Bio::EMBL

# File lib/bio/db/embl/embl.rb, line 327
def cc
  get('CC').to_s.gsub(/^CC   /, '')
end

# File lib/bio/db/embl/embl.rb, line 130
def data_class
  id_line('DATA_CLASS')
end

# File lib/bio/db/embl/embl.rb, line 387
def date_created
  parse_date(self.dt['created'])
end

# File lib/bio/db/embl/embl.rb, line 382
def date_modified
  parse_date(self.dt['updated'])
end

# File lib/bio/db/embl/embl.rb, line 437
def dblinks
  get('DR').split(/\n/).collect { |x|
    Bio::Sequence::DBLink.parse_embl_DR_line(x)
  }
end

# File lib/bio/db/embl/embl.rb, line 140
def division
  id_line('DIVISION')
end

# File lib/bio/db/embl/embl.rb, line 182
def dt(key=nil)
  unless @data['DT']
    tmp = Hash.new
    dt_line = self.get('DT').split(/\n/)
    tmp['created'] = dt_line[0].sub(/\w{2}   /,'').strip
    tmp['updated'] = dt_line[1].sub(/\w{2}   /,'').strip
    @data['DT'] = tmp
  end
  if key
    @data['DT'][key]
  else
    @data['DT']
  end
end

# File lib/bio/db/embl/embl.rb, line 306
def each_cds
  ft.each do |cds_feature|
    if cds_feature.feature == 'CDS'
      yield cds_feature
    end
  end
end

# File lib/bio/db/embl/embl.rb, line 315
def each_gene
  ft.each do |gene_feature|
    if gene_feature.feature == 'gene'
      yield gene_feature
    end
  end
end

# File lib/bio/db/embl/embl.rb, line 117
def entry
  id_line('ENTRY_NAME')
end

# File lib/bio/db/embl/embl.rb, line 402
def entry_version
  parse_release_version(self.dt['updated'])[1]
end

# File lib/bio/db/embl/embl.rb, line 251
def fh
  fetch('FH')
end

# File lib/bio/db/embl/embl.rb, line 262
def ft
  unless @data['FT']
    ary = Array.new
    in_quote = false
    @orig['FT'].each_line do |line|
      next if line =~ /^FEATURES/

      head = line[0,20].strip  # feature key (source, CDS, ...)
      body = line[20,60].chomp # feature value (position, /qualifier=)
      if line =~ /^FT {3}(\S+)/
        ary.push([ $1, body ]) # [ feature, position, /q="data", ... ]
      elsif body =~ /^ \// and not in_quote
        ary.last.push(body)    # /q="data..., /q=data, /q

        if body =~ /=" / and body !~ /"$/
          in_quote = true
        end

      else
        ary.last.last << body # ...data..., ...data..."

        if body =~ /"$/
          in_quote = false
        end
      end
    end

    ary.map! do |subary|
      parse_qualifiers(subary)
    end

    @data['FT'] = ary.extend(Bio::Features::BackwardCompatibility)
  end
  if block_given?
    @data['FT'].each do |feature|
      yield feature
    end
  else
    @data['FT']
  end
end

# File lib/bio/db/embl/embl.rb, line 89
def id_line(key=nil)
  unless @data['ID']
    tmp = Hash.new
    idline = fetch('ID').split(/; +/)         
    tmp['ENTRY_NAME'], tmp['DATA_CLASS'] = idline.shift.split(/ +/)
    if idline.first =~ /^SV/
      tmp['SEQUENCE_VERSION'] = idline.shift.split(' ').last
      tmp['TOPOLOGY'] = idline.shift
      tmp['MOLECULE_TYPE'] = idline.shift
      tmp['DATA_CLASS'] = idline.shift
    else
      tmp['MOLECULE_TYPE'] = idline.shift
    end
    tmp['DIVISION'] = idline.shift
    tmp['SEQUENCE_LENGTH'] = idline.shift.strip.split(' ').first.to_i

    @data['ID'] = tmp
  end
  
  if key
    @data['ID'][key]
  else
    @data['ID']
  end
end

# File lib/bio/db/embl/embl.rb, line 125
def molecule
  id_line('MOLECULE_TYPE')
end

# File lib/bio/db/embl/embl.rb, line 397
def release_created
  parse_release_version(self.dt['created'])[0]
end

# File lib/bio/db/embl/embl.rb, line 392
def release_modified
  parse_release_version(self.dt['updated'])[0]
end

# File lib/bio/db/embl/embl.rb, line 371
def seq
  Bio::Sequence::NA.new( fetch('').gsub(/ /,'').gsub(/\d+/,'') )
end

# File lib/bio/db/embl/embl.rb, line 146
def sequence_length
  id_line('SEQUENCE_LENGTH')
end

# File lib/bio/db/embl/embl.rb, line 444
def species
  self.fetch('OS')
end

# File lib/bio/db/embl/embl.rb, line 348
def sq(base = nil)
  unless @data['SQ']
    fetch('SQ') =~               /(\d+) BP\; (\d+) A; (\d+) C; (\d+) G; (\d+) T; (\d+) other;/
    @data['SQ'] = {'ntlen' => $1.to_i, 'other' => $6.to_i,
                   'a' => $2.to_i, 'c' => $3.to_i , 'g' => $4.to_i, 't' => $5.to_i}
  else
    @data['SQ']
  end

  if base
    @data['SQ'][base.downcase]
  else
    @data['SQ']
  end
end

# File lib/bio/db/embl/embl.rb, line 162
def sv
  if (v = field_fetch('SV').sub(/;/,'')) == ""
    [id_line['ENTRY_NAME'], id_line['SEQUENCE_VERSION']].join('.') 
  else
    v
  end  
end

# File lib/bio/db/embl/embl.rb, line 456
def to_biosequence
  Bio::Sequence.adapter(self, Bio::Sequence::Adapter::EMBL)
end

# File lib/bio/db/embl/embl.rb, line 134
def topology
  id_line('TOPOLOGY')
end

# File lib/bio/db/embl/embl.rb, line 169
def version
  (sv.split(".")[1] || id_line['SEQUENCE_VERSION']).to_i
end