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 + + * 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 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 # Copyright:: Copyright (C) 2003 Masumi Itoh # --- 1,6 ---- # ! # = bio/db/kegg/ortholog.rb - KEGG ORTHOLOG database class # ! # Copyright:: Copyright (C) 2003-2007 Toshiaki Katayama # Copyright:: Copyright (C) 2003 Masumi Itoh # *************** *** 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 # Copyright:: Copyright (C) 2003 Masumi Itoh # # $Id$ --- 1,8 ---- # ! # = bio/db/kegg/orthology.rb - KEGG ORTHOLOGY database class # # Copyright:: Copyright (C) 2003-2007 Toshiaki Katayama # Copyright:: Copyright (C) 2003 Masumi Itoh + # 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 ! # ! # 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 ! # 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 ! # ! # 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 ! # 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 # License:: Ruby's # --- 2,7 ---- # test/unit/bio/test_feature.rb - Unit test for Features/Feature classes # ! # Copyright:: Copyright (C) 2005 ! # Mitsuteru Nakao # 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 ! # Copyright (C) 2006 Mitsuteru C. Nakao ! # ! # 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 ! # 2006 Mitsuteru C. Nakao ! # 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 ! # Copyright (C) 2005 Naohisa Goto ! # ! # 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 ! # 2005 Naohisa Goto ! # 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 ! # ! # 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 ! # 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 ! # ! # 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 ! # 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 ! # ! # 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 ! # 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 ! # License:: Ruby's # # $Id$ --- 13,17 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 16,20 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 14,18 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru C. Nakao ! # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 25,29 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 18,22 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # 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 # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005,2006 Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright: Copyright (C) 2005 Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru Nakao ! # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 23,27 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 23,27 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 21,25 **** # Author:: Trevor Wennblom # 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 # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2007 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005,2007 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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 # ! # License:: Ruby's # # $ I d: $ --- 80,84 ---- # Copyright:: Copyright (C) 2006 Chem R. Hacker # ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001-2006 # Toshiaki Katayama ! # 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 # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # 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 , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Naohisa Goto , # Toshiaki Katayama ! # 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 # 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (c) 2002, 2005 Toshiaki Katayama # 2006 Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Naohisa Goto ! # 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 # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # ! # 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 , # Jan Aerts ! # License:: Ruby's # # $Id$ --- 8,12 ---- # Ryan Raaum , # Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2002, 2005 # Toshiaki Katayama ! # 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 , # Shuichi Kawashima ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Shuichi Kawashima ! # 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 , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 GOTO Naohisa ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2004, 2005 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2003 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2002 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2002 # Naohisa Goto ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # 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 # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 7,11 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2003-2006 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # 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 # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2002,2003 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 41,45 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 28,32 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 22,26 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 18,22 **** # Author:: Trevor Wennblom # 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 # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003, 2006 # Naohisa Goto ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003, 2006 # Naohisa Goto ! # 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 ! # License: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # 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 ! # Licence:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Jan Aerts ! # 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 ! # License: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/flatfile.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** flatfile.rb 9 Feb 2006 20:48:53 -0000 1.12 --- flatfile.rb 5 Apr 2007 23:45:11 -0000 1.13 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # 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/db/pdb test_pdb.rb,1.2,1.3 Message-ID: <200704052335.l35NZj1x020381@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db/pdb Modified Files: test_pdb.rb Log Message: Standardize on The Ruby License Index: test_pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/pdb/test_pdb.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_pdb.rb 27 Jun 2006 14:25:40 -0000 1.2 --- test_pdb.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 5,9 **** # Naohisa Goto # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Naohisa Goto # ! # License:: The Ruby License # # $Id$ 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/sim4 report.rb,1.8,1.9 Message-ID: <200704052336.l35NZgN0020151@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/sim4 In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/sim4 Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4/report.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** report.rb 30 Apr 2006 05:50:19 -0000 1.8 --- report.rb 5 Apr 2007 23:35:40 -0000 1.9 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: The Ruby License # # $Id$ 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/spidey report.rb,1.9,1.10 Message-ID: <200704052336.l35NZgk0020158@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/spidey In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/spidey Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/spidey/report.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** report.rb 22 Feb 2006 08:46:15 -0000 1.9 --- report.rb 5 Apr 2007 23:35:40 -0000 1.10 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: The Ruby License # # $Id$ 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/mafft report.rb,1.11,1.12 Message-ID: <200704052336.l35NZgWM020141@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/mafft In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/mafft Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft/report.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** report.rb 15 Dec 2006 16:23:18 -0000 1.11 --- report.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ 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/tmhmm report.rb,1.7,1.8 Message-ID: <200704052336.l35NZgW0020167@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/tmhmm Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm/report.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** report.rb 30 Apr 2006 07:11:29 -0000 1.7 --- report.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # 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/db/kegg test_genes.rb,1.4,1.5 Message-ID: <200704052335.l35NZjn8020366@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db/kegg In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db/kegg Modified Files: test_genes.rb Log Message: Standardize on The Ruby License Index: test_genes.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/kegg/test_genes.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_genes.rb 24 Dec 2006 17:19:05 -0000 1.4 --- test_genes.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ 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/targetp report.rb,1.8,1.9 Message-ID: <200704052336.l35NZgxu020162@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/targetp In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/targetp Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/targetp/report.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** report.rb 30 Apr 2006 07:11:28 -0000 1.8 --- report.rb 5 Apr 2007 23:35:40 -0000 1.9 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ 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/sosui report.rb,1.10,1.11 Message-ID: <200704052336.l35NZgG1020154@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/sosui In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/sosui Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sosui/report.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** report.rb 30 Apr 2006 07:13:39 -0000 1.10 --- report.rb 5 Apr 2007 23:35:40 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ 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/psort report.rb,1.14,1.15 Message-ID: <200704052336.l35NZgVj020148@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/psort In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/psort Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort/report.rb,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** report.rb 25 Jul 2006 18:41:23 -0000 1.14 --- report.rb 5 Apr 2007 23:35:40 -0000 1.15 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ 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/iprscan report.rb,1.5,1.6 Message-ID: <200704052336.l35NZgrE020137@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/iprscan In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/iprscan Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/iprscan/report.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** report.rb 29 Mar 2007 09:02:44 -0000 1.5 --- report.rb 5 Apr 2007 23:35:40 -0000 1.6 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # 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/tmhmm test_report.rb, 1.3, 1.4 Message-ID: <200704052335.l35NZjRJ020326@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/tmhmm In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/tmhmm 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/tmhmm/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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ 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/hmmer report.rb,1.12,1.13 Message-ID: <200704052336.l35NZgpK020133@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/hmmer In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/hmmer Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/hmmer/report.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** report.rb 30 Mar 2007 22:26:15 -0000 1.12 --- report.rb 5 Apr 2007 23:35:40 -0000 1.13 *************** *** 6,10 **** # Copyright:: Copyright (C) 2005 # Masashi Fujita ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2005 # Masashi Fujita ! # 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/shell/plugin test_seq.rb, 1.8, 1.9 Message-ID: <200704052335.l35NZkBF020413@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/shell/plugin Modified Files: test_seq.rb Log Message: Standardize on The Ruby License Index: test_seq.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin/test_seq.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** test_seq.rb 24 Dec 2006 09:30:23 -0000 1.8 --- test_seq.rb 5 Apr 2007 23:35:44 -0000 1.9 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # 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/single_strand test_cut_locations_in_enzyme_notation.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZkPq020448@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/single_strand In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util/restriction_enzyme/single_strand Modified Files: 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/single_strand/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 # 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 # 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 19:35:42 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/phylip alignment.rb, 1.1, 1.2 distance_matrix.rb, 1.2, 1.3 Message-ID: <200704052336.l35NZgdB020145@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/phylip In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/phylip Modified Files: alignment.rb distance_matrix.rb Log Message: Standardize on The Ruby License Index: distance_matrix.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/phylip/distance_matrix.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** distance_matrix.rb 15 Dec 2006 14:59:26 -0000 1.2 --- distance_matrix.rb 5 Apr 2007 23:35:40 -0000 1.3 *************** *** 5,9 **** # GOTO Naohisa # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # ! # License:: The Ruby License # # $Id$ Index: alignment.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/phylip/alignment.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** alignment.rb 14 Dec 2006 22:38:53 -0000 1.1 --- alignment.rb 5 Apr 2007 23:35:40 -0000 1.2 *************** *** 5,9 **** # GOTO Naohisa # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # ! # 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/blast test_report.rb, 1.4, 1.5 test_xmlparser.rb, 1.6, 1.7 Message-ID: <200704052335.l35NZjx2020305@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/blast Modified Files: test_report.rb test_xmlparser.rb Log Message: Standardize on The Ruby License Index: test_xmlparser.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/test_xmlparser.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_xmlparser.rb 28 Dec 2006 06:25:21 -0000 1.6 --- test_xmlparser.rb 5 Apr 2007 23:35:43 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ 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/data aa.rb, 0.19, 0.20 codontable.rb, 0.17, 0.18 na.rb, 0.21, 0.22 Message-ID: <200704052336.l35NZgd2020171@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/data In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/data Modified Files: aa.rb codontable.rb na.rb Log Message: Standardize on The Ruby License Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/aa.rb,v retrieving revision 0.19 retrieving revision 0.20 diff -C2 -d -r0.19 -r0.20 *** aa.rb 24 Dec 2006 10:06:07 -0000 0.19 --- aa.rb 5 Apr 2007 23:35:40 -0000 0.20 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v retrieving revision 0.21 retrieving revision 0.22 diff -C2 -d -r0.21 -r0.22 *** na.rb 5 Apr 2007 23:10:09 -0000 0.21 --- na.rb 5 Apr 2007 23:35:40 -0000 0.22 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: codontable.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/codontable.rb,v retrieving revision 0.17 retrieving revision 0.18 diff -C2 -d -r0.17 -r0.18 *** codontable.rb 8 May 2006 14:21:46 -0000 0.17 --- codontable.rb 5 Apr 2007 23:35:40 -0000 0.18 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2004 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2004 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/io/flatfile bdb.rb, 1.9, 1.10 index.rb, 1.18, 1.19 indexer.rb, 1.24, 1.25 Message-ID: <200704052336.l35NZhNS020214@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/io/flatfile In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/io/flatfile Modified Files: bdb.rb index.rb indexer.rb Log Message: Standardize on The Ruby License Index: bdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/bdb.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** bdb.rb 30 Apr 2006 05:58:50 -0000 1.9 --- bdb.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: index.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/index.rb,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -d -r1.18 -r1.19 *** index.rb 22 Feb 2006 08:40:31 -0000 1.18 --- index.rb 5 Apr 2007 23:35:41 -0000 1.19 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002 # GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002 # GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: indexer.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/indexer.rb,v retrieving revision 1.24 retrieving revision 1.25 diff -C2 -d -r1.24 -r1.25 *** indexer.rb 22 Mar 2006 10:19:22 -0000 1.24 --- indexer.rb 5 Apr 2007 23:35:41 -0000 1.25 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # 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/sequence test_aa.rb, 1.2, 1.3 test_common.rb, 1.3, 1.4 test_compat.rb, 1.2, 1.3 test_na.rb, 1.4, 1.5 Message-ID: <200704052335.l35NZkYZ020401@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/sequence Modified Files: test_aa.rb test_common.rb test_compat.rb test_na.rb Log Message: Standardize on The Ruby License Index: test_common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_common.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_common.rb 24 Dec 2006 17:19:05 -0000 1.3 --- test_common.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_compat.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_compat.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_compat.rb 24 Dec 2006 17:19:05 -0000 1.2 --- test_compat.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_na.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_na.rb 5 Apr 2007 23:10:10 -0000 1.4 --- test_na.rb 5 Apr 2007 23:35:44 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_aa.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_aa.rb 31 Dec 2006 21:54:49 -0000 1.2 --- test_aa.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # 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/analysis test_calculated_cuts.rb, 1.3, 1.4 test_cut_ranges.rb, 1.1, 1.2 test_sequence_range.rb, 1.3, 1.4 Message-ID: <200704052335.l35NZka8020434@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util/restriction_enzyme/analysis Modified Files: test_calculated_cuts.rb test_cut_ranges.rb test_sequence_range.rb Log Message: Standardize on The Ruby License Index: test_sequence_range.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_sequence_range.rb 2 Jan 2007 00:22:27 -0000 1.3 --- test_sequence_range.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_cut_ranges.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_cut_ranges.rb 2 Jan 2007 06:18:07 -0000 1.1 --- test_cut_ranges.rb 5 Apr 2007 23:35:44 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_calculated_cuts.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_calculated_cuts.rb 2 Jan 2007 00:22:27 -0000 1.3 --- test_calculated_cuts.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # 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 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/genbank common.rb, 1.10, 1.11 ddbj.rb, 1.8, 1.9 genbank.rb, 0.39, 0.40 genpept.rb, 1.11, 1.12 refseq.rb, 1.7, 1.8 Message-ID: <200704052336.l35NZhrA020187@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/genbank Modified Files: common.rb ddbj.rb genbank.rb genpept.rb refseq.rb Log Message: Standardize on The Ruby License Index: genpept.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genpept.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** genpept.rb 19 Sep 2006 05:59:34 -0000 1.11 --- genpept.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002-2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002-2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: genbank.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v retrieving revision 0.39 retrieving revision 0.40 diff -C2 -d -r0.39 -r0.40 *** genbank.rb 19 Sep 2006 05:59:07 -0000 0.39 --- genbank.rb 5 Apr 2007 23:35:40 -0000 0.40 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2000-2005 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2000-2005 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: ddbj.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/ddbj.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** ddbj.rb 19 Sep 2006 05:57:54 -0000 1.8 --- ddbj.rb 5 Apr 2007 23:35:40 -0000 1.9 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/common.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** common.rb 19 Sep 2006 05:57:20 -0000 1.10 --- common.rb 5 Apr 2007 23:35:40 -0000 1.11 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: refseq.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/refseq.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** refseq.rb 19 Sep 2006 06:00:06 -0000 1.7 --- refseq.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # 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/db/embl test_common.rb, 1.3, 1.4 test_embl.rb, 1.4, 1.5 test_embl_rel89.rb, 1.1, 1.2 test_sptr.rb, 1.6, 1.7 test_uniprot.rb, 1.4, 1.5 Message-ID: <200704052335.l35NZjqD020354@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db/embl In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db/embl Modified Files: test_common.rb test_embl.rb test_embl_rel89.rb test_sptr.rb test_uniprot.rb Log Message: Standardize on The Ruby License Index: test_uniprot.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_uniprot.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_uniprot.rb 24 Dec 2006 17:19:04 -0000 1.4 --- test_uniprot.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_embl_rel89.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl_rel89.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_embl_rel89.rb 13 Mar 2007 17:03:55 -0000 1.1 --- test_embl_rel89.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2007 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2007 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_common.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_common.rb 24 Dec 2006 17:19:04 -0000 1.3 --- test_common.rb 5 Apr 2007 23:35:43 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_sptr.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_sptr.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_sptr.rb 31 Dec 2006 21:54:49 -0000 1.6 --- test_sptr.rb 5 Apr 2007 23:35:43 -0000 1.7 *************** *** 3,7 **** # # Copyright::: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright::: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_embl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_embl.rb 24 Dec 2006 17:19:04 -0000 1.4 --- test_embl.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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/io test_ddbjxml.rb, 1.3, 1.4 test_ensembl.rb, 1.5, 1.6 test_fastacmd.rb, 1.2, 1.3 test_flatfile.rb, 1.1, 1.2 test_soapwsdl.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZkjN020384@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/io In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/io Modified Files: test_ddbjxml.rb test_ensembl.rb test_fastacmd.rb test_flatfile.rb test_soapwsdl.rb Log Message: Standardize on The Ruby License Index: test_flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_flatfile.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_flatfile.rb 15 Jun 2006 14:28:55 -0000 1.1 --- test_flatfile.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 4,8 **** # Copyright (C) 2006 Naohisa Goto # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright (C) 2006 Naohisa Goto # ! # License:: The Ruby License # # $Id$ Index: test_fastacmd.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_fastacmd.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_fastacmd.rb 24 Dec 2006 17:19:05 -0000 1.2 --- test_fastacmd.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2006 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_ensembl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_ensembl.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_ensembl.rb 29 Mar 2007 14:14:17 -0000 1.5 --- test_ensembl.rb 5 Apr 2007 23:35:43 -0000 1.6 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006, 2007 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006, 2007 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_soapwsdl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_soapwsdl.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_soapwsdl.rb 5 Jun 2006 02:51:59 -0000 1.2 --- test_soapwsdl.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 3,7 **** # # Copytight:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copytight:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_ddbjxml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_ddbjxml.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_ddbjxml.rb 28 Mar 2007 11:21:20 -0000 1.3 --- test_ddbjxml.rb 5 Apr 2007 23:35:43 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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 test_color_scheme.rb, 1.2, 1.3 test_contingency_table.rb, 1.3, 1.4 test_restriction_enzyme.rb, 1.2, 1.3 test_sirna.rb, 1.3, 1.4 Message-ID: <200704052335.l35NZkom020418@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util Modified Files: test_color_scheme.rb test_contingency_table.rb test_restriction_enzyme.rb test_sirna.rb Log Message: Standardize on The Ruby License Index: test_contingency_table.