# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 58
  def initialize(size=nil, circular=false)
    @size = size
    @circular = circular
    @vc_primary = []
    @vc_complement = []
    @hc_between_strands = []
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 73
  def add_cuts_from_cut_ranges(cut_ranges)
    @strands_for_display_current = false

    cut_ranges.each do |cut_range|
      @vc_primary += [cut_range.p_cut_left, cut_range.p_cut_right]
      @vc_complement += [cut_range.c_cut_left, cut_range.c_cut_right]

      # Add horizontal cut ranges.  This may happen from cuts made inbetween a
      # VerticalCutRange or may be specifically defined by a HorizontalCutRange.
      if cut_range.class == VerticalCutRange
        ( cut_range.min + 1 ).upto( cut_range.max ){|i| @hc_between_strands << i} if cut_range.min < cut_range.max
      elsif cut_range.class == HorizontalCutRange
        ( cut_range.hcuts.first ).upto( cut_range.hcuts.last ){|i| @hc_between_strands << i}
      end
    end
    clean_all
    #return
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 120
  def remove_incomplete_cuts(size=nil)
    @strands_for_display_current = false
    @size = size if size
    raise IndexError, "Size of the strand must be provided here or during initalization." if !@size.kind_of?(Fixnum) and not @circular

    vcuts = (@vc_primary + @vc_complement).uniq.sort
    hcuts = @hc_between_strands
    last_index = @size - 1
    good_hcuts = []
    potential_hcuts = []

    if @circular
    # NOTE
    # if it's circular we should start at the beginning of a cut for orientation,
    # scan for it, hack off the first set of hcuts and move them to the back
    else
      vcuts.unshift(-1) unless vcuts.include?(-1)
      vcuts.push(last_index) unless vcuts.include?(last_index)
    end

    hcuts.each do |hcut|
      raise IndexError if hcut < -1 or hcut > last_index
      # skipped a nucleotide
      potential_hcuts.clear if !potential_hcuts.empty? and (hcut - potential_hcuts.last).abs > 1

      if potential_hcuts.empty?
        if vcuts.include?( hcut ) and vcuts.include?( hcut - 1 )
          good_hcuts += [hcut]
        elsif vcuts.include?( hcut - 1 )
          potential_hcuts << hcut
        end
      else
        if vcuts.include?( hcut )
          good_hcuts += potential_hcuts + [hcut]
          potential_hcuts.clear
        else
          potential_hcuts << hcut
        end
      end
    end

    check_vc = lambda do |vertical_cuts, opposing_vcuts|
      # opposing_vcuts is here only to check for blunt cuts, so there shouldn't
      # be any out-of-order problems with this
      good_vc = []
      vertical_cuts.each { |vc| good_vc << vc if good_hcuts.include?( vc ) or good_hcuts.include?( vc + 1 ) or opposing_vcuts.include?( vc ) }
      good_vc
    end

    @vc_primary = check_vc.call(@vc_primary, @vc_complement)
    @vc_complement = check_vc.call(@vc_complement, @vc_primary)
    @hc_between_strands = good_hcuts

    clean_all
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 187
  def strands_for_display(str1 = nil, str2 = nil, vcp=nil, vcc=nil, hc=nil)
    return @strands_for_display if @strands_for_display_current
    vcs = '|'   # Vertical cut symbol
    hcs = '-'   # Horizontal cut symbol
    vhcs = '+'  # Intersection of vertical and horizontal cut symbol
      
    num_txt_repeat = lambda { num_txt = '0123456789'; (num_txt * ( @size / num_txt.size.to_f ).ceil)[0..@size-1] }
    (str1 == nil) ? a = num_txt_repeat.call : a = str1.dup
    (str2 == nil) ? b = num_txt_repeat.call : b = str2.dup

    vcp = @vc_primary if vcp==nil
    vcc = @vc_complement if vcc==nil
    hc = @hc_between_strands if hc==nil

    vcuts = (vcp + vcc).uniq.sort

    vcp.reverse.each { |c| a.insert(c+1, vcs) }
    vcc.reverse.each { |c| b.insert(c+1, vcs) }

    between = ' ' * @size
    hc.each {|hcut| between[hcut,1] = hcs }

    s_a = add_spacing(a, vcs)
    s_b = add_spacing(b, vcs)
    s_bet = add_spacing(between)

    # NOTE watch this for circular
    i = 0
    0.upto( s_a.size-1 ) do
      if (s_a[i,1] == vcs) or (s_b[i,1] == vcs)
        s_bet[i] = vhcs 
      elsif i != 0 and s_bet[i-1,1] == hcs and s_bet[i+1,1] == hcs
        s_bet[i] = hcs 
      end
      i+=1
    end

    @strands_for_display_current = true
    @strands_for_display = [s_a, s_bet, s_b]
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 234
  def clean_all
    [@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! }
  end