Class: Bio::Big::FrameCodonHelpers::FrameCodonSequence

Inherits:
Object
  • Object
show all
Includes:
TrackSequenceTrait, Enumerable
Defined in:
lib/bigbio/db/emitters/orf_emitter.rb

Instance Attribute Summary collapse

Attributes included from TrackSequenceTrait

#track_ntseq_pos

Instance Method Summary collapse

Methods included from TrackSequenceTrait

update_reversed_sequence_pos, update_sequence_pos

Constructor Details

#initialize(seq, pos = 0) ⇒ FrameCodonSequence

Returns a new instance of FrameCodonSequence.



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# 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

Instance Attribute Details

#codons ⇒ Object (readonly)

Returns the value of attribute codons.



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 75

def codons
  @codons
end

#pos ⇒ Object (readonly)

codon position in short parent sequence



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 74

def pos
  @pos
end

Instance Method Details

#[](index) ⇒ Object 



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 90

def [] index
  @codons[index]
end

#each ⇒ Object 



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 101

def each
  @codons.each { | c| yield c }
end

#rpos ⇒ Object 



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 87

def rpos
  pos + size
end

#shift ⇒ Object 



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 93

def shift
  list = @codons
  list.shift
  FrameCodonSequence.new(list,@pos+1)
end

#size ⇒ Object 



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 84

def size
  @codons.size
end

#to_seq ⇒ Object 



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# File 'lib/bigbio/db/emitters/orf_emitter.rb', line 98

def to_seq
  @codons.join
end