From ngoto at dev.open-bio.org  Mon Apr  2 08:55:28 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 02 Apr 2007 12:55:28 +0000
Subject: [BioRuby-cvs] bioruby ChangeLog,1.62,1.63
Message-ID: <200704021255.l32CtSGM005165@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv5141

Modified Files:
	ChangeLog 
Log Message:
Incompatible change: Bio::MAFFT#output is changed to return
a string of multi-fasta formmatted text. To get an array of
Bio::FastaFormat objects (as of 1.0 or before), please use
report.data instead.


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.62
retrieving revision 1.63
diff -C2 -d -r1.62 -r1.63
*** ChangeLog	27 Mar 2007 09:26:02 -0000	1.62
--- ChangeLog	2 Apr 2007 12:55:26 -0000	1.63
***************
*** 1,2 ****
--- 1,11 ----
+ 2007-04-02  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/appl/mafft.rb
+ 
+ 	Incompatible change: Bio::MAFFT#output is changed to return
+ 	a string of multi-fasta formmatted text. To get an array of
+ 	Bio::FastaFormat objects (as of 1.0 or before), please use
+ 	report.data instead.
+ 
  2007-03-27  Naohisa Goto <ng at bioruby.org>
  


From ngoto at dev.open-bio.org  Mon Apr  2 08:55:28 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 02 Apr 2007 12:55:28 +0000
Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.18,1.19
Message-ID: <200704021255.l32CtSP8005170@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/doc
In directory dev.open-bio.org:/tmp/cvs-serv5141/doc

Modified Files:
	Changes-0.7.rd 
Log Message:
Incompatible change: Bio::MAFFT#output is changed to return
a string of multi-fasta formmatted text. To get an array of
Bio::FastaFormat objects (as of 1.0 or before), please use
report.data instead.


Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** Changes-0.7.rd	28 Dec 2006 15:35:50 -0000	1.18
--- Changes-0.7.rd	2 Apr 2007 12:55:26 -0000	1.19
***************
*** 292,295 ****
--- 292,304 ----
    No replacements/alternatives are available.
  
+ --- Bio::MAFFT
+ 
+ In 1.1.0:
+ 
+ * Bio::MAFFT#output is changed to return a string of multi-fasta
+   formmatted text instead of Array of Bio::FastaFormat objects.
+   To get an array of Bio::FastaFormat objects, please use
+   report.data instead.
+ 
  --- Bio::MAFFT::Report
  


From ngoto at dev.open-bio.org  Mon Apr  2 08:55:28 2007
From: ngoto at dev.open-bio.org (Naohisa Goto)
Date: Mon, 02 Apr 2007 12:55:28 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl mafft.rb,1.15,1.16
Message-ID: <200704021255.l32CtSrM005175@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv5141/lib/bio/appl

Modified Files:
	mafft.rb 
Log Message:
Incompatible change: Bio::MAFFT#output is changed to return
a string of multi-fasta formmatted text. To get an array of
Bio::FastaFormat objects (as of 1.0 or before), please use
report.data instead.


Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** mafft.rb	14 Dec 2006 16:08:46 -0000	1.15
--- mafft.rb	2 Apr 2007 12:55:26 -0000	1.16
***************
*** 143,149 ****
  
      # Shows latest raw alignment result.
!     # Since a result of MAFFT is simply a multiple-fasta format,
!     # it returns an array of Bio::FastaFormat instances
!     # instead of raw string.
      attr_reader :output
  
--- 143,150 ----
  
      # Shows latest raw alignment result.
!     # Return a string. (Changed in bioruby-1.1.0).
!     # Compatibility note:
!     # If you want an array of Bio::FastaFormat instances,
!     # you should use report.data instead.
      attr_reader :output
  
***************
*** 202,207 ****
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         ff = Bio::FlatFile.new(Bio::FastaFormat, io)
!         @output = ff.to_a
        end
      end
--- 203,207 ----
        Bio::Command.call_command(@command) do |io|
          io.close_write
!         @output = io.read
        end
      end


From trevor at dev.open-bio.org  Wed Apr  4 14:07:46 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 18:07:46 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/util/restriction_enzyme/double_stranded
	aligned_strands.rb, 1.3, 1.4 cut_location_pair.rb, 1.5,
	1.6 cut_location_pair_in_enzyme_notation.rb, 1.3,
	1.4 cut_locations.rb, 1.3,
	1.4 cut_locations_in_enzyme_notation.rb, 1.3, 1.4
Message-ID: <200704041807.l34I7kOO013499@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded
In directory dev.open-bio.org:/tmp/cvs-serv13464/lib/bio/util/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:
Removed independent path awareness.


Index: aligned_strands.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** aligned_strands.rb	1 Jan 2007 05:07:04 -0000	1.3
--- aligned_strands.rb	4 Apr 2007 18:07:44 -0000	1.4
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/single_strand'
--- 8,11 ----

Index: cut_locations.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** cut_locations.rb	1 Jan 2007 05:07:04 -0000	1.3
--- cut_locations.rb	4 Apr 2007 18:07:44 -0000	1.4
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
--- 8,11 ----

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 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** cut_locations_in_enzyme_notation.rb	1 Jan 2007 05:07:04 -0000	1.3
--- cut_locations_in_enzyme_notation.rb	4 Apr 2007 18:07:44 -0000	1.4
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
--- 8,11 ----

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 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** cut_location_pair_in_enzyme_notation.rb	1 Jan 2007 05:07:04 -0000	1.3
--- cut_location_pair_in_enzyme_notation.rb	4 Apr 2007 18:07:44 -0000	1.4
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
--- 8,11 ----

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 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** cut_location_pair.rb	29 Mar 2007 02:48:15 -0000	1.5
--- cut_location_pair.rb	4 Apr 2007 18:07:44 -0000	1.6
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/cut_symbol'
--- 8,11 ----


From trevor at dev.open-bio.org  Wed Apr  4 14:07:46 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 18:07:46 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/util/restriction_enzyme/range/sequence_range
	calculated_cuts.rb, 1.4, 1.5 fragment.rb, 1.2,
	1.3 fragments.rb, 1.2, 1.3
Message-ID: <200704041807.l34I7kHT013514@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range
In directory dev.open-bio.org:/tmp/cvs-serv13464/lib/bio/util/restriction_enzyme/range/sequence_range

Modified Files:
	calculated_cuts.rb fragment.rb fragments.rb 
Log Message:
Removed independent path awareness.


Index: calculated_cuts.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** calculated_cuts.rb	29 Mar 2007 02:48:15 -0000	1.4
--- calculated_cuts.rb	4 Apr 2007 18:07:44 -0000	1.5
***************
*** 9,16 ****
  #
  
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
- 
  require 'bio/util/restriction_enzyme'  # test/runner.rb wont load without this
  require 'bio/util/restriction_enzyme/cut_symbol'
--- 9,12 ----

Index: fragment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** fragment.rb	2 Jan 2007 00:19:06 -0000	1.2
--- fragment.rb	4 Apr 2007 18:07:44 -0000	1.3
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/range/cut_ranges'
--- 8,11 ----

Index: fragments.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** fragments.rb	2 Jan 2007 00:19:06 -0000	1.2
--- fragments.rb	4 Apr 2007 18:07:44 -0000	1.3
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  module Bio; end
--- 8,11 ----


From trevor at dev.open-bio.org  Wed Apr  4 14:07:46 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 18:07:46 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb,
	1.15, 1.16 analysis_basic.rb, 1.9, 1.10 double_stranded.rb,
	1.8, 1.9 single_strand.rb, 1.3,
	1.4 single_strand_complement.rb, 1.2, 1.3 string_formatting.rb,
	1.3, 1.4
Message-ID: <200704041807.l34I7kwV013492@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv13464/lib/bio/util/restriction_enzyme

Modified Files:
	analysis.rb analysis_basic.rb double_stranded.rb 
	single_strand.rb single_strand_complement.rb 
	string_formatting.rb 
Log Message:
Removed independent path awareness.


Index: analysis_basic.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** analysis_basic.rb	28 Mar 2007 19:45:27 -0000	1.9
--- analysis_basic.rb	4 Apr 2007 18:07:43 -0000	1.10
***************
*** 9,16 ****
  #
  
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
- 
  require 'bio'
  class Bio::Sequence::NA
--- 9,12 ----

Index: string_formatting.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/string_formatting.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** string_formatting.rb	1 Jan 2007 03:36:37 -0000	1.3
--- string_formatting.rb	4 Apr 2007 18:07:43 -0000	1.4
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/cut_symbol'
--- 8,11 ----

Index: single_strand_complement.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand_complement.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** single_strand_complement.rb	31 Dec 2006 21:50:31 -0000	1.2
--- single_strand_complement.rb	4 Apr 2007 18:07:43 -0000	1.3
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/single_strand'
--- 8,11 ----

Index: double_stranded.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** double_stranded.rb	28 Mar 2007 19:45:27 -0000	1.8
--- double_stranded.rb	4 Apr 2007 18:07:43 -0000	1.9
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/db/rebase'
--- 8,11 ----

Index: single_strand.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** single_strand.rb	1 Jan 2007 03:36:37 -0000	1.3
--- single_strand.rb	4 Apr 2007 18:07:43 -0000	1.4
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'
--- 8,11 ----

Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** analysis.rb	5 Jan 2007 06:33:01 -0000	1.15
--- analysis.rb	4 Apr 2007 18:07:43 -0000	1.16
***************
*** 9,16 ****
  #
  
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
- 
  require 'bio/util/restriction_enzyme/analysis_basic'
  
--- 9,12 ----


From trevor at dev.open-bio.org  Wed Apr  4 14:07:46 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 18:07:46 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range
	cut_range.rb, 1.1, 1.2 cut_ranges.rb, 1.2,
	1.3 horizontal_cut_range.rb, 1.2, 1.3 sequence_range.rb, 1.5,
	1.6 vertical_cut_range.rb, 1.2, 1.3
Message-ID: <200704041807.l34I7kXB013506@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range
In directory dev.open-bio.org:/tmp/cvs-serv13464/lib/bio/util/restriction_enzyme/range

Modified Files:
	cut_range.rb cut_ranges.rb horizontal_cut_range.rb 
	sequence_range.rb vertical_cut_range.rb 
Log Message:
Removed independent path awareness.


