[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range sequence_range.rb, 1.3, 1.4

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range
In directory dev.open-bio.org:/tmp/cvs-serv18362/restriction_enzyme/range

Modified Files:
	sequence_range.rb 
Log Message:


Index: sequence_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** sequence_range.rb	6 Jan 2007 05:35:04 -0000	1.3
--- sequence_range.rb	6 Jan 2007 05:52:52 -0000	1.4
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/range/sequence_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restrction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 24,43 ****
  class Range
  #
! # bio/util/restrction_enzyme/range/sequence_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
  # License::   Distributes under the same terms as Ruby
  class SequenceRange
  
!   attr_reader :p_left, :p_right
!   attr_reader :c_left, :c_right
  
!   attr_reader :left, :right
    attr_reader :size
    attr_reader :cut_ranges
  
    def initialize( p_left = nil, p_right = nil, c_left = nil, c_right = nil )
-     @__fragments_current = false
      raise ArgumentError if p_left == nil and c_left == nil
      raise ArgumentError if p_right == nil and c_right == nil
--- 24,64 ----
  class Range
  #
! # bio/util/restrction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
  # License::   Distributes under the same terms as Ruby
+ #
+ # A defined range over a nucleotide sequence.
+ #
+ # This class accomadates having cuts defined on a sequence and returning the
+ # fragments made by those cuts.
  class SequenceRange
  
!   # Left-most index of primary strand
!   attr_reader :p_left
!   
!   # Right-most index of primary strand
!   attr_reader :p_right
!   
!   # Left-most index of complementary strand
!   attr_reader :c_left
!   
!   # Right-most index of complementary strand
!   attr_reader :c_right
  
!   # Left-most index of DNA sequence
!   attr_reader :left
!   
!   # Right-most index of DNA sequence
!   attr_reader :right
!   
!   # Size of DNA sequence
    attr_reader :size
+   
+   # CutRanges in this SequenceRange
    attr_reader :cut_ranges
  
    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
***************
*** 45,68 ****
      (raise ArgumentError unless c_left <= c_right) unless c_left == nil or c_right == nil
  
!     @p_left  = p_left
!     @p_right = p_right
!     @c_left  = c_left
!     @c_right = c_right
! 
!     tmp = [p_left, c_left]
!     tmp.delete(nil)
!     @left = tmp.sort.first
! 
!     tmp = [p_right, c_right]
!     tmp.delete(nil)
!     @right = tmp.sort.last
! 
      @size = (@right - @left) + 1 unless @left == nil or @right == nil
- 
      @cut_ranges = CutRanges.new
    end
  
    # Cut occurs immediately after the index supplied.
!   # For example, a cut at '0' would mean a cut occurs between 0 and 1.
    def add_cut_range( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil )
      @__fragments_current = false
--- 66,79 ----
      (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
  
    # Cut occurs immediately after the index supplied.
!   # For example, a cut at '0' would mean a cut occurs between bases 0 and 1.
    def add_cut_range( p_cut_left=nil, p_cut_right=nil, c_cut_left=nil, c_cut_right=nil )
      @__fragments_current = false
***************
*** 81,86 ****
  
    def add_cut_ranges(*cut_ranges)
!     cut_ranges.flatten!
!     cut_ranges.each do |cut_range|
        raise TypeError, "Not of type CutRange" unless cut_range.kind_of? CutRange
        self.add_cut_range( cut_range )
--- 92,96 ----
  
    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 )
***************
*** 93,98 ****
--- 103,137 ----
    end
    
+   # 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]>}
    Bin = Struct.new(:c, :p)
  
+   # 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
    def fragments
      return @__fragments if @__fragments_current == true