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_contingency_table.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_contingency_table.rb 31 Dec 2006 18:46:14 -0000 1.3 --- test_contingency_table.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_color_scheme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_color_scheme.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_color_scheme.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_color_scheme.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_restriction_enzyme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_restriction_enzyme.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_restriction_enzyme.rb 1 Jan 2007 00:12:54 -0000 1.2 --- test_restriction_enzyme.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_sirna.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_sirna.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_sirna.rb 24 Dec 2006 17:19:05 -0000 1.3 --- test_sirna.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru C. Nakap ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru C. Nakap ! # License:: The Ruby License # # $Id$ 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/db/embl common.rb, 1.11, 1.12 embl.rb, 1.28, 1.29 sptr.rb, 1.35, 1.36 swissprot.rb, 1.6, 1.7 trembl.rb, 1.6, 1.7 uniprot.rb, 1.4, 1.5 Message-ID: <200704052336.l35NZgJM020183@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/embl In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/embl Modified Files: common.rb embl.rb sptr.rb swissprot.rb trembl.rb uniprot.rb Log Message: Standardize on The Ruby License Index: sptr.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -d -r1.35 -r1.36 *** sptr.rb 5 Oct 2006 07:39:29 -0000 1.35 --- sptr.rb 5 Apr 2007 23:35:40 -0000 1.36 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001-2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001-2006 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: uniprot.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/uniprot.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** uniprot.rb 19 Sep 2006 06:01:48 -0000 1.4 --- uniprot.rb 5 Apr 2007 23:35:40 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: embl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v retrieving revision 1.28 retrieving revision 1.29 diff -C2 -d -r1.28 -r1.29 *** embl.rb 13 Mar 2007 17:03:55 -0000 1.28 --- embl.rb 5 Apr 2007 23:35:40 -0000 1.29 *************** *** 4,8 **** # # Copyright:: Copyright (C) 2001-2007 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # # Copyright:: Copyright (C) 2001-2007 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** common.rb 30 Apr 2006 07:11:29 -0000 1.11 --- common.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001-2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001-2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: trembl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/trembl.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** trembl.rb 19 Sep 2006 06:01:48 -0000 1.6 --- trembl.rb 5 Apr 2007 23:35:40 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: swissprot.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/swissprot.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** swissprot.rb 19 Sep 2006 06:01:48 -0000 1.6 --- swissprot.rb 5 Apr 2007 23:35:40 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # 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 format0.rb, 1.19, 1.20 format8.rb, 1.6, 1.7 report.rb, 1.10, 1.11 rexml.rb, 1.11, 1.12 wublast.rb, 1.8, 1.9 xmlparser.rb, 1.16, 1.17 Message-ID: <200704052336.l35NZffI020112@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/blast Modified Files: format0.rb format8.rb report.rb rexml.rb wublast.rb xmlparser.rb Log Message: Standardize on The Ruby License Index: xmlparser.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/xmlparser.rb,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -d -r1.16 -r1.17 *** xmlparser.rb 31 Dec 2006 21:54:49 -0000 1.16 --- xmlparser.rb 5 Apr 2007 23:35:39 -0000 1.17 *************** *** 6,10 **** # Copyright:: Copyright (C) 2003 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2003 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/report.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** report.rb 19 Sep 2006 06:09:20 -0000 1.10 --- report.rb 5 Apr 2007 23:35:39 -0000 1.11 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: format8.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format8.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** format8.rb 19 Sep 2006 06:08:26 -0000 1.6 --- format8.rb 5 Apr 2007 23:35:39 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: format0.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** format0.rb 19 Sep 2006 06:12:37 -0000 1.19 --- format0.rb 5 Apr 2007 23:35:39 -0000 1.20 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003-2006 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003-2006 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: wublast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** wublast.rb 19 Sep 2006 06:12:37 -0000 1.8 --- wublast.rb 5 Apr 2007 23:35:39 -0000 1.9 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: rexml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/rexml.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** rexml.rb 19 Sep 2006 06:10:19 -0000 1.11 --- rexml.rb 5 Apr 2007 23:35:39 -0000 1.12 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/sequence aa.rb, 1.3, 1.4 common.rb, 1.3, 1.4 compat.rb, 1.3, 1.4 format.rb, 1.3, 1.4 generic.rb, 1.4, 1.5 na.rb, 1.5, 1.6 Message-ID: <200704052336.l35NZhd1020220@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/sequence Modified Files: aa.rb common.rb compat.rb format.rb generic.rb na.rb Log Message: Standardize on The Ruby License Index: compat.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/compat.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** compat.rb 26 Mar 2006 02:27:59 -0000 1.3 --- compat.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ Index: common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/common.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** common.rb 26 Mar 2006 02:27:59 -0000 1.3 --- common.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ Index: format.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** format.rb 26 Mar 2006 02:27:59 -0000 1.3 --- format.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 6,10 **** # Naohisa Goto , # Ryan Raaum ! # License:: Ruby's # # = TODO --- 6,10 ---- # Naohisa Goto , # Ryan Raaum ! # License:: The Ruby License # # = TODO Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/aa.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** aa.rb 26 Mar 2006 02:27:59 -0000 1.3 --- aa.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ Index: generic.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/generic.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** generic.rb 26 Mar 2006 02:27:59 -0000 1.4 --- generic.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/na.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** na.rb 20 Jul 2006 03:45:22 -0000 1.5 --- na.rb 5 Apr 2007 23:35:41 -0000 1.6 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb, 1.7, 1.8 chain.rb, 1.7, 1.8 chemicalcomponent.rb, 1.2, 1.3 model.rb, 1.8, 1.9 pdb.rb, 1.20, 1.21 residue.rb, 1.11, 1.12 utils.rb, 1.6, 1.7 Message-ID: <200704052336.l35NZhNO020198@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/pdb Modified Files: atom.rb chain.rb chemicalcomponent.rb model.rb pdb.rb residue.rb utils.rb Log Message: Standardize on The Ruby License Index: atom.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/atom.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** atom.rb 29 Mar 2007 12:50:49 -0000 1.7 --- atom.rb 5 Apr 2007 23:35:41 -0000 1.8 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: residue.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** residue.rb 29 Mar 2007 12:50:49 -0000 1.11 --- residue.rb 5 Apr 2007 23:35:41 -0000 1.12 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: model.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/model.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** model.rb 29 Mar 2007 12:50:49 -0000 1.8 --- model.rb 5 Apr 2007 23:35:41 -0000 1.9 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** pdb.rb 29 Mar 2007 12:50:49 -0000 1.20 --- pdb.rb 5 Apr 2007 23:35:41 -0000 1.21 *************** *** 5,9 **** # GOTO Naohisa # Alex Gutteridge ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # Alex Gutteridge ! # License:: The Ruby License # # $Id$ Index: utils.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/utils.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** utils.rb 29 Mar 2007 12:50:49 -0000 1.6 --- utils.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: chemicalcomponent.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/chemicalcomponent.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** chemicalcomponent.rb 29 Mar 2007 12:50:49 -0000 1.2 --- chemicalcomponent.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: chain.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/chain.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** chain.rb 29 Mar 2007 12:50:49 -0000 1.7 --- chain.rb 5 Apr 2007 23:35:41 -0000 1.8 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util color_scheme.rb, 1.3, 1.4 contingency_table.rb, 1.6, 1.7 restriction_enzyme.rb, 1.12, 1.13 sirna.rb, 1.10, 1.11 Message-ID: <200704052336.l35NZhGf020237@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util Modified Files: color_scheme.rb contingency_table.rb restriction_enzyme.rb sirna.rb Log Message: Standardize on The Ruby License Index: restriction_enzyme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** restriction_enzyme.rb 2 Feb 2007 06:42:14 -0000 1.12 --- restriction_enzyme.rb 5 Apr 2007 23:35:41 -0000 1.13 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 22,26 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # = Description --- 22,26 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # = Description Index: color_scheme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** color_scheme.rb 31 Dec 2006 19:47:35 -0000 1.3 --- color_scheme.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Index: sirna.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/sirna.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** sirna.rb 29 Mar 2007 12:52:54 -0000 1.10 --- sirna.rb 5 Apr 2007 23:35:41 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004, 2005 # Itoshi NIKAIDO ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004, 2005 # Itoshi NIKAIDO ! # License:: The Ruby License # # $Id$ Index: contingency_table.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/contingency_table.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** contingency_table.rb 31 Dec 2006 23:04:04 -0000 1.6 --- contingency_table.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # = Description --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # = Description From trevor at dev.open-bio.org Thu Apr 5 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/shell core.rb, 1.23, 1.24 demo.rb, 1.3, 1.4 interface.rb, 1.15, 1.16 irb.rb, 1.2, 1.3 object.rb, 1.2, 1.3 script.rb, 1.2, 1.3 setup.rb, 1.2, 1.3 web.rb, 1.3, 1.4 Message-ID: <200704052336.l35NZhP4020225@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/shell In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/shell Modified Files: core.rb demo.rb interface.rb irb.rb object.rb script.rb setup.rb web.rb Log Message: Standardize on The Ruby License Index: interface.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/interface.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** interface.rb 24 Dec 2006 08:36:45 -0000 1.15 --- interface.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: object.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/object.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** object.rb 24 Dec 2006 08:40:00 -0000 1.2 --- object.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 5,9 **** # Nobuya Tanaka , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Nobuya Tanaka , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: irb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/irb.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** irb.rb 14 Mar 2007 19:54:51 -0000 1.2 --- irb.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: script.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/script.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** script.rb 28 Mar 2007 20:21:26 -0000 1.2 --- script.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: core.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/core.rb,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** core.rb 28 Mar 2007 20:14:14 -0000 1.23 --- core.rb 5 Apr 2007 23:35:41 -0000 1.24 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: web.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/web.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** web.rb 14 Mar 2007 19:55:10 -0000 1.3 --- web.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Nobuya Tanaka , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Nobuya Tanaka , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: setup.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/setup.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** setup.rb 28 Mar 2007 20:21:26 -0000 1.2 --- setup.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: demo.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/demo.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** demo.rb 24 Dec 2006 08:40:43 -0000 1.3 --- demo.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # 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 test_analysis.rb, 1.9, 1.10 test_cut_symbol.rb, 1.1, 1.2 test_double_stranded.rb, 1.4, 1.5 test_single_strand.rb, 1.2, 1.3 test_single_strand_complement.rb, 1.2, 1.3 test_string_formatting.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZkht020424@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util/restriction_enzyme Modified Files: test_analysis.rb test_cut_symbol.rb test_double_stranded.rb test_single_strand.rb test_single_strand_complement.rb test_string_formatting.rb Log Message: Standardize on The Ruby License Index: test_analysis.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_analysis.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** test_analysis.rb 28 Mar 2007 19:45:27 -0000 1.9 --- test_analysis.rb 5 Apr 2007 23:35:44 -0000 1.10 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_double_stranded.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_double_stranded.rb 2 Jan 2007 06:18:07 -0000 1.4 --- test_double_stranded.rb 5 Apr 2007 23:35:44 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_cut_symbol.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_cut_symbol.rb 1 Jan 2007 02:16:05 -0000 1.1 --- test_cut_symbol.rb 5 Apr 2007 23:35:44 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_single_strand.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_single_strand.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_single_strand.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_single_strand.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_string_formatting.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_string_formatting.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_string_formatting.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_single_strand_complement.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_single_strand_complement.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_single_strand_complement.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # 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 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin blast.rb, 1.2, 1.3 codon.rb, 1.15, 1.16 das.rb, 1.2, 1.3 emboss.rb, 1.2, 1.3 entry.rb, 1.9, 1.10 keggapi.rb, 1.11, 1.12 midi.rb, 1.8, 1.9 psort.rb, 1.2, 1.3 seq.rb, 1.20, 1.21 Message-ID: <200704052336.l35NZhfv020231@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/shell/plugin Modified Files: blast.rb codon.rb das.rb emboss.rb entry.rb keggapi.rb midi.rb psort.rb seq.rb Log Message: Standardize on The Ruby License Index: emboss.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/emboss.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** emboss.rb 9 Feb 2006 20:48:53 -0000 1.2 --- emboss.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: blast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/blast.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** blast.rb 24 Dec 2006 08:50:18 -0000 1.2 --- blast.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: psort.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/psort.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** psort.rb 24 Dec 2006 08:50:18 -0000 1.2 --- psort.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: keggapi.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/keggapi.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** keggapi.rb 24 Dec 2006 08:49:12 -0000 1.11 --- keggapi.rb 5 Apr 2007 23:35:41 -0000 1.12 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: das.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/das.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** das.rb 28 Mar 2007 19:50:28 -0000 1.2 --- das.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: codon.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** codon.rb 24 Dec 2006 08:46:50 -0000 1.15 --- codon.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: midi.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/midi.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** midi.rb 24 Dec 2006 08:50:37 -0000 1.8 --- midi.rb 5 Apr 2007 23:35:41 -0000 1.9 *************** *** 5,9 **** # Natsuhiro Ichinose , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Natsuhiro Ichinose , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: seq.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** seq.rb 24 Dec 2006 09:30:22 -0000 1.20 --- seq.rb 5 Apr 2007 23:35:41 -0000 1.21 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: entry.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/entry.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** entry.rb 24 Dec 2006 08:50:18 -0000 1.9 --- entry.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # 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/db test_aaindex.rb, 1.3, 1.4 test_fasta.rb, 1.4, 1.5 test_gff.rb, 1.5, 1.6 test_lasergene.rb, 1.1, 1.2 test_newick.rb, 1.4, 1.5 test_nexus.rb, 1.1, 1.2 test_prosite.rb, 1.5, 1.6 test_rebase.rb, 1.4, 1.5 test_soft.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZjgb020340@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db Modified Files: test_aaindex.rb test_fasta.rb test_gff.rb test_lasergene.rb test_newick.rb test_nexus.rb test_prosite.rb test_rebase.rb test_soft.rb Log Message: Standardize on The Ruby License Index: test_soft.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_soft.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_soft.rb 29 Mar 2007 03:18:26 -0000 1.2 --- test_soft.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_aaindex.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_aaindex.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_aaindex.rb 22 Feb 2006 07:35:19 -0000 1.3 --- test_aaindex.rb 5 Apr 2007 23:35:43 -0000 1.4 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_fasta.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_fasta.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_fasta.rb 24 Dec 2006 17:19:04 -0000 1.4 --- test_fasta.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_nexus.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_nexus.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_nexus.rb 19 Dec 2006 05:17:27 -0000 1.1 --- test_nexus.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: The Ruby License # # $Id$ Index: test_prosite.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_prosite.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_prosite.rb 24 Dec 2006 17:19:04 -0000 1.5 --- test_prosite.rb 5 Apr 2007 23:35:43 -0000 1.6 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_rebase.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_rebase.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_rebase.rb 1 Jan 2007 00:12:54 -0000 1.4 --- test_rebase.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_lasergene.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_lasergene.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_lasergene.rb 8 Jan 2007 06:38:39 -0000 1.1 --- test_lasergene.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: Distributes under the same terms as Ruby # # $Id$ --- 4,8 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: The Ruby License # # $Id$ Index: test_newick.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_newick.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_newick.rb 12 Jan 2007 16:19:24 -0000 1.4 --- test_newick.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 5,9 **** # Daniel Amelang # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Daniel Amelang # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_gff.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_gff.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_gff.rb 24 Dec 2006 17:19:04 -0000 1.5 --- test_gff.rb 5 Apr 2007 23:35:43 -0000 1.6 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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/color_scheme buried.rb, 1.3, 1.4 helix.rb, 1.3, 1.4 hydropathy.rb, 1.3, 1.4 nucleotide.rb, 1.3, 1.4 strand.rb, 1.4, 1.5 taylor.rb, 1.3, 1.4 turn.rb, 1.3, 1.4 zappo.rb, 1.3, 1.4 Message-ID: <200704052336.l35NZi3i020243@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/color_scheme In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util/color_scheme Modified Files: buried.rb helix.rb hydropathy.rb nucleotide.rb strand.rb taylor.rb turn.rb zappo.rb Log Message: Standardize on The Ruby License Index: strand.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/strand.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** strand.rb 31 Dec 2006 19:47:35 -0000 1.4 --- strand.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: turn.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/turn.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** turn.rb 31 Dec 2006 19:47:35 -0000 1.3 --- turn.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: hydropathy.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/hydropathy.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** hydropathy.rb 31 Dec 2006 19:47:35 -0000 1.3 --- hydropathy.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: nucleotide.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/nucleotide.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** nucleotide.rb 31 Dec 2006 19:47:35 -0000 1.3 --- nucleotide.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: buried.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/buried.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** buried.rb 31 Dec 2006 19:47:35 -0000 1.3 --- buried.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: helix.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/helix.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** helix.rb 31 Dec 2006 19:47:35 -0000 1.3 --- helix.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: taylor.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/taylor.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** taylor.rb 31 Dec 2006 19:47:35 -0000 1.3 --- taylor.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: zappo.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/zappo.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** zappo.rb 31 Dec 2006 19:47:35 -0000 1.3 --- zappo.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # 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 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/kegg brite.rb, 0.7, 0.8 compound.rb, 0.14, 0.15 drug.rb, 1.1, 1.2 enzyme.rb, 0.10, 0.11 expression.rb, 1.10, 1.11 genes.rb, 0.24, 0.25 genome.rb, 0.16, 0.17 glycan.rb, 1.4, 1.5 keggtab.rb, 1.9, 1.10 kgml.rb, 1.6, 1.7 reaction.rb, 1.4, 1.5 Message-ID: <200704052336.l35NZhxY020193@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/kegg Modified Files: brite.rb compound.rb drug.rb enzyme.rb expression.rb genes.rb genome.rb glycan.rb keggtab.rb kgml.rb reaction.rb Log Message: Standardize on The Ruby License Index: drug.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/drug.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** drug.rb 8 Mar 2007 00:11:49 -0000 1.1 --- drug.rb 5 Apr 2007 23:35:41 -0000 1.2 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: keggtab.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/keggtab.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** keggtab.rb 19 Sep 2006 05:54:29 -0000 1.9 --- keggtab.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001 Mitsuteru C. Nakao # Copyright (C) 2003, 2006 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001 Mitsuteru C. Nakao # Copyright (C) 2003, 2006 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: glycan.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/glycan.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** glycan.rb 8 Mar 2007 00:14:16 -0000 1.4 --- glycan.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: compound.