[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range cut_range.rb, 1.3, 1.4 cut_ranges.rb, 1.4, 1.5 horizontal_cut_range.rb, 1.4, 1.5 sequence_range.rb, 1.8, 1.9 vertical_cut_range.rb, 1.4, 1.5

Mon Jul 16 19:28:50 UTC 2007

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

Modified Files:
	cut_range.rb cut_ranges.rb horizontal_cut_range.rb 
	sequence_range.rb vertical_cut_range.rb 
Log Message:
* autoloadified

Index: vertical_cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** vertical_cut_range.rb	5 Apr 2007 23:35:42 -0000	1.4
--- vertical_cut_range.rb	16 Jul 2007 19:28:48 -0000	1.5
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/range/vertical_cut_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/range/vertical_cut_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #

! require 'bio/util/restriction_enzyme/range/cut_range'

! module Bio; end
! class Bio::RestrictionEnzyme
  class Range

- #
- # bio/util/restrction_enzyme/range/vertical_cut_range.rb - 
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # FIXME docs are kind of out of date.  Change this to VerticalAndHorizontalCutRange
  class VerticalCutRange < CutRange
--- 9,18 ----
  #

! require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme
  class Range

  # FIXME docs are kind of out of date.  Change this to VerticalAndHorizontalCutRange
  class VerticalCutRange < CutRange
***************
*** 81,83 ****
  end # VerticalCutRange
  end # Range
! end # Bio::RestrictionEnzyme
--- 74,77 ----
  end # VerticalCutRange
  end # Range
! end # RestrictionEnzyme
! end # Bio

Index: horizontal_cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** horizontal_cut_range.rb	5 Apr 2007 23:35:42 -0000	1.4
--- horizontal_cut_range.rb	16 Jul 2007 19:28:48 -0000	1.5
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/range/horizontal_cut_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/range/horizontal_cut_range.rb - 
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,25 ****
  #

! require 'bio/util/restriction_enzyme/range/cut_range'

! module Bio; end
! class Bio::RestrictionEnzyme
  class Range

- #
- # bio/util/restrction_enzyme/range/horizontal_cut_range.rb - 
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  class HorizontalCutRange < CutRange
    attr_reader :p_cut_left, :p_cut_right
--- 9,18 ----
  #

! require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme
  class Range

  class HorizontalCutRange < CutRange
    attr_reader :p_cut_left, :p_cut_right
***************
*** 71,73 ****
  end # HorizontalCutRange
  end # Range
! end # Bio::RestrictionEnzyme
--- 64,67 ----
  end # HorizontalCutRange
  end # Range
! end # RestrictionEnzyme
! end # Bio

Index: sequence_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** sequence_range.rb	13 May 2007 04:08:02 -0000	1.8
--- sequence_range.rb	16 Jul 2007 19:28:48 -0000	1.9
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,30 ****
  #

! require 'bio/util/restriction_enzyme/range/cut_ranges'
! require 'bio/util/restriction_enzyme/range/horizontal_cut_range'
! require 'bio/util/restriction_enzyme/range/vertical_cut_range'
! require 'bio/util/restriction_enzyme/range/sequence_range/calculated_cuts'
! require 'bio/util/restriction_enzyme/range/sequence_range/fragments'
! require 'bio/util/restriction_enzyme/range/sequence_range/fragment'
! require 'bio'

! module Bio; end
! class Bio::RestrictionEnzyme
  class Range
! #
! # bio/util/restrction_enzyme/range/sequence_range.rb - A defined range over a nucleotide 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 defined range over a nucleotide sequence.
  #
--- 9,23 ----
  #

! require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme
  class Range
! 
!   autoload :CutRange,                'bio/util/restriction_enzyme/range/cut_range'
!   autoload :CutRanges,               'bio/util/restriction_enzyme/range/cut_ranges'
!   autoload :HorizontalCutRange,      'bio/util/restriction_enzyme/range/horizontal_cut_range'
!   autoload :VerticalCutRange,        'bio/util/restriction_enzyme/range/vertical_cut_range'
! 
  # A defined range over a nucleotide sequence.
  #
***************
*** 33,36 ****
--- 26,33 ----
  class SequenceRange

+   autoload :Fragment,                'bio/util/restriction_enzyme/range/sequence_range/fragment'
+   autoload :Fragments,               'bio/util/restriction_enzyme/range/sequence_range/fragments'
+   autoload :CalculatedCuts,          'bio/util/restriction_enzyme/range/sequence_range/calculated_cuts'
+ 
    # Left-most index of primary strand
    attr_reader :p_left
***************
*** 257,259 ****
  end # SequenceRange
  end # Range
! end # Bio::RestrictionEnzyme
\ No newline at end of file
--- 254,257 ----
  end # SequenceRange
  end # Range
! end # RestrictionEnzyme
! end # Bio

Index: cut_ranges.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/cut_ranges.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** cut_ranges.rb	5 Apr 2007 23:35:42 -0000	1.4
--- cut_ranges.rb	16 Jul 2007 19:28:48 -0000	1.5
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child objects.
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child objects.
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,23 ****
  #

! module Bio; end
! class Bio::RestrictionEnzyme
  class Range

- #
- # bio/util/restrction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child objects.
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Container for many CutRange objects or CutRange child objects.  Inherits from array.
  #
--- 9,18 ----
  #

! require 'bio/util/restriction_enzyme'
! 
! module Bio
! class RestrictionEnzyme
  class Range

  # Container for many CutRange objects or CutRange child objects.  Inherits from array.
  #
***************
*** 49,51 ****
  end # CutRanges
  end # Range
! end # Bio::RestrictionEnzyme
--- 44,47 ----
  end # CutRanges
  end # Range
! end # RestrictionEnzyme
! end # Bio

Index: cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/cut_range.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** cut_range.rb	5 Apr 2007 23:35:42 -0000	1.3
--- cut_range.rb	16 Jul 2007 19:28:48 -0000	1.4
***************
*** 1,4 ****
  #
! # bio/util/restrction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
--- 1,4 ----
  #
! # bio/util/restriction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange
  #
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
***************
*** 9,29 ****
  #

! require 'bio'

! module Bio; end
! class Bio::RestrictionEnzyme
  class Range

- #
- # bio/util/restrction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange
- #
- # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
- # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
- # License::   The Ruby License
- #
  # Abstract base class for HorizontalCutRange and VerticalCutRange
  #
  class CutRange
  end # CutRange
  end # Range
! end # Bio::RestrictionEnzyme
\ No newline at end of file
--- 9,24 ----
  #

! require 'bio/util/restriction_enzyme'

! module Bio
! class RestrictionEnzyme
  class Range

  # Abstract base class for HorizontalCutRange and VerticalCutRange
  #
  class CutRange
  end # CutRange
+ 
  end # Range
! end # RestrictionEnzyme
! end # Bio