Index: vertical_cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** vertical_cut_range.rb	5 Jan 2007 06:03:22 -0000	1.2
--- vertical_cut_range.rb	4 Apr 2007 18:07:44 -0000	1.3
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/range/cut_range'
--- 8,11 ----

Index: horizontal_cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** horizontal_cut_range.rb	2 Jan 2007 06:18:38 -0000	1.2
--- horizontal_cut_range.rb	4 Apr 2007 18:07:44 -0000	1.3
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/range/cut_range'
--- 8,11 ----

Index: sequence_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** sequence_range.rb	6 Jan 2007 06:13:22 -0000	1.5
--- sequence_range.rb	4 Apr 2007 18:07:44 -0000	1.6
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/range/cut_ranges'
--- 8,11 ----

Index: cut_ranges.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/cut_ranges.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** cut_ranges.rb	2 Jan 2007 06:18:38 -0000	1.2
--- cut_ranges.rb	4 Apr 2007 18:07:44 -0000	1.3
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  module Bio; end
--- 8,11 ----

Index: cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/cut_range.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** cut_range.rb	2 Jan 2007 00:13:07 -0000	1.1
--- cut_range.rb	4 Apr 2007 18:07:44 -0000	1.2
***************
*** 9,16 ****
  #
  
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
- 
  require 'bio'
  
--- 9,12 ----


From trevor at dev.open-bio.org  Wed Apr  4 14:07:46 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 18:07:46 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand
	cut_locations_in_enzyme_notation.rb, 1.3, 1.4
Message-ID: <200704041807.l34I7kI0013519@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand
In directory dev.open-bio.org:/tmp/cvs-serv13464/lib/bio/util/restriction_enzyme/single_strand

Modified Files:
	cut_locations_in_enzyme_notation.rb 
Log Message:
Removed independent path awareness.


Index: cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** cut_locations_in_enzyme_notation.rb	1 Jan 2007 03:36:37 -0000	1.3
--- cut_locations_in_enzyme_notation.rb	4 Apr 2007 18:07:44 -0000	1.4
***************
*** 8,14 ****
  #  $Id$
  #
- require 'pathname'
- libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
- $:.unshift(libpath) unless $:.include?(libpath)
  
  require 'bio/util/restriction_enzyme/cut_symbol'
--- 8,11 ----


From trevor at dev.open-bio.org  Wed Apr  4 16:05:08 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 20:05:08 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme
	single_strand.rb, 1.4, 1.5 integer.rb, 1.2, NONE
Message-ID: <200704042005.l34K58e6013907@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv13881/lib/bio/util/restriction_enzyme

Modified Files:
	single_strand.rb 
Removed Files:
	integer.rb 
Log Message:
Removed "negative?" Integer extension

--- integer.rb DELETED ---

Index: single_strand.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** single_strand.rb	4 Apr 2007 18:07:43 -0000	1.4
--- single_strand.rb	4 Apr 2007 20:05:05 -0000	1.5
***************
*** 136,140 ****
    def pattern
      return stripped if @cut_locations_in_enzyme_notation.min == nil
!     left = (@cut_locations_in_enzyme_notation.min.negative? ? 'n' * @cut_locations_in_enzyme_notation.min.abs : '')
  
      # Add one more 'n' if a cut is at the last position 
--- 136,140 ----
    def pattern
      return stripped if @cut_locations_in_enzyme_notation.min == nil
!     left = (@cut_locations_in_enzyme_notation.min < 0 ? 'n' * @cut_locations_in_enzyme_notation.min.abs : '')
  
      # Add one more 'n' if a cut is at the last position 


From trevor at dev.open-bio.org  Wed Apr  4 16:05:08 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 20:05:08 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/util/restriction_enzyme/double_stranded
	cut_location_pair.rb, 1.6,
	1.7 cut_location_pair_in_enzyme_notation.rb, 1.4,
	1.5 cut_locations_in_enzyme_notation.rb, 1.4, 1.5
Message-ID: <200704042005.l34K58Yi013912@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded
In directory dev.open-bio.org:/tmp/cvs-serv13881/lib/bio/util/restriction_enzyme/double_stranded

Modified Files:
	cut_location_pair.rb cut_location_pair_in_enzyme_notation.rb 
	cut_locations_in_enzyme_notation.rb 
Log Message:
Removed "negative?" Integer extension

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 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** cut_location_pair.rb	4 Apr 2007 18:07:44 -0000	1.6
--- cut_location_pair.rb	4 Apr 2007 20:05:06 -0000	1.7
***************
*** 10,14 ****
  
  require 'bio/util/restriction_enzyme/cut_symbol'
- require 'bio/util/restriction_enzyme/integer'
  
  module Bio; end
--- 10,13 ----
***************
*** 98,102 ****
  
    def validate_2( a, b )
!     if (a != nil and a.negative?) or (b != nil and b.negative?)
        raise ArgumentError, "0-based index notation only.  Negative values are illegal."
      end
--- 97,101 ----
  
    def validate_2( a, b )
!     if (a != nil and a < 0) or (b != nil and b < 0)
        raise ArgumentError, "0-based index notation only.  Negative values are illegal."
      end

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 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** cut_locations_in_enzyme_notation.rb	4 Apr 2007 18:07:44 -0000	1.4
--- cut_locations_in_enzyme_notation.rb	4 Apr 2007 20:05:06 -0000	1.5
***************
*** 82,89 ****
      return [] if minimum == nil  # no elements
  
!     if minimum.negative?
        calc = lambda do |n|
          unless n == nil
!           n -= 1 unless n.negative?
            n += minimum.abs
          end
--- 82,89 ----
      return [] if minimum == nil  # no elements
  
!     if minimum < 0
        calc = lambda do |n|
          unless n == nil
!           n -= 1 unless n < 0
            n += minimum.abs
          end

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 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** cut_location_pair_in_enzyme_notation.rb	4 Apr 2007 18:07:44 -0000	1.4
--- cut_location_pair_in_enzyme_notation.rb	4 Apr 2007 20:05:06 -0000	1.5
***************
*** 10,14 ****
  
  require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
- require 'bio/util/restriction_enzyme/integer'
  
  module Bio; end
--- 10,13 ----


From trevor at dev.open-bio.org  Wed Apr  4 16:05:08 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 20:05:08 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme
	test_integer.rb, 1.2, NONE
Message-ID: <200704042005.l34K58jh013924@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv13881/test/unit/bio/util/restriction_enzyme

Removed Files:
	test_integer.rb 
Log Message:
Removed "negative?" Integer extension

--- test_integer.rb DELETED ---


From trevor at dev.open-bio.org  Wed Apr  4 16:05:08 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 20:05:08 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand
	cut_locations_in_enzyme_notation.rb, 1.4, 1.5
Message-ID: <200704042005.l34K58Nf013919@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand
In directory dev.open-bio.org:/tmp/cvs-serv13881/lib/bio/util/restriction_enzyme/single_strand

Modified Files:
	cut_locations_in_enzyme_notation.rb 
Log Message:
Removed "negative?" Integer extension

Index: cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** cut_locations_in_enzyme_notation.rb	4 Apr 2007 18:07:44 -0000	1.4
--- cut_locations_in_enzyme_notation.rb	4 Apr 2007 20:05:06 -0000	1.5
***************
*** 10,14 ****
  
  require 'bio/util/restriction_enzyme/cut_symbol'
- require 'bio/util/restriction_enzyme/integer'
  require 'bio/sequence'
  
--- 10,13 ----
***************
*** 103,109 ****
    def to_array_index
      return [] if @min == nil
!     if @min.negative?
        calc = lambda do |n| 
!         n -= 1 unless n.negative?
          n + @min.abs
        end
--- 102,108 ----
    def to_array_index
      return [] if @min == nil
!     if @min < 0
        calc = lambda do |n| 
!         n -= 1 unless n < 0
          n + @min.abs
        end


From trevor at dev.open-bio.org  Wed Apr  4 16:10:33 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Wed, 04 Apr 2007 20:10:33 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme
	analysis_basic.rb, 1.10, 1.11
Message-ID: <200704042010.l34KAXR9013973@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv13953/lib/bio/util/restriction_enzyme

Modified Files:
	analysis_basic.rb 
Log Message:
Remove "require pp"


Index: analysis_basic.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** analysis_basic.rb	4 Apr 2007 18:07:43 -0000	1.10
--- analysis_basic.rb	4 Apr 2007 20:10:31 -0000	1.11
***************
*** 30,35 ****
  end
  
- require 'pp'
- 
  require 'set'  # for method create_enzyme_actions
  require 'bio/util/restriction_enzyme'
--- 30,33 ----


From k at dev.open-bio.org  Thu Apr  5 11:16:03 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Thu, 05 Apr 2007 15:16:03 +0000
Subject: [BioRuby-cvs] bioruby COPYING, 1.1.1.1, NONE COPYING.LIB, 1.1.1.1,
	NONE
Message-ID: <200704051516.l35FG37P015810@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv15806

Removed Files:
	COPYING COPYING.LIB 
Log Message:
* The BioRuby is now distributed under the same terms as Ruby


--- COPYING.LIB DELETED ---

--- COPYING DELETED ---


From k at dev.open-bio.org  Thu Apr  5 11:18:53 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Thu, 05 Apr 2007 15:18:53 +0000
Subject: [BioRuby-cvs] bioruby README,1.14,1.15 README.DEV,1.12,1.13
Message-ID: <200704051518.l35FIr8h015834@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv15830

Modified Files:
	README README.DEV 
Log Message:
* BioRuby is now distributed under the same terms as Ruby


Index: README
===================================================================
RCS file: /home/repository/bioruby/bioruby/README,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** README	27 Feb 2006 12:28:03 -0000	1.14
--- README	5 Apr 2007 15:18:51 -0000	1.15
***************
*** 167,172 ****
  == LICENSE
  
! BioRuby can be freely distributed under the GNU LGPL license.
! We are trying to change the lincense to Ruby's now.
  
