[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.6, 1.7 cut_symbol.rb, 1.2, 1.3

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv512/lib/bio/util/restriction_enzyme

Modified Files:
	analysis.rb cut_symbol.rb 
Log Message:


Index: cut_symbol.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/cut_symbol.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** cut_symbol.rb	31 Dec 2006 21:50:31 -0000	1.2
--- cut_symbol.rb	1 Jan 2007 02:16:05 -0000	1.3
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/cut_symbol.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restrction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,13 ****
  #
  
! nil # separate file-level rdoc from following statement
  
  module Bio; end
--- 9,13 ----
  #
  
! nil # to separate file-level rdoc from following statement # !> useless use of nil in void context
  
  module Bio; end
***************
*** 15,19 ****
  
  #
! # bio/util/restrction_enzyme/cut_symbol.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 15,19 ----
  
  #
! # bio/util/restrction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 21,57 ****
  # License::   Distributes under the same terms as Ruby
  #
  module CutSymbol
  
!   require 'singleton'
! 
!   class CutSymbol__
!     include Singleton
!     attr_accessor :cut_symbol
!     attr_accessor :escaped_cut_symbol
!   end
! 
!   # NOTE verify this sometime
!   def cut_symbol=(c)
!     CutSymbol__.instance.cut_symbol = c
    end
  
!   def cut_symbol
!     CutSymbol__.instance.cut_symbol ||= '^'
!   end
  
!   def escaped_cut_symbol
!     CutSymbol__.instance.escaped_cut_symbol ||= "\\#{cut_symbol}"  # \^
!   end
  
!   # Used to check if multiple cut symbols are next to each other
    def re_cut_symbol_adjacent
      %r"#{escaped_cut_symbol}{2}"
    end
  
!   # A Regexp of the cut_symbol.  Convenience method.
    def re_cut_symbol
      %r"#{escaped_cut_symbol}"
    end
  
  end # CutSymbol
! end # Bio::RestrictionEnzyme
\ No newline at end of file
--- 21,115 ----
  # License::   Distributes under the same terms as Ruby
  #
+ # = Usage
+ #
+ #   #require 'bio/util/restriction_enzyme/cut_symbol'
+ #   require 'cut_symbol'
+ #   include Bio::RestrictionEnzyme::CutSymbol
+ #   
+ #   cut_symbol                            # => "^"
+ #   set_cut_symbol('|')                   # => "|"
+ #   cut_symbol                            # => "|"
+ #   escaped_cut_symbol                    # => "\\|"
+ #   re_cut_symbol                         # => /\|/
+ #   set_cut_symbol('^')                   # => "^"
+ #   "abc^de" =~ re_cut_symbol             # => 3
+ #   "abc^de" =~ re_cut_symbol_adjacent    # => nil
+ #   "abc^^de" =~ re_cut_symbol_adjacent   # => 3
+ #   "a^bc^^de" =~ re_cut_symbol_adjacent  # => 4
+ #   "a^bc^de" =~ re_cut_symbol_adjacent   # => nil
+ #
  module CutSymbol
  
!   # Set the token to be used as the cut symbol in a restriction enzyme sequece
!   #
!   # Starts as +^+ character
!   #
!   # ---
!   # *Arguments*
!   # * +glyph+: The single character to be used as the cut symbol in an enzyme sequence
!   # *Returns*:: +glyph+
!   def set_cut_symbol(glyph)
!     CutSymbol__.cut_symbol = glyph
    end
  
!   # Get the token that's used as the cut symbol in a restriction enzyme sequece
!   #
!   # ---
!   # *Arguments*
!   # * _none_
!   # *Returns*:: +glyph+
!   def cut_symbol; CutSymbol__.cut_symbol; end
  
!   # Get the token that's used as the cut symbol in a restriction enzyme sequece with
!   # a back-slash preceding it.
!   #
!   # ---
!   # *Arguments*
!   # * _none_
!   # *Returns*:: +\glyph+
!   def escaped_cut_symbol; CutSymbol__.escaped_cut_symbol; end
  
!   # Used to check if multiple cut symbols are next to each other.
!   #
!   # ---
!   # *Arguments*
!   # * _none_
!   # *Returns*:: +RegExp+
    def re_cut_symbol_adjacent
      %r"#{escaped_cut_symbol}{2}"
    end
  
!   # A Regexp of the cut_symbol.
!   #
!   # ---
!   # *Arguments*
!   # * _none_
!   # *Returns*:: +RegExp+
    def re_cut_symbol
      %r"#{escaped_cut_symbol}"
    end
  
+   #########
+   protected
+   #########
+   
+   require 'singleton'
+   
+   # Class to keep state
+   class CutSymbol__
+     include Singleton
+ 
+     @cut_symbol = '^'
+     
+     def self.cut_symbol; @cut_symbol; end
+     
+     def self.cut_symbol=(glyph);
+       raise ArgumentError if glyph.size != 1
+       @cut_symbol = glyph
+     end
+     
+     def self.escaped_cut_symbol; "\\" + self.cut_symbol; end
+   end
+   
  end # CutSymbol
! end # Bio::RestrictionEnzyme

Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** analysis.rb	31 Dec 2006 21:50:31 -0000	1.6
--- analysis.rb	1 Jan 2007 02:16:05 -0000	1.7
***************
*** 33,37 ****
  
  require 'bio/util/restriction_enzyme'
! require 'bio/util/restriction_enzyme/analysis/sequence_range.rb'
  
  class Bio::RestrictionEnzyme
--- 33,37 ----
  
  require 'bio/util/restriction_enzyme'
! require 'bio/util/restriction_enzyme/analysis/sequence_range'
  
  class Bio::RestrictionEnzyme