### Home Classes Methods

### In Files

- lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb

### Parent

Object

### Methods

- ::new
- #add_cuts_from_cut_ranges
- #clean_all
- #hc_between_strands
- #hc_between_strands_as_original_class
- #remove_incomplete_cuts
- #strands_for_display
- #vc_complement
- #vc_complement_as_original_class
- #vc_primary
- #vc_primary_as_original_class

### Included Modules

- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::StringFormatting

### Files

- KNOWN_ISSUES.rdoc
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

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No matching classes.

# Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts

cc = CalculatedCuts.new(@size) cc.add_cuts_from_cut_ranges(@cut_ranges) cc.remove_incomplete_cuts

    1 2 3 4 5 6 7
    G A|T T A C A
       +-----+
    C T A A T|G T
    1 2 3 4 5 6 7

Primary cut = 2 Complement cut = 5 Horizontal cuts = 3, 4, 5

### Attributes

circular[RW]

Set to `true` if the fragment CalculatedCuts is working on is circular

size[R]

Size of the sequence being digested.

strands_for_display_current[R]

If `false` the strands_for_display method needs to be called to update the contents of @strands_for_display. Becomes out of date whenever add_cuts_from_cut_ranges is called.

### Public Class Methods

new(size=nil, circular=false) click to toggle source

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 86
    def initialize(size=nil, circular=false)
      @size = size
      @circular = circular
      @vc_primary = SortedNumArray[]
      @vc_complement = SortedNumArray[]
      @hc_between_strands = SortedNumArray[]
    end

### Public Instance Methods

add_cuts_from_cut_ranges(cut_ranges) click to toggle source

Accepts an `Array` of CutRange type objects and applies them to @vc_complement, @vc_primary, and @hc_between_strands.

Arguments

- `cut_ranges`: An `Array` of HorizontalCutRange or VerticalCutRange objects

Returns | nothing

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 101
    def add_cuts_from_cut_ranges(cut_ranges)
      @strands_for_display_current = false

      @vc_primary = @vc_primary.dup
      @vc_complement = @vc_complement.dup

      cut_ranges.each do |cut_range|
        @vc_primary.concat [cut_range.p_cut_left, cut_range.p_cut_right]
        @vc_complement.concat [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

hc_between_strands() click to toggle source

`Array` of horizontal cuts between strands in 0-based index notation

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 60
    def hc_between_strands
      #$stderr.puts caller[0].inspect ###DEBUG
      @hc_between_strands.to_a
    end

hc_between_strands_as_original_class() click to toggle source

Returns the same contents as hc_between_strands, but returns original data structure used in the class.

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 67
    def hc_between_strands_as_original_class
      @hc_between_strands
    end

remove_incomplete_cuts(size=nil) click to toggle source

There may be incomplete cuts made, this method removes the cuts that don't create sub-sequences for easier processing.

For example, stray horizontal cuts that do not end with a left and right separation:

    G A T T A C A
       +--  ---
    C T|A A T G T

Or stray vertical cuts:

    G A T T A C A
       +--   +
    C T|A A T|G T

However note that for non-circular sequences this would be a successful cut which would result in a floating 'GT' sub-sequence:

    G A T T A C A
             +---
    C T A A T|G T

Blunt cuts are also complete cuts.

Arguments

- `size`: (optional) Size of the sequence being digested. Defined here or during initalization of CalculatedCuts.

Returns | nothing

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 151
    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
      hcuts = @hc_between_strands
      last_index = @size - 1
      good_hcuts = SortedNumArray[]
      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.concat(potential_hcuts)
            good_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 = SortedNumArray[]
        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

strands_for_display(str1 = nil, str2 = nil, vcp=nil, vcc=nil, hc=nil) click to toggle source

Sets @strands_for_display_current to `true` and populates @strands_for_display.

Arguments

- `str1`: (optional) For displaying a primary strand. If `nil` a numbered sequence will be used in place.

- `str2`: (optional) For displaying a complementary strand. If `nil` a numbered sequence will be used in place.

- `vcp`: (optional) An array of vertical cut locations on the primary strand. If `nil` the contents of @vc_primary is used.

- `vcc`: (optional) An array of vertical cut locations on the complementary strand. If `nil` the contents of @vc_complementary is used.

- `hc`: (optional) An array of horizontal cut locations between strands. If `nil` the contents of @hc_between_strands is used.

Returns | `Array` An array with the primary strand with vertical cuts, the horizontal cuts, and the complementary strand with vertical cuts.

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 219
    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.div(num_txt.size) + 1))[0..@size-1] }
      (str1 == nil) ? a = num_txt_repeat.call : a = str1.dup
      (str2 == nil) ? b = num_txt_repeat.call : b = str2.dup

      if vcp and !vcp.is_a?(SortedNumArray) then
        vcp = SortedNumArray.new.concat(vcp)
      end
      if vcc and !vcc.is_a?(SortedNumArray) then
        vcc = SortedNumArray.new.concat(vcc)
      end
      if hc and !hc.is_a?(SortedNumArray) then
        hc = SortedNumArray.new.concat(hc)
      end

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

      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

vc_complement() click to toggle source

`Array` of vertical cuts on the complementary strand in 0-based index notation

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 48
    def vc_complement
      #$stderr.puts caller[0].inspect ###DEBUG
      @vc_complement.to_a
    end

vc_complement_as_original_class() click to toggle source

Returns the same contents as vc_complement, but returns original data structure used in the class.

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 55
    def vc_complement_as_original_class
      @vc_complement
    end

vc_primary() click to toggle source

`Array` of vertical cuts on the primary strand in 0-based index notation

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 36
    def vc_primary
      #$stderr.puts caller[0].inspect ###DEBUG
      @vc_primary.to_a
    end

vc_primary_as_original_class() click to toggle source

Returns the same contents as vc_primary, but returns original data structure used in the class.

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 43
    def vc_primary_as_original_class
      @vc_primary
    end

### Protected Instance Methods

clean_all() click to toggle source

remove nil values, remove duplicate values, and sort @vc_primary, @vc_complement, and @hc_between_strands

    # File lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb, line 274
    def clean_all
      [@vc_primary, @vc_complement, @hc_between_strands].collect { |a| a.delete(nil); a.uniq!; a.sort! }
    end

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