  Note that, install.rb included in the BioRuby package comes from
--- 167,171 ----
  == LICENSE
  
! BioRuby can be freely distributed under the same terms as Ruby.
  
  Note that, install.rb included in the BioRuby package comes from

Index: README.DEV
===================================================================
RCS file: /home/repository/bioruby/bioruby/README.DEV,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** README.DEV	24 Dec 2006 10:11:11 -0000	1.12
--- README.DEV	5 Apr 2007 15:18:51 -0000	1.13
***************
*** 28,33 ****
  compatible with other modules in BioRuby.
  
! BioRuby was previously distributed under the GNU GPL license, but now we
! are changing the license to Ruby's. 
  
  = CODING STYLE
--- 28,33 ----
  compatible with other modules in BioRuby.
  
! BioRuby was previously distributed under the LGPL license, but now is
! distributed under the same terms as Ruby.
  
  = CODING STYLE


From k at dev.open-bio.org  Thu Apr  5 11:37:52 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Thu, 05 Apr 2007 15:37:52 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/kegg ortholog.rb,1.7,1.8
Message-ID: <200704051537.l35FbqoJ016308@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv16283

Modified Files:
	ortholog.rb 
Log Message:
* Recently, KEGG KO database is renamed to KEGG ORTHOLOG, so we follow the change as
  * ko.rb is renamed to ortholog.rb
  * Bio::KEGG::KO is renamed to Bio::KEGG::ORTHOLOG
* genes and dblinks methods are rewrited to use lines_fetch


Index: ortholog.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/ortholog.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** ortholog.rb	8 Mar 2007 00:20:21 -0000	1.7
--- ortholog.rb	5 Apr 2007 15:37:50 -0000	1.8
***************
*** 1,6 ****
  #
! # = bio/db/kegg/ko.rb - KO (KEGG Orthology) database class
  #
! # Copyright::  Copyright (C) 2003 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
  #
--- 1,6 ----
  #
! # = bio/db/kegg/ortholog.rb - KEGG ORTHOLOG database class
  #
! # Copyright::  Copyright (C) 2003-2007 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
  #
***************
*** 22,26 ****
  # * ftp://ftp.genome.jp/pub/kegg/tarfiles/ko
  #
! class KO < KEGGDB
    
    DELIMITER	= RS = "\n///\n"
--- 22,26 ----
  # * ftp://ftp.genome.jp/pub/kegg/tarfiles/ko
  #
! class ORTHOLOG < KEGGDB
    
    DELIMITER	= RS = "\n///\n"
***************
*** 70,80 ****
    def dblinks
      unless @data['DBLINKS']
!       hash = {}
!       get('DBLINKS').scan(/(\S+):\s*(.*)\n/).each do |k, v|
!         hash[k] = v.split(/\s+/)
!       end
!       @data['DBLINKS'] = hash
      end
!     @data['DBLINKS']		# Hash of DB:ID in DBLINKS
    end
  
--- 70,76 ----
    def dblinks
      unless @data['DBLINKS']
!       @data['DBLINKS'] = lines_fetch('DBLINKS')
      end
!     @data['DBLINKS']
    end
  
***************
*** 82,102 ****
    def genes
      unless @data['GENES']
!       hash = {}
!       k = ''
!       get('GENES').each_line do |line|
!         line.chomp!
!         line[0, @tagsize] = '' 
!         if line =~ /(\S+):/
!           k = $1
!           hash[k] = []
!         end
!         line[0, 5] = ''
!         line.gsub(/\(\S+/, '').each(' ') do |u|
!           hash[k] << u.strip
!         end
!       end
!       @data['GENES'] = hash
      end
!     @data['GENES']		# Hash of DB:ID in DBLINKS
    end
    
--- 78,84 ----
    def genes
      unless @data['GENES']
!       @data['GENES'] = lines_fetch('GENES')
      end
!     @data['GENES']
    end
    


From k at dev.open-bio.org  Thu Apr  5 11:43:01 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Thu, 05 Apr 2007 15:43:01 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/db/kegg orthology.rb,1.8,1.9
Message-ID: <200704051543.l35Fh1BI016361@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg
In directory dev.open-bio.org:/tmp/cvs-serv16350/bio/db/kegg

Modified Files:
	orthology.rb 
Log Message:
* The official name of the KEGG KO database is determined to KEGG ORTHOLOGY,
  so the module is renamed. I made CVS trick that mv the file in the repository
  so that we can track the history.


Index: orthology.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/orthology.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** orthology.rb	5 Apr 2007 15:37:50 -0000	1.8
--- orthology.rb	5 Apr 2007 15:42:59 -0000	1.9
***************
*** 1,7 ****
  #
! # = bio/db/kegg/ortholog.rb - KEGG ORTHOLOG database class
  #
  # Copyright::  Copyright (C) 2003-2007 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
  #
  # $Id$
--- 1,8 ----
  #
! # = bio/db/kegg/orthology.rb - KEGG ORTHOLOGY database class
  #
  # Copyright::  Copyright (C) 2003-2007 Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2003 Masumi Itoh <m at bioruby.org>
+ # License::    The Ruby License
  #
  # $Id$
***************
*** 20,26 ****
  #
  # * http://www.genome.jp/dbget-bin/get_htext?KO
! # * ftp://ftp.genome.jp/pub/kegg/tarfiles/ko
  #
! class ORTHOLOG < KEGGDB
    
    DELIMITER	= RS = "\n///\n"
--- 21,27 ----
  #
  # * http://www.genome.jp/dbget-bin/get_htext?KO
! # * ftp://ftp.genome.jp/pub/kegg/genes/ko
  #
! class ORTHOLOGY < KEGGDB
    
    DELIMITER	= RS = "\n///\n"
***************
*** 83,87 ****
    end
    
! end # KO
      
  end # KEGG
--- 84,88 ----
    end
    
! end # ORTHOLOGY
      
  end # KEGG
***************
*** 95,99 ****
  
    flat = Bio::Fetch.query('ko', 'K00001')
!   entry = Bio::KEGG::KO.new(flat)
  
    p entry.entry_id
--- 96,100 ----
  
    flat = Bio::Fetch.query('ko', 'K00001')
!   entry = Bio::KEGG::ORTHOLOGY.new(flat)
  
    p entry.entry_id


From k at dev.open-bio.org  Thu Apr  5 11:43:01 2007
From: k at dev.open-bio.org (Katayama Toshiaki)
Date: Thu, 05 Apr 2007 15:43:01 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.82,1.83
Message-ID: <200704051543.l35Fh1J1016356@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv16350

Modified Files:
	bio.rb 
Log Message:
* The official name of the KEGG KO database is determined to KEGG ORTHOLOGY,
  so the module is renamed. I made CVS trick that mv the file in the repository
  so that we can track the history.


Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.82
retrieving revision 1.83
diff -C2 -d -r1.82 -r1.83
*** bio.rb	8 Mar 2007 00:25:26 -0000	1.82
--- bio.rb	5 Apr 2007 15:42:59 -0000	1.83
***************
*** 95,99 ****
      autoload :CELL,         'bio/db/kegg/cell'
      autoload :EXPRESSION,   'bio/db/kegg/expression'
!     autoload :ORTHOLOG,     'bio/db/kegg/ortholog'
      autoload :KGML,         'bio/db/kegg/kgml'
      autoload :Keggtab,      'bio/db/kegg/keggtab'
--- 95,99 ----
      autoload :CELL,         'bio/db/kegg/cell'
      autoload :EXPRESSION,   'bio/db/kegg/expression'
!     autoload :ORTHOLOGY,    'bio/db/kegg/orthology'
      autoload :KGML,         'bio/db/kegg/kgml'
      autoload :Keggtab,      'bio/db/kegg/keggtab'


From nakao at dev.open-bio.org  Thu Apr  5 13:12:02 2007
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 05 Apr 2007 17:12:02 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_alignment.rb, 1.9,
	1.10 test_feature.rb, 1.3, 1.4 test_location.rb, 1.2,
	1.3 test_pathway.rb, 1.3, 1.4 test_sequence.rb, 1.6, 1.7
Message-ID: <200704051712.l35HC2BV016629@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory dev.open-bio.org:/tmp/cvs-serv16609/test/unit/bio

Modified Files:
	test_alignment.rb test_feature.rb test_location.rb 
	test_pathway.rb test_sequence.rb 
Log Message:
* Chaged license LGPL to Ruby's