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/compound.rb,v retrieving revision 0.14 retrieving revision 0.15 diff -C2 -d -r0.14 -r0.15 *** compound.rb 8 Mar 2007 00:10:05 -0000 0.14 --- compound.rb 5 Apr 2007 23:35:41 -0000 0.15 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002, 2004, 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002, 2004, 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: kgml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/kgml.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** kgml.rb 24 Dec 2006 09:18:43 -0000 1.6 --- kgml.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: enzyme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/enzyme.rb,v retrieving revision 0.10 retrieving revision 0.11 diff -C2 -d -r0.10 -r0.11 *** enzyme.rb 15 Jan 2007 04:50:05 -0000 0.10 --- enzyme.rb 5 Apr 2007 23:35:41 -0000 0.11 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: expression.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/expression.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** expression.rb 8 May 2006 14:25:25 -0000 1.10 --- expression.rb 5 Apr 2007 23:35:41 -0000 1.11 *************** *** 5,9 **** # Shuichi Kawashima , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Shuichi Kawashima , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: genome.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/genome.rb,v retrieving revision 0.16 retrieving revision 0.17 diff -C2 -d -r0.16 -r0.17 *** genome.rb 15 Jan 2007 04:37:29 -0000 0.16 --- genome.rb 5 Apr 2007 23:35:41 -0000 0.17 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: genes.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/genes.rb,v retrieving revision 0.24 retrieving revision 0.25 diff -C2 -d -r0.24 -r0.25 *** genes.rb 8 Mar 2007 00:10:50 -0000 0.24 --- genes.rb 5 Apr 2007 23:35:41 -0000 0.25 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2002, 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2002, 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: reaction.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/reaction.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** reaction.rb 19 Sep 2006 05:56:38 -0000 1.4 --- reaction.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: brite.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/brite.rb,v retrieving revision 0.7 retrieving revision 0.8 diff -C2 -d -r0.7 -r0.8 *** brite.rb 19 Sep 2006 05:50:45 -0000 0.7 --- brite.rb 5 Apr 2007 23:35:41 -0000 0.8 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # 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 test_alignment.rb, 1.10, 1.11 test_command.rb, 1.4, 1.5 test_db.rb, 1.3, 1.4 test_feature.rb, 1.4, 1.5 test_location.rb, 1.3, 1.4 test_map.rb, 1.4, 1.5 test_pathway.rb, 1.4, 1.5 test_reference.rb, 1.2, 1.3 test_sequence.rb, 1.8, 1.9 test_shell.rb, 1.6, 1.7 test_tree.rb, 1.4, 1.5 Message-ID: <200704052335.l35NZjem020289@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio Modified Files: test_alignment.rb test_command.rb test_db.rb test_feature.rb test_location.rb test_map.rb test_pathway.rb test_reference.rb test_sequence.rb test_shell.rb test_tree.rb Log Message: Standardize on The Ruby License Index: test_pathway.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_pathway.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_pathway.rb 5 Apr 2007 17:12:00 -0000 1.4 --- test_pathway.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: The Ruby License # # $Id$ Index: test_command.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_command.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_command.rb 29 Mar 2007 12:14:46 -0000 1.4 --- test_command.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 5,9 **** # Mitsuteru Nakao , # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Mitsuteru Nakao , # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_map.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_map.rb 28 Mar 2007 21:25:02 -0000 1.4 --- test_map.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Jan Aerts ! # License:: Ruby's # # $Id: --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Jan Aerts ! # License:: The Ruby License # # $Id: Index: test_alignment.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_alignment.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** test_alignment.rb 5 Apr 2007 17:12:00 -0000 1.10 --- test_alignment.rb 5 Apr 2007 23:35:42 -0000 1.11 *************** *** 5,9 **** # Moses Hohman # 2005 Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Moses Hohman # 2005 Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_feature.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_feature.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_feature.rb 5 Apr 2007 17:12:00 -0000 1.4 --- test_feature.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_shell.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_shell.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_shell.rb 24 Dec 2006 17:19:04 -0000 1.6 --- test_shell.rb 5 Apr 2007 23:35:42 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_location.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_location.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_location.rb 5 Apr 2007 17:12:00 -0000 1.3 --- test_location.rb 5 Apr 2007 23:35:42 -0000 1.4 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: The Ruby License # # $Id$ Index: test_db.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_db.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_db.rb 24 Dec 2006 17:19:04 -0000 1.3 --- test_db.rb 5 Apr 2007 23:35:42 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_reference.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_reference.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_reference.rb 31 Dec 2006 21:54:49 -0000 1.2 --- test_reference.rb 5 Apr 2007 23:35:42 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_tree.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_tree.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_tree.rb 12 Jan 2007 16:12:05 -0000 1.4 --- test_tree.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_sequence.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_sequence.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** test_sequence.rb 5 Apr 2007 23:10:09 -0000 1.8 --- test_sequence.rb 5 Apr 2007 23:35:42 -0000 1.9 *************** *** 5,9 **** # Moses Hohman # 2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Moses Hohman # 2006 Mitsuteru C. Nakao ! # 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/double_stranded aligned_strands.rb, 1.4, 1.5 cut_location_pair.rb, 1.7, 1.8 cut_location_pair_in_enzyme_notation.rb, 1.5, 1.6 cut_locations.rb, 1.4, 1.5 cut_locations_in_enzyme_notation.rb, 1.5, 1.6 Message-ID: <200704052336.l35NZivJ020253@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-serv20013/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: Standardize on The Ruby License Index: aligned_strands.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** aligned_strands.rb 4 Apr 2007 18:07:44 -0000 1.4 --- aligned_strands.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 22,26 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Align two SingleStrand objects and return a Result --- 22,26 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Align two SingleStrand objects and return a Result Index: cut_locations.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** cut_locations.rb 4 Apr 2007 18:07:44 -0000 1.4 --- cut_locations.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Contains an +Array+ of CutLocationPair objects. --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Contains an +Array+ of CutLocationPair objects. 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 1.5 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 21,25 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Inherits from DoubleStranded::CutLocations. Contains CutLocationPairInEnzymeNotation objects. --- 21,25 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Inherits from DoubleStranded::CutLocations. Contains CutLocationPairInEnzymeNotation objects. 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 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** cut_location_pair_in_enzyme_notation.rb 4 Apr 2007 20:05:06 -0000 1.5 --- cut_location_pair_in_enzyme_notation.rb 5 Apr 2007 23:35:42 -0000 1.6 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in 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 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** cut_location_pair.rb 4 Apr 2007 20:05:06 -0000 1.7 --- cut_location_pair.rb 5 Apr 2007 23:35:42 -0000 1.8 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Stores a single cut location pair in 0-based index notation for use with --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Stores a single cut location pair in 0-based index notation for use with From trevor at dev.open-bio.org Thu Apr 5 19:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/io das.rb, 1.15, 1.16 dbget.rb, 1.12, 1.13 ddbjxml.rb, 1.13, 1.14 ebisoap.rb, 1.2, 1.3 ensembl.rb, 1.10, 1.11 fastacmd.rb, 1.15, 1.16 fetch.rb, 1.9, 1.10 flatfile.rb, 1.57, 1.58 keggapi.rb, 1.13, 1.14 ncbisoap.rb, 1.2, 1.3 pubmed.rb, 1.15, 1.16 registry.rb, 1.18, 1.19 soapwsdl.rb, 1.6, 1.7 sql.rb, 1.7, 1.8 Message-ID: <200704052336.l35NZhJW020207@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/io In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/io Modified Files: das.rb dbget.rb ddbjxml.rb ebisoap.rb ensembl.rb fastacmd.rb fetch.rb flatfile.rb keggapi.rb ncbisoap.rb pubmed.rb registry.rb soapwsdl.rb sql.rb Log Message: Standardize on The Ruby License Index: registry.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/registry.rb,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -d -r1.18 -r1.19 *** registry.rb 14 Jul 2006 14:48:56 -0000 1.18 --- registry.rb 5 Apr 2007 23:35:41 -0000 1.19 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002, 2003, 2004, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002, 2003, 2004, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: dbget.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/dbget.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** dbget.rb 8 May 2006 14:29:58 -0000 1.12 --- dbget.rb 5 Apr 2007 23:35:41 -0000 1.13 *************** *** 5,9 **** # Mitsuteru C. Nakao , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Mitsuteru C. Nakao , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: pubmed.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/pubmed.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** pubmed.rb 19 Sep 2006 05:47:52 -0000 1.15 --- pubmed.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: The Ruby License # # $Id$ Index: keggapi.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/keggapi.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** keggapi.rb 19 Sep 2006 05:45:48 -0000 1.13 --- keggapi.rb 5 Apr 2007 23:35:41 -0000 1.14 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: ebisoap.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ebisoap.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** ebisoap.rb 28 Mar 2007 09:11:02 -0000 1.2 --- ebisoap.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: sql.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/sql.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** sql.rb 15 Dec 2006 16:53:20 -0000 1.7 --- sql.rb 5 Apr 2007 23:35:41 -0000 1.8 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Raoul Jean Pierre Bonnal ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Raoul Jean Pierre Bonnal ! # License:: The Ruby License # # $Id$ Index: ddbjxml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ddbjxml.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** ddbjxml.rb 28 Mar 2007 09:11:02 -0000 1.13 --- ddbjxml.rb 5 Apr 2007 23:35:41 -0000 1.14 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003, 2004 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003, 2004 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: fetch.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fetch.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** fetch.rb 14 Jul 2006 14:28:44 -0000 1.9 --- fetch.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama , # Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama , # Copyright (C) 2006 Jan Aerts ! # License:: The Ruby License # # $Id$ Index: ensembl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ensembl.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** ensembl.rb 29 Mar 2007 14:14:17 -0000 1.10 --- ensembl.rb 5 Apr 2007 23:35:41 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: soapwsdl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/soapwsdl.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** soapwsdl.rb 19 Sep 2006 05:43:06 -0000 1.6 --- soapwsdl.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v retrieving revision 1.57 retrieving revision 1.58 diff -C2 -d -r1.57 -r1.58 *** flatfile.rb 27 Mar 2007 09:26:03 -0000 1.57 --- flatfile.rb 5 Apr 2007 23:35:41 -0000 1.58 *************** *** 4,8 **** # Copyright (C) 2001-2006 Naohisa Goto # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright (C) 2001-2006 Naohisa Goto # ! # License:: The Ruby License # # $Id$ Index: das.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/das.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** das.rb 28 Mar 2007 19:51:24 -0000 1.15 --- das.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 5,9 **** # Shuichi Kawashima , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Shuichi Kawashima , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: fastacmd.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fastacmd.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** fastacmd.rb 29 Mar 2007 12:44:25 -0000 1.15 --- fastacmd.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 7,11 **** # Mitsuteru C. Nakao , # Jan Aerts ! # License:: Ruby's # # $Id$ --- 7,11 ---- # Mitsuteru C. Nakao , # Jan Aerts ! # License:: The Ruby License # # $Id$ Index: ncbisoap.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ncbisoap.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** ncbisoap.rb 28 Mar 2007 09:11:02 -0000 1.2 --- ncbisoap.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004, 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004, 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ 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/db aaindex.rb, 1.19, 1.20 fantom.rb, 1.13, 1.14 fasta.rb, 1.27, 1.28 gff.rb, 1.7, 1.8 go.rb, 1.10, 1.11 lasergene.rb, 1.2, 1.3 litdb.rb, 0.9, 0.10 medline.rb, 1.15, 1.16 nbrf.rb, 1.9, 1.10 newick.rb, 1.6, 1.7 nexus.rb, 1.2, 1.3 pdb.rb, 1.7, 1.8 rebase.rb, 1.7, 1.8 soft.rb, 1.1, 1.2 transfac.rb, 1.11, 1.12 Message-ID: <200704052336.l35NZgfH020178@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db Modified Files: aaindex.rb fantom.rb fasta.rb gff.rb go.rb lasergene.rb litdb.rb medline.rb nbrf.rb newick.rb nexus.rb pdb.rb rebase.rb soft.rb transfac.rb Log Message: Standardize on The Ruby License Index: aaindex.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/aaindex.rb,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** aaindex.rb 8 May 2006 14:34:52 -0000 1.19 --- aaindex.rb 5 Apr 2007 23:35:40 -0000 1.20 *************** *** 6,10 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: soft.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/soft.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** soft.rb 2 Feb 2007 06:13:10 -0000 1.1 --- soft.rb 5 Apr 2007 23:35:40 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # $Id$ --- 4,8 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Index: go.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/go.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** go.rb 30 Apr 2006 07:11:28 -0000 1.10 --- go.rb 5 Apr 2007 23:35:40 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: litdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/litdb.rb,v retrieving revision 0.9 retrieving revision 0.10 diff -C2 -d -r0.9 -r0.10 *** litdb.rb 19 Sep 2006 06:03:51 -0000 0.9 --- litdb.rb 5 Apr 2007 23:35:40 -0000 0.10 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: fasta.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fasta.rb,v retrieving revision 1.27 retrieving revision 1.28 diff -C2 -d -r1.27 -r1.28 *** fasta.rb 31 Dec 2006 21:54:49 -0000 1.27 --- fasta.rb 5 Apr 2007 23:35:40 -0000 1.28 *************** *** 5,9 **** # GOTO Naohisa , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: newick.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/newick.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** newick.rb 15 Dec 2006 14:59:25 -0000 1.6 --- newick.rb 5 Apr 2007 23:35:40 -0000 1.7 *************** *** 5,9 **** # Naohisa Goto # Daniel Amelang ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Naohisa Goto # Daniel Amelang ! # License:: The Ruby License # # $Id$ Index: pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** pdb.rb 29 Mar 2007 12:50:49 -0000 1.7 --- pdb.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: rebase.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/rebase.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** rebase.rb 1 Jan 2007 00:12:54 -0000 1.7 --- rebase.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Index: nexus.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nexus.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** nexus.rb 19 Dec 2006 05:37:50 -0000 1.2 --- nexus.rb 5 Apr 2007 23:35:40 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: The Ruby License # # $Id$ Index: medline.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/medline.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** medline.rb 19 Sep 2006 06:03:51 -0000 1.15 --- medline.rb 5 Apr 2007 23:35:40 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: lasergene.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/lasergene.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** lasergene.rb 1 Feb 2007 05:23:01 -0000 1.2 --- lasergene.rb 5 Apr 2007 23:35:40 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: Distributes under the same terms as Ruby # # $Id$ --- 4,8 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: Distributes under the same terms as Ruby # # = Description --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: The Ruby License # # = Description Index: gff.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/gff.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** gff.rb 8 May 2006 14:31:58 -0000 1.7 --- gff.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 5,9 **** # Toshiaki Katayama # 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama # 2006 Jan Aerts ! # License:: The Ruby License # # $Id$ Index: fantom.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fantom.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** fantom.rb 14 Jul 2006 14:48:55 -0000 1.13 --- fantom.rb 5 Apr 2007 23:35:40 -0000 1.14 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: transfac.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/transfac.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** transfac.rb 29 Mar 2007 12:46:58 -0000 1.11 --- transfac.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001 # Shuichi Kawashima ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001 # Shuichi Kawashima ! # License:: The Ruby License # # $Id$ Index: nbrf.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nbrf.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** nbrf.rb 19 Sep 2006 06:03:51 -0000 1.9 --- nbrf.rb 5 Apr 2007 23:35:40 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001-2003,2006 Naohisa Goto # Copyright (C) 2001-2002 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001-2003,2006 Naohisa Goto # Copyright (C) 2001-2002 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From k at dev.open-bio.org Fri Apr 6 00:41:30 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 04:41:30 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/data aa.rb, 0.20, 0.21 na.rb, 0.22, 0.23 Message-ID: <200704060441.l364fUa0021024@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/data In directory dev.open-bio.org:/tmp/cvs-serv21020 Modified Files: aa.rb na.rb Log Message: * AA#to_re is rewrited symmetrically to NA#to_re * default value '.' is assigned for to_re replacement Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/aa.rb,v retrieving revision 0.20 retrieving revision 0.21 diff -C2 -d -r0.20 -r0.21 *** aa.rb 5 Apr 2007 23:35:40 -0000 0.20 --- aa.rb 6 Apr 2007 04:41:28 -0000 0.21 *************** *** 218,225 **** def to_re(seq) str = seq.to_s.upcase ! str.gsub!(/[^BZACDEFGHIKLMNPQRSTVWYU]/, ".") ! str.gsub!("B", "[DN]") ! str.gsub!("Z", "[EQ]") Regexp.new(str) end --- 218,233 ---- def to_re(seq) + replace = { + 'B' => '[DNB]', + 'Z' => '[EQZ]', + 'J' => '[ILJ]', + 'X' => '[ACDEFGHIKLMNPQRSTVWYUO]', + } + replace.default = '.' + str = seq.to_s.upcase ! str.gsub!(/[^ACDEFGHIKLMNPQRSTVWYUO]/) { |aa| ! replace[aa] ! } Regexp.new(str) end Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v retrieving revision 0.22 retrieving revision 0.23 diff -C2 -d -r0.22 -r0.23 *** na.rb 5 Apr 2007 23:35:40 -0000 0.22 --- na.rb 6 Apr 2007 04:41:28 -0000 0.23 *************** *** 172,179 **** 'n' => '[atgcyrwskmbdhvn]' } str = seq.to_s.downcase ! str.gsub!(/[^atgcu]/) { |base| ! replace[base] || base } if rna --- 172,180 ---- 'n' => '[atgcyrwskmbdhvn]' } + replace.default = '.' str = seq.to_s.downcase ! str.gsub!(/[^atgcu]/) { |na| ! replace[na] } if rna From k at dev.open-bio.org Fri Apr 6 00:44:53 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 04:44:53 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/data aa.rb,0.21,0.22 Message-ID: <200704060444.l364irau021086@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/data In directory dev.open-bio.org:/tmp/cvs-serv21082 Modified Files: aa.rb Log Message: * replacement of X should include X itself. Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/aa.rb,v retrieving revision 0.21 retrieving revision 0.22 diff -C2 -d -r0.21 -r0.22 *** aa.rb 6 Apr 2007 04:41:28 -0000 0.21 --- aa.rb 6 Apr 2007 04:44:51 -0000 0.22 *************** *** 222,226 **** 'Z' => '[EQZ]', 'J' => '[ILJ]', ! 'X' => '[ACDEFGHIKLMNPQRSTVWYUO]', } replace.default = '.' --- 222,226 ---- 'Z' => '[EQZ]', 'J' => '[ILJ]', ! 'X' => '[ACDEFGHIKLMNPQRSTVWYUOX]', } replace.default = '.' From k at dev.open-bio.org Fri Apr 6 00:46:38 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 04:46:38 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio/data test_aa.rb,1.6,1.7 Message-ID: <200704060446.l364kcik021111@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/data In directory dev.open-bio.org:/tmp/cvs-serv21107/test/unit/bio/data Modified Files: test_aa.rb Log Message: * followed the change of AA#to_re spec. Index: test_aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/data/test_aa.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_aa.rb 5 Apr 2007 23:35:43 -0000 1.6 --- test_aa.rb 6 Apr 2007 04:46:36 -0000 1.7 *************** *** 85,89 **** def test_to_re ! assert_equal(/[DN][EQ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU')) end end --- 85,89 ---- def test_to_re ! assert_equal(/[DNB][EQZ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU')) end end From k at dev.open-bio.org Fri Apr 6 08:04:07 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 12:04:07 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/fasta format10.rb,1.6,1.7 Message-ID: <200704061204.l36C47EV022099@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/fasta In directory dev.open-bio.org:/tmp/cvs-serv22095/lib/bio/appl/fasta Modified Files: format10.rb Log Message: * Licensed under the same terms as Ruby * converted to RDoc Index: format10.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/fasta/format10.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** format10.rb 26 Sep 2005 13:00:05 -0000 1.6 --- format10.rb 6 Apr 2007 12:04:05 -0000 1.7 *************** *** 1,22 **** # ! # bio/appl/fasta/format10.rb - FASTA output (-m 10) parser # ! # Copyright (C) 2002 KATAYAMA Toshiaki ! # ! # 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 # ! # $Id$ # --- 1,9 ---- # ! # = bio/appl/fasta/format10.rb - FASTA output (-m 10) parser # ! # Copyright:: Copyright (C) 2002 Toshiaki Katayama ! # License:: The Ruby License # ! # $Id$ # *************** *** 24,267 **** module Bio ! class Fasta ! class Report ! def initialize(data) ! # header lines - brief list of the hits ! if data.sub!(/.*\nThe best scores are/m, '') ! data.sub!(/(.*)\n\n>>>/m, '') ! @list = "The best scores are" + $1 ! else ! data.sub!(/.*\n!!\s+/m, '') ! data.sub!(/.*/) { |x| @list = x; '' } ! end ! # body lines - fasta execution result ! program, *hits = data.split(/\n>>/) ! # trailing lines - log messages of the execution ! @log = hits.pop ! @log.sub!(/.*<\n/m, '') ! @log.strip! ! # parse results ! @program = Program.new(program) ! @hits = [] ! hits.each do |x| ! @hits.push(Hit.new(x)) ! end ! end ! attr_reader :list, :log, :program, :hits ! def each ! @hits.each do |x| ! yield x ! end ! end ! def threshold(evalue_max = 0.1) ! list = [] ! @hits.each do |x| ! list.push(x) if x.evalue < evalue_max ! end ! return list ! end ! def lap_over(length_min = 0) ! list = [] ! @hits.each do |x| ! list.push(x) if x.overlap > length_min ! end ! return list ! end ! class Program ! def initialize(data) ! @definition, *program = data.split(/\n/) ! @program = {} ! pat = /;\s+([^:]+):\s+(.*)/ ! program.each do |x| ! if pat.match(x) ! @program[$1] = $2 ! end ! end end - attr_reader :definition, :program end - class Hit - def initialize(data) - score, query, target = data.split(/\n>/) ! @definition, *score = score.split(/\n/) ! @score = {} ! pat = /;\s+([^:]+):\s+(.