[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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