Index: test_pathway.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_pathway.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_pathway.rb	18 Dec 2005 16:50:56 -0000	1.3
--- test_pathway.rb	5 Apr 2007 17:12:00 -0000	1.4
***************
*** 2,20 ****
  # test/bio/tc_pathway.rb - Unit test for Bio::Pathway
  #
! #   Copyright (C) 2004 Moses Hohman <mmhohman at northwestern.edu>
! #
! #  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
  #
  #  $Id$
--- 2,8 ----
  # test/bio/tc_pathway.rb - Unit test for Bio::Pathway
  #
! # Copyright::  Copyright (C) 2004
! #              Moses Hohman <mmhohman at northwestern.edu>
! # License::    Ruby's
  #
  #  $Id$

Index: test_location.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_location.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_location.rb	24 Sep 2005 03:12:55 -0000	1.2
--- test_location.rb	5 Apr 2007 17:12:00 -0000	1.3
***************
*** 2,20 ****
  # test/unit/bio/test_location.rb - Unit test for Bio::Location
  #
! #   Copyright (C) 2004 Moses Hohman <mmhohman at northwestern.edu>
! #
! #  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
  #
  #  $Id$
--- 2,8 ----
  # test/unit/bio/test_location.rb - Unit test for Bio::Location
  #
! # Copyright::  Copyright (C) 2004 
! #              Moses Hohman <mmhohman at northwestern.edu>
! # License::    Ruby's
  #
  #  $Id$

Index: test_feature.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_feature.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_feature.rb	24 Dec 2006 17:19:04 -0000	1.3
--- test_feature.rb	5 Apr 2007 17:12:00 -0000	1.4
***************
*** 2,6 ****
  # test/unit/bio/test_feature.rb - Unit test for Features/Feature classes
  #
! # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
  # License::    Ruby's
  #
--- 2,7 ----
  # test/unit/bio/test_feature.rb - Unit test for Features/Feature classes
  #
! # Copyright::  Copyright (C) 2005 
! #              Mitsuteru Nakao <n at bioruby.org>
  # License::    Ruby's
  #

Index: test_sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_sequence.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** test_sequence.rb	5 Feb 2006 17:39:27 -0000	1.6
--- test_sequence.rb	5 Apr 2007 17:12:00 -0000	1.7
***************
*** 2,21 ****
  # test/unit/bio/test_sequence.rb - Unit test for Bio::Sequencce
  #
! #   Copyright (C) 2004 Moses Hohman <mmhohman at northwestern.edu>
! #   Copyright (C) 2006 Mitsuteru C. Nakao <n at bioruby.org>
! #
! #  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
  #
  #  $Id$
--- 2,9 ----
  # test/unit/bio/test_sequence.rb - Unit test for Bio::Sequencce
  #
! # Copyright::  Copyright (C) 2004
! #              Moses Hohman <mmhohman at northwestern.edu>
! #              2006 Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$

Index: test_alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_alignment.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** test_alignment.rb	24 Dec 2006 17:19:04 -0000	1.9
--- test_alignment.rb	5 Apr 2007 17:12:00 -0000	1.10
***************
*** 2,21 ****
  # test/unit/bio/test_alignment.rb - Unit test for Bio::Alignment
  #
! # Copyright::  Copyright (C) 2004 Moses Hohman <mmhohman at northwestern.edu>
! #              Copyright (C) 2005 Naohisa Goto <ng at bioruby.org>
! #
! #  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
  #
  #  $Id$
--- 2,9 ----
  # test/unit/bio/test_alignment.rb - Unit test for Bio::Alignment
  #
! # Copyright::  Copyright (C) 2004
! #              Moses Hohman <mmhohman at northwestern.edu>
! #              2005 Naohisa Goto <ng at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$


From nakao at dev.open-bio.org  Thu Apr  5 13:22:16 2007
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 05 Apr 2007 17:22:16 +0000
Subject: [BioRuby-cvs] bioruby/sample goslim.rb,1.3,1.4
Message-ID: <200704051722.l35HMGiJ016718@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv16698/sample

Modified Files:
	goslim.rb 
Log Message:
* Chaged license LGPL to Ruby's


Index: goslim.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/goslim.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** goslim.rb	13 May 2003 10:45:42 -0000	1.3
--- goslim.rb	5 Apr 2007 17:22:14 -0000	1.4
***************
*** 11,25 ****
  #    % gv mgi.pdf
  #
! #   Copyright (C) 2003 Mitsuteru C. Nakao <n at bioruby.org>
! #
! #  This program is free software; you can redistribute it and/or modify
! #  it under the terms of the GNU General Public License as published by
! #  the Free Software Foundation; either version 2 of the License, or
! #  (at your option) any later version.
! #
! #  This program 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 General Public License for more details.
  #
  #  $Id$
--- 11,17 ----
  #    % gv mgi.pdf
  #
! # Copyright::  Copyright (C) 2003
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$


From nakao at dev.open-bio.org  Thu Apr  5 13:23:44 2007
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 05 Apr 2007 17:23:44 +0000
Subject: [BioRuby-cvs] bioruby/sample psortplot_html.rb,1.1,1.2
Message-ID: <200704051723.l35HNh7H016746@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv16726/sample

Modified Files:
	psortplot_html.rb 
Log Message:
Chagend license LPGL to Ruby's


Index: psortplot_html.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/psortplot_html.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** psortplot_html.rb	12 Oct 2005 02:10:11 -0000	1.1
--- psortplot_html.rb	5 Apr 2007 17:23:41 -0000	1.2
***************
*** 12,26 ****
  #   % cat eco00010_psort2.html
  #
! # Copyright (C) 2005 Mitsuteru C. Nakao <n at bioruby.org>
! #
! #  This program is free software; you can redistribute it and/or modify
! #  it under the terms of the GNU General Public License as published by
! #  the Free Software Foundation; either version 2 of the License, or
! #  (at your option) any later version.
! #
! #  This program 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 General Public License for more details.
  #
  #  $Id$
--- 12,18 ----
  #   % cat eco00010_psort2.html
  #
! # Copyright::  Copyright (C) 2005
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$


From nakao at dev.open-bio.org  Thu Apr  5 13:26:31 2007
From: nakao at dev.open-bio.org (Mitsuteru C. Nakao)
Date: Thu, 05 Apr 2007 17:26:31 +0000
Subject: [BioRuby-cvs] bioruby/sample color_scheme_na.rb,1.1,1.2
Message-ID: <200704051726.l35HQVfx016795@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv16775/sample

Modified Files:
	color_scheme_na.rb 
Log Message:
Chaged lincense LPGL to Ruby's


Index: color_scheme_na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/color_scheme_na.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** color_scheme_na.rb	31 Oct 2005 07:39:13 -0000	1.1
--- color_scheme_na.rb	5 Apr 2007 17:26:29 -0000	1.2
***************
*** 14,28 ****
  #
  #
! # Copyright (C) 2005 Mitsuteru C. Nakao <n at bioruby.org>
! #
! #  This program is free software; you can redistribute it and/or modify
! #  it under the terms of the GNU General Public License as published by
! #  the Free Software Foundation; either version 2 of the License, or
! #  (at your option) any later version.
! #
! #  This program 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 General Public License for more details.
  #
  #  $Id$
--- 14,20 ----
  #
  #
! # Copyright::  Copyright (C) 2005
! #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:10:11 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:10:11 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_sequence.rb,1.7,1.8
Message-ID: <200704052310.l35NABc1019950@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory dev.open-bio.org:/tmp/cvs-serv19921/test/unit/bio

Modified Files:
	test_sequence.rb 
Log Message:
Integrate Toshiaki's improvements of to_re in Bio::Sequence::NA

Index: test_sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_sequence.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** test_sequence.rb	5 Apr 2007 17:12:00 -0000	1.7
--- test_sequence.rb	5 Apr 2007 23:10:09 -0000	1.8
***************
*** 191,199 ****
  
      def test_dna_to_re
!       assert_equal(/atgc[ag][tc][ac][tg][atg][atc][agc][tgc][gc][at][atgc]/, Sequence::NA.new('atgcrymkdhvbswn').to_re)
      end
  
      def test_rna_to_re
!       assert_equal(/augc[ag][uc][ac][ug][aug][auc][agc][ugc][gc][au][augc]/, Sequence::NA.new('augcrymkdhvbswn').to_re)
      end
  
--- 191,199 ----
  
      def test_dna_to_re
!       assert_equal(/atgc[agr][tcy][acm][tgk][atgrwkd][atcwmyh][agcmrsv][tgcyskb][gcw][atw][atgcyrwskmbdhvn]/, Sequence::NA.new('atgcrymkdhvbswn').to_re)
      end
  
      def test_rna_to_re
!       assert_equal(/augc[agr][ucy][acm][ugk][augrwkd][aucwmyh][agcmrsv][ugcyskb][gcw][auw][augcyrwskmbdhvn]/, Sequence::NA.new('augcrymkdhvbswn').to_re)
      end
  


From trevor at dev.open-bio.org  Thu Apr  5 19:10:12 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:10:12 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/sequence test_na.rb,1.3,1.4
Message-ID: <200704052310.l35NACJd019960@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/sequence
In directory dev.open-bio.org:/tmp/cvs-serv19921/test/unit/bio/sequence

Modified Files:
	test_na.rb 
Log Message:
Integrate Toshiaki's improvements of to_re in Bio::Sequence::NA

Index: test_na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_na.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_na.rb	31 Dec 2006 21:54:49 -0000	1.3
--- test_na.rb	5 Apr 2007 23:10:10 -0000	1.4
***************
*** 142,146 ****
        @obj[4,1] = 'y'
        @obj[5,1] = 'w'
!       assert_equal(/a[atgc][ag][gc][tc][at]gcatgcatgcaaaa/, @obj.to_re)
      end
  
--- 142,146 ----
        @obj[4,1] = 'y'
        @obj[5,1] = 'w'
!       assert_equal(/a[atgcyrwskmbdhvn][agr][gcw][tcy][atw]gcatgcatgcaaaa/, @obj.to_re)
      end
  