*)/ ! score.each do |x| ! if pat.match(x) ! @score[$1] = $2 ! end ! end ! @query = Query.new(query) ! @target = Target.new(target) end ! attr_reader :definition, :score, :query, :target ! def evalue ! if @score['fa_expect'] ! @score['fa_expect'].to_f ! elsif @score['sw_expect'] ! @score['sw_expect'].to_f ! elsif @score['fx_expect'] ! @score['fx_expect'].to_f ! elsif @score['tx_expect'] ! @score['tx_expect'].to_f ! end ! end ! def bit_score ! if @score['fa_bits'] ! @score['fa_bits'].to_f ! elsif @score['sw_bits'] ! @score['sw_bits'].to_f ! elsif @score['fx_bits'] ! @score['fx_bits'].to_f ! elsif @score['tx_bits'] ! @score['tx_bits'].to_f ! end ! end ! def direction ! @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame'] ! end ! def sw ! @score['sw_score'].to_i ! end ! def identity ! @score['sw_ident'].to_f ! end ! def overlap ! @score['sw_overlap'].to_i ! end ! def query_id ! @query.entry_id ! end ! def target_id ! @target.entry_id ! end ! def query_def ! @query.definition ! end ! def target_def ! @target.definition ! end ! def query_len ! @query.length ! end ! def target_len ! @target.length ! end ! def query_seq ! @query.sequence ! end ! def target_seq ! @target.sequence ! end ! def query_type ! @query.moltype ! end ! def target_type ! @target.moltype ! end ! def query_start ! @query.start ! end ! def query_end ! @query.stop ! end ! def target_start ! @target.start ! end ! def target_end ! @target.stop ! end ! def lap_at ! [ query_start, query_end, target_start, target_end ] ! end ! class Query ! def initialize(data) ! @definition, *data = data.split(/\n/) ! @data = {} ! @sequence = '' ! pat = /;\s+([^:]+):\s+(.*)/ ! data.each do |x| ! if pat.match(x) ! @data[$1] = $2 ! else ! @sequence += x ! end ! end ! end ! attr_reader :definition, :data, :sequence - def entry_id - @definition[/\S+/] - end ! def length ! @data['sq_len'].to_i ! end ! def moltype ! @data['sq_type'] ! end ! def start ! @data['al_start'].to_i end ! def stop ! @data['al_stop'].to_i ! end ! end ! class Target < Query; end end end end ! end --- 11,312 ---- module Bio ! class Fasta ! # Summarized results of the fasta execution results. ! class Report ! def initialize(data) ! # header lines - brief list of the hits ! if data.sub!(/.*\nThe best scores are/m, '') ! data.sub!(/(.*)\n\n>>>/m, '') ! @list = "The best scores are" + $1 ! else ! data.sub!(/.*\n!!\s+/m, '') ! data.sub!(/.*/) { |x| @list = x; '' } ! end ! # body lines - fasta execution result ! program, *hits = data.split(/\n>>/) ! # trailing lines - log messages of the execution ! @log = hits.pop ! @log.sub!(/.*<\n/m, '') ! @log.strip! ! # parse results ! @program = Program.new(program) ! @hits = [] ! hits.each do |x| ! @hits.push(Hit.new(x)) ! end ! end ! ! # Returns the 'The best scores are' lines as a String. ! attr_reader :list ! # Returns the trailing lines including library size, execution date, ! # fasta function used, and fasta versions as a String. ! attr_reader :log ! # Returns a Bio::Fasta::Report::Program object. ! attr_reader :program ! # Returns an Array of Bio::Fasta::Report::Hit objects. ! attr_reader :hits + # Iterates on each Bio::Fasta::Report::Hit object. + def each + @hits.each do |x| + yield x + end + end ! # Returns an Array of Bio::Fasta::Report::Hit objects having ! # better evalue than 'evalue_max'. ! def threshold(evalue_max = 0.1) ! list = [] ! @hits.each do |x| ! list.push(x) if x.evalue < evalue_max ! end ! return list ! end ! # Returns an Array of Bio::Fasta::Report::Hit objects having ! # longer overlap length than 'length_min'. ! def lap_over(length_min = 0) ! list = [] ! @hits.each do |x| ! list.push(x) if x.overlap > length_min ! end ! return list ! end ! # Log of the fasta execution environments. ! class Program ! def initialize(data) ! @definition, *program = data.split(/\n/) ! @program = {} ! ! pat = /;\s+([^:]+):\s+(.*)/ ! ! program.each do |x| ! if pat.match(x) ! @program[$1] = $2 end end + end + + # Returns a String containing query and library filenames. + attr_reader :definition + # Accessor for a Hash containing 'mp_name', 'mp_ver', 'mp_argv', + # 'pg_name', 'pg_ver, 'pg_matrix', 'pg_gap-pen', 'pg_ktup', + # 'pg_optcut', 'pg_cgap', 'mp_extrap', 'mp_stats', and 'mp_KS' values. + attr_reader :program + end ! class Hit ! def initialize(data) ! score, query, target = data.split(/\n>/) ! @definition, *score = score.split(/\n/) ! @score = {} ! pat = /;\s+([^:]+):\s+(.*)/ ! score.each do |x| ! if pat.match(x) ! @score[$1] = $2 end ! end ! @query = Query.new(query) ! @target = Target.new(target) ! end ! attr_reader :definition, :score, :query, :target ! # E-value score ! def evalue ! if @score['fa_expect'] ! @score['fa_expect'].to_f ! elsif @score['sw_expect'] ! @score['sw_expect'].to_f ! elsif @score['fx_expect'] ! @score['fx_expect'].to_f ! elsif @score['tx_expect'] ! @score['tx_expect'].to_f ! end ! end ! # Bit score ! def bit_score ! if @score['fa_bits'] ! @score['fa_bits'].to_f ! elsif @score['sw_bits'] ! @score['sw_bits'].to_f ! elsif @score['fx_bits'] ! @score['fx_bits'].to_f ! elsif @score['tx_bits'] ! @score['tx_bits'].to_f ! end ! end ! def direction ! @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame'] ! end ! # Smith-Waterman score ! def sw ! @score['sw_score'].to_i ! end ! # percent identity ! def identity ! @score['sw_ident'].to_f ! end ! # overlap length ! def overlap ! @score['sw_overlap'].to_i ! end ! # Shortcuts for the methods of Bio::Fasta::Report::Hit::Query ! def query_id ! @query.entry_id ! end ! def target_id ! @target.entry_id ! end ! def query_def ! @query.definition ! end ! def target_def ! @target.definition ! end ! def query_len ! @query.length ! end ! # Shortcuts for the methods of Bio::Fasta::Report::Hit::Target ! def target_len ! @target.length ! end ! def query_seq ! @query.sequence ! end ! def target_seq ! @target.sequence ! end ! def query_type ! @query.moltype ! end ! def target_type ! @target.moltype ! end ! # Information on matching region ! def query_start ! @query.start ! end + def query_end + @query.stop + end ! def target_start ! @target.start ! end ! def target_end ! @target.stop ! end ! def lap_at ! [ query_start, query_end, target_start, target_end ] ! end ! class Query ! def initialize(data) ! @definition, *data = data.split(/\n/) ! @data = {} ! @sequence = '' ! pat = /;\s+([^:]+):\s+(.*)/ ! data.each do |x| ! if pat.match(x) ! @data[$1] = $2 ! else ! @sequence += x end + end + end ! # Returns the definition of the entry as a String. ! # You can access this value by Report::Hit#query_def method. ! attr_reader :definition ! # Returns a Hash containing 'sq_len', 'sq_offset', 'sq_type', ! # 'al_start', 'al_stop', and 'al_display_start' values. ! # You can access most of these values by Report::Hit#query_* methods. ! attr_reader :data ! # Returns the sequence (with gaps) as a String. ! # You can access this value by the Report::Hit#query_seq method. ! attr_reader :sequence ! ! # Returns the first word in the definition as a String. ! # You can get this value by Report::Hit#query_id method. ! def entry_id ! @definition[/\S+/] ! end ! ! # Returns the sequence length. ! # You can access this value by the Report::Hit#query_len method. ! def length ! @data['sq_len'].to_i ! end ! ! # Returns 'p' for protein sequence, 'D' for nucleotide sequence. ! def moltype ! @data['sq_type'] ! end ! ! # Returns alignment start position. You can also access this value ! # by Report::Hit#query_start method for shortcut. ! def start ! @data['al_start'].to_i ! end ! ! # Returns alignment end position. You can access this value ! # by Report::Hit#query_end method for shortcut. ! def stop ! @data['al_stop'].to_i end end + # Same as Bio::Fasta::Report::Hit::Query but for Target. + class Target < Query; end end ! ! end # Report ! ! end # Fasta ! end # Bio *************** *** 279,428 **** - =begin - - = Bio::Fasta::Report - - Summarized results of the fasta execution hits. - - --- Bio::Fasta::Report.new(data) - --- Bio::Fasta::Report#each - - Iterates on each Bio::Fasta::Report::Hit object. - - --- Bio::Fasta::Report#hits - - Returns an Array of Bio::Fasta::Report::Hit objects. - - --- Bio::Fasta::Report#threshold(evalue_max = 0.1) - - Returns an Array of Bio::Fasta::Report::Hit objects having - better evalue than 'evalue_max'. - - --- Bio::Fasta::Report#lap_over(length_min = 0) - - Returns an Array of Bio::Fasta::Report::Hit objects having - longer overlap length than 'length_min'. - - --- Bio::Fasta::Report#program - - Returns a Bio::Fasta::Report::Program object. - - --- Bio::Fasta::Report#list - - Returns the 'The best scores are' lines as a String. - - --- Bio::Fasta::Report#log - - Returns the trailing lines including library size, execution date, - fasta function used, and fasta versions as a String. - - - == Bio::Fasta::Report::Program - - Log of the fasta execution environments. - - --- Bio::Fasta::Report::Program#definition - - Returns a String containing query and library filenames. - - --- Bio::Fasta::Report::Program#program - - Accessor for a Hash containing 'mp_name', 'mp_ver', 'mp_argv', - 'pg_name', 'pg_ver, 'pg_matrix', 'pg_gap-pen', 'pg_ktup', - 'pg_optcut', 'pg_cgap', 'mp_extrap', 'mp_stats', and 'mp_KS' values. - - - == Bio::Fasta::Report::Hit - - --- Bio::Fasta::Report::Hit#definition - --- Bio::Fasta::Report::Hit#score - --- Bio::Fasta::Report::Hit#query - --- Bio::Fasta::Report::Hit#target - - Accessors for the internal structures. - - --- Bio::Fasta::Report::Hit#evalue - --- Bio::Fasta::Report::Hit#bit_score - --- Bio::Fasta::Report::Hit#sw - --- Bio::Fasta::Report::Hit#identity - - Matching scores. - - --- Bio::Fasta::Report::Hit#query_id - --- Bio::Fasta::Report::Hit#query_def - --- Bio::Fasta::Report::Hit#query_len - --- Bio::Fasta::Report::Hit#query_seq - --- Bio::Fasta::Report::Hit#query_type - --- Bio::Fasta::Report::Hit#target_id - --- Bio::Fasta::Report::Hit#target_def - --- Bio::Fasta::Report::Hit#target_len - --- Bio::Fasta::Report::Hit#target_seq - --- Bio::Fasta::Report::Hit#target_type - - Matching subjects. - Shortcuts for the methods of Hit::Query and the Hit::Target. - - --- Bio::Fasta::Report::Hit#query_start - --- Bio::Fasta::Report::Hit#query_end - --- Bio::Fasta::Report::Hit#target_start - --- Bio::Fasta::Report::Hit#target_end - --- Bio::Fasta::Report::Hit#overlap - --- Bio::Fasta::Report::Hit#lap_at - --- Bio::Fasta::Report::Hit#direction - - Matching regions. - - - == Bio::Fasta::Report::Hit::Query - - --- Bio::Fasta::Report::Hit::Query#entry_id - - Returns the first word in the definition as a String. - You can get this value by Report::Hit#query_id method. - - --- Bio::Fasta::Report::Hit::Query#definition - - Returns the definition of the entry as a String. - You can access this value by Report::Hit#query_def method. - - --- Bio::Fasta::Report::Hit::Query#sequence - - Returns the sequence (with gaps) as a String. - You can access this value by the Report::Hit#query_seq method. - - --- Bio::Fasta::Report::Hit::Query#length - - Returns the sequence length. - You can access this value by the Report::Hit#query_len method. - - --- Bio::Fasta::Report::Hit::Query#moltype - - Returns 'p' for protein sequence, 'D' for nucleotide sequence. - - --- Bio::Fasta::Report::Hit::Query#start - --- Bio::Fasta::Report::Hit::Query#stop - - Returns alignment start and stop position. - You can access these values by Report::Hit#query_start and - Report::Hit#query_end methods. - - --- Bio::Fasta::Report::Hit::Query#data - - Returns a Hash containing 'sq_len', 'sq_offset', 'sq_type', - 'al_start', 'al_stop', and 'al_display_start' values. - You can access most of these values by Report::Hit#query_* methods. - - - == Bio::Fasta::Report::Hit::Target - - --- Bio::Fasta::Report::Hit::Target#entry_id - --- Bio::Fasta::Report::Hit::Target#definition - --- Bio::Fasta::Report::Hit::Target#data - --- Bio::Fasta::Report::Hit::Target#sequence - --- Bio::Fasta::Report::Hit::Target#length - --- Bio::Fasta::Report::Hit::Target#start - --- Bio::Fasta::Report::Hit::Target#stop - - Same as Bio::Fasta::Report::Hit::Query but for Target. - - =end --- 324,325 ---- From k at dev.open-bio.org Fri Apr 6 09:13:39 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 13:13:39 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/fasta format6.rb,1.2,NONE Message-ID: <200704061313.l36DDdTd022257@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/fasta In directory dev.open-bio.org:/tmp/cvs-serv22253 Removed Files: format6.rb Log Message: * deprecated --- format6.rb DELETED --- From aerts at dev.open-bio.org Thu Apr 12 08:19:18 2007 From: aerts at dev.open-bio.org (Jan Aerts) Date: Thu, 12 Apr 2007 12:19:18 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.10,1.11 Message-ID: <200704121219.l3CCJIDQ032222@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio In directory dev.open-bio.org:/tmp/cvs-serv32200/lib/bio Modified Files: map.rb Log Message: * Added mappings_on method to Bio::Map::ActsLikeMarker. * Extended unit tests to get 100% coverage. Index: map.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** map.rb 5 Apr 2007 23:45:10 -0000 1.10 --- map.rb 12 Apr 2007 12:19:16 -0000 1.11 *************** *** 263,266 **** --- 263,286 ---- return positions end + + # Return all mappings of this marker on a given map. + # --- + # *Arguments*: + # * _map_: an object that mixes in Bio::Map::ActsLikeMap + # *Returns*:: array of Bio::Map::Mapping objects + def mappings_on(map) + unless map.class.include?(Bio::Map::ActsLikeMap) + raise "[Error] map is not object that implements Bio::Map::ActsLikeMap" + end + + m = Array.new + self.mappings_as_marker.each do |mapping| + if mapping.map == map + m.push(mapping) + end + end + + return m + end *************** *** 304,308 **** end ! return self.location.<=>(other.location) end end # Mapping --- 324,328 ---- end ! return self.location[0].<=>(other.location[0]) end end # Mapping From aerts at dev.open-bio.org Thu Apr 12 08:19:19 2007 From: aerts at dev.open-bio.org (Jan Aerts) Date: Thu, 12 Apr 2007 12:19:19 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio test_map.rb,1.5,1.6 Message-ID: <200704121219.l3CCJJxi032225@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio In directory dev.open-bio.org:/tmp/cvs-serv32200/test/unit/bio Modified Files: test_map.rb Log Message: * Added mappings_on method to Bio::Map::ActsLikeMarker. * Extended unit tests to get 100% coverage. Index: test_map.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_map.rb 5 Apr 2007 23:35:42 -0000 1.5 --- test_map.rb 12 Apr 2007 12:19:16 -0000 1.6 *************** *** 41,44 **** --- 41,45 ---- @marker3 = Bio::Map::Marker.new('marker3') @map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit') + @map2 = Bio::Map::SimpleMap.new('map2', 'some_other_type', 'some_other_unit') end *************** *** 101,104 **** --- 102,108 ---- @marker1.add_mapping_as_marker(@map1, '53') # This mapping should _not_ be added, because it's already defined. assert_equal(3, @marker1.mappings_as_marker.length) + + @map1.add_mapping_as_map(@marker1, '53') + assert_equal(3, @marker1.mappings_as_marker.length) end *************** *** 110,113 **** --- 114,159 ---- assert_equal('5,37', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.sort{|a,b| a.to_i <=> b.to_i}.join(',')) # FIXME: Test is not correct (uses Location.first) end + + def test_mappings_on + @map1.add_mapping_as_map(@marker1, '5') + @map1.add_mapping_as_map(@marker1, '37') + assert_equal('5,37', @marker1.mappings_on(@map1).sort{|a,b| a.location[0].from.to_i <=> b.location[0].from.to_i}.collect{|m| m.location[0].from}.join(',')) # FIXME: Test is not correct (uses Location.first) + end + + def test_mapping_location_comparison + @map1.add_mapping_as_map(@marker1, '5') + @map1.add_mapping_as_map(@marker2, '5') + @map1.add_mapping_as_map(@marker3, '17') + + mapping1 = @marker1.mappings_on(@map1)[0] + mapping2 = @marker2.mappings_on(@map1)[0] + mapping3 = @marker3.mappings_on(@map1)[0] + assert_equal(true, mapping1 == mapping2) + assert_equal(false, mapping1 < mapping2) + assert_equal(false, mapping1 > mapping2) + assert_equal(false, mapping1 == mapping3) + assert_equal(true, mapping1 < mapping3) + assert_equal(false, mapping1 > mapping3) + + @map2.add_mapping_as_map(@marker1, '23') + mapping4 = @marker1.mappings_on(@map2)[0] + assert_raise(RuntimeError) { mapping2 < mapping4 } + end + + def test_raise_error_kind_of + marker_without_class = 'marker1' + assert_raise(RuntimeError) { @map1.add_mapping_as_map(marker_without_class, '5') } + assert_raise(RuntimeError) { @map1.contains_marker?(marker_without_class) } + + map_without_class = 'map1' + assert_raise(RuntimeError) { @marker1.add_mapping_as_marker(map_without_class, '5') } + assert_raise(RuntimeError) { @marker1.mapped_to?(map_without_class) } + assert_raise(RuntimeError) { @marker1.positions_on(map_without_class) } + assert_raise(RuntimeError) { @marker1.mappings_on(map_without_class) } + + @map1.add_mapping_as_map(@marker1, '5') + mapping1 = @marker1.mappings_on(@map1)[0] + assert_raise(RuntimeError) { mapping1 > 'some_mapping' } + end end From k at dev.open-bio.org Fri Apr 13 22:29:47 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Sat, 14 Apr 2007 02:29:47 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.58,1.59 Message-ID: <200704140229.l3E2Tl8w004766@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/io In directory dev.open-bio.org:/tmp/cvs-serv4757/lib/bio/io Modified Files: flatfile.rb Log Message: * KEGG::ORTHOLOG is renamed to KEGG::ORTHOLOGY Index: flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v retrieving revision 1.58 retrieving revision 1.59 diff -C2 -d -r1.58 -r1.59 *** flatfile.rb 5 Apr 2007 23:35:41 -0000 1.58 --- flatfile.rb 14 Apr 2007 02:29:45 -0000 1.59 *************** *** 1146,1150 **** brite = RuleRegexp[ 'Bio::KEGG::BRITE', /^Entry [A-Z0-9]+/ ], ! ortholog = RuleRegexp[ 'Bio::KEGG::ORTHOLOG', /^ENTRY .+ KO\s*/ ], drug = RuleRegexp[ 'Bio::KEGG::DRUG', --- 1146,1150 ---- brite = RuleRegexp[ 'Bio::KEGG::BRITE', /^Entry [A-Z0-9]+/ ], ! orthology = RuleRegexp[ 'Bio::KEGG::ORTHOLOGY', /^ENTRY .+ KO\s*/ ], drug = RuleRegexp[ 'Bio::KEGG::DRUG', *************** *** 1250,1255 **** #aaindex.is_prior_to litdb #litdb.is_prior_to brite ! brite.is_prior_to ortholog ! ortholog.is_prior_to drug drug.is_prior_to glycan glycan.is_prior_to enzyme --- 1250,1255 ---- #aaindex.is_prior_to litdb #litdb.is_prior_to brite ! brite.is_prior_to orthology ! orthology.is_prior_to drug drug.is_prior_to glycan glycan.is_prior_to enzyme From k at dev.open-bio.org Sat Apr 14 01:09:25 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Sat, 14 Apr 2007 05:09:25 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio/sequence test_aa.rb,1.3,1.4 Message-ID: <200704140509.l3E59Px2005968@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv5963/test/unit/bio/sequence Modified Files: test_aa.rb Log Message: * follow the change in to_re method that the regexp includes ambiguous amino acid itself Index: test_aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_aa.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_aa.rb 5 Apr 2007 23:35:44 -0000 1.3 --- test_aa.rb 14 Apr 2007 05:09:23 -0000 1.4 *************** *** 68,72 **** assert_equal(re, @obj.to_re) @obj[1, 1] = 'B' ! re = /R[DN]LEHTFVFLRNFSLMLLRY/ assert_equal(re, @obj.to_re) end --- 68,72 ---- assert_equal(re, @obj.to_re) @obj[1, 1] = 'B' ! re = /R[DNB]LEHTFVFLRNFSLMLLRY/ assert_equal(re, @obj.to_re) end From ngoto at dev.open-bio.org Thu Apr 19 09:59:31 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Thu, 19 Apr 2007 13:59:31 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.21,1.22 Message-ID: <200704191359.l3JDxV0e017218@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv17198/lib/bio/db/pdb Modified Files: pdb.rb Log Message: BUG: When parsing a pdb file with many models, but only one chain per model, all atoms are added to residues in the first Bio::PDB::Model of the Bio::PDB structure. ([BioRuby] bug in pdb.rb bio-1.0.0) reported by Mikael Borg. Index: pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -d -r1.21 -r1.22 *** pdb.rb 5 Apr 2007 23:35:41 -0000 1.21 --- pdb.rb 19 Apr 2007 13:59:29 -0000 1.22 *************** *** 1536,1539 **** --- 1536,1540 ---- when 'MODEL' c_atom = nil + cChain = nil if cModel.model_serial or cModel.chains.size > 0 then self.addModel(cModel) From ngoto at dev.open-bio.org Sat Apr 21 04:25:15 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Sat, 21 Apr 2007 08:25:15 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.20, 1.21 wublast.rb, 1.9, 1.10 Message-ID: <200704210825.l3L8PF8k021508@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv21488/lib/bio/appl/blast Modified Files: format0.rb wublast.rb Log Message: * Incompatible Changes: In Bio::BLAST::Default::Report#expect and and Bio::BLAST::WU::Report#expect are changed to return a Float or nil instead of a String or nil. * Incompatible Changes: In Bio::BLAST::Default::Report::Hit, Bio::BLAST::Default::Report::HSP, Bio::BLAST::WU::Report::Hit, and Bio::BLAST::WU::Report::HSP, following methods are changed to return a Float object instead of a String object: evalue, pvalue (note that pvalue is only available in WU-BLAST). Index: wublast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** wublast.rb 5 Apr 2007 23:35:39 -0000 1.9 --- wublast.rb 21 Apr 2007 08:25:13 -0000 1.10 *************** *** 138,141 **** --- 138,145 ---- end end + if ev = @parameters['E'] then + ev = '1' + ev if ev[0] == ?e + @parameters['E'] = ev.to_f + end @parse_parameters = true end *************** *** 251,256 **** scr = z.pop.to_s pval = z.pop.to_s nnum = z.pop.to_i - #ev = '1' + ev if ev[0] == ?e h.instance_eval { @score = scr --- 255,261 ---- scr = z.pop.to_s pval = z.pop.to_s + pval = '1' + pval if pval[0] == ?e + pval = (pval.empty? ? (1.0/0.0) : pval.to_f) nnum = z.pop.to_i h.instance_eval { @score = scr Index: format0.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** format0.rb 5 Apr 2007 23:35:39 -0000 1.20 --- format0.rb 21 Apr 2007 08:25:13 -0000 1.21 *************** *** 328,332 **** while sc.rest? if sc.match?(/Number of sequences better than +([e\-\.\d]+) *\: *(.+)/) then ! @expect = sc[1] @num_hits = sc[2].tr(',', '').to_i end --- 328,334 ---- while sc.rest? if sc.match?(/Number of sequences better than +([e\-\.\d]+) *\: *(.+)/) then ! ev = sc[1] ! ev = '1' + ev if ev[0] == ?e ! @expect = ev.to_f @num_hits = sc[2].tr(',', '').to_i end *************** *** 659,663 **** bs = z.pop.to_s ev = z.pop.to_s ! #ev = '1' + ev if ev[0] == ?e h.instance_eval { @bit_score = bs; @evalue = ev } @hits << h --- 661,666 ---- bs = z.pop.to_s ev = z.pop.to_s ! ev = '1' + ev if ev[0] == ?e ! ev = (ev.empty? ? (1.0/0.0) : ev.to_f) h.instance_eval { @bit_score = bs; @evalue = ev } @hits << h *************** *** 950,955 **** sc.skip(/\s*/) if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then ! @evalue = sc[1] ! #@evalue = '1' + @evalue if @evalue[0] == ?e elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then @bit_score = sc[1] --- 953,959 ---- sc.skip(/\s*/) if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then ! ev = sc[1].to_s ! ev = '1' + ev if ev[0] == ?e ! @evalue = ev.to_f elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then @bit_score = sc[1] *************** *** 1001,1009 **** #WU-BLAST @p_sum_n = nil ! @pvalue = sc[1] elsif sc.skip(/Sum +P *\( *(\d+) *\) *\= *([e\-\.\d]+)/) then #WU-BLAST @p_sum_n = sc[1].to_i ! @pvalue = sc[2] else raise ScanError --- 1005,1017 ---- #WU-BLAST @p_sum_n = nil ! pv = sc[1] ! pv = '1' + pv if pv[0] == ?e ! @pvalue = pv.to_f elsif sc.skip(/Sum +P *\( *(\d+) *\) *\= *([e\-\.\d]+)/) then #WU-BLAST @p_sum_n = sc[1].to_i ! pv = sc[2] ! pv = '1' + pv if pv[0] == ?e ! @pvalue = pv.to_f else raise ScanError From ngoto at dev.open-bio.org Sat Apr 21 04:58:19 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Sat, 21 Apr 2007 08:58:19 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.21, 1.22 wublast.rb, 1.10, 1.11 Message-ID: <200704210858.l3L8wJn9021602@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv21582/lib/bio/appl/blast Modified Files: format0.rb wublast.rb Log Message: * Incompatible changes: Hit#bit_score, and HSP#bit_score are changed to return a Float object or nil instead of a String object or nil. * Incompatible changes: Following methods are changed to return an integer value or nil instead of a String object or nil: score, percent_identity, percent_positive, percent_gaps. Index: wublast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** wublast.rb 21 Apr 2007 08:25:13 -0000 1.10 --- wublast.rb 21 Apr 2007 08:58:17 -0000 1.11 *************** *** 253,257 **** end z.pop if flag_tblast #ignore Reading Frame ! scr = z.pop.to_s pval = z.pop.to_s pval = '1' + pval if pval[0] == ?e --- 253,258 ---- end z.pop if flag_tblast #ignore Reading Frame ! scr = z.pop ! scr = (scr ? scr.to_i : nil) pval = z.pop.to_s pval = '1' + pval if pval[0] == ?e Index: format0.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -d -r1.21 -r1.22 *** format0.rb 21 Apr 2007 08:25:13 -0000 1.21 --- format0.rb 21 Apr 2007 08:58:17 -0000 1.22 *************** *** 660,663 **** --- 660,665 ---- h = Hit.new([ z.pop.to_s.sub(/\.+\z/, '') ]) bs = z.pop.to_s + bs = '1' + bs if bs[0] == ?e + bs = (bs.empty? ? nil : bs.to_f) ev = z.pop.to_s ev = '1' + ev if ev[0] == ?e *************** *** 957,962 **** @evalue = ev.to_f elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then ! @bit_score = sc[1] ! @score = sc[2] elsif sc.skip(/(Identities|Positives|Gaps) *\= (\d+) *\/ *(\d+) *\(([\.\d]+) *\% *\)/) then alen = sc[3].to_i --- 959,966 ---- @evalue = ev.to_f elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then ! bs = sc[1] ! bs = '1' + bs if bs[0] == ?e ! @bit_score = bs.to_f ! @score = sc[2].to_i elsif sc.skip(/(Identities|Positives|Gaps) *\= (\d+) *\/ *(\d+) *\(([\.\d]+) *\% *\)/) then alen = sc[3].to_i *************** *** 966,976 **** when 'Identities' @identity = sc[2].to_i ! @percent_identity = sc[4] when 'Positives' @positive = sc[2].to_i ! @percent_positive = sc[4] when 'Gaps' @gaps = sc[2].to_i ! @percent_gaps = sc[4] else raise ScanError --- 970,980 ---- when 'Identities' @identity = sc[2].to_i ! @percent_identity = sc[4].to_i when 'Positives' @positive = sc[2].to_i ! @percent_positive = sc[4].to_i when 'Gaps' @gaps = sc[2].to_i ! @percent_gaps = sc[4].to_i else raise ScanError *************** *** 1000,1005 **** elsif sc.skip(/Score *\= *([e\-\.