[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/double_stranded aligned_strands.rb, 1.1, 1.2 cut_location_pair.rb, 1.1, 1.2 cut_location_pair_in_enzyme_notation.rb, 1.1, 1.2 cut_locations.rb, 1.1, 1.2 cut_locations_in_enzyme_notation.rb, 1.1, 1.2

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded
In directory dev.open-bio.org:/tmp/cvs-serv32395/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:
Updated license for RestrictionEnzyme.

Index: aligned_strands.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** aligned_strands.rb	1 Feb 2006 07:34:11 -0000	1.1
--- aligned_strands.rb	31 Dec 2006 21:50:31 -0000	1.2
***************
*** 1,2 ****
--- 1,11 ----
+ #
+ # bio/util/restrction_enzyme/double_stranded/aligned_strands.rb - 
+ #
+ # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
+ # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+ # License::   Distributes under the same terms as Ruby
+ #
+ #  $Id$
+ #
  require 'pathname'
  libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
***************
*** 12,48 ****
  
  #
! # bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - 
! #
! # Copyright::  Copyright (C) 2006 Trevor Wennblom <trevor at corevx.com>
! # License::    LGPL
! #
! #  $Id$
! #
! #
! #--
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
  #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
- 
- =begin rdoc
- bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - 
- 
- Align two SingleStrand::Pattern objects and return a Result
- object with +primary+ and +complement+ accessors.
- =end
  class AlignedStrands
    extend CutSymbol
--- 21,33 ----
  
  #
! # bio/util/restrction_enzyme/double_stranded/aligned_strands.rb - 
  #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   Distributes under the same terms as Ruby
  #
! # Align two SingleStrand::Pattern objects and return a Result
! # object with +primary+ and +complement+ accessors.
  #
  class AlignedStrands
    extend CutSymbol
***************
*** 142,148 ****
      end
    end
! 
! end
! 
! end
! end
--- 127,131 ----
      end
    end
! end # AlignedStrands
! end # DoubleStranded
! end # Bio::RestrictionEnzyme

Index: cut_locations.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** cut_locations.rb	1 Feb 2006 07:34:11 -0000	1.1
--- cut_locations.rb	31 Dec 2006 21:50:31 -0000	1.2
***************
*** 1,2 ****
--- 1,11 ----
+ #
+ # bio/util/restrction_enzyme/double_stranded/cut_locations.rb - 
+ #
+ # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
+ # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+ # License::   Distributes under the same terms as Ruby
+ #
+ #  $Id$
+ #
  require 'pathname'
  libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
***************
*** 10,43 ****
  
  #
! # bio/util/restriction_enzyme/double_stranded/cut_locations.rb - 
! #
! # Copyright::  Copyright (C) 2006 Trevor Wennblom <trevor at corevx.com>
! # License::    LGPL
! #
! #  $Id$
! #
! #
! #--
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
- 
- =begin rdoc
- bio/util/restriction_enzyme/double_stranded/cut_locations.rb - 
- =end
  class CutLocations < Array
  
--- 19,28 ----
  
  #
! # bio/util/restrction_enzyme/double_stranded/cut_locations.rb - 
  #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   Distributes under the same terms as Ruby
  #
  class CutLocations < Array
  
***************
*** 69,76 ****
      end
    end
! 
! 
! end
! 
! end
! end
--- 54,58 ----
      end
    end
! end # CutLocations
! end # DoubleStranded
! end # Bio::RestrictionEnzyme

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 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** cut_locations_in_enzyme_notation.rb	1 Feb 2006 07:34:11 -0000	1.1
--- cut_locations_in_enzyme_notation.rb	31 Dec 2006 21:50:31 -0000	1.2
***************
*** 1,2 ****
--- 1,11 ----
+ #
+ # bio/util/restrction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - 
+ #
+ # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
+ # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+ # License::   Distributes under the same terms as Ruby
+ #
+ #  $Id$
+ #
  require 'pathname'
  libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
***************
*** 11,44 ****
  
  #
! # bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - 
! #
! # Copyright::  Copyright (C) 2006 Trevor Wennblom <trevor at corevx.com>
! # License::    LGPL
! #
! #  $Id$
! #
! #
! #--
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
- 
- =begin rdoc
- bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - 
- =end
  class CutLocationsInEnzymeNotation < CutLocations
  