From trevor at dev.open-bio.org  Thu Apr  5 19:10:11 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:10:11 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/data na.rb,0.20,0.21
Message-ID: <200704052310.l35NABQM019947@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/data
In directory dev.open-bio.org:/tmp/cvs-serv19921/lib/bio/data

Modified Files:
	na.rb 
Log Message:
Integrate Toshiaki's improvements of to_re in Bio::Sequence::NA

Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v
retrieving revision 0.20
retrieving revision 0.21
diff -C2 -d -r0.20 -r0.21
*** na.rb	8 Feb 2006 12:15:42 -0000	0.20
--- na.rb	5 Apr 2007 23:10:09 -0000	0.21
***************
*** 159,165 ****
  
      def to_re(seq, rna = false)
        str = seq.to_s.downcase
        str.gsub!(/[^atgcu]/) { |base|
!         NAMES[base] || '.'
        }
        if rna
--- 159,179 ----
  
      def to_re(seq, rna = false)
+       replace = {
+         'y' => '[tcy]',
+         'r' => '[agr]',
+         'w' => '[atw]',
+         's' => '[gcw]',
+         'k' => '[tgk]',
+         'm' => '[acm]',
+         'b' => '[tgcyskb]',
+         'd' => '[atgrwkd]',
+         'h' => '[atcwmyh]',
+         'v' => '[agcmrsv]',
+         'n' => '[atgcyrwskmbdhvn]'
+       }
+ 
        str = seq.to_s.downcase
        str.gsub!(/[^atgcu]/) { |base|
!         replace[base] || base
        }
        if rna


From trevor at dev.open-bio.org  Thu Apr  5 19:10:12 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:10:12 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/data test_na.rb,1.7,1.8
Message-ID: <200704052310.l35NACFb019953@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/data
In directory dev.open-bio.org:/tmp/cvs-serv19921/test/unit/bio/data

Modified Files:
	test_na.rb 
Log Message:
Integrate Toshiaki's improvements of to_re in Bio::Sequence::NA

Index: test_na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/data/test_na.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** test_na.rb	31 Dec 2006 21:54:49 -0000	1.7
--- test_na.rb	5 Apr 2007 23:10:09 -0000	1.8
***************
*** 41,45 ****
  
      def test_to_re
!       re = /[tc][ag][at][gc][tg][ac][tgc][atg][agc][atgc]atgc/
        str = 'yrwskmbdvnatgc'
        str0 = str.clone
--- 41,45 ----
  
      def test_to_re
!       re = /[tcy][agr][atw][gcw][tgk][acm][tgcyskb][atgrwkd][agcmrsv][atgcyrwskmbdhvn]atgc/
        str = 'yrwskmbdvnatgc'
        str0 = str.clone


From trevor at dev.open-bio.org  Thu Apr  5 19:35:44 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:44 +0000
Subject: [BioRuby-cvs] bioruby/sample color_scheme_na.rb, 1.2, 1.3 goslim.rb,
	1.4, 1.5 psortplot_html.rb, 1.2, 1.3
Message-ID: <200704052335.l35NZicD020280@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/sample
In directory dev.open-bio.org:/tmp/cvs-serv20013/sample

Modified Files:
	color_scheme_na.rb goslim.rb psortplot_html.rb 
Log Message:
Standardize on The Ruby License

Index: goslim.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/goslim.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** goslim.rb	5 Apr 2007 17:22:14 -0000	1.4
--- goslim.rb	5 Apr 2007 23:35:42 -0000	1.5
***************
*** 13,17 ****
  # Copyright::  Copyright (C) 2003
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 13,17 ----
  # Copyright::  Copyright (C) 2003
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$

Index: color_scheme_na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/color_scheme_na.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** color_scheme_na.rb	5 Apr 2007 17:26:29 -0000	1.2
--- color_scheme_na.rb	5 Apr 2007 23:35:42 -0000	1.3
***************
*** 16,20 ****
  # Copyright::  Copyright (C) 2005
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 16,20 ----
  # Copyright::  Copyright (C) 2005
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$

Index: psortplot_html.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/sample/psortplot_html.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** psortplot_html.rb	5 Apr 2007 17:23:41 -0000	1.2
--- psortplot_html.rb	5 Apr 2007 23:35:42 -0000	1.3
***************
*** 14,18 ****
  # Copyright::  Copyright (C) 2005
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 14,18 ----
  # Copyright::  Copyright (C) 2005
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:44 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:44 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range
	cut_range.rb, 1.2, 1.3 cut_ranges.rb, 1.3,
	1.4 horizontal_cut_range.rb, 1.3, 1.4 sequence_range.rb, 1.6,
	1.7 vertical_cut_range.rb, 1.3, 1.4
Message-ID: <200704052335.l35NZiVS020265@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util/restriction_enzyme/range

Modified Files:
	cut_range.rb cut_ranges.rb horizontal_cut_range.rb 
	sequence_range.rb vertical_cut_range.rb 
Log Message:
Standardize on The Ruby License

Index: vertical_cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** vertical_cut_range.rb	4 Apr 2007 18:07:44 -0000	1.3
--- vertical_cut_range.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 20,24 ****
  # 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
  #
  # FIXME docs are kind of out of date.  Change this to VerticalAndHorizontalCutRange
--- 20,24 ----
  # 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

Index: horizontal_cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** horizontal_cut_range.rb	4 Apr 2007 18:07:44 -0000	1.3
--- horizontal_cut_range.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 20,24 ****
  # 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 HorizontalCutRange < CutRange
--- 20,24 ----
  # 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

Index: sequence_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** sequence_range.rb	4 Apr 2007 18:07:44 -0000	1.6
--- sequence_range.rb	5 Apr 2007 23:35:42 -0000	1.7
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 25,29 ****
  # 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
  #
  # A defined range over a nucleotide sequence.
--- 25,29 ----
  # 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.

Index: cut_ranges.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/cut_ranges.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** cut_ranges.rb	4 Apr 2007 18:07:44 -0000	1.3
--- cut_ranges.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 18,22 ****
  # 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
  #
  # Container for many CutRange objects or CutRange child objects.  Inherits from array.
--- 18,22 ----
  # 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.

Index: cut_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/cut_range.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** cut_range.rb	4 Apr 2007 18:07:44 -0000	1.2
--- cut_range.rb	5 Apr 2007 23:35:42 -0000	1.3
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 20,24 ****
  # 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
  #
  # Abstract base class for HorizontalCutRange and VerticalCutRange
--- 20,24 ----
  # 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


From trevor at dev.open-bio.org  Thu Apr  5 19:35:45 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:45 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/bl2seq test_report.rb, 1.2,
	1.3
Message-ID: <200704052335.l35NZjNg020302@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/bl2seq
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/bl2seq

Modified Files:
	test_report.rb 
Log Message:
Standardize on The Ruby License

Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/bl2seq/test_report.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_report.rb	23 Feb 2006 22:25:30 -0000	1.2
--- test_report.rb	5 Apr 2007 23:35:43 -0000	1.3
***************
*** 5,9 ****
  #  Copyright::   Copyright (C) 2006 
  #                Mitsuteru C. Nakao <n at bioruby.org>
! #  License::     Ruby's
  #
  #  $Id$
--- 5,9 ----
  #  Copyright::   Copyright (C) 2006 
  #                Mitsuteru C. Nakao <n at bioruby.org>
! #  License::     The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:45 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:45 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/data test_aa.rb, 1.5,
	1.6 test_codontable.rb, 1.5, 1.6 test_na.rb, 1.8, 1.9
Message-ID: <200704052335.l35NZj7p020329@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/data
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/data

Modified Files:
	test_aa.rb test_codontable.rb test_na.rb 
Log Message:
Standardize on The Ruby License

Index: test_codontable.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/data/test_codontable.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** test_codontable.rb	24 Dec 2006 17:19:04 -0000	1.5
--- test_codontable.rb	5 Apr 2007 23:35:43 -0000	1.6
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$

Index: test_na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/data/test_na.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** test_na.rb	5 Apr 2007 23:10:09 -0000	1.8
--- test_na.rb	5 Apr 2007 23:35:43 -0000	1.9
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2005,2006 Mitsuteru Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2005,2006 Mitsuteru Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$

Index: test_aa.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/data/test_aa.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** test_aa.rb	24 Dec 2006 17:19:04 -0000	1.5
--- test_aa.rb	5 Apr 2007 23:35:43 -0000	1.6
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:46 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:46 +0000
Subject: [BioRuby-cvs]
	bioruby/test/unit/bio/util/restriction_enzyme/double_stranded
	test_aligned_strands.rb, 1.2, 1.3 test_cut_location_pair.rb,
	1.2, 1.3 test_cut_location_pair_in_enzyme_notation.rb, 1.2,
	1.3 test_cut_locations.rb, 1.2,
	1.3 test_cut_locations_in_enzyme_notation.rb, 1.2, 1.3
Message-ID: <200704052335.l35NZkFq020441@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/double_stranded
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util/restriction_enzyme/double_stranded

Modified Files:
	test_aligned_strands.rb test_cut_location_pair.rb 
	test_cut_location_pair_in_enzyme_notation.rb 
	test_cut_locations.rb test_cut_locations_in_enzyme_notation.rb 
Log Message:
Standardize on The Ruby License

Index: test_cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_cut_locations_in_enzyme_notation.rb	31 Dec 2006 18:46:15 -0000	1.2
--- test_cut_locations_in_enzyme_notation.rb	5 Apr 2007 23:35:44 -0000	1.3
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$

