# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 56
  def initialize( p_left = nil, p_right = nil, c_left = nil, c_right = nil )
    raise ArgumentError if p_left == nil and c_left == nil
    raise ArgumentError if p_right == nil and c_right == nil
    (raise ArgumentError unless p_left <= p_right) unless p_left == nil or p_right == nil
    (raise ArgumentError unless c_left <= c_right) unless c_left == nil or c_right == nil

    @p_left, @p_right, @c_left, @c_right = p_left, p_right, c_left, c_right
    @left = [p_left, c_left].compact.sort.first
    @right = [p_right, c_right].compact.sort.last
    @size = (@right - @left) + 1 unless @left == nil or @right == nil
    @cut_ranges = CutRanges.new
    @__fragments_current = false
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 86
  def add_cut_range( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil )
    @__fragments_current = false
    if p_cut_left.kind_of? CutRange # shortcut
      @cut_ranges << p_cut_left
    else
      [p_cut_left, p_cut_right, c_cut_left, c_cut_right].each { |n| (raise IndexError unless n >= @left and n <= @right) unless n == nil }
      @cut_ranges << VerticalCutRange.new( p_cut_left, p_cut_right, c_cut_left, c_cut_right )
    end
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 102
  def add_cut_ranges(*cut_ranges)
    cut_ranges.flatten.each do |cut_range|
      raise TypeError, "Not of type CutRange" unless cut_range.kind_of? CutRange
      self.add_cut_range( cut_range )
    end
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 116
  def add_horizontal_cut_range( left, right=left )
    @__fragments_current = false
    @cut_ranges << HorizontalCutRange.new( left, right )
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 158
  def fragments
    return @__fragments if @__fragments_current == true
    @__fragments_current = true
    
    num_txt = '0123456789'
    num_txt_repeat = (num_txt * ( @size / num_txt.size.to_f ).ceil)[0..@size-1]
    fragments = Fragments.new(num_txt_repeat, num_txt_repeat)

    cc = Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts.new(@size)
    cc.add_cuts_from_cut_ranges(@cut_ranges)
    cc.remove_incomplete_cuts
    
    create_bins(cc).sort.each { |k, bin| fragments << Fragment.new( bin.p, bin.c ) }
    @__fragments = fragments
    return fragments
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 195
  def create_bins(cc)
    p_cut = cc.vc_primary
    c_cut = cc.vc_complement
    h_cut = cc.hc_between_strands
    
    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
  
      unique_id = 0
    else
      p_cut.unshift(-1) unless p_cut.include?(-1)
      c_cut.unshift(-1) unless c_cut.include?(-1)
      unique_id = -1
    end

    p_bin_id = c_bin_id = unique_id
    bins = {}
    setup_new_bin(bins, unique_id)

    -1.upto(@size-1) do |idx| # NOTE - circular, for the future - should '-1' be replace with 'unique_id'?
      
      # if bin_ids are out of sync but the strands are attached
      if (p_bin_id != c_bin_id) and !h_cut.include?(idx)
        min_id, max_id = [p_bin_id, c_bin_id].sort
        bins.delete(max_id)
        p_bin_id = c_bin_id = min_id
      end

      bins[ p_bin_id ].p << idx
      bins[ c_bin_id ].c << idx
      
      if p_cut.include? idx
        p_bin_id = (unique_id += 1)
        setup_new_bin(bins, p_bin_id)
      end

      if c_cut.include? idx             # repetition
        c_bin_id = (unique_id += 1)     # repetition
        setup_new_bin(bins, c_bin_id)   # repetition
      end                               # repetition
       
    end
  
    # Bin "-1" is an easy way to indicate the start of a strand just in case
    # there is a horizontal cut at position 0
    bins.delete(-1) unless @circular
    bins
  end

# File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 248
  def setup_new_bin(bins, bin_id)
    bins[ bin_id ] = Bin.new
    bins[ bin_id ].p = []
    bins[ bin_id ].c = []
  end