class Orf

Attributes

frame[RW]
more_than_one_frame[RW]
score[RW]
seq[RW]
status[RW]
stop_codon[RW]
t_end[RW]
t_start[RW]
type[RW]

Public Class Methods

new(orf_seq, t_start, t_end, frame, stop_codon, type) click to toggle source
# File lib/full_lengther_next/orf.rb, line 6
def initialize(orf_seq, t_start, t_end, frame, stop_codon, type)
        @seq=orf_seq
        @t_start=t_start
        @t_end=t_end
        @frame=frame
        @stop_codon=stop_codon
        @type=type # :N_terminus,:C_terminus,:Complete,:Internal,:Putative_Complete,:Putative_N_terminus
        @status = :unknown # :unknown,:putative_coding,:coding
        @score = 0
        @more_than_one_frame = false
end

Public Instance Methods

overlaps?(other_orf) click to toggle source
# File lib/full_lengther_next/orf.rb, line 18
def overlaps?(other_orf)
        overlap_status = false
        i1 = self.t_start
        i2 = other_orf.t_start
        e1 = self.t_end
        e2 = other_orf.t_end
        
        if (e1 > i2) && (e1 < e2)
                overlap_status = true
        end
        
        return overlap_status
end