[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.19, 1.20 analysis_basic.rb, 1.15, 1.16 cut_symbol.rb, 1.5, 1.6 double_stranded.rb, 1.10, 1.11 single_strand.rb, 1.6, 1.7 single_strand_complement.rb, 1.4, 1.5 string_formatting.rb, 1.5, 1.6

Mon Jul 16 19:28:50 UTC 2007

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv21244/restriction_enzyme

Modified Files:
	analysis.rb analysis_basic.rb cut_symbol.rb double_stranded.rb 
	single_strand.rb single_strand_complement.rb 
	string_formatting.rb 
Log Message:
* autoloadified

Index: analysis_basic.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** analysis_basic.rb	13 May 2007 04:08:02 -0000	1.15
--- analysis_basic.rb	16 Jul 2007 19:28:48 -0000	1.16
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/analysis_basic.rb - Does the work of fragmenting the DNA from the enzymes
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/analysis_basic.rb - Does the work of fragmenting the DNA from the enzymes
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 11,25 ****
  require 'set'  # for method create_enzyme_actions
  require 'bio/util/restriction_enzyme'
- require 'bio/util/restriction_enzyme/range/sequence_range'

! class Bio::RestrictionEnzyme

- #
- # bio/util/restrction_enzyme/analysis_basic.rb - Does the work of fragmenting the DNA from the enzymes
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  class Analysis

--- 11,18 ----
  require 'set'  # for method create_enzyme_actions
  require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme

  class Analysis

***************
*** 221,223 ****

  end # Analysis
! end # Bio::RestrictionEnzyme
--- 214,217 ----

  end # Analysis
! end # RestrictionEnzyme
! end # Bio

Index: string_formatting.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/string_formatting.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** string_formatting.rb	5 Apr 2007 23:35:42 -0000	1.5
--- string_formatting.rb	16 Jul 2007 19:28:48 -0000	1.6
***************
*** 9,24 ****
  #

! require 'bio/util/restriction_enzyme/cut_symbol'

! module Bio; end
! class Bio::RestrictionEnzyme

- #
- # bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  module StringFormatting
    include CutSymbol
--- 9,17 ----
  #

! require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme

  module StringFormatting
    include CutSymbol
***************
*** 115,117 ****
    end
  end # StringFormatting
! end # Bio::RestrictionEnzyme
--- 108,111 ----
    end
  end # StringFormatting
! end # RestrictionEnzyme
! end # Bio

Index: cut_symbol.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/cut_symbol.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** cut_symbol.rb	5 Apr 2007 23:35:42 -0000	1.5
--- cut_symbol.rb	16 Jul 2007 19:28:48 -0000	1.6
***************
*** 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>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,24 ****
  #

! nil # to separate file-level rdoc from following statement # !> useless use of nil in void context
! 
! module Bio; end
! class Bio::RestrictionEnzyme

- #
- # 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>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # = Usage
  #
--- 9,15 ----
  #

! module Bio
! class RestrictionEnzyme

  # = Usage
  #
***************
*** 113,115 ****

  end # CutSymbol
! end # Bio::RestrictionEnzyme
--- 104,107 ----

  end # CutSymbol
! end # RestrictionEnzyme
! end # Bio

Index: single_strand_complement.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand_complement.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** single_strand_complement.rb	5 Apr 2007 23:35:42 -0000	1.4
--- single_strand_complement.rb	16 Jul 2007 19:28:48 -0000	1.5
***************
*** 9,24 ****
  #

! require 'bio/util/restriction_enzyme/single_strand'

! module Bio; end
! class Bio::RestrictionEnzyme

- #
- # bio/util/restriction_enzyme/single_strand_complement.rb - Single strand restriction enzyme sequence in complement orientation
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # A single strand of restriction enzyme sequence pattern with a 3' to 5' orientation.
  #
--- 9,17 ----
  #

! require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme

  # A single strand of restriction enzyme sequence pattern with a 3' to 5' orientation.
  #
***************
*** 27,29 ****
    def orientation; [3, 5]; end
  end # SingleStrandComplement
! end # Bio::RestrictionEnzyme
--- 20,23 ----
    def orientation; [3, 5]; end
  end # SingleStrandComplement
! end # RestrictionEnzyme
! end # Bio

