[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand cut_locations_in_enzyme_notation.rb, 1.2, 1.3

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand
In directory dev.open-bio.org:/tmp/cvs-serv728/lib/bio/util/restriction_enzyme/single_strand

Modified Files:
	cut_locations_in_enzyme_notation.rb 
Log Message:


Index: cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** cut_locations_in_enzyme_notation.rb	31 Dec 2006 21:50:31 -0000	1.2
--- cut_locations_in_enzyme_notation.rb	1 Jan 2007 03:36:37 -0000	1.3
***************
*** 33,36 ****
--- 33,42 ----
  # 
  # Enzyme index notation:: 1.._n_, value before 1 is -1
+ #
+ # example:: [-3][-2][-1][1][2][3][4][5]
+ #
+ # Negative values are used to indicate when a cut may occur at a specified
+ # distance before the sequence begins.  This would be padded with 'n'
+ # nucleotides to represent wildcards.
  # 
  # Notes:
***************
*** 38,43 ****
  # * +nil+ is not allowed here as it has no meaning
  # * +nil+ values are kept track of in DoubleStranded::CutLocations as they
! #   need a reference point on the correlating strand.  +nil+ represents no
! #   cut or a partial digestion.
  # 
  class CutLocationsInEnzymeNotation < Array
--- 44,50 ----
  # * +nil+ is not allowed here as it has no meaning
  # * +nil+ values are kept track of in DoubleStranded::CutLocations as they
! #   need a reference point on the correlating strand.  In 
! #   DoubleStranded::CutLocations +nil+ represents no cut or a partial 
! #   digestion.
  # 
  class CutLocationsInEnzymeNotation < Array
***************
*** 45,55 ****
    extend CutSymbol
  
!   attr_reader :min, :max
  
    def initialize(*a)
      a.flatten! # in case an array was passed as an argument
  
      if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol
!     # Initialize with a cut symbol pattern such as 'n^ng^arraxt^n'
        s = a[0]
        a = []
--- 52,77 ----
    extend CutSymbol
  
!   # First cut, in enzyme-index notation
!   attr_reader :min
!   
!   # Last cut, in enzyme-index notation
!   attr_reader :max
  
+   # Constructor for CutLocationsInEnzymeNotation
+   #
+   # ---
+   # *Arguments*
+   # * +a+: Locations of cuts represented as a string with cuts or an array of values
+   # Examples:
+   # * n^ng^arraxt^n
+   # * 2
+   # * -1, 5
+   # * [-1, 5]
+   # *Returns*:: nothing
    def initialize(*a)
      a.flatten! # in case an array was passed as an argument
  
      if a.size == 1 and a[0].kind_of? String and a[0] =~ re_cut_symbol
!       # Initialize with a cut symbol pattern such as 'n^ng^arraxt^n'
        s = a[0]
        a = []
***************
*** 78,81 ****
--- 100,107 ----
    #   [ -2, 1, 3 ] -> [ 0, 2, 4 ]
    #
+   # ---
+   # *Arguments*
+   # * _none_
+   # *Returns*:: +Array+ of cuts in 0-based index notation
    def to_array_index
      return [] if @min == nil