Index: test_aligned_strands.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_aligned_strands.rb	31 Dec 2006 18:46:15 -0000	1.2
--- test_aligned_strands.rb	5 Apr 2007 23:35:44 -0000	1.3
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$

Index: test_cut_locations.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_cut_locations.rb	31 Dec 2006 18:46:15 -0000	1.2
--- test_cut_locations.rb	5 Apr 2007 23:35:44 -0000	1.3
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$

Index: test_cut_location_pair_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_cut_location_pair_in_enzyme_notation.rb	31 Dec 2006 18:46:15 -0000	1.2
--- test_cut_location_pair_in_enzyme_notation.rb	5 Apr 2007 23:35:44 -0000	1.3
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$

Index: test_cut_location_pair.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_cut_location_pair.rb	31 Dec 2006 18:46:15 -0000	1.2
--- test_cut_location_pair.rb	5 Apr 2007 23:35:44 -0000	1.3
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:45 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:45 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/targetp test_report.rb, 1.4,
	1.5
Message-ID: <200704052335.l35NZjAb020323@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/targetp
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/targetp

Modified Files:
	test_report.rb 
Log Message:
Standardize on The Ruby License

Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/targetp/test_report.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_report.rb	24 Dec 2006 17:19:04 -0000	1.4
--- test_report.rb	5 Apr 2007 23:35:43 -0000	1.5
***************
*** 3,7 ****
  #
  # Copyright:  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::   The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:45 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:45 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/genscan test_report.rb, 1.3,
	1.4
Message-ID: <200704052335.l35NZjsa020314@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/genscan
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/genscan

Modified Files:
	test_report.rb 
Log Message:
Standardize on The Ruby License

Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/genscan/test_report.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_report.rb	24 Dec 2006 17:19:04 -0000	1.3
--- test_report.rb	5 Apr 2007 23:35:43 -0000	1.4
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:45 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:45 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/hmmer test_report.rb, 1.2,
	1.3
Message-ID: <200704052335.l35NZjfJ020317@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/hmmer
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/hmmer

Modified Files:
	test_report.rb 
Log Message:
Standardize on The Ruby License

Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/hmmer/test_report.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_report.rb	24 Dec 2006 17:19:04 -0000	1.2
--- test_report.rb	5 Apr 2007 23:35:43 -0000	1.3
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2006 Mitsuteru Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2006 Mitsuteru Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:44 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:44 +0000
Subject: [BioRuby-cvs]
	bioruby/lib/bio/util/restriction_enzyme/range/sequence_range
	calculated_cuts.rb, 1.5, 1.6 fragment.rb, 1.3,
	1.4 fragments.rb, 1.3, 1.4
Message-ID: <200704052335.l35NZi7A020272@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util/restriction_enzyme/range/sequence_range

Modified Files:
	calculated_cuts.rb fragment.rb fragments.rb 
Log Message:
Standardize on The Ruby License

Index: calculated_cuts.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** calculated_cuts.rb	4 Apr 2007 18:07:44 -0000	1.5
--- calculated_cuts.rb	5 Apr 2007 23:35:42 -0000	1.6
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 23,27 ****
  # 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
  # 
  # cc = CalculatedCuts.new(@size)
--- 23,27 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  # 
  # cc = CalculatedCuts.new(@size)

Index: fragment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** fragment.rb	4 Apr 2007 18:07:44 -0000	1.3
--- fragment.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 23,27 ****
  # 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 Fragment
--- 23,27 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  class Fragment

Index: fragments.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** fragments.rb	4 Apr 2007 18:07:44 -0000	1.3
--- fragments.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 19,23 ****
  # 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 Fragments < Array
--- 19,23 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  class Fragments < Array


From trevor at dev.open-bio.org  Thu Apr  5 19:35:44 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:44 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand
	cut_locations_in_enzyme_notation.rb, 1.5, 1.6
Message-ID: <200704052335.l35NZi89020277@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util/restriction_enzyme/single_strand

Modified Files:
	cut_locations_in_enzyme_notation.rb 
Log Message:
Standardize on The Ruby License

Index: cut_locations_in_enzyme_notation.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** cut_locations_in_enzyme_notation.rb	4 Apr 2007 20:05:06 -0000	1.5
--- cut_locations_in_enzyme_notation.rb	5 Apr 2007 23:35:42 -0000	1.6
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 21,25 ****
  # 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 the cut location in thier enzyme index notation
--- 21,25 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  # Stores the cut location in thier enzyme index notation


From trevor at dev.open-bio.org  Thu Apr  5 19:35:44 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:44 +0000
Subject: [BioRuby-cvs] bioruby/test/functional/bio/io test_ensembl.rb, 1.3,
	1.4 test_soapwsdl.rb, 1.3, 1.4
Message-ID: <200704052335.l35NZiUR020285@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/functional/bio/io
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/functional/bio/io

Modified Files:
	test_ensembl.rb test_soapwsdl.rb 
Log Message:
Standardize on The Ruby License

Index: test_ensembl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/functional/bio/io/test_ensembl.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_ensembl.rb	29 Mar 2007 08:00:04 -0000	1.3
--- test_ensembl.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2007
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2007
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     The Ruby License
  #
  #  $Id$

Index: test_soapwsdl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/functional/bio/io/test_soapwsdl.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_soapwsdl.rb	28 Mar 2007 20:48:11 -0000	1.3
--- test_soapwsdl.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2005,2007
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$ 
--- 4,8 ----
  # Copyright::   Copyright (C) 2005,2007
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     The Ruby License
  #
  #  $Id$ 


From trevor at dev.open-bio.org  Thu Apr  5 19:35:45 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:45 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/sosui test_report.rb, 1.4,
	1.5
Message-ID: <200704052335.l35NZjM3020320@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/sosui
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/sosui

Modified Files:
	test_report.rb 
Log Message:
Standardize on The Ruby License

Index: test_report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/sosui/test_report.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_report.rb	24 Dec 2006 17:19:04 -0000	1.4
--- test_report.rb	5 Apr 2007 23:35:43 -0000	1.5
***************
*** 3,7 ****
  #
  # Copyright::   Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::   Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::     The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:45 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:45 +0000
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl test_blast.rb, 1.4,
	1.5 test_fasta.rb, 1.2, 1.3 test_pts1.rb, 1.2, 1.3
Message-ID: <200704052335.l35NZjTX020295@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/test/unit/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl

Modified Files:
	test_blast.rb test_fasta.rb test_pts1.rb 
Log Message:
Standardize on The Ruby License

Index: test_fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/test_fasta.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_fasta.rb	29 Mar 2007 13:08:46 -0000	1.2
--- test_fasta.rb	5 Apr 2007 23:35:43 -0000	1.3
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2006
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  #  $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2006
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     The Ruby License
  #
  #  $Id$

Index: test_pts1.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/test_pts1.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_pts1.rb	5 Jun 2006 02:54:42 -0000	1.2
--- test_pts1.rb	5 Apr 2007 23:35:43 -0000	1.3
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2006 
  #               Mitsuteru Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2006 
  #               Mitsuteru Nakao <n at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: test_blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/test_blast.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_blast.rb	24 Dec 2006 17:19:04 -0000	1.4
--- test_blast.rb	5 Apr 2007 23:35:43 -0000	1.5
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2005 Mitsuteru Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby README.DEV,1.13,1.14
Message-ID: <200704052336.l35NZfWb020085@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv20013

Modified Files:
	README.DEV 
Log Message:
Standardize on The Ruby License

Index: README.DEV
===================================================================
RCS file: /home/repository/bioruby/bioruby/README.DEV,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** README.DEV	5 Apr 2007 15:18:51 -0000	1.13
--- README.DEV	5 Apr 2007 23:35:39 -0000	1.14
***************
*** 80,84 ****
    # Copyright::  Copyright (C) 2006 Chem R. Hacker <crh at example.org>
    #
!   # License::    Ruby's
    #
    # $ I d: $
--- 80,84 ----
    # Copyright::  Copyright (C) 2006 Chem R. Hacker <crh at example.org>
    #
!   # License::    The Ruby License
    #
    # $ I d: $


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.83,1.84
Message-ID: <200704052336.l35NZfce020092@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib

Modified Files:
	bio.rb 
Log Message:
Standardize on The Ruby License

Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.83
retrieving revision 1.84
diff -C2 -d -r1.83 -r1.84
*** bio.rb	5 Apr 2007 15:42:59 -0000	1.83
--- bio.rb	5 Apr 2007 23:35:39 -0000	1.84
***************
*** 4,8 ****
  # Copyright::	Copyright (C) 2001-2006
  #		Toshiaki Katayama <k at bioruby.org>
! # License::	Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::	Copyright (C) 2001-2006
  #		Toshiaki Katayama <k at bioruby.org>
! # License::	The Ruby License
  #
  # $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio alignment.rb, 1.21, 1.22 command.rb,
	1.16, 1.17 db.rb, 0.36, 0.37 feature.rb, 1.12,
	1.13 location.rb, 0.27, 0.28 pathway.rb, 1.35,
	1.36 reference.rb, 1.23, 1.24 sequence.rb, 0.57, 0.58 tree.rb,
	1.7, 1.8
Message-ID: <200704052336.l35NZfht020097@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio

Modified Files:
	alignment.rb command.rb db.rb feature.rb location.rb 
	pathway.rb reference.rb sequence.rb tree.rb 
Log Message:
Standardize on The Ruby License

Index: location.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/location.rb,v
retrieving revision 0.27
retrieving revision 0.28
diff -C2 -d -r0.27 -r0.28
*** location.rb	24 Dec 2006 10:10:08 -0000	0.27
--- location.rb	5 Apr 2007 23:35:39 -0000	0.28
***************
*** 4,8 ****
  # Copyright::	Copyright (C) 2001, 2005 Toshiaki Katayama <k at bioruby.org>
  # Copyright::   Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::	Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::	Copyright (C) 2001, 2005 Toshiaki Katayama <k at bioruby.org>
  # Copyright::   Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::	The Ruby License
  #
  # $Id$

