[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/double_stranded aligned_strands.rb, 1.5, 1.6 cut_location_pair.rb, 1.8, 1.9 cut_location_pair_in_enzyme_notation.rb, 1.6, 1.7 cut_locations.rb, 1.5, 1.6 cut_locations_in_enzyme_notation.rb, 1.6, 1.7

Katayama Toshiaki k at dev.open-bio.org
Mon Jul 16 19:28:50 UTC 2007


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

Modified Files:
	aligned_strands.rb cut_location_pair.rb 
	cut_location_pair_in_enzyme_notation.rb cut_locations.rb 
	cut_locations_in_enzyme_notation.rb 
Log Message:
* autoloadified


Index: aligned_strands.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** aligned_strands.rb	5 Apr 2007 23:35:42 -0000	1.5
--- aligned_strands.rb	16 Jul 2007 19:28:48 -0000	1.6
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,27 ****
  #
  
! require 'bio/util/restriction_enzyme/single_strand'
! require 'bio/util/restriction_enzyme/cut_symbol'
! require 'bio/util/restriction_enzyme/string_formatting'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Align two SingleStrand objects and return a Result
  # object with +primary+ and +complement+ accessors.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Align two SingleStrand objects and return a Result
  # object with +primary+ and +complement+ accessors.
***************
*** 136,138 ****
  end # AlignedStrands
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 127,130 ----
  end # AlignedStrands
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_locations.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** cut_locations.rb	5 Apr 2007 23:35:42 -0000	1.5
--- cut_locations.rb	16 Jul 2007 19:28:48 -0000	1.6
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #
  
! require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Contains an +Array+ of CutLocationPair objects.
  #
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Contains an +Array+ of CutLocationPair objects.
  #
***************
*** 80,82 ****
  end # CutLocations
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 73,76 ----
  end # CutLocations
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** cut_locations_in_enzyme_notation.rb	5 Apr 2007 23:35:42 -0000	1.6
--- cut_locations_in_enzyme_notation.rb	16 Jul 2007 19:28:48 -0000	1.7
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,26 ****
  #
  
! require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
! require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Inherits from DoubleStranded::CutLocations.  Contains CutLocationPairInEnzymeNotation objects.
  # Adds helper methods to convert from enzyme index notation to 0-based array index notation.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Inherits from DoubleStranded::CutLocations.  Contains CutLocationPairInEnzymeNotation objects.
  # Adds helper methods to convert from enzyme index notation to 0-based array index notation.
***************
*** 112,114 ****
  end # CutLocationsInEnzymeNotation
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 104,107 ----
  end # CutLocationsInEnzymeNotation
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_location_pair_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** cut_location_pair_in_enzyme_notation.rb	5 Apr 2007 23:35:42 -0000	1.6
--- cut_location_pair_in_enzyme_notation.rb	16 Jul 2007 19:28:48 -0000	1.7
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #
  
! require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
  
- #
- # bio/util/restrction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in
  # enzyme notation instead of 0-based.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
  
  # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in
  # enzyme notation instead of 0-based.
***************
*** 42,44 ****
  end # CutLocationPair
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 35,38 ----
  end # CutLocationPair
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio

Index: cut_location_pair.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** cut_location_pair.rb	5 Apr 2007 23:35:42 -0000	1.8
--- cut_location_pair.rb	16 Jul 2007 19:28:48 -0000	1.9
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #
  
! require 'bio/util/restriction_enzyme/cut_symbol'
  
! module Bio; end
! class Bio::RestrictionEnzyme
  class DoubleStranded
    
- #
- # bio/util/restrction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Stores a single cut location pair in 0-based index notation for use with
  # DoubleStranded enzyme sequences.
--- 9,18 ----
  #
  
! require 'bio/util/restriction_enzyme'
  
! module Bio
! class RestrictionEnzyme
  class DoubleStranded
    
  # Stores a single cut location pair in 0-based index notation for use with
  # DoubleStranded enzyme sequences.
***************
*** 107,109 ****
  end # CutLocationPair
  end # DoubleStranded
! end # Bio::RestrictionEnzyme
--- 100,103 ----
  end # CutLocationPair
  end # DoubleStranded
! end # RestrictionEnzyme
! end # Bio




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