\d]+) +\(([e\-\.\d]+) *bits *\)/) then #WU-BLAST ! @score = sc[1] ! @bit_score = sc[2] elsif sc.skip(/P *\= * ([e\-\.\d]+)/) then #WU-BLAST --- 1004,1011 ---- elsif sc.skip(/Score *\= *([e\-\.\d]+) +\(([e\-\.\d]+) *bits *\)/) then #WU-BLAST ! @score = sc[1].to_i ! bs = sc[2] ! bs = '1' + bs if bs[0] == ?e ! @bit_score = bs.to_f elsif sc.skip(/P *\= * ([e\-\.\d]+)/) then #WU-BLAST From ngoto at dev.open-bio.org Sat Apr 21 04:59:47 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Sat, 21 Apr 2007 08:59:47 +0000 Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.19,1.20 Message-ID: <200704210859.l3L8xlXC021652@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/doc In directory dev.open-bio.org:/tmp/cvs-serv21632/doc Modified Files: Changes-0.7.rd Log Message: incompatible changes in Bio::BLAST::Default and Bio::BLAST::WU are added. Index: Changes-0.7.rd =================================================================== RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** Changes-0.7.rd 2 Apr 2007 12:55:26 -0000 1.19 --- Changes-0.7.rd 21 Apr 2007 08:59:45 -0000 1.20 *************** *** 308,311 **** --- 308,325 ---- formmatted text instead of Array. + --- Bio::BLAST::Default::Report, Bio::BLAST::Default::Report::Hit, + Bio::BLAST::Default::Report::HSP, Bio::BLAST::WU::Report, + Bio::BLAST::WU::Report::Hit, Bio::BLAST::WU::Report::HSP + + In 1.1.0: + + * Hit#evalue, HSP#evalue, WU::Hit#pvalue, and WU::HSP#pvalue are + changed to return a Float object instead of a String object. + * Report#expect, Hit#bit_score, and HSP#bit_score are changed to return + a Float object or nil instead of a String object or nil. + * Following methods are changed to return an integer value or nil + instead of a string or nil: score, percent_identity, percent_positive, + percent_gaps. + === Deleted files From ngoto at dev.open-bio.org Mon Apr 23 12:03:27 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Mon, 23 Apr 2007 16:03:27 +0000 Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.20,1.21 Message-ID: <200704231603.l3NG3RZh023014@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/doc In directory dev.open-bio.org:/tmp/cvs-serv22990/doc Modified Files: Changes-0.7.rd Log Message: Bio::PDB::Residue#[] (and Bio::PDB::Heterogen#[]) are changed to use the name field for selecting atoms, because the element field is not useful for selecting atoms and is not used in many pdb files. (reported by Alex Gutteridge in [BioRuby] Bio::PDB::Residue patch) Index: Changes-0.7.rd =================================================================== RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** Changes-0.7.rd 21 Apr 2007 08:59:45 -0000 1.20 --- Changes-0.7.rd 23 Apr 2007 16:03:24 -0000 1.21 *************** *** 256,259 **** --- 256,262 ---- are also subject to the above changes, because Bio::PDB::HETATM inherits Bio::PDB::ATOM. + * Bio::PDB::Residue#[] and Bio::PDB::Heterogen#[] are changed to use the + name field for selecting atoms, because the element field is not useful + for selecting atoms and is not used in many pdb files. --- Bio::FlatFile From ngoto at dev.open-bio.org Mon Apr 23 12:03:27 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Mon, 23 Apr 2007 16:03:27 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb residue.rb,1.12,1.13 Message-ID: <200704231603.l3NG3RIa023017@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv22990/lib/bio/db/pdb Modified Files: residue.rb Log Message: Bio::PDB::Residue#[] (and Bio::PDB::Heterogen#[]) are changed to use the name field for selecting atoms, because the element field is not useful for selecting atoms and is not used in many pdb files. (reported by Alex Gutteridge in [BioRuby] Bio::PDB::Residue patch) Index: residue.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** residue.rb 5 Apr 2007 23:35:41 -0000 1.12 --- residue.rb 23 Apr 2007 16:03:25 -0000 1.13 *************** *** 66,72 **** alias id residue_id ! #Keyed access to atoms based on element e.g. ["CA"] def [](key) ! atom = @atoms.find{ |atom| key == atom.element } end --- 66,72 ---- alias id residue_id ! #Keyed access to atoms based on atom name e.g. ["CA"] def [](key) ! atom = @atoms.find{ |atom| key == atom.name } end From trevor at dev.open-bio.org Mon Apr 23 12:43:53 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 16:43:53 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/sequence na.rb,1.6,1.7 Message-ID: <200704231643.l3NGhr9r023198@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv23176/bio/sequence Modified Files: na.rb Log Message: Move cut_with_enzyme to Bio::Sequence::NA Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/na.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** na.rb 5 Apr 2007 23:35:41 -0000 1.6 --- na.rb 23 Apr 2007 16:43:51 -0000 1.7 *************** *** 468,471 **** --- 468,487 ---- protected :rna? + # Example: + # + # seq = Bio::Sequence::NA.new('gaattc') + # cuts = seq.cut_with_enzyme('EcoRI') + # + # _or_ + # + # seq = Bio::Sequence::NA.new('gaattc') + # cuts = seq.cut_with_enzyme('g^aattc') + # --- + # See Bio::RestrictionEnzyme::Analysis.cut + def cut_with_enzyme(*args) + Bio::RestrictionEnzyme::Analysis.cut(self, *args) + end + alias cut_with_enzymes cut_with_enzyme + end # NA From trevor at dev.open-bio.org Mon Apr 23 12:43:53 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 16:43:53 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis_basic.rb, 1.12, 1.13 Message-ID: <200704231643.l3NGhrs5023203@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23176/bio/util/restriction_enzyme Modified Files: analysis_basic.rb Log Message: Move cut_with_enzyme to Bio::Sequence::NA Index: analysis_basic.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** analysis_basic.rb 5 Apr 2007 23:35:42 -0000 1.12 --- analysis_basic.rb 23 Apr 2007 16:43:51 -0000 1.13 *************** *** 10,32 **** require 'bio' - class Bio::Sequence::NA - # Example: - # - # seq = Bio::Sequence::NA.new('gaattc') - # cuts = seq.cut_with_enzyme('EcoRI') - # - # _or_ - # - # seq = Bio::Sequence::NA.new('gaattc') - # cuts = seq.cut_with_enzyme('g^aattc') - # --- - # See Bio::RestrictionEnzyme::Analysis.cut - # - # NOTE: move this into Bio::Sequence::NA - def cut_with_enzyme(*args) - Bio::RestrictionEnzyme::Analysis.cut(self, *args) - end - alias cut_with_enzymes cut_with_enzyme - end require 'set' # for method create_enzyme_actions --- 10,13 ---- From trevor at dev.open-bio.org Mon Apr 23 13:11:13 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 17:11:13 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis_basic.rb, 1.13, 1.14 Message-ID: <200704231711.l3NHBD7F023254@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23234/lib/bio/util/restriction_enzyme Modified Files: analysis_basic.rb Log Message: Index: analysis_basic.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** analysis_basic.rb 23 Apr 2007 16:43:51 -0000 1.13 --- analysis_basic.rb 23 Apr 2007 17:11:11 -0000 1.14 *************** *** 9,14 **** # - require 'bio' - require 'set' # for method create_enzyme_actions require 'bio/util/restriction_enzyme' --- 9,12 ---- From trevor at dev.open-bio.org Mon Apr 23 15:42:57 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 19:42:57 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_analysis.rb, 1.10, 1.11 Message-ID: <200704231943.l3NJgvm6023491@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23466/test/unit/bio/util/restriction_enzyme Modified Files: test_analysis.rb Log Message: Support user specification of maximum allowable permutations. It's becoming apparent that we need some sort of standardized logging mechanism for warnings. Index: test_analysis.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_analysis.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** test_analysis.rb 5 Apr 2007 23:35:44 -0000 1.10 --- test_analysis.rb 23 Apr 2007 19:42:55 -0000 1.11 *************** *** 160,164 **** assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary ) assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag').primary ) ! assert_equal([], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('EcoRII').primary ) assert_equal(["ag", "ag", "cag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag', 'EcoRII').primary ) --- 160,164 ---- assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary ) assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag').primary ) ! assert_equal(:no_cuts_found, Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('EcoRII') ) assert_equal(["ag", "ag", "cag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag', 'EcoRII').primary ) *************** *** 170,172 **** end ! end \ No newline at end of file --- 170,172 ---- end ! end From trevor at dev.open-bio.org Mon Apr 23 15:42:57 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 19:42:57 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.17, 1.18 Message-ID: <200704231943.l3NJgvhU023488@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23466/lib/bio/util/restriction_enzyme Modified Files: analysis.rb Log Message: Support user specification of maximum allowable permutations. It's becoming apparent that we need some sort of standardized logging mechanism for warnings. Index: analysis.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 *** analysis.rb 5 Apr 2007 23:35:42 -0000 1.17 --- analysis.rb 23 Apr 2007 19:42:55 -0000 1.18 *************** *** 47,55 **** # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. ! # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments) def cut( sequence, *args ) ! return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty? # Format the fragments for the user ! fragments_for_display( cut_and_return_by_permutations( sequence, *args ) ) end --- 47,56 ---- # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. ! # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments) or a +Symbol+ containing an error code def cut( sequence, *args ) ! res = cut_and_return_by_permutations( sequence, *args ) ! return res if res.class == Symbol # Format the fragments for the user ! fragments_for_display( res ) end *************** *** 64,76 **** # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. # *Returns*:: +Hash+ Keys are a permutation ID, values are SequenceRange objects that have cuts applied. def cut_and_return_by_permutations( sequence, *args ) my_hash = {} ! return my_hash if !sequence.kind_of?(String) or sequence.empty? sequence = Bio::Sequence::NA.new( sequence ) enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args ) ! return my_hash if enzyme_actions.empty? and initial_cuts.empty? if enzyme_actions.size > 1 --- 65,113 ---- # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. + # May also supply a +Hash+ with the key ":max_permutations" to specificy how many permutations are allowed - a value of 0 indicates no permutations are allowed. # *Returns*:: +Hash+ Keys are a permutation ID, values are SequenceRange objects that have cuts applied. + # _also_ may return the +Symbol+ ':sequence_empty', ':no_cuts_found', or ':too_many_permutations' def cut_and_return_by_permutations( sequence, *args ) my_hash = {} + maximum_permutations = nil + + hashes_in_args = args.select { |i| i.class == Hash } + args.delete_if { |i| i.class == Hash } + hashes_in_args.each do |hsh| + hsh.each do |key, value| + case key + when :max_permutations, 'max_permutations', :maximum_permutations, 'maximum_permutations' + maximum_permutations = value.to_i unless value == nil + else + raise ArgumentError, "Received key #{key.inspect} in argument - I only know the key ':max_permutations' currently. Hash passed: #{hsh.inspect}" + end + end + end ! if !sequence.kind_of?(String) or sequence.empty? ! logger.warn "The supplied sequence is empty." if defined?(logger) ! return :sequence_empty ! end sequence = Bio::Sequence::NA.new( sequence ) enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args ) ! ! if enzyme_actions.empty? and initial_cuts.empty? ! logger.warn "This enzyme does not make any cuts on this sequence." if defined?(logger) ! return :no_cuts_found ! end ! ! # * When enzyme_actions.size is equal to '1' that means there are no permutations. ! # * If enzyme_actions.size is equal to '2' there is one ! # permutation ("[0, 1]") ! # * If enzyme_actions.size is equal to '3' there are two ! # permutations ("[0, 1, 2]") ! # * and so on.. ! if maximum_permutations and enzyme_actions.size > 1 ! if (enzyme_actions.size - 1) > maximum_permutations.to_i ! logger.warn "More permutations than maximum, skipping. Found: #{enzyme_actions.size-1} Max: #{maximum_permutations.to_i}" if defined?(logger) ! return :too_many_permutations ! end ! end if enzyme_actions.size > 1 From trevor at dev.open-bio.org Mon Apr 23 15:53:36 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 19:53:36 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme enzymes.yaml, 1.2, 1.3 Message-ID: <200704231953.l3NJraJu023521@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23501/lib/bio/util/restriction_enzyme Modified Files: enzymes.yaml Log Message: Update enzymes.yaml to version 704 Index: enzymes.yaml =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/enzymes.yaml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** enzymes.yaml 31 Dec 2006 20:50:43 -0000 1.2 --- enzymes.yaml 23 Apr 2007 19:53:34 -0000 1.3 *************** *** 1,7001 **** --- TspRI: ! :blunt: "0" ! :c2: "-3" ! :c4: "0" :c1: "7" :pattern: CASTG ! :len: "5" :name: TspRI :c3: "0" [...14033 lines suppressed...] BseMI: ! :len: "6" :c1: "8" + :c4: "0" + :ncuts: "2" :pattern: GCAATG ! :c2: "6" :name: BseMI + :blunt: "0" :c3: "0" EcoRII: ! :len: "5" :c1: "-1" + :c4: "0" + :ncuts: "2" :pattern: CCWGG ! :c2: "5" :name: EcoRII + :blunt: "0" :c3: "0" From trevor at dev.open-bio.org Mon Apr 23 16:05:36 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 20:05:36 +0000 Subject: [BioRuby-cvs] bioruby README,1.15,1.16 Message-ID: <200704232005.l3NK5a5C023571@dev.open-bio.org> Update of /home/repository/bioruby/bioruby In directory dev.open-bio.org:/tmp/cvs-serv23551 Modified Files: README Log Message: Index: README =================================================================== RCS file: /home/repository/bioruby/bioruby/README,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** README 5 Apr 2007 15:18:51 -0000 1.15 --- README 23 Apr 2007 20:05:34 -0000 1.16 *************** *** 1,4 **** - =begin - $Id$ --- 1,2 ---- *************** *** 177,182 **** Current staffs of the BioRuby project can be reached by sending e-mail to . - - - =end - --- 175,176 ---- From ngoto at dev.open-bio.org Mon Apr 2 12:55:28 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 + + * 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 From ngoto at dev.open-bio.org Mon Apr 2 12:55:28 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 12:55:28 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 18:07:46 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 18:07:46 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 18:07:46 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 18:07:46 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 18:07:46 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 20:05:08 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 20:05:08 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 20:05:08 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 20:05:08 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 20:10:33 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 15:16:03 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 15:18:53 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 15:37:52 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 # Copyright:: Copyright (C) 2003 Masumi Itoh # --- 1,6 ---- # ! # = bio/db/kegg/ortholog.rb - KEGG ORTHOLOG database class # ! # Copyright:: Copyright (C) 2003-2007 Toshiaki Katayama # Copyright:: Copyright (C) 2003 Masumi Itoh # *************** *** 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 15:43:01 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 # Copyright:: Copyright (C) 2003 Masumi Itoh # # $Id$ --- 1,8 ---- # ! # = bio/db/kegg/orthology.rb - KEGG ORTHOLOGY database class # # Copyright:: Copyright (C) 2003-2007 Toshiaki Katayama # Copyright:: Copyright (C) 2003 Masumi Itoh + # 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 15:43:01 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 17:12:02 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 ! # ! # 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 ! # 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 ! # ! # 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 ! # 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 # License:: Ruby's # --- 2,7 ---- # test/unit/bio/test_feature.rb - Unit test for Features/Feature classes # ! # Copyright:: Copyright (C) 2005 ! # Mitsuteru Nakao # 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 ! # Copyright (C) 2006 Mitsuteru C. Nakao ! # ! # 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 ! # 2006 Mitsuteru C. Nakao ! # 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 ! # Copyright (C) 2005 Naohisa Goto ! # ! # 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 ! # 2005 Naohisa Goto ! # License:: Ruby's # # $Id$ From nakao at dev.open-bio.org Thu Apr 5 17:22:16 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 ! # ! # 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 ! # License:: Ruby's # # $Id$ From nakao at dev.open-bio.org Thu Apr 5 17:23:44 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 ! # ! # 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 ! # License:: Ruby's # # $Id$ From nakao at dev.open-bio.org Thu Apr 5 17:26:31 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 ! # ! # 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 ! # License:: Ruby's # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:10:11 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 23:10:12 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 23:10:11 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 23:10:12 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 23:35:44 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 ! # License:: Ruby's # # $Id$ --- 13,17 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 16,20 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 14,18 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:44 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 25,29 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 18,22 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # 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 # 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 23:35:45 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005,2006 Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 # 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 23:35:45 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:44 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 23,27 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 23,27 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 23:35:44 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 21,25 **** # Author:: Trevor Wennblom # 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 # 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 23:35:44 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2007 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005,2007 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 # ! # License:: Ruby's # # $ I d: $ --- 80,84 ---- # Copyright:: Copyright (C) 2006 Chem R. Hacker # ! # License:: The Ruby License # # $ I d: $ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001-2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # 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 , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Naohisa Goto , # Toshiaki Katayama ! # 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 # 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (c) 2002, 2005 Toshiaki Katayama # 2006 Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Naohisa Goto ! # 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 # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # ! # 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 , # Jan Aerts ! # License:: Ruby's # # $Id$ --- 8,12 ---- # Ryan Raaum , # Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2002, 2005 # Toshiaki Katayama ! # 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 , # Shuichi Kawashima ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Shuichi Kawashima ! # 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 , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2004, 2005 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2003 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2002 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2002 # Naohisa Goto ! # 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 ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 7,11 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2003-2006 # Mitsuteru C. Nakao ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # 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 # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Copyright:: Copyright (C) 2002,2003 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002 # Toshiaki Katayama ! # 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:44 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 41,45 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 19,23 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 28,32 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 22,26 **** # Author:: Trevor Wennblom # 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 # 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 18,22 **** # Author:: Trevor Wennblom # 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 # 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 23:35:42 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003, 2006 # Naohisa Goto ! # 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 ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003, 2006 # Naohisa Goto ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:45:13 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 ! # License: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # 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 ! # Licence:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:45:13 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 ! # License: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/flatfile.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** flatfile.rb 9 Feb 2006 20:48:53 -0000 1.12 --- flatfile.rb 5 Apr 2007 23:45:11 -0000 1.13 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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/db/pdb test_pdb.rb,1.2,1.3 Message-ID: <200704052335.l35NZj1x020381@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db/pdb Modified Files: test_pdb.rb Log Message: Standardize on The Ruby License Index: test_pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/pdb/test_pdb.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_pdb.rb 27 Jun 2006 14:25:40 -0000 1.2 --- test_pdb.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 5,9 **** # Naohisa Goto # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Naohisa Goto # ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/sim4 report.rb,1.8,1.9 Message-ID: <200704052336.l35NZgN0020151@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/sim4 In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/sim4 Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4/report.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** report.rb 30 Apr 2006 05:50:19 -0000 1.8 --- report.rb 5 Apr 2007 23:35:40 -0000 1.9 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/spidey report.rb,1.9,1.10 Message-ID: <200704052336.l35NZgk0020158@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/spidey In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/spidey Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/spidey/report.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** report.rb 22 Feb 2006 08:46:15 -0000 1.9 --- report.rb 5 Apr 2007 23:35:40 -0000 1.10 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/mafft report.rb,1.11,1.12 Message-ID: <200704052336.l35NZgWM020141@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/mafft In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/mafft Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft/report.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** report.rb 15 Dec 2006 16:23:18 -0000 1.11 --- report.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/tmhmm report.rb,1.7,1.8 Message-ID: <200704052336.l35NZgW0020167@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/tmhmm Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm/report.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** report.rb 30 Apr 2006 07:11:29 -0000 1.7 --- report.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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/db/kegg test_genes.rb,1.4,1.5 Message-ID: <200704052335.l35NZjn8020366@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db/kegg In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db/kegg Modified Files: test_genes.rb Log Message: Standardize on The Ruby License Index: test_genes.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/kegg/test_genes.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_genes.rb 24 Dec 2006 17:19:05 -0000 1.4 --- test_genes.