Index: command.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/command.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** command.rb	29 Mar 2007 12:14:46 -0000	1.16
--- command.rb	5 Apr 2007 23:35:39 -0000	1.17
***************
*** 5,9 ****
  # 		Naohisa Goto <ng at bioruby.org>,
  #		Toshiaki Katayama <k at bioruby.org>
! # License::	Ruby's
  #
  #  $Id$
--- 5,9 ----
  # 		Naohisa Goto <ng at bioruby.org>,
  #		Toshiaki Katayama <k at bioruby.org>
! # License::	The Ruby License
  #
  #  $Id$

Index: feature.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/feature.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** feature.rb	9 May 2006 11:52:30 -0000	1.12
--- feature.rb	5 Apr 2007 23:35:39 -0000	1.13
***************
*** 4,8 ****
  # Copyright::	Copyright (c) 2002, 2005  Toshiaki Katayama <k at bioruby.org>
  #                             2006        Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::	Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::	Copyright (c) 2002, 2005  Toshiaki Katayama <k at bioruby.org>
  #                             2006        Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::	The Ruby License
  #
  # $Id$

Index: tree.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/tree.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** tree.rb	12 Jan 2007 16:10:28 -0000	1.7
--- tree.rb	5 Apr 2007 23:35:39 -0000	1.8
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2006
  #               Naohisa Goto <ng at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2006
  #               Naohisa Goto <ng at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** alignment.rb	14 Dec 2006 19:52:53 -0000	1.21
--- alignment.rb	5 Apr 2007 23:35:39 -0000	1.22
***************
*** 5,9 ****
  #             GOTO Naohisa <ng at bioruby.org>
  #
! # License:: Ruby's
  #
  #  $Id$
--- 5,9 ----
  #             GOTO Naohisa <ng at bioruby.org>
  #
! # License:: The Ruby License
  #
  #  $Id$

Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.57
retrieving revision 0.58
diff -C2 -d -r0.57 -r0.58
*** sequence.rb	26 Mar 2006 02:27:59 -0000	0.57
--- sequence.rb	5 Apr 2007 23:35:39 -0000	0.58
***************
*** 8,12 ****
  #               Ryan Raaum <ryan at raaum.org>,
  #               Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::     Ruby's
  #
  # $Id$
--- 8,12 ----
  #               Ryan Raaum <ryan at raaum.org>,
  #               Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::     The Ruby License
  #
  # $Id$

Index: db.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db.rb,v
retrieving revision 0.36
retrieving revision 0.37
diff -C2 -d -r0.36 -r0.37
*** db.rb	15 Jan 2007 04:33:52 -0000	0.36
--- db.rb	5 Apr 2007 23:35:39 -0000	0.37
***************
*** 4,8 ****
  # Copyright::  Copyright (C) 2001, 2002, 2005
  #              Toshiaki Katayama <k at bioruby.org>
! # License::    Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::  Copyright (C) 2001, 2002, 2005
  #              Toshiaki Katayama <k at bioruby.org>
! # License::    The Ruby License
  #
  # $Id$

Index: pathway.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/pathway.rb,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** pathway.rb	25 Jul 2006 18:21:26 -0000	1.35
--- pathway.rb	5 Apr 2007 23:35:39 -0000	1.36
***************
*** 5,9 ****
  #               Toshiaki Katayama <k at bioruby.org>,
  #               Shuichi Kawashima <shuichi at hgc.jp>
! # License::     Ruby's
  #
  #  $Id$
--- 5,9 ----
  #               Toshiaki Katayama <k at bioruby.org>,
  #               Shuichi Kawashima <shuichi at hgc.jp>
! # License::     The Ruby License
  #
  #  $Id$

Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** reference.rb	31 Dec 2006 21:54:49 -0000	1.23
--- reference.rb	5 Apr 2007 23:35:39 -0000	1.24
***************
*** 5,9 ****
  #               Toshiaki Katayama <k at bioruby.org>,
  #               Ryan Raaum <ryan at raaum.org>
! # License::     Ruby's
  #
  # $Id$
--- 5,9 ----
  #               Toshiaki Katayama <k at bioruby.org>,
  #               Ryan Raaum <ryan at raaum.org>
! # License::     The Ruby License
  #
  # $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/bl2seq report.rb,1.7,1.8
Message-ID: <200704052336.l35NZfRh020107@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/bl2seq

Modified Files:
	report.rb 
Log Message:
Standardize on The Ruby License

Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb	30 Apr 2006 05:40:23 -0000	1.7
--- report.rb	5 Apr 2007 23:35:39 -0000	1.8
***************
*** 3,7 ****
  # 
  # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$
--- 3,7 ----
  # 
  # Copyright:: Copyright (C) 2005 GOTO Naohisa <ng at bioruby.org>
! # License::   The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.11,1.12
Message-ID: <200704052336.l35NZfKr020120@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/clustalw
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/clustalw

Modified Files:
	report.rb 
Log Message:
Standardize on The Ruby License

Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw/report.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** report.rb	14 Dec 2006 15:22:05 -0000	1.11
--- report.rb	5 Apr 2007 23:35:39 -0000	1.12
***************
*** 3,7 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/bin bioruby, 1.18, 1.19 br_biofetch.rb, 1.3,
	1.4 br_bioflat.rb, 1.16, 1.17 br_biogetseq.rb, 1.3,
	1.4 br_pmfetch.rb, 1.6, 1.7
Message-ID: <200704052336.l35NZfpm020089@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/bin
In directory dev.open-bio.org:/tmp/cvs-serv20013/bin

Modified Files:
	bioruby br_biofetch.rb br_bioflat.rb br_biogetseq.rb 
	br_pmfetch.rb 
Log Message:
Standardize on The Ruby License

Index: br_pmfetch.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/bin/br_pmfetch.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** br_pmfetch.rb	9 Feb 2006 16:29:41 -0000	1.6
--- br_pmfetch.rb	5 Apr 2007 23:35:39 -0000	1.7
***************
*** 5,9 ****
  # Copyright::   Copyright (C) 2004, 2005
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 5,9 ----
  # Copyright::   Copyright (C) 2004, 2005
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: br_biogetseq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/bin/br_biogetseq.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** br_biogetseq.rb	9 Feb 2006 16:29:41 -0000	1.3
--- br_biogetseq.rb	5 Apr 2007 23:35:39 -0000	1.4
***************
*** 5,9 ****
  # Copyright::   Copyright (C) 2003
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 5,9 ----
  # Copyright::   Copyright (C) 2003
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: br_biofetch.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/bin/br_biofetch.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** br_biofetch.rb	9 Feb 2006 16:29:41 -0000	1.3
--- br_biofetch.rb	5 Apr 2007 23:35:39 -0000	1.4
***************
*** 5,9 ****
  # Copyright::   Copyright (C) 2002
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 5,9 ----
  # Copyright::   Copyright (C) 2002
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: br_bioflat.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/bin/br_bioflat.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** br_bioflat.rb	22 Feb 2006 07:01:05 -0000	1.16
--- br_bioflat.rb	5 Apr 2007 23:35:39 -0000	1.17
***************
*** 5,9 ****
  # Copyright::   Copyright (C) 2002
  #               Naohisa Goto <ng at bioruby.org>
! # License::     Ruby's
  #
  # $Id$ 
--- 5,9 ----
  # Copyright::   Copyright (C) 2002
  #               Naohisa Goto <ng at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$ 

Index: bioruby
===================================================================
RCS file: /home/repository/bioruby/bioruby/bin/bioruby,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** bioruby	24 Dec 2006 14:55:53 -0000	1.18
--- bioruby	5 Apr 2007 23:35:39 -0000	1.19
***************
*** 5,9 ****
  # Copyright::   Copyright (C) 2005, 2006
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 5,9 ----
  # Copyright::   Copyright (C) 2005, 2006
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl blast.rb, 1.32, 1.33 clustalw.rb,
	1.17, 1.18 emboss.rb, 1.7, 1.8 fasta.rb, 1.23, 1.24 hmmer.rb,
	1.8, 1.9 mafft.rb, 1.16, 1.17 psort.rb, 1.12, 1.13 pts1.rb,
	1.4, 1.5 sim4.rb, 1.9, 1.10
Message-ID: <200704052336.l35NZfec020102@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl

Modified Files:
	blast.rb clustalw.rb emboss.rb fasta.rb hmmer.rb mafft.rb 
	psort.rb pts1.rb sim4.rb 
Log Message:
Standardize on The Ruby License

Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/emboss.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** emboss.rb	19 Sep 2006 06:31:08 -0000	1.7
--- emboss.rb	5 Apr 2007 23:35:39 -0000	1.8
***************
*** 4,8 ****
  # Copyright::  Copyright (C) 2002, 2005 Toshiaki Katayama<k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::    Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::  Copyright (C) 2002, 2005 Toshiaki Katayama<k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::    The Ruby License
  #
  # $Id$

