
# File 'lib/bio/db/fantom.rb', line 77

def to_s
  @elem.to_s
end