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/targetp report.rb,1.8,1.9 Message-ID: <200704052336.l35NZgxu020162@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/targetp In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/targetp Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/targetp/report.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** report.rb 30 Apr 2006 07:11:28 -0000 1.8 --- report.rb 5 Apr 2007 23:35:40 -0000 1.9 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/sosui report.rb,1.10,1.11 Message-ID: <200704052336.l35NZgG1020154@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/sosui In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/sosui Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sosui/report.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** report.rb 30 Apr 2006 07:13:39 -0000 1.10 --- report.rb 5 Apr 2007 23:35:40 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/psort report.rb,1.14,1.15 Message-ID: <200704052336.l35NZgVj020148@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/psort In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/psort Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort/report.rb,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** report.rb 25 Jul 2006 18:41:23 -0000 1.14 --- report.rb 5 Apr 2007 23:35:40 -0000 1.15 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/iprscan report.rb,1.5,1.6 Message-ID: <200704052336.l35NZgrE020137@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/iprscan In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/iprscan Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/iprscan/report.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** report.rb 29 Mar 2007 09:02:44 -0000 1.5 --- report.rb 5 Apr 2007 23:35:40 -0000 1.6 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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/tmhmm test_report.rb, 1.3, 1.4 Message-ID: <200704052335.l35NZjRJ020326@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/tmhmm In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/tmhmm 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/tmhmm/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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/hmmer report.rb,1.12,1.13 Message-ID: <200704052336.l35NZgpK020133@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/hmmer In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/hmmer Modified Files: report.rb Log Message: Standardize on The Ruby License Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/hmmer/report.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** report.rb 30 Mar 2007 22:26:15 -0000 1.12 --- report.rb 5 Apr 2007 23:35:40 -0000 1.13 *************** *** 6,10 **** # Copyright:: Copyright (C) 2005 # Masashi Fujita ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2005 # Masashi Fujita ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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/shell/plugin test_seq.rb, 1.8, 1.9 Message-ID: <200704052335.l35NZkBF020413@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/shell/plugin Modified Files: test_seq.rb Log Message: Standardize on The Ruby License Index: test_seq.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin/test_seq.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** test_seq.rb 24 Dec 2006 09:30:23 -0000 1.8 --- test_seq.rb 5 Apr 2007 23:35:44 -0000 1.9 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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/single_strand test_cut_locations_in_enzyme_notation.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZkPq020448@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/single_strand In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util/restriction_enzyme/single_strand Modified Files: 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/single_strand/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 # 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 # 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 23:35:42 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/phylip alignment.rb, 1.1, 1.2 distance_matrix.rb, 1.2, 1.3 Message-ID: <200704052336.l35NZgdB020145@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/phylip In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/phylip Modified Files: alignment.rb distance_matrix.rb Log Message: Standardize on The Ruby License Index: distance_matrix.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/phylip/distance_matrix.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** distance_matrix.rb 15 Dec 2006 14:59:26 -0000 1.2 --- distance_matrix.rb 5 Apr 2007 23:35:40 -0000 1.3 *************** *** 5,9 **** # GOTO Naohisa # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # ! # License:: The Ruby License # # $Id$ Index: alignment.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/phylip/alignment.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** alignment.rb 14 Dec 2006 22:38:53 -0000 1.1 --- alignment.rb 5 Apr 2007 23:35:40 -0000 1.2 *************** *** 5,9 **** # GOTO Naohisa # ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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/blast test_report.rb, 1.4, 1.5 test_xmlparser.rb, 1.6, 1.7 Message-ID: <200704052335.l35NZjx2020305@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/appl/blast Modified Files: test_report.rb test_xmlparser.rb Log Message: Standardize on The Ruby License Index: test_xmlparser.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/test_xmlparser.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_xmlparser.rb 28 Dec 2006 06:25:21 -0000 1.6 --- test_xmlparser.rb 5 Apr 2007 23:35:43 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/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 ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/data aa.rb, 0.19, 0.20 codontable.rb, 0.17, 0.18 na.rb, 0.21, 0.22 Message-ID: <200704052336.l35NZgd2020171@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/data In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/data Modified Files: aa.rb codontable.rb na.rb Log Message: Standardize on The Ruby License Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/aa.rb,v retrieving revision 0.19 retrieving revision 0.20 diff -C2 -d -r0.19 -r0.20 *** aa.rb 24 Dec 2006 10:06:07 -0000 0.19 --- aa.rb 5 Apr 2007 23:35:40 -0000 0.20 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v retrieving revision 0.21 retrieving revision 0.22 diff -C2 -d -r0.21 -r0.22 *** na.rb 5 Apr 2007 23:10:09 -0000 0.21 --- na.rb 5 Apr 2007 23:35:40 -0000 0.22 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: codontable.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/codontable.rb,v retrieving revision 0.17 retrieving revision 0.18 diff -C2 -d -r0.17 -r0.18 *** codontable.rb 8 May 2006 14:21:46 -0000 0.17 --- codontable.rb 5 Apr 2007 23:35:40 -0000 0.18 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2004 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2004 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/io/flatfile bdb.rb, 1.9, 1.10 index.rb, 1.18, 1.19 indexer.rb, 1.24, 1.25 Message-ID: <200704052336.l35NZhNS020214@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/io/flatfile In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/io/flatfile Modified Files: bdb.rb index.rb indexer.rb Log Message: Standardize on The Ruby License Index: bdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/bdb.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** bdb.rb 30 Apr 2006 05:58:50 -0000 1.9 --- bdb.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: index.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/index.rb,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -d -r1.18 -r1.19 *** index.rb 22 Feb 2006 08:40:31 -0000 1.18 --- index.rb 5 Apr 2007 23:35:41 -0000 1.19 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002 # GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002 # GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: indexer.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/indexer.rb,v retrieving revision 1.24 retrieving revision 1.25 diff -C2 -d -r1.24 -r1.25 *** indexer.rb 22 Mar 2006 10:19:22 -0000 1.24 --- indexer.rb 5 Apr 2007 23:35:41 -0000 1.25 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002 GOTO Naohisa ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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/sequence test_aa.rb, 1.2, 1.3 test_common.rb, 1.3, 1.4 test_compat.rb, 1.2, 1.3 test_na.rb, 1.4, 1.5 Message-ID: <200704052335.l35NZkYZ020401@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/sequence Modified Files: test_aa.rb test_common.rb test_compat.rb test_na.rb Log Message: Standardize on The Ruby License Index: test_common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_common.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_common.rb 24 Dec 2006 17:19:05 -0000 1.3 --- test_common.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_compat.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_compat.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_compat.rb 24 Dec 2006 17:19:05 -0000 1.2 --- test_compat.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_na.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_na.rb 5 Apr 2007 23:10:10 -0000 1.4 --- test_na.rb 5 Apr 2007 23:35:44 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_aa.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_aa.rb 31 Dec 2006 21:54:49 -0000 1.2 --- test_aa.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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/analysis test_calculated_cuts.rb, 1.3, 1.4 test_cut_ranges.rb, 1.1, 1.2 test_sequence_range.rb, 1.3, 1.4 Message-ID: <200704052335.l35NZka8020434@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util/restriction_enzyme/analysis Modified Files: test_calculated_cuts.rb test_cut_ranges.rb test_sequence_range.rb Log Message: Standardize on The Ruby License Index: test_sequence_range.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_sequence_range.rb 2 Jan 2007 00:22:27 -0000 1.3 --- test_sequence_range.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_cut_ranges.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_cut_ranges.rb 2 Jan 2007 06:18:07 -0000 1.1 --- test_cut_ranges.rb 5 Apr 2007 23:35:44 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_calculated_cuts.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_calculated_cuts.rb 2 Jan 2007 00:22:27 -0000 1.3 --- test_calculated_cuts.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # 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 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/genbank common.rb, 1.10, 1.11 ddbj.rb, 1.8, 1.9 genbank.rb, 0.39, 0.40 genpept.rb, 1.11, 1.12 refseq.rb, 1.7, 1.8 Message-ID: <200704052336.l35NZhrA020187@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/genbank Modified Files: common.rb ddbj.rb genbank.rb genpept.rb refseq.rb Log Message: Standardize on The Ruby License Index: genpept.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genpept.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** genpept.rb 19 Sep 2006 05:59:34 -0000 1.11 --- genpept.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002-2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002-2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: genbank.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v retrieving revision 0.39 retrieving revision 0.40 diff -C2 -d -r0.39 -r0.40 *** genbank.rb 19 Sep 2006 05:59:07 -0000 0.39 --- genbank.rb 5 Apr 2007 23:35:40 -0000 0.40 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2000-2005 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2000-2005 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: ddbj.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/ddbj.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** ddbj.rb 19 Sep 2006 05:57:54 -0000 1.8 --- ddbj.rb 5 Apr 2007 23:35:40 -0000 1.9 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/common.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** common.rb 19 Sep 2006 05:57:20 -0000 1.10 --- common.rb 5 Apr 2007 23:35:40 -0000 1.11 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: refseq.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/refseq.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** refseq.rb 19 Sep 2006 06:00:06 -0000 1.7 --- refseq.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2000-2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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/db/embl test_common.rb, 1.3, 1.4 test_embl.rb, 1.4, 1.5 test_embl_rel89.rb, 1.1, 1.2 test_sptr.rb, 1.6, 1.7 test_uniprot.rb, 1.4, 1.5 Message-ID: <200704052335.l35NZjqD020354@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db/embl In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db/embl Modified Files: test_common.rb test_embl.rb test_embl_rel89.rb test_sptr.rb test_uniprot.rb Log Message: Standardize on The Ruby License Index: test_uniprot.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_uniprot.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_uniprot.rb 24 Dec 2006 17:19:04 -0000 1.4 --- test_uniprot.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_embl_rel89.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl_rel89.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_embl_rel89.rb 13 Mar 2007 17:03:55 -0000 1.1 --- test_embl_rel89.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2007 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2007 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_common.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_common.rb 24 Dec 2006 17:19:04 -0000 1.3 --- test_common.rb 5 Apr 2007 23:35:43 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_sptr.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_sptr.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_sptr.rb 31 Dec 2006 21:54:49 -0000 1.6 --- test_sptr.rb 5 Apr 2007 23:35:43 -0000 1.7 *************** *** 3,7 **** # # Copyright::: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright::: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_embl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_embl.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_embl.rb 24 Dec 2006 17:19:04 -0000 1.4 --- test_embl.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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/io test_ddbjxml.rb, 1.3, 1.4 test_ensembl.rb, 1.5, 1.6 test_fastacmd.rb, 1.2, 1.3 test_flatfile.rb, 1.1, 1.2 test_soapwsdl.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZkjN020384@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/io In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/io Modified Files: test_ddbjxml.rb test_ensembl.rb test_fastacmd.rb test_flatfile.rb test_soapwsdl.rb Log Message: Standardize on The Ruby License Index: test_flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_flatfile.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_flatfile.rb 15 Jun 2006 14:28:55 -0000 1.1 --- test_flatfile.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 4,8 **** # Copyright (C) 2006 Naohisa Goto # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright (C) 2006 Naohisa Goto # ! # License:: The Ruby License # # $Id$ Index: test_fastacmd.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_fastacmd.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_fastacmd.rb 24 Dec 2006 17:19:05 -0000 1.2 --- test_fastacmd.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2006 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2006 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_ensembl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_ensembl.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_ensembl.rb 29 Mar 2007 14:14:17 -0000 1.5 --- test_ensembl.rb 5 Apr 2007 23:35:43 -0000 1.6 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006, 2007 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006, 2007 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_soapwsdl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_soapwsdl.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_soapwsdl.rb 5 Jun 2006 02:51:59 -0000 1.2 --- test_soapwsdl.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 3,7 **** # # Copytight:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copytight:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_ddbjxml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/io/test_ddbjxml.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_ddbjxml.rb 28 Mar 2007 11:21:20 -0000 1.3 --- test_ddbjxml.rb 5 Apr 2007 23:35:43 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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 test_color_scheme.rb, 1.2, 1.3 test_contingency_table.rb, 1.3, 1.4 test_restriction_enzyme.rb, 1.2, 1.3 test_sirna.rb, 1.3, 1.4 Message-ID: <200704052335.l35NZkom020418@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util Modified Files: test_color_scheme.rb test_contingency_table.rb test_restriction_enzyme.rb test_sirna.rb Log Message: Standardize on The Ruby License Index: test_contingency_table.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_contingency_table.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_contingency_table.rb 31 Dec 2006 18:46:14 -0000 1.3 --- test_contingency_table.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_color_scheme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_color_scheme.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_color_scheme.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_color_scheme.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_restriction_enzyme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_restriction_enzyme.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_restriction_enzyme.rb 1 Jan 2007 00:12:54 -0000 1.2 --- test_restriction_enzyme.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_sirna.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_sirna.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_sirna.rb 24 Dec 2006 17:19:05 -0000 1.3 --- test_sirna.rb 5 Apr 2007 23:35:44 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru C. Nakap ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru C. Nakap ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/db/embl common.rb, 1.11, 1.12 embl.rb, 1.28, 1.29 sptr.rb, 1.35, 1.36 swissprot.rb, 1.6, 1.7 trembl.rb, 1.6, 1.7 uniprot.rb, 1.4, 1.5 Message-ID: <200704052336.l35NZgJM020183@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/embl In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/embl Modified Files: common.rb embl.rb sptr.rb swissprot.rb trembl.rb uniprot.rb Log Message: Standardize on The Ruby License Index: sptr.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -d -r1.35 -r1.36 *** sptr.rb 5 Oct 2006 07:39:29 -0000 1.35 --- sptr.rb 5 Apr 2007 23:35:40 -0000 1.36 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001-2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001-2006 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: uniprot.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/uniprot.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** uniprot.rb 19 Sep 2006 06:01:48 -0000 1.4 --- uniprot.rb 5 Apr 2007 23:35:40 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: embl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/embl.rb,v retrieving revision 1.28 retrieving revision 1.29 diff -C2 -d -r1.28 -r1.29 *** embl.rb 13 Mar 2007 17:03:55 -0000 1.28 --- embl.rb 5 Apr 2007 23:35:40 -0000 1.29 *************** *** 4,8 **** # # Copyright:: Copyright (C) 2001-2007 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # # Copyright:: Copyright (C) 2001-2007 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/common.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** common.rb 30 Apr 2006 07:11:29 -0000 1.11 --- common.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001-2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001-2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: trembl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/trembl.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** trembl.rb 19 Sep 2006 06:01:48 -0000 1.6 --- trembl.rb 5 Apr 2007 23:35:40 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: swissprot.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/swissprot.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** swissprot.rb 19 Sep 2006 06:01:48 -0000 1.6 --- swissprot.rb 5 Apr 2007 23:35:40 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:41 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 format0.rb, 1.19, 1.20 format8.rb, 1.6, 1.7 report.rb, 1.10, 1.11 rexml.rb, 1.11, 1.12 wublast.rb, 1.8, 1.9 xmlparser.rb, 1.16, 1.17 Message-ID: <200704052336.l35NZffI020112@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/appl/blast Modified Files: format0.rb format8.rb report.rb rexml.rb wublast.rb xmlparser.rb Log Message: Standardize on The Ruby License Index: xmlparser.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/xmlparser.rb,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -d -r1.16 -r1.17 *** xmlparser.rb 31 Dec 2006 21:54:49 -0000 1.16 --- xmlparser.rb 5 Apr 2007 23:35:39 -0000 1.17 *************** *** 6,10 **** # Copyright:: Copyright (C) 2003 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2003 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: report.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/report.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** report.rb 19 Sep 2006 06:09:20 -0000 1.10 --- report.rb 5 Apr 2007 23:35:39 -0000 1.11 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: format8.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format8.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** format8.rb 19 Sep 2006 06:08:26 -0000 1.6 --- format8.rb 5 Apr 2007 23:35:39 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: format0.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** format0.rb 19 Sep 2006 06:12:37 -0000 1.19 --- format0.rb 5 Apr 2007 23:35:39 -0000 1.20 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003-2006 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003-2006 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: wublast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** wublast.rb 19 Sep 2006 06:12:37 -0000 1.8 --- wublast.rb 5 Apr 2007 23:35:39 -0000 1.9 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: rexml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/rexml.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** rexml.rb 19 Sep 2006 06:10:19 -0000 1.11 --- rexml.rb 5 Apr 2007 23:35:39 -0000 1.12 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/sequence aa.rb, 1.3, 1.4 common.rb, 1.3, 1.4 compat.rb, 1.3, 1.4 format.rb, 1.3, 1.4 generic.rb, 1.4, 1.5 na.rb, 1.5, 1.6 Message-ID: <200704052336.l35NZhd1020220@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/sequence Modified Files: aa.rb common.rb compat.rb format.rb generic.rb na.rb Log Message: Standardize on The Ruby License Index: compat.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/compat.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** compat.rb 26 Mar 2006 02:27:59 -0000 1.3 --- compat.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ Index: common.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/common.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** common.rb 26 Mar 2006 02:27:59 -0000 1.3 --- common.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ Index: format.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/format.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** format.rb 26 Mar 2006 02:27:59 -0000 1.3 --- format.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 6,10 **** # Naohisa Goto , # Ryan Raaum ! # License:: Ruby's # # = TODO --- 6,10 ---- # Naohisa Goto , # Ryan Raaum ! # License:: The Ruby License # # = TODO Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/aa.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** aa.rb 26 Mar 2006 02:27:59 -0000 1.3 --- aa.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ Index: generic.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/generic.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** generic.rb 26 Mar 2006 02:27:59 -0000 1.4 --- generic.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/na.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** na.rb 20 Jul 2006 03:45:22 -0000 1.5 --- na.rb 5 Apr 2007 23:35:41 -0000 1.6 *************** *** 5,9 **** # Toshiaki Katayama , # Ryan Raaum ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama , # Ryan Raaum ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb, 1.7, 1.8 chain.rb, 1.7, 1.8 chemicalcomponent.rb, 1.2, 1.3 model.rb, 1.8, 1.9 pdb.rb, 1.20, 1.21 residue.rb, 1.11, 1.12 utils.rb, 1.6, 1.7 Message-ID: <200704052336.l35NZhNO020198@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/pdb Modified Files: atom.rb chain.rb chemicalcomponent.rb model.rb pdb.rb residue.rb utils.rb Log Message: Standardize on The Ruby License Index: atom.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/atom.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** atom.rb 29 Mar 2007 12:50:49 -0000 1.7 --- atom.rb 5 Apr 2007 23:35:41 -0000 1.8 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: residue.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** residue.rb 29 Mar 2007 12:50:49 -0000 1.11 --- residue.rb 5 Apr 2007 23:35:41 -0000 1.12 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: model.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/model.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** model.rb 29 Mar 2007 12:50:49 -0000 1.8 --- model.rb 5 Apr 2007 23:35:41 -0000 1.9 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** pdb.rb 29 Mar 2007 12:50:49 -0000 1.20 --- pdb.rb 5 Apr 2007 23:35:41 -0000 1.21 *************** *** 5,9 **** # GOTO Naohisa # Alex Gutteridge ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa # Alex Gutteridge ! # License:: The Ruby License # # $Id$ Index: utils.