### Home Classes Methods

### In Files

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

### Parent

Object

### Namespace

- CLASS Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- CLASS Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- CLASS Bio::RestrictionEnzyme::Range::SequenceRange::Fragments

### Methods

- ::new
- #add_cut_range
- #add_cut_ranges
- #add_horizontal_cut_range
- #create_bins
- #fragments
- #setup_new_bin

### 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

A defined range over a nucleotide sequence.

This class accomadates having cuts defined on a sequence and returning the fragments made by those cuts.

### Constants

Bin

  A Bio::RestrictionEnzyme::Range::SequenceRange::Bin holds an `Array` of indexes for the primary and complement strands (`p` and `c` accessors).

  Example hash with Bin values:

      {0=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[0, 1], p=[0]>,
       2=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[], p=[1, 2]>,
       3=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[2, 3], p=[]>,
       4=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[4, 5], p=[3, 4, 5]>}

  Note that the bin cannot be easily stored as a range since there may be nucleotides excised in the middle of a range.

  TODO: Perhaps store the bins as one-or-many ranges since missing nucleotides due to enzyme cutting is a special case.

### Attributes

c_left[R]

Left-most index of complementary strand

c_right[R]

Right-most index of complementary strand

cut_ranges[R]

CutRanges in this SequenceRange

left[R]

Left-most index of DNA sequence

p_left[R]

Left-most index of primary strand

p_right[R]

Right-most index of primary strand

right[R]

Right-most index of DNA sequence

size[R]

Size of DNA sequence

### Public Class Methods

new( p_left = nil, p_right = nil, c_left = nil, c_right = nil ) click to toggle source

    # File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 55
    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

### Public Instance Methods

add_cut_range( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil ) click to toggle source

If the first object is HorizontalCutRange or VerticalCutRange, that is added to the SequenceRange. Otherwise this method builds a VerticalCutRange object and adds it to the SequenceRange.

Note: Cut occurs immediately after the index supplied. For example, a cut at '0' would mean a cut occurs between bases 0 and 1.

Arguments

- `p_cut_left`: (optional) Left-most cut on the primary strand or a CutRange object. `nil` to skip

- `p_cut_right`: (optional) Right-most cut on the primary strand. `nil` to skip

- `c_cut_left`: (optional) Left-most cut on the complementary strand. `nil` to skip

- `c_cut_right`: (optional) Right-most cut on the complementary strand. `nil` to skip

Returns | nothing

    # File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 85
    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

add_cut_ranges(*cut_ranges) click to toggle source

Add a series of CutRange objects (HorizontalCutRange or VerticalCutRange).

Arguments

- `cut_ranges`: A series of CutRange objects

Returns | nothing

    # File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 101
    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

add_horizontal_cut_range( left, right=left ) click to toggle source

Builds a HorizontalCutRange object and adds it to the SequenceRange.

Arguments

- `left`: Left-most cut

- `right`: (optional) Right side - by default this equals the left side, default is recommended.

Returns | nothing

    # File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 115
    def add_horizontal_cut_range( left, right=left )
      @__fragments_current = false
      @cut_ranges << HorizontalCutRange.new( left, right )
    end

fragments() click to toggle source

Calculates the fragments over this sequence range as defined after using the methods add_cut_range, add_cut_ranges, and/or add_horizontal_cut_range

Example return value:

    [#<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277bdc
      @complement_bin=[0, 1],
      @primary_bin=[0]>,
     #<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277bc8
      @complement_bin=[],
      @primary_bin=[1, 2]>,
     #<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277bb4
      @complement_bin=[2, 3],
      @primary_bin=[]>,
     #<Bio::RestrictionEnzyme::Range::SequenceRange::Fragment:0x277ba0
      @complement_bin=[4, 5],
      @primary_bin=[3, 4, 5]>]

Arguments

- none

Returns | Bio::RestrictionEnzyme::Range::SequenceRange::Fragments

    # File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 157
    def fragments
      return @__fragments if @__fragments_current == true
      @__fragments_current = true

      num_txt = '0123456789'
      num_txt_repeat = (num_txt * ( @size.div(num_txt.size) + 1))[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

### Protected Instance Methods

create_bins(cc) click to toggle source

Example:

    cc = Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts.new(@size)
    cc.add_cuts_from_cut_ranges(@cut_ranges)
    cc.remove_incomplete_cuts
    bins = create_bins(cc)

Example return value:

    {0=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[0, 1], p=[0]>,
     2=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[], p=[1, 2]>,
     3=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[2, 3], p=[]>,
     4=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[4, 5], p=[3, 4, 5]>}

Arguments

- `cc`: Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts

Returns | `Hash` Keys are unique, values are Bio::RestrictionEnzyme::Range::SequenceRange::Bin objects filled with indexes of the sequence locations they represent.

    # File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 194
    def create_bins(cc)
      p_cut = cc.vc_primary_as_original_class
      c_cut = cc.vc_complement_as_original_class
      h_cut = cc.hc_between_strands_as_original_class

      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

setup_new_bin(bins, bin_id) click to toggle source

Modifies bins in place by creating a new element with key bin_id and initializing the bin.

    # File lib/bio/util/restriction_enzyme/range/sequence_range.rb, line 247
    def setup_new_bin(bins, bin_id)
      bins[ bin_id ] = Bin.new
      bins[ bin_id ].p = DenseIntArray[] #could be replaced by SortedNumArray[]
      bins[ bin_id ].c = DenseIntArray[] #could be replaced by SortedNumArray[]
    end

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