Index: double_stranded.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** double_stranded.rb	5 Apr 2007 23:35:42 -0000	1.10
--- double_stranded.rb	16 Jul 2007 19:28:48 -0000	1.11
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded.rb - DoubleStranded restriction enzyme sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded.rb - DoubleStranded restriction enzyme sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,33 ****
  #

- require 'bio/db/rebase'
  require 'bio/util/restriction_enzyme'
- require 'bio/util/restriction_enzyme/range/sequence_range'
- 
- require 'bio/util/restriction_enzyme/cut_symbol'
- require 'bio/util/restriction_enzyme/single_strand'
- require 'bio/util/restriction_enzyme/single_strand_complement'
- require 'bio/util/restriction_enzyme/double_stranded/aligned_strands'
- require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
- require 'bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation'

! module Bio; end
! class Bio::RestrictionEnzyme

- #
- # bio/util/restrction_enzyme/double_stranded.rb - DoubleStranded restriction enzyme sequence
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # A pair of SingleStrand and SingleStrandComplement objects with methods to
  # add utility to their relation.
--- 9,17 ----
  #

  require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme

  # A pair of SingleStrand and SingleStrandComplement objects with methods to
  # add utility to their relation.
***************
*** 41,44 ****
--- 25,35 ----
  # FIXME needs better docs
  class DoubleStranded
+ 
+   autoload :AlignedStrands,  'bio/util/restriction_enzyme/double_stranded/aligned_strands'
+   autoload :CutLocations,    'bio/util/restriction_enzyme/double_stranded/cut_locations'
+   autoload :CutLocationPair, 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
+   autoload :CutLocationsInEnzymeNotation,    'bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation'
+   autoload :CutLocationPairInEnzymeNotation, 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'
+ 
    include CutSymbol
    extend CutSymbol
***************
*** 327,329 ****

  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 318,321 ----

  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: single_strand.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** single_strand.rb	5 Apr 2007 23:35:42 -0000	1.6
--- single_strand.rb	16 Jul 2007 19:28:48 -0000	1.7
***************
*** 9,27 ****
  #

! require 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'
! require 'bio/util/restriction_enzyme/cut_symbol'
! require 'bio/util/restriction_enzyme/string_formatting'
  require 'bio/sequence'

! module Bio; end
! class Bio::RestrictionEnzyme

- #
- # bio/util/restriction_enzyme/single_strand.rb - Single strand of a restriction enzyme sequence
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # A single strand of restriction enzyme sequence pattern with a 5' to 3' 
  # orientation.
--- 9,18 ----
  #

! require 'bio/util/restriction_enzyme'
  require 'bio/sequence'

! module Bio
! class RestrictionEnzyme

  # A single strand of restriction enzyme sequence pattern with a 5' to 3' 
  # orientation.
***************
*** 31,34 ****
--- 22,28 ----
  #
  class SingleStrand < Bio::Sequence::NA
+ 
+   autoload :CutLocationsInEnzymeNotation, 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'
+ 
    include CutSymbol
    include StringFormatting
***************
*** 202,204 ****

  end # SingleStrand
! end # Bio::RestrictionEnzyme
\ No newline at end of file
--- 196,199 ----

  end # SingleStrand
! end # RestrictionEnzyme
! end # Bio

Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** analysis.rb	13 May 2007 04:08:02 -0000	1.19
--- analysis.rb	16 Jul 2007 19:28:48 -0000	1.20
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,23 ****
  #

  require 'bio/util/restriction_enzyme/analysis_basic'

! class Bio::RestrictionEnzyme

- #
- # bio/util/restrction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  class Analysis

--- 9,18 ----
  #

+ require 'bio/util/restriction_enzyme'
  require 'bio/util/restriction_enzyme/analysis_basic'

! module Bio
! class RestrictionEnzyme

  class Analysis

***************
*** 251,253 ****

  end # Analysis
! end # Bio::RestrictionEnzyme
--- 246,249 ----

  end # Analysis
! end # RestrictionEnzyme
! end # Bio