Index: pts1.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/pts1.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** pts1.rb	14 Jul 2006 14:28:44 -0000	1.4
--- pts1.rb	5 Apr 2007 23:35:39 -0000	1.5
***************
*** 7,11 ****
  # Copyright::   Copyright (C) 2006 
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 7,11 ----
  # Copyright::   Copyright (C) 2006 
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: psort.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** psort.rb	19 Sep 2006 06:30:42 -0000	1.12
--- psort.rb	5 Apr 2007 23:35:39 -0000	1.13
***************
*** 6,10 ****
  # Copyright::   Copyright (C) 2003-2006
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 6,10 ----
  # Copyright::   Copyright (C) 2003-2006
  #               Mitsuteru C. Nakao <n at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/fasta.rb,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** fasta.rb	19 Sep 2006 06:28:56 -0000	1.23
--- fasta.rb	5 Apr 2007 23:35:39 -0000	1.24
***************
*** 3,7 ****
  #
  # Copyright::  Copyright (C) 2001, 2002 Toshiaki Katayama <k at bioruby.org>
! # License::    Ruby's
  #
  # $Id$
--- 3,7 ----
  #
  # Copyright::  Copyright (C) 2001, 2002 Toshiaki Katayama <k at bioruby.org>
! # License::    The Ruby License
  #
  # $Id$

Index: sim4.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** sim4.rb	14 Dec 2006 15:59:21 -0000	1.9
--- sim4.rb	5 Apr 2007 23:35:39 -0000	1.10
***************
*** 3,7 ****
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License::   The Ruby License
  #
  #  $Id$

Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** blast.rb	19 Sep 2006 06:31:08 -0000	1.32
--- blast.rb	5 Apr 2007 23:35:39 -0000	1.33
***************
*** 5,9 ****
  # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::    Ruby's
  #
  # $Id$
--- 5,9 ----
  # Copyright::  Copyright (C) 2002,2003  Toshiaki Katayama <k at bioruby.org>
  # Copyright::  Copyright (C) 2006       Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::    The Ruby License
  #
  # $Id$

Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** clustalw.rb	14 Dec 2006 16:08:46 -0000	1.17
--- clustalw.rb	5 Apr 2007 23:35:39 -0000	1.18
***************
*** 3,7 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   The Ruby License
  #
  #  $Id$

Index: hmmer.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/hmmer.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** hmmer.rb	31 Dec 2006 21:54:49 -0000	1.8
--- hmmer.rb	5 Apr 2007 23:35:39 -0000	1.9
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2002 
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2002 
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** mafft.rb	2 Apr 2007 12:55:26 -0000	1.16
--- mafft.rb	5 Apr 2007 23:35:39 -0000	1.17
***************
*** 3,7 ****
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2003 GOTO Naohisa <ngoto at gen-info.osaka-u.ac.jp>
! # License::   The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.12,1.13
Message-ID: <200704052336.l35NZfAo020116@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/blat

Modified Files:
	report.rb 
Log Message:
Standardize on The Ruby License

Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** report.rb	29 Jun 2006 11:54:33 -0000	1.12
--- report.rb	5 Apr 2007 23:35:39 -0000	1.13
***************
*** 3,7 ****
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License:: Ruby's
  #
  #  $Id$
--- 3,7 ----
  #
  # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # License:: The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:44 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:44 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb,
	1.16, 1.17 analysis_basic.rb, 1.11, 1.12 cut_symbol.rb, 1.4,
	1.5 double_stranded.rb, 1.9, 1.10 single_strand.rb, 1.5,
	1.6 single_strand_complement.rb, 1.3, 1.4 string_formatting.rb,
	1.4, 1.5
Message-ID: <200704052336.l35NZiPq020248@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util/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:
Standardize on The Ruby License

Index: analysis_basic.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** analysis_basic.rb	4 Apr 2007 20:10:31 -0000	1.11
--- analysis_basic.rb	5 Apr 2007 23:35:42 -0000	1.12
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 41,45 ****
  # 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 Analysis
--- 41,45 ----
  # 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

Index: string_formatting.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/string_formatting.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** string_formatting.rb	4 Apr 2007 18:07:43 -0000	1.4
--- string_formatting.rb	5 Apr 2007 23:35:42 -0000	1.5
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 19,23 ****
  # 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
  #
  module StringFormatting
--- 19,23 ----
  # 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

Index: cut_symbol.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/cut_symbol.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** cut_symbol.rb	1 Jan 2007 05:07:04 -0000	1.4
--- cut_symbol.rb	5 Apr 2007 23:35:42 -0000	1.5
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 19,23 ****
  # 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
  #
  # = Usage
--- 19,23 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  # = Usage

Index: single_strand_complement.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand_complement.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** single_strand_complement.rb	4 Apr 2007 18:07:43 -0000	1.3
--- single_strand_complement.rb	5 Apr 2007 23:35:42 -0000	1.4
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 19,23 ****
  # 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
  #
  # A single strand of restriction enzyme sequence pattern with a 3' to 5' orientation.
--- 19,23 ----
  # 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.

Index: double_stranded.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** double_stranded.rb	4 Apr 2007 18:07:43 -0000	1.9
--- double_stranded.rb	5 Apr 2007 23:35:42 -0000	1.10
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 28,32 ****
  # 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
  #
  # A pair of SingleStrand and SingleStrandComplement objects with methods to
--- 28,32 ----
  # 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

Index: single_strand.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/single_strand.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** single_strand.rb	4 Apr 2007 20:05:05 -0000	1.5
--- single_strand.rb	5 Apr 2007 23:35:42 -0000	1.6
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 22,26 ****
  # 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
  #
  # A single strand of restriction enzyme sequence pattern with a 5' to 3' 
--- 22,26 ----
  # 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' 

Index: analysis.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** analysis.rb	4 Apr 2007 18:07:43 -0000	1.16
--- analysis.rb	5 Apr 2007 23:35:42 -0000	1.17
***************
*** 4,8 ****
  # 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
  #
  #  $Id$
--- 4,8 ----
  # Author::    Trevor Wennblom  <mailto:trevor at corevx.com>
  # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
! # License::   The Ruby License
  #
  #  $Id$
***************
*** 18,22 ****
  # 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 Analysis
--- 18,22 ----
  # 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


From trevor at dev.open-bio.org  Thu Apr  5 19:35:42 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:42 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/genscan report.rb,1.9,1.10
Message-ID: <200704052336.l35NZgkl020128@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/genscan
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/genscan

Modified Files:
	report.rb 
Log Message:
Standardize on The Ruby License

Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/genscan/report.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** report.rb	30 Apr 2006 07:11:29 -0000	1.9
--- report.rb	5 Apr 2007 23:35:39 -0000	1.10
***************
*** 4,8 ****
  # Copyright::  Copyright (C) 2003 
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    Ruby's
  #
  #  $Id$
--- 4,8 ----
  # Copyright::  Copyright (C) 2003 
  #              Mitsuteru C. Nakao <n at bioruby.org>
! # License::    The Ruby License
  #
  #  $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:35:41 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:35:41 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/gcg msf.rb, 1.1, 1.2 seq.rb, 1.2,
	1.3
Message-ID: <200704052336.l35NZfNH020124@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/appl/gcg
In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/gcg

Modified Files:
	msf.rb seq.rb 
Log Message:
Standardize on The Ruby License

Index: msf.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/gcg/msf.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** msf.rb	14 Dec 2006 19:52:53 -0000	1.1
--- msf.rb	5 Apr 2007 23:35:39 -0000	1.2
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2003, 2006
  #               Naohisa Goto <ng at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2003, 2006
  #               Naohisa Goto <ng at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/gcg/seq.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** seq.rb	14 Dec 2006 19:55:10 -0000	1.2
--- seq.rb	5 Apr 2007 23:35:39 -0000	1.3
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2003, 2006
  #               Naohisa Goto <ng at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2003, 2006
  #               Naohisa Goto <ng at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:45:13 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:45:13 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.9,1.10 shell.rb,1.18,1.19
Message-ID: <200704052345.l35NjDqn020699@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio
In directory dev.open-bio.org:/tmp/cvs-serv20677/lib/bio

Modified Files:
	map.rb shell.rb 
Log Message:
More license changes.

Index: shell.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell.rb,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** shell.rb	28 Mar 2007 20:23:39 -0000	1.18
--- shell.rb	5 Apr 2007 23:45:10 -0000	1.19
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2005, 2006
  #               Toshiaki Katayama <k at bioruby.org>
! # License:      Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2005, 2006
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     The Ruby License
  #
  # $Id$

Index: map.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** map.rb	24 Dec 2006 10:10:08 -0000	1.9
--- map.rb	5 Apr 2007 23:45:10 -0000	1.10
***************
*** 3,7 ****
  #
  # Copyright::   Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # Licence::     Ruby's
  #
  # $Id$
--- 3,7 ----
  #
  # Copyright::   Copyright (C) 2006 Jan Aerts <jan.aerts at bbsrc.ac.uk>
! # License::     The Ruby License
  #
  # $Id$


From trevor at dev.open-bio.org  Thu Apr  5 19:45:13 2007
From: trevor at dev.open-bio.org (Trevor Wennblom)
Date: Thu, 05 Apr 2007 23:45:13 +0000
Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin flatfile.rb, 1.12,
	1.13 obda.rb, 1.9, 1.10
Message-ID: <200704052345.l35NjDJa020705@dev.open-bio.org>

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory dev.open-bio.org:/tmp/cvs-serv20677/lib/bio/shell/plugin

Modified Files:
	flatfile.rb obda.rb 
Log Message:
More license changes.

Index: obda.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/obda.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** obda.rb	9 Feb 2006 20:48:53 -0000	1.9
--- obda.rb	5 Apr 2007 23:45:11 -0000	1.10
***************
*** 4,8 ****
  # Copyright::   Copyright (C) 2005
  #               Toshiaki Katayama <k at bioruby.org>
! # License:      Ruby's
  #
  # $Id$
--- 4,8 ----
  # Copyright::   Copyright (C) 2005
  #               Toshiaki Katayama <k at bioruby.org>
! # License::     The Ruby License 
  #
  # $Id$

Index: flatfile.rb
===================================================================
RCS fil