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/utils.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** utils.rb 29 Mar 2007 12:50:49 -0000 1.6 --- utils.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: chemicalcomponent.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/chemicalcomponent.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** chemicalcomponent.rb 29 Mar 2007 12:50:49 -0000 1.2 --- chemicalcomponent.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: chain.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/chain.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** chain.rb 29 Mar 2007 12:50:49 -0000 1.7 --- chain.rb 5 Apr 2007 23:35:41 -0000 1.8 *************** *** 5,9 **** # Alex Gutteridge # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Alex Gutteridge # Naohisa Goto ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util color_scheme.rb, 1.3, 1.4 contingency_table.rb, 1.6, 1.7 restriction_enzyme.rb, 1.12, 1.13 sirna.rb, 1.10, 1.11 Message-ID: <200704052336.l35NZhGf020237@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util Modified Files: color_scheme.rb contingency_table.rb restriction_enzyme.rb sirna.rb Log Message: Standardize on The Ruby License Index: restriction_enzyme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** restriction_enzyme.rb 2 Feb 2007 06:42:14 -0000 1.12 --- restriction_enzyme.rb 5 Apr 2007 23:35:41 -0000 1.13 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 22,26 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # = Description --- 22,26 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # = Description Index: color_scheme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** color_scheme.rb 31 Dec 2006 19:47:35 -0000 1.3 --- color_scheme.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Index: sirna.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/sirna.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** sirna.rb 29 Mar 2007 12:52:54 -0000 1.10 --- sirna.rb 5 Apr 2007 23:35:41 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004, 2005 # Itoshi NIKAIDO ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004, 2005 # Itoshi NIKAIDO ! # License:: The Ruby License # # $Id$ Index: contingency_table.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/contingency_table.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** contingency_table.rb 31 Dec 2006 23:04:04 -0000 1.6 --- contingency_table.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # = Description --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # = Description From trevor at dev.open-bio.org Thu Apr 5 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/shell core.rb, 1.23, 1.24 demo.rb, 1.3, 1.4 interface.rb, 1.15, 1.16 irb.rb, 1.2, 1.3 object.rb, 1.2, 1.3 script.rb, 1.2, 1.3 setup.rb, 1.2, 1.3 web.rb, 1.3, 1.4 Message-ID: <200704052336.l35NZhP4020225@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/shell In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/shell Modified Files: core.rb demo.rb interface.rb irb.rb object.rb script.rb setup.rb web.rb Log Message: Standardize on The Ruby License Index: interface.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/interface.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** interface.rb 24 Dec 2006 08:36:45 -0000 1.15 --- interface.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: object.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/object.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** object.rb 24 Dec 2006 08:40:00 -0000 1.2 --- object.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 5,9 **** # Nobuya Tanaka , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Nobuya Tanaka , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: irb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/irb.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** irb.rb 14 Mar 2007 19:54:51 -0000 1.2 --- irb.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: script.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/script.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** script.rb 28 Mar 2007 20:21:26 -0000 1.2 --- script.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: core.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/core.rb,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -d -r1.23 -r1.24 *** core.rb 28 Mar 2007 20:14:14 -0000 1.23 --- core.rb 5 Apr 2007 23:35:41 -0000 1.24 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005, 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: web.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/web.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** web.rb 14 Mar 2007 19:55:10 -0000 1.3 --- web.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 5,9 **** # Nobuya Tanaka , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Nobuya Tanaka , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: setup.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/setup.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** setup.rb 28 Mar 2007 20:21:26 -0000 1.2 --- setup.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: demo.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/demo.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** demo.rb 24 Dec 2006 08:40:43 -0000 1.3 --- demo.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:46 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 test_analysis.rb, 1.9, 1.10 test_cut_symbol.rb, 1.1, 1.2 test_double_stranded.rb, 1.4, 1.5 test_single_strand.rb, 1.2, 1.3 test_single_strand_complement.rb, 1.2, 1.3 test_string_formatting.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZkht020424@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/util/restriction_enzyme Modified Files: test_analysis.rb test_cut_symbol.rb test_double_stranded.rb test_single_strand.rb test_single_strand_complement.rb test_string_formatting.rb Log Message: Standardize on The Ruby License Index: test_analysis.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_analysis.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** test_analysis.rb 28 Mar 2007 19:45:27 -0000 1.9 --- test_analysis.rb 5 Apr 2007 23:35:44 -0000 1.10 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_double_stranded.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_double_stranded.rb 2 Jan 2007 06:18:07 -0000 1.4 --- test_double_stranded.rb 5 Apr 2007 23:35:44 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_cut_symbol.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_cut_symbol.rb 1 Jan 2007 02:16:05 -0000 1.1 --- test_cut_symbol.rb 5 Apr 2007 23:35:44 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_single_strand.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_single_strand.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_single_strand.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_single_strand.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_string_formatting.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_string_formatting.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_string_formatting.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_single_strand_complement.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_single_strand_complement.rb 31 Dec 2006 18:46:14 -0000 1.2 --- test_single_strand_complement.rb 5 Apr 2007 23:35:44 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # 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 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin blast.rb, 1.2, 1.3 codon.rb, 1.15, 1.16 das.rb, 1.2, 1.3 emboss.rb, 1.2, 1.3 entry.rb, 1.9, 1.10 keggapi.rb, 1.11, 1.12 midi.rb, 1.8, 1.9 psort.rb, 1.2, 1.3 seq.rb, 1.20, 1.21 Message-ID: <200704052336.l35NZhfv020231@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/shell/plugin Modified Files: blast.rb codon.rb das.rb emboss.rb entry.rb keggapi.rb midi.rb psort.rb seq.rb Log Message: Standardize on The Ruby License Index: emboss.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/emboss.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** emboss.rb 9 Feb 2006 20:48:53 -0000 1.2 --- emboss.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: blast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/blast.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** blast.rb 24 Dec 2006 08:50:18 -0000 1.2 --- blast.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: psort.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/psort.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** psort.rb 24 Dec 2006 08:50:18 -0000 1.2 --- psort.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: keggapi.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/keggapi.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** keggapi.rb 24 Dec 2006 08:49:12 -0000 1.11 --- keggapi.rb 5 Apr 2007 23:35:41 -0000 1.12 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: das.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/das.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** das.rb 28 Mar 2007 19:50:28 -0000 1.2 --- das.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: codon.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** codon.rb 24 Dec 2006 08:46:50 -0000 1.15 --- codon.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: midi.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/midi.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** midi.rb 24 Dec 2006 08:50:37 -0000 1.8 --- midi.rb 5 Apr 2007 23:35:41 -0000 1.9 *************** *** 5,9 **** # Natsuhiro Ichinose , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Natsuhiro Ichinose , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: seq.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** seq.rb 24 Dec 2006 09:30:22 -0000 1.20 --- seq.rb 5 Apr 2007 23:35:41 -0000 1.21 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: entry.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/entry.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** entry.rb 24 Dec 2006 08:50:18 -0000 1.9 --- entry.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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/db test_aaindex.rb, 1.3, 1.4 test_fasta.rb, 1.4, 1.5 test_gff.rb, 1.5, 1.6 test_lasergene.rb, 1.1, 1.2 test_newick.rb, 1.4, 1.5 test_nexus.rb, 1.1, 1.2 test_prosite.rb, 1.5, 1.6 test_rebase.rb, 1.4, 1.5 test_soft.rb, 1.2, 1.3 Message-ID: <200704052335.l35NZjgb020340@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/db In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio/db Modified Files: test_aaindex.rb test_fasta.rb test_gff.rb test_lasergene.rb test_newick.rb test_nexus.rb test_prosite.rb test_rebase.rb test_soft.rb Log Message: Standardize on The Ruby License Index: test_soft.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_soft.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_soft.rb 29 Mar 2007 03:18:26 -0000 1.2 --- test_soft.rb 5 Apr 2007 23:35:43 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_aaindex.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_aaindex.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_aaindex.rb 22 Feb 2006 07:35:19 -0000 1.3 --- test_aaindex.rb 5 Apr 2007 23:35:43 -0000 1.4 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_fasta.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_fasta.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_fasta.rb 24 Dec 2006 17:19:04 -0000 1.4 --- test_fasta.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_nexus.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_nexus.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_nexus.rb 19 Dec 2006 05:17:27 -0000 1.1 --- test_nexus.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: The Ruby License # # $Id$ Index: test_prosite.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_prosite.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_prosite.rb 24 Dec 2006 17:19:04 -0000 1.5 --- test_prosite.rb 5 Apr 2007 23:35:43 -0000 1.6 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_rebase.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_rebase.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_rebase.rb 1 Jan 2007 00:12:54 -0000 1.4 --- test_rebase.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: test_lasergene.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_lasergene.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** test_lasergene.rb 8 Jan 2007 06:38:39 -0000 1.1 --- test_lasergene.rb 5 Apr 2007 23:35:43 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: Distributes under the same terms as Ruby # # $Id$ --- 4,8 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: The Ruby License # # $Id$ Index: test_newick.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_newick.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_newick.rb 12 Jan 2007 16:19:24 -0000 1.4 --- test_newick.rb 5 Apr 2007 23:35:43 -0000 1.5 *************** *** 5,9 **** # Daniel Amelang # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Daniel Amelang # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_gff.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_gff.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_gff.rb 24 Dec 2006 17:19:04 -0000 1.5 --- test_gff.rb 5 Apr 2007 23:35:43 -0000 1.6 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:44 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/color_scheme buried.rb, 1.3, 1.4 helix.rb, 1.3, 1.4 hydropathy.rb, 1.3, 1.4 nucleotide.rb, 1.3, 1.4 strand.rb, 1.4, 1.5 taylor.rb, 1.3, 1.4 turn.rb, 1.3, 1.4 zappo.rb, 1.3, 1.4 Message-ID: <200704052336.l35NZi3i020243@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/color_scheme In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/util/color_scheme Modified Files: buried.rb helix.rb hydropathy.rb nucleotide.rb strand.rb taylor.rb turn.rb zappo.rb Log Message: Standardize on The Ruby License Index: strand.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/strand.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** strand.rb 31 Dec 2006 19:47:35 -0000 1.4 --- strand.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: turn.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/turn.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** turn.rb 31 Dec 2006 19:47:35 -0000 1.3 --- turn.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: hydropathy.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/hydropathy.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** hydropathy.rb 31 Dec 2006 19:47:35 -0000 1.3 --- hydropathy.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: nucleotide.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/nucleotide.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** nucleotide.rb 31 Dec 2006 19:47:35 -0000 1.3 --- nucleotide.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: buried.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/buried.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** buried.rb 31 Dec 2006 19:47:35 -0000 1.3 --- buried.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: helix.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/helix.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** helix.rb 31 Dec 2006 19:47:35 -0000 1.3 --- helix.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: taylor.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/taylor.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** taylor.rb 31 Dec 2006 19:47:35 -0000 1.3 --- taylor.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ Index: zappo.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/color_scheme/zappo.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** zappo.rb 31 Dec 2006 19:47:35 -0000 1.3 --- zappo.rb 5 Apr 2007 23:35:41 -0000 1.4 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # 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 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/kegg brite.rb, 0.7, 0.8 compound.rb, 0.14, 0.15 drug.rb, 1.1, 1.2 enzyme.rb, 0.10, 0.11 expression.rb, 1.10, 1.11 genes.rb, 0.24, 0.25 genome.rb, 0.16, 0.17 glycan.rb, 1.4, 1.5 keggtab.rb, 1.9, 1.10 kgml.rb, 1.6, 1.7 reaction.rb, 1.4, 1.5 Message-ID: <200704052336.l35NZhxY020193@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/kegg In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db/kegg Modified Files: brite.rb compound.rb drug.rb enzyme.rb expression.rb genes.rb genome.rb glycan.rb keggtab.rb kgml.rb reaction.rb Log Message: Standardize on The Ruby License Index: drug.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/drug.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** drug.rb 8 Mar 2007 00:11:49 -0000 1.1 --- drug.rb 5 Apr 2007 23:35:41 -0000 1.2 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: keggtab.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/keggtab.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** keggtab.rb 19 Sep 2006 05:54:29 -0000 1.9 --- keggtab.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001 Mitsuteru C. Nakao # Copyright (C) 2003, 2006 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001 Mitsuteru C. Nakao # Copyright (C) 2003, 2006 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: glycan.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/glycan.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** glycan.rb 8 Mar 2007 00:14:16 -0000 1.4 --- glycan.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: compound.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/compound.rb,v retrieving revision 0.14 retrieving revision 0.15 diff -C2 -d -r0.14 -r0.15 *** compound.rb 8 Mar 2007 00:10:05 -0000 0.14 --- compound.rb 5 Apr 2007 23:35:41 -0000 0.15 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002, 2004, 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002, 2004, 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: kgml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/kgml.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** kgml.rb 24 Dec 2006 09:18:43 -0000 1.6 --- kgml.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: enzyme.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/enzyme.rb,v retrieving revision 0.10 retrieving revision 0.11 diff -C2 -d -r0.10 -r0.11 *** enzyme.rb 15 Jan 2007 04:50:05 -0000 0.10 --- enzyme.rb 5 Apr 2007 23:35:41 -0000 0.11 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: expression.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/expression.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** expression.rb 8 May 2006 14:25:25 -0000 1.10 --- expression.rb 5 Apr 2007 23:35:41 -0000 1.11 *************** *** 5,9 **** # Shuichi Kawashima , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Shuichi Kawashima , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: genome.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/genome.rb,v retrieving revision 0.16 retrieving revision 0.17 diff -C2 -d -r0.16 -r0.17 *** genome.rb 15 Jan 2007 04:37:29 -0000 0.16 --- genome.rb 5 Apr 2007 23:35:41 -0000 0.17 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001, 2002, 2007 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: genes.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/genes.rb,v retrieving revision 0.24 retrieving revision 0.25 diff -C2 -d -r0.24 -r0.25 *** genes.rb 8 Mar 2007 00:10:50 -0000 0.24 --- genes.rb 5 Apr 2007 23:35:41 -0000 0.25 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2002, 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2002, 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: reaction.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/reaction.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** reaction.rb 19 Sep 2006 05:56:38 -0000 1.4 --- reaction.rb 5 Apr 2007 23:35:41 -0000 1.5 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: brite.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/kegg/brite.rb,v retrieving revision 0.7 retrieving revision 0.8 diff -C2 -d -r0.7 -r0.8 *** brite.rb 19 Sep 2006 05:50:45 -0000 0.7 --- brite.rb 5 Apr 2007 23:35:41 -0000 0.8 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:45 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 test_alignment.rb, 1.10, 1.11 test_command.rb, 1.4, 1.5 test_db.rb, 1.3, 1.4 test_feature.rb, 1.4, 1.5 test_location.rb, 1.3, 1.4 test_map.rb, 1.4, 1.5 test_pathway.rb, 1.4, 1.5 test_reference.rb, 1.2, 1.3 test_sequence.rb, 1.8, 1.9 test_shell.rb, 1.6, 1.7 test_tree.rb, 1.4, 1.5 Message-ID: <200704052335.l35NZjem020289@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio In directory dev.open-bio.org:/tmp/cvs-serv20013/test/unit/bio Modified Files: test_alignment.rb test_command.rb test_db.rb test_feature.rb test_location.rb test_map.rb test_pathway.rb test_reference.rb test_sequence.rb test_shell.rb test_tree.rb Log Message: Standardize on The Ruby License Index: test_pathway.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_pathway.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_pathway.rb 5 Apr 2007 17:12:00 -0000 1.4 --- test_pathway.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: The Ruby License # # $Id$ Index: test_command.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_command.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_command.rb 29 Mar 2007 12:14:46 -0000 1.4 --- test_command.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 5,9 **** # Mitsuteru Nakao , # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Mitsuteru Nakao , # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_map.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_map.rb 28 Mar 2007 21:25:02 -0000 1.4 --- test_map.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Jan Aerts ! # License:: Ruby's # # $Id: --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Jan Aerts ! # License:: The Ruby License # # $Id: Index: test_alignment.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_alignment.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** test_alignment.rb 5 Apr 2007 17:12:00 -0000 1.10 --- test_alignment.rb 5 Apr 2007 23:35:42 -0000 1.11 *************** *** 5,9 **** # Moses Hohman # 2005 Naohisa Goto ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Moses Hohman # 2005 Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_feature.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_feature.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_feature.rb 5 Apr 2007 17:12:00 -0000 1.4 --- test_feature.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2005 # Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_shell.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_shell.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_shell.rb 24 Dec 2006 17:19:04 -0000 1.6 --- test_shell.rb 5 Apr 2007 23:35:42 -0000 1.7 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_location.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_location.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_location.rb 5 Apr 2007 17:12:00 -0000 1.3 --- test_location.rb 5 Apr 2007 23:35:42 -0000 1.4 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # Moses Hohman ! # License:: The Ruby License # # $Id$ Index: test_db.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_db.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_db.rb 24 Dec 2006 17:19:04 -0000 1.3 --- test_db.rb 5 Apr 2007 23:35:42 -0000 1.4 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2005 Mitsuteru Nakao ! # License:: The Ruby License # # $Id$ Index: test_reference.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_reference.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** test_reference.rb 31 Dec 2006 21:54:49 -0000 1.2 --- test_reference.rb 5 Apr 2007 23:35:42 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: test_tree.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_tree.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** test_tree.rb 12 Jan 2007 16:12:05 -0000 1.4 --- test_tree.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Naohisa Goto ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Naohisa Goto ! # License:: The Ruby License # # $Id$ Index: test_sequence.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_sequence.rb,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -d -r1.8 -r1.9 *** test_sequence.rb 5 Apr 2007 23:10:09 -0000 1.8 --- test_sequence.rb 5 Apr 2007 23:35:42 -0000 1.9 *************** *** 5,9 **** # Moses Hohman # 2006 Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Moses Hohman # 2006 Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:44 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/double_stranded aligned_strands.rb, 1.4, 1.5 cut_location_pair.rb, 1.7, 1.8 cut_location_pair_in_enzyme_notation.rb, 1.5, 1.6 cut_locations.rb, 1.4, 1.5 cut_locations_in_enzyme_notation.rb, 1.5, 1.6 Message-ID: <200704052336.l35NZivJ020253@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-serv20013/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: Standardize on The Ruby License Index: aligned_strands.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** aligned_strands.rb 4 Apr 2007 18:07:44 -0000 1.4 --- aligned_strands.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 22,26 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Align two SingleStrand objects and return a Result --- 22,26 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Align two SingleStrand objects and return a Result Index: cut_locations.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** cut_locations.rb 4 Apr 2007 18:07:44 -0000 1.4 --- cut_locations.rb 5 Apr 2007 23:35:42 -0000 1.5 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Contains an +Array+ of CutLocationPair objects. --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Contains an +Array+ of CutLocationPair objects. 