Class: Bio::RestrictionEnzyme::Range::SequenceRange

Inherits:

Object

• Object
• Bio::RestrictionEnzyme::Range::SequenceRange

show all

Defined in:

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

Overview

Defined Under Namespace

Classes: Bin, CalculatedCuts, Fragment, Fragments

Instance Attribute Summary (collapse)

• - (Object) c_left readonly

  Left-most index of complementary strand.

• - (Object) c_right readonly

  Right-most index of complementary strand.

• - (Object) cut_ranges readonly

  CutRanges in this SequenceRange.

• - (Object) left readonly

  Left-most index of DNA sequence.

• - (Object) p_left readonly

  Left-most index of primary strand.

• - (Object) p_right readonly

  Right-most index of primary strand.

• - (Object) right readonly

  Right-most index of DNA sequence.

• - (Object) size readonly

  Size of DNA sequence.

Instance Method Summary (collapse)

• - (Object) add_cut_range(p_cut_left = nil, p_cut_right = nil, c_cut_left = nil, c_cut_right = nil)

  If the first object is HorizontalCutRange or VerticalCutRange, that is added to the SequenceRange.

• - (Object) add_cut_ranges(*cut_ranges)

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

• - (Object) add_horizontal_cut_range(left, right = left)

  Builds a HorizontalCutRange object and adds it to the SequenceRange.

• - (Object) fragments

  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.

• - (SequenceRange) initialize(p_left = nil, p_right = nil, c_left = nil, c_right = nil) constructor

  A new instance of SequenceRange.

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# 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

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 39

def c_left
  @c_left
end

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 42

def c_right
  @c_right
end

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 54

def cut_ranges
  @cut_ranges
end

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 45

def left
  @left
end

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 33

def p_left
  @p_left
end

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 36

def p_right
  @p_right
end

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 48

def right
  @right
end

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# File 'lib/bio/util/restriction_enzyme/range/sequence_range.rb', line 51

def size
  @size
end

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# 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

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# 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

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# 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

[#<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]>]

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# 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.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