class Bio::FANTOM::MaXML::Cluster

Constants

Data_XPath

(MaXML cluster) fantom2.gsc.riken.go.jp/fantom/2.1/allclust.sep.xml.gz

Public Instance Methods

representative_annotations() click to toggle source
# File lib/bio/db/fantom.rb, line 145
def representative_annotations
  e = representative_sequence
  e ? e.annotations : nil
end
representative_clone()
representative_cloneid() click to toggle source
# File lib/bio/db/fantom.rb, line 150
def representative_cloneid
  e = representative_sequence
  e ? e.cloneid : nil
end
representative_seqid() click to toggle source
# File lib/bio/db/fantom.rb, line 116
def representative_seqid
  unless defined?(@representative_seqid)
    @representative_seqid =
      gsub_entities(@elem.text('representative-seqid'))
  end
  @representative_seqid
end
representative_sequence() click to toggle source
# File lib/bio/db/fantom.rb, line 135
def representative_sequence
  unless defined?(@representative_sequence)
    rid = representative_seqid
    @representative_sequence =
      rid ? sequences[representative_seqid] : nil
  end
  @representative_sequence
end
Also aliased as: representative_clone
sequence(idstr = nil) click to toggle source
# File lib/bio/db/fantom.rb, line 131
def sequence(idstr = nil)
  idstr ? sequences[idstr] : representative_sequence
end
sequences() click to toggle source
# File lib/bio/db/fantom.rb, line 124
def sequences
  unless defined?(@sequences)
    @sequences = MaXML::Sequences.new(@elem)
  end
  @sequences
end