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 1.5 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 # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 21,25 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Inherits from DoubleStranded::CutLocations. Contains CutLocationPairInEnzymeNotation objects. --- 21,25 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Inherits from DoubleStranded::CutLocations. Contains CutLocationPairInEnzymeNotation objects. 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 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** cut_location_pair_in_enzyme_notation.rb 4 Apr 2007 20:05:06 -0000 1.5 --- cut_location_pair_in_enzyme_notation.rb 5 Apr 2007 23:35:42 -0000 1.6 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Inherits from DoubleStranded::CutLocationPair , stores the cut location pair in 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 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** cut_location_pair.rb 4 Apr 2007 20:05:06 -0000 1.7 --- cut_location_pair.rb 5 Apr 2007 23:35:42 -0000 1.8 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # Stores a single cut location pair in 0-based index notation for use with --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Stores a single cut location pair in 0-based index notation for use with From trevor at dev.open-bio.org Thu Apr 5 23:35:43 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Thu, 05 Apr 2007 23:35:43 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/io das.rb, 1.15, 1.16 dbget.rb, 1.12, 1.13 ddbjxml.rb, 1.13, 1.14 ebisoap.rb, 1.2, 1.3 ensembl.rb, 1.10, 1.11 fastacmd.rb, 1.15, 1.16 fetch.rb, 1.9, 1.10 flatfile.rb, 1.57, 1.58 keggapi.rb, 1.13, 1.14 ncbisoap.rb, 1.2, 1.3 pubmed.rb, 1.15, 1.16 registry.rb, 1.18, 1.19 soapwsdl.rb, 1.6, 1.7 sql.rb, 1.7, 1.8 Message-ID: <200704052336.l35NZhJW020207@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/io In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/io Modified Files: das.rb dbget.rb ddbjxml.rb ebisoap.rb ensembl.rb fastacmd.rb fetch.rb flatfile.rb keggapi.rb ncbisoap.rb pubmed.rb registry.rb soapwsdl.rb sql.rb Log Message: Standardize on The Ruby License Index: registry.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/registry.rb,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -d -r1.18 -r1.19 *** registry.rb 14 Jul 2006 14:48:56 -0000 1.18 --- registry.rb 5 Apr 2007 23:35:41 -0000 1.19 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002, 2003, 2004, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002, 2003, 2004, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: dbget.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/dbget.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** dbget.rb 8 May 2006 14:29:58 -0000 1.12 --- dbget.rb 5 Apr 2007 23:35:41 -0000 1.13 *************** *** 5,9 **** # Mitsuteru C. Nakao , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Mitsuteru C. Nakao , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: pubmed.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/pubmed.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** pubmed.rb 19 Sep 2006 05:47:52 -0000 1.15 --- pubmed.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Jan Aerts ! # License:: The Ruby License # # $Id$ Index: keggapi.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/keggapi.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** keggapi.rb 19 Sep 2006 05:45:48 -0000 1.13 --- keggapi.rb 5 Apr 2007 23:35:41 -0000 1.14 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: ebisoap.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ebisoap.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** ebisoap.rb 28 Mar 2007 09:11:02 -0000 1.2 --- ebisoap.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: sql.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/sql.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** sql.rb 15 Dec 2006 16:53:20 -0000 1.7 --- sql.rb 5 Apr 2007 23:35:41 -0000 1.8 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Raoul Jean Pierre Bonnal ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002 Toshiaki Katayama # Copyright:: Copyright (C) 2006 Raoul Jean Pierre Bonnal ! # License:: The Ruby License # # $Id$ Index: ddbjxml.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ddbjxml.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** ddbjxml.rb 28 Mar 2007 09:11:02 -0000 1.13 --- ddbjxml.rb 5 Apr 2007 23:35:41 -0000 1.14 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003, 2004 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003, 2004 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: fetch.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fetch.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** fetch.rb 14 Jul 2006 14:28:44 -0000 1.9 --- fetch.rb 5 Apr 2007 23:35:41 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama , # Copyright (C) 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2002, 2005 Toshiaki Katayama , # Copyright (C) 2006 Jan Aerts ! # License:: The Ruby License # # $Id$ Index: ensembl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ensembl.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** ensembl.rb 29 Mar 2007 14:14:17 -0000 1.10 --- ensembl.rb 5 Apr 2007 23:35:41 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: soapwsdl.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/soapwsdl.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** soapwsdl.rb 19 Sep 2006 05:43:06 -0000 1.6 --- soapwsdl.rb 5 Apr 2007 23:35:41 -0000 1.7 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v retrieving revision 1.57 retrieving revision 1.58 diff -C2 -d -r1.57 -r1.58 *** flatfile.rb 27 Mar 2007 09:26:03 -0000 1.57 --- flatfile.rb 5 Apr 2007 23:35:41 -0000 1.58 *************** *** 4,8 **** # Copyright (C) 2001-2006 Naohisa Goto # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright (C) 2001-2006 Naohisa Goto # ! # License:: The Ruby License # # $Id$ Index: das.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/das.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** das.rb 28 Mar 2007 19:51:24 -0000 1.15 --- das.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 5,9 **** # Shuichi Kawashima , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Shuichi Kawashima , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: fastacmd.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fastacmd.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** fastacmd.rb 29 Mar 2007 12:44:25 -0000 1.15 --- fastacmd.rb 5 Apr 2007 23:35:41 -0000 1.16 *************** *** 7,11 **** # Mitsuteru C. Nakao , # Jan Aerts ! # License:: Ruby's # # $Id$ --- 7,11 ---- # Mitsuteru C. Nakao , # Jan Aerts ! # License:: The Ruby License # # $Id$ Index: ncbisoap.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/ncbisoap.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** ncbisoap.rb 28 Mar 2007 09:11:02 -0000 1.2 --- ncbisoap.rb 5 Apr 2007 23:35:41 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004, 2006 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004, 2006 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From trevor at dev.open-bio.org Thu Apr 5 23:35:42 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/db aaindex.rb, 1.19, 1.20 fantom.rb, 1.13, 1.14 fasta.rb, 1.27, 1.28 gff.rb, 1.7, 1.8 go.rb, 1.10, 1.11 lasergene.rb, 1.2, 1.3 litdb.rb, 0.9, 0.10 medline.rb, 1.15, 1.16 nbrf.rb, 1.9, 1.10 newick.rb, 1.6, 1.7 nexus.rb, 1.2, 1.3 pdb.rb, 1.7, 1.8 rebase.rb, 1.7, 1.8 soft.rb, 1.1, 1.2 transfac.rb, 1.11, 1.12 Message-ID: <200704052336.l35NZgfH020178@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db In directory dev.open-bio.org:/tmp/cvs-serv20013/lib/bio/db Modified Files: aaindex.rb fantom.rb fasta.rb gff.rb go.rb lasergene.rb litdb.rb medline.rb nbrf.rb newick.rb nexus.rb pdb.rb rebase.rb soft.rb transfac.rb Log Message: Standardize on The Ruby License Index: aaindex.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/aaindex.rb,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** aaindex.rb 8 May 2006 14:34:52 -0000 1.19 --- aaindex.rb 5 Apr 2007 23:35:40 -0000 1.20 *************** *** 6,10 **** # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 6,10 ---- # Copyright:: Copyright (C) 2006 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: soft.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/soft.rb,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** soft.rb 2 Feb 2007 06:13:10 -0000 1.1 --- soft.rb 5 Apr 2007 23:35:40 -0000 1.2 *************** *** 4,8 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # $Id$ --- 4,8 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Index: go.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/go.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** go.rb 30 Apr 2006 07:11:28 -0000 1.10 --- go.rb 5 Apr 2007 23:35:40 -0000 1.11 *************** *** 4,8 **** # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2003 # Mitsuteru C. Nakao ! # License:: The Ruby License # # $Id$ Index: litdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/litdb.rb,v retrieving revision 0.9 retrieving revision 0.10 diff -C2 -d -r0.9 -r0.10 *** litdb.rb 19 Sep 2006 06:03:51 -0000 0.9 --- litdb.rb 5 Apr 2007 23:35:40 -0000 0.10 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2001 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: fasta.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fasta.rb,v retrieving revision 1.27 retrieving revision 1.28 diff -C2 -d -r1.27 -r1.28 *** fasta.rb 31 Dec 2006 21:54:49 -0000 1.27 --- fasta.rb 5 Apr 2007 23:35:40 -0000 1.28 *************** *** 5,9 **** # GOTO Naohisa , # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 5,9 ---- # GOTO Naohisa , # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: newick.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/newick.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** newick.rb 15 Dec 2006 14:59:25 -0000 1.6 --- newick.rb 5 Apr 2007 23:35:40 -0000 1.7 *************** *** 5,9 **** # Naohisa Goto # Daniel Amelang ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Naohisa Goto # Daniel Amelang ! # License:: The Ruby License # # $Id$ Index: pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** pdb.rb 29 Mar 2007 12:50:49 -0000 1.7 --- pdb.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 4,8 **** # Copyright:: Copyright (C) 2004 # GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2004 # GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: rebase.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/rebase.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** rebase.rb 1 Jan 2007 00:12:54 -0000 1.7 --- rebase.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 4,8 **** # Author:: Trevor Wennblom # 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 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # $Id$ *************** *** 20,24 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: Distributes under the same terms as Ruby # # --- 20,24 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com) ! # License:: The Ruby License # # Index: nexus.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nexus.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** nexus.rb 19 Dec 2006 05:37:50 -0000 1.2 --- nexus.rb 5 Apr 2007 23:35:40 -0000 1.3 *************** *** 4,8 **** # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2006 Christian M Zmasek # ! # License:: The Ruby License # # $Id$ Index: medline.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/medline.rb,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** medline.rb 19 Sep 2006 06:03:51 -0000 1.15 --- medline.rb 5 Apr 2007 23:35:40 -0000 1.16 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001, 2005 # Toshiaki Katayama ! # License:: The Ruby License # # $Id$ Index: lasergene.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/lasergene.rb,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** lasergene.rb 1 Feb 2007 05:23:01 -0000 1.2 --- lasergene.rb 5 Apr 2007 23:35:40 -0000 1.3 *************** *** 4,8 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: Distributes under the same terms as Ruby # # $Id$ --- 4,8 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: The Ruby License # # $Id$ *************** *** 16,20 **** # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: Distributes under the same terms as Ruby # # = Description --- 16,20 ---- # Author:: Trevor Wennblom # Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu) ! # License:: The Ruby License # # = Description Index: gff.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/gff.rb,v retrieving revision 1.7 retrieving revision 1.8 diff -C2 -d -r1.7 -r1.8 *** gff.rb 8 May 2006 14:31:58 -0000 1.7 --- gff.rb 5 Apr 2007 23:35:40 -0000 1.8 *************** *** 5,9 **** # Toshiaki Katayama # 2006 Jan Aerts ! # License:: Ruby's # # $Id$ --- 5,9 ---- # Toshiaki Katayama # 2006 Jan Aerts ! # License:: The Ruby License # # $Id$ Index: fantom.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/fantom.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** fantom.rb 14 Jul 2006 14:48:55 -0000 1.13 --- fantom.rb 5 Apr 2007 23:35:40 -0000 1.14 *************** *** 3,7 **** # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: Ruby's # # $Id$ --- 3,7 ---- # # Copyright:: Copyright (C) 2003 GOTO Naohisa ! # License:: The Ruby License # # $Id$ Index: transfac.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/transfac.rb,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** transfac.rb 29 Mar 2007 12:46:58 -0000 1.11 --- transfac.rb 5 Apr 2007 23:35:40 -0000 1.12 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001 # Shuichi Kawashima ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001 # Shuichi Kawashima ! # License:: The Ruby License # # $Id$ Index: nbrf.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nbrf.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** nbrf.rb 19 Sep 2006 06:03:51 -0000 1.9 --- nbrf.rb 5 Apr 2007 23:35:40 -0000 1.10 *************** *** 4,8 **** # Copyright:: Copyright (C) 2001-2003,2006 Naohisa Goto # Copyright (C) 2001-2002 Toshiaki Katayama ! # License:: Ruby's # # $Id$ --- 4,8 ---- # Copyright:: Copyright (C) 2001-2003,2006 Naohisa Goto # Copyright (C) 2001-2002 Toshiaki Katayama ! # License:: The Ruby License # # $Id$ From k at dev.open-bio.org Fri Apr 6 04:41:30 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 04:41:30 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/data aa.rb, 0.20, 0.21 na.rb, 0.22, 0.23 Message-ID: <200704060441.l364fUa0021024@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/data In directory dev.open-bio.org:/tmp/cvs-serv21020 Modified Files: aa.rb na.rb Log Message: * AA#to_re is rewrited symmetrically to NA#to_re * default value '.' is assigned for to_re replacement Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/aa.rb,v retrieving revision 0.20 retrieving revision 0.21 diff -C2 -d -r0.20 -r0.21 *** aa.rb 5 Apr 2007 23:35:40 -0000 0.20 --- aa.rb 6 Apr 2007 04:41:28 -0000 0.21 *************** *** 218,225 **** def to_re(seq) str = seq.to_s.upcase ! str.gsub!(/[^BZACDEFGHIKLMNPQRSTVWYU]/, ".") ! str.gsub!("B", "[DN]") ! str.gsub!("Z", "[EQ]") Regexp.new(str) end --- 218,233 ---- def to_re(seq) + replace = { + 'B' => '[DNB]', + 'Z' => '[EQZ]', + 'J' => '[ILJ]', + 'X' => '[ACDEFGHIKLMNPQRSTVWYUO]', + } + replace.default = '.' + str = seq.to_s.upcase ! str.gsub!(/[^ACDEFGHIKLMNPQRSTVWYUO]/) { |aa| ! replace[aa] ! } Regexp.new(str) end Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v retrieving revision 0.22 retrieving revision 0.23 diff -C2 -d -r0.22 -r0.23 *** na.rb 5 Apr 2007 23:35:40 -0000 0.22 --- na.rb 6 Apr 2007 04:41:28 -0000 0.23 *************** *** 172,179 **** 'n' => '[atgcyrwskmbdhvn]' } str = seq.to_s.downcase ! str.gsub!(/[^atgcu]/) { |base| ! replace[base] || base } if rna --- 172,180 ---- 'n' => '[atgcyrwskmbdhvn]' } + replace.default = '.' str = seq.to_s.downcase ! str.gsub!(/[^atgcu]/) { |na| ! replace[na] } if rna From k at dev.open-bio.org Fri Apr 6 04:44:53 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 04:44:53 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/data aa.rb,0.21,0.22 Message-ID: <200704060444.l364irau021086@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/data In directory dev.open-bio.org:/tmp/cvs-serv21082 Modified Files: aa.rb Log Message: * replacement of X should include X itself. Index: aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/data/aa.rb,v retrieving revision 0.21 retrieving revision 0.22 diff -C2 -d -r0.21 -r0.22 *** aa.rb 6 Apr 2007 04:41:28 -0000 0.21 --- aa.rb 6 Apr 2007 04:44:51 -0000 0.22 *************** *** 222,226 **** 'Z' => '[EQZ]', 'J' => '[ILJ]', ! 'X' => '[ACDEFGHIKLMNPQRSTVWYUO]', } replace.default = '.' --- 222,226 ---- 'Z' => '[EQZ]', 'J' => '[ILJ]', ! 'X' => '[ACDEFGHIKLMNPQRSTVWYUOX]', } replace.default = '.' From k at dev.open-bio.org Fri Apr 6 04:46:38 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 04:46:38 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio/data test_aa.rb,1.6,1.7 Message-ID: <200704060446.l364kcik021111@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/data In directory dev.open-bio.org:/tmp/cvs-serv21107/test/unit/bio/data Modified Files: test_aa.rb Log Message: * followed the change of AA#to_re spec. Index: test_aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/data/test_aa.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** test_aa.rb 5 Apr 2007 23:35:43 -0000 1.6 --- test_aa.rb 6 Apr 2007 04:46:36 -0000 1.7 *************** *** 85,89 **** def test_to_re ! assert_equal(/[DN][EQ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU')) end end --- 85,89 ---- def test_to_re ! assert_equal(/[DNB][EQZ]ACDEFGHIKLMNPQRSTVWYU/, @obj.to_re('BZACDEFGHIKLMNPQRSTVWYU')) end end From k at dev.open-bio.org Fri Apr 6 12:04:07 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 12:04:07 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/fasta format10.rb,1.6,1.7 Message-ID: <200704061204.l36C47EV022099@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/fasta In directory dev.open-bio.org:/tmp/cvs-serv22095/lib/bio/appl/fasta Modified Files: format10.rb Log Message: * Licensed under the same terms as Ruby * converted to RDoc Index: format10.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/fasta/format10.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** format10.rb 26 Sep 2005 13:00:05 -0000 1.6 --- format10.rb 6 Apr 2007 12:04:05 -0000 1.7 *************** *** 1,22 **** # ! # bio/appl/fasta/format10.rb - FASTA output (-m 10) parser # ! # Copyright (C) 2002 KATAYAMA Toshiaki ! # ! # 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 # ! # $Id$ # --- 1,9 ---- # ! # = bio/appl/fasta/format10.rb - FASTA output (-m 10) parser # ! # Copyright:: Copyright (C) 2002 Toshiaki Katayama ! # License:: The Ruby License # ! # $Id$ # *************** *** 24,267 **** module Bio ! class Fasta ! class Report ! def initialize(data) ! # header lines - brief list of the hits ! if data.sub!(/.*\nThe best scores are/m, '') ! data.sub!(/(.*)\n\n>>>/m, '') ! @list = "The best scores are" + $1 ! else ! data.sub!(/.*\n!!\s+/m, '') ! data.sub!(/.*/) { |x| @list = x; '' } ! end ! # body lines - fasta execution result ! program, *hits = data.split(/\n>>/) ! # trailing lines - log messages of the execution ! @log = hits.pop ! @log.sub!(/.*<\n/m, '') ! @log.strip! ! # parse results ! @program = Program.new(program) ! @hits = [] ! hits.each do |x| ! @hits.push(Hit.new(x)) ! end ! end ! attr_reader :list, :log, :program, :hits ! def each ! @hits.each do |x| ! yield x ! end ! end ! def threshold(evalue_max = 0.1) ! list = [] ! @hits.each do |x| ! list.push(x) if x.evalue < evalue_max ! end ! return list ! end ! def lap_over(length_min = 0) ! list = [] ! @hits.each do |x| ! list.push(x) if x.overlap > length_min ! end ! return list ! end ! class Program ! def initialize(data) ! @definition, *program = data.split(/\n/) ! @program = {} ! pat = /;\s+([^:]+):\s+(.*)/ ! program.each do |x| ! if pat.match(x) ! @program[$1] = $2 ! end ! end end - attr_reader :definition, :program end - class Hit - def initialize(data) - score, query, target = data.split(/\n>/) ! @definition, *score = score.split(/\n/) ! @score = {} ! pat = /;\s+([^:]+):\s+(.*)/ ! score.each do |x| ! if pat.match(x) ! @score[$1] = $2 ! end ! end ! @query = Query.new(query) ! @target = Target.new(target) end ! attr_reader :definition, :score, :query, :target ! def evalue ! if @score['fa_expect'] ! @score['fa_expect'].to_f ! elsif @score['sw_expect'] ! @score['sw_expect'].to_f ! elsif @score['fx_expect'] ! @score['fx_expect'].to_f ! elsif @score['tx_expect'] ! @score['tx_expect'].to_f ! end ! end ! def bit_score ! if @score['fa_bits'] ! @score['fa_bits'].to_f ! elsif @score['sw_bits'] ! @score['sw_bits'].to_f ! elsif @score['fx_bits'] ! @score['fx_bits'].to_f ! elsif @score['tx_bits'] ! @score['tx_bits'].to_f ! end ! end ! def direction ! @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame'] ! end ! def sw ! @score['sw_score'].to_i ! end ! def identity ! @score['sw_ident'].to_f ! end ! def overlap ! @score['sw_overlap'].to_i ! end ! def query_id ! @query.entry_id ! end ! def target_id ! @target.entry_id ! end ! def query_def ! @query.definition ! end ! def target_def ! @target.definition ! end ! def query_len ! @query.length ! end ! def target_len ! @target.length ! end ! def query_seq ! @query.sequence ! end ! def target_seq ! @target.sequence ! end ! def query_type ! @query.moltype ! end ! def target_type ! @target.moltype ! end ! def query_start ! @query.start ! end ! def query_end ! @query.stop ! end ! def target_start ! @target.start ! end ! def target_end ! @target.stop ! end ! def lap_at ! [ query_start, query_end, target_start, target_end ] ! end ! class Query ! def initialize(data) ! @definition, *data = data.split(/\n/) ! @data = {} ! @sequence = '' ! pat = /;\s+([^:]+):\s+(.*)/ ! data.each do |x| ! if pat.match(x) ! @data[$1] = $2 ! else ! @sequence += x ! end ! end ! end ! attr_reader :definition, :data, :sequence - def entry_id - @definition[/\S+/] - end ! def length ! @data['sq_len'].to_i ! end ! def moltype ! @data['sq_type'] ! end ! def start ! @data['al_start'].to_i end ! def stop ! @data['al_stop'].to_i ! end ! end ! class Target < Query; end end end end ! end --- 11,312 ---- module Bio ! class Fasta ! # Summarized results of the fasta execution results. ! class Report ! def initialize(data) ! # header lines - brief list of the hits ! if data.sub!(/.*\nThe best scores are/m, '') ! data.sub!(/(.*)\n\n>>>/m, '') ! @list = "The best scores are" + $1 ! else ! data.sub!(/.*\n!!\s+/m, '') ! data.sub!(/.*/) { |x| @list = x; '' } ! end ! # body lines - fasta execution result ! program, *hits = data.split(/\n>>/) ! # trailing lines - log messages of the execution ! @log = hits.pop ! @log.sub!(/.*<\n/m, '') ! @log.strip! ! # parse results ! @program = Program.new(program) ! @hits = [] ! hits.each do |x| ! @hits.push(Hit.new(x)) ! end ! end ! ! # Returns the 'The best scores are' lines as a String. ! attr_reader :list ! # Returns the trailing lines including library size, execution date, ! # fasta function used, and fasta versions as a String. ! attr_reader :log ! # Returns a Bio::Fasta::Report::Program object. ! attr_reader :program ! # Returns an Array of Bio::Fasta::Report::Hit objects. ! attr_reader :hits + # Iterates on each Bio::Fasta::Report::Hit object. + def each + @hits.each do |x| + yield x + end + end ! # Returns an Array of Bio::Fasta::Report::Hit objects having ! # better evalue than 'evalue_max'. ! def threshold(evalue_max = 0.1) ! list = [] ! @hits.each do |x| ! list.push(x) if x.evalue < evalue_max ! end ! return list ! end ! # Returns an Array of Bio::Fasta::Report::Hit objects having ! # longer overlap length than 'length_min'. ! def lap_over(length_min = 0) ! list = [] ! @hits.each do |x| ! list.push(x) if x.overlap > length_min ! end ! return list ! end ! # Log of the fasta execution environments. ! class Program ! def initialize(data) ! @definition, *program = data.split(/\n/) ! @program = {} ! ! pat = /;\s+([^:]+):\s+(.*)/ ! ! program.each do |x| ! if pat.match(x) ! @program[$1] = $2 end end + end + + # Returns a String containing query and library filenames. + attr_reader :definition + # Accessor for a Hash containing 'mp_name', 'mp_ver', 'mp_argv', + # 'pg_name', 'pg_ver, 'pg_matrix', 'pg_gap-pen', 'pg_ktup', + # 'pg_optcut', 'pg_cgap', 'mp_extrap', 'mp_stats', and 'mp_KS' values. + attr_reader :program + end ! class Hit ! def initialize(data) ! score, query, target = data.split(/\n>/) ! @definition, *score = score.split(/\n/) ! @score = {} ! pat = /;\s+([^:]+):\s+(.*)/ ! score.each do |x| ! if pat.match(x) ! @score[$1] = $2 end ! end ! @query = Query.new(query) ! @target = Target.new(target) ! end ! attr_reader :definition, :score, :query, :target ! # E-value score ! def evalue ! if @score['fa_expect'] ! @score['fa_expect'].to_f ! elsif @score['sw_expect'] ! @score['sw_expect'].to_f ! elsif @score['fx_expect'] ! @score['fx_expect'].to_f ! elsif @score['tx_expect'] ! @score['tx_expect'].to_f ! end ! end ! # Bit score ! def bit_score ! if @score['fa_bits'] ! @score['fa_bits'].to_f ! elsif @score['sw_bits'] ! @score['sw_bits'].to_f ! elsif @score['fx_bits'] ! @score['fx_bits'].to_f ! elsif @score['tx_bits'] ! @score['tx_bits'].to_f ! end ! end ! def direction ! @score['fa_frame'] || @score['sw_frame'] || @score['fx_frame'] || @score['tx_frame'] ! end ! # Smith-Waterman score ! def sw ! @score['sw_score'].to_i ! end ! # percent identity ! def identity ! @score['sw_ident'].to_f ! end ! # overlap length ! def overlap ! @score['sw_overlap'].to_i ! end ! # Shortcuts for the methods of Bio::Fasta::Report::Hit::Query ! def query_id ! @query.entry_id ! end ! def target_id ! @target.entry_id ! end ! def query_def ! @query.definition ! end ! def target_def ! @target.definition ! end ! def query_len ! @query.length ! end