--- 20,29 ----
  
  #
! # bio/util/restrction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - 
  #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   Distributes under the same terms as Ruby
  #
  class CutLocationsInEnzymeNotation < CutLocations
  
***************
*** 103,109 ****
      end
    end
! 
! end
! 
! end
! end
--- 88,92 ----
      end
    end
! end # CutLocationsInEnzymeNotation
! end # DoubleStranded
! end # Bio::RestrictionEnzyme

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 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** cut_location_pair_in_enzyme_notation.rb	1 Feb 2006 07:34:11 -0000	1.1
--- cut_location_pair_in_enzyme_notation.rb	31 Dec 2006 21:50:31 -0000	1.2
***************
*** 1,2 ****
--- 1,11 ----
+ #
+ # bio/util/restrction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - 
+ #
+ # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
+ # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+ # License::   Distributes under the same terms as Ruby
+ #
+ #  $Id$
+ #
  require 'pathname'
  libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
***************
*** 11,46 ****
  
  #
! # bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - 
! #
! # Copyright::  Copyright (C) 2006 Trevor Wennblom <trevor at corevx.com>
! # License::    LGPL
! #
! #  $Id$
! #
! #
! #--
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
  #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
- 
- =begin rdoc
- bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - 
- 
- See CutLocationPair
- =end
  class CutLocationPairInEnzymeNotation < CutLocationPair
  
--- 20,31 ----
  
  #
! # bio/util/restrction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - 
  #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   Distributes under the same terms as Ruby
  #
! # See CutLocationPair
  #
  class CutLocationPairInEnzymeNotation < CutLocationPair
  
***************
*** 62,68 ****
      end
    end
! 
! end
! 
! end
! end
--- 47,51 ----
      end
    end
! end # CutLocationPair
! end # DoubleStranded
! end # Bio::RestrictionEnzyme

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 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** cut_location_pair.rb	1 Feb 2006 07:34:11 -0000	1.1
--- cut_location_pair.rb	31 Dec 2006 21:50:31 -0000	1.2
***************
*** 1,2 ****
--- 1,11 ----
+ #
+ # bio/util/restrction_enzyme/double_stranded/cut_location_pair.rb - 
+ #
+ # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
+ # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+ # License::   Distributes under the same terms as Ruby
+ #
+ #  $Id$
+ #
  require 'pathname'
  libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
***************
*** 9,60 ****
  class Bio::RestrictionEnzyme
  class DoubleStranded
! 
! #
! # bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - 
! #
! # Copyright::  Copyright (C) 2006 Trevor Wennblom <trevor at corevx.com>
! # License::    LGPL
! #
! #  $Id$
! #
! #
! #--
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
  #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
  #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
- 
- =begin rdoc
- bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - 
- 
- Stores a cut location pair in 0-based index notation
- 
- Input:
- +pair+:: May be two values represented as an Array, a Range, or a
-          combination of Integer and nil values.  The first value
-          represents a cut on the primary strand, the second represents
-          a cut on the complement strand.
- 
- Example:
-   clp = CutLocationPair.new(3,2)
-   clp.primary                    # 3
-   clp.complement                 # 2
- 
- Notes:
- * a value of +nil+ is an explicit representation of 'no cut'
- =end
  class CutLocationPair < Array
    attr_reader :primary, :complement
--- 18,45 ----
  class Bio::RestrictionEnzyme
  class DoubleStranded
!   
  #
! # bio/util/restrction_enzyme/double_stranded/cut_location_pair.rb - 
  #
! # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
! # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   Distributes under the same terms as Ruby
  #
! # Stores a cut location pair in 0-based index notation
! # 
! # Input:
! # +pair+:: May be two values represented as an Array, a Range, or a
! #          combination of Integer and nil values.  The first value
! #          represents a cut on the primary strand, the second represents
! #          a cut on the complement strand.
! # 
! # Example:
! #   clp = CutLocationPair.new(3,2)
! #   clp.primary                    # 3
! #   clp.complement                 # 2
! # 
! # Notes:
! # * a value of +nil+ is an explicit representation of 'no cut'
  #
  class CutLocationPair < Array
    attr_reader :primary, :complement
***************
*** 112,118 ****
      end
    end
! 
! end
! 
! end
! end
--- 97,101 ----
      end
    end
! end # CutLocationPair
! end # DoubleStranded
! end # Bio::RestrictionEnzyme
\ No newline at end of file