class Bio::Big::FrameCodonHelpers::FrameCodonSequence

Attributes

codons[R]
pos[R]

Public Class Methods

new(seq, pos=0) click to toggle source
# File lib/bigbio/db/emitters/orf_emitter.rb, line 76
def initialize seq, pos=0
  if seq.kind_of?(String)
    @codons = seq.upcase.scan(/(\w\w\w)/).flatten
  else
    @codons = seq
  end
  @pos = pos
end

Public Instance Methods

[](index) click to toggle source
# File lib/bigbio/db/emitters/orf_emitter.rb, line 90
def [] index
  @codons[index]
end
each() { |c| ... } click to toggle source
# File lib/bigbio/db/emitters/orf_emitter.rb, line 101
def each
  @codons.each { | c| yield c }
end
rpos() click to toggle source
# File lib/bigbio/db/emitters/orf_emitter.rb, line 87
def rpos
  pos + size
end
shift() click to toggle source
# File lib/bigbio/db/emitters/orf_emitter.rb, line 93
def shift
  list = @codons
  list.shift
  FrameCodonSequence.new(list,@pos+1)
end
size() click to toggle source
# File lib/bigbio/db/emitters/orf_emitter.rb, line 84
def size
  @codons.size
end
to_seq() click to toggle source
# File lib/bigbio/db/emitters/orf_emitter.rb, line 98
def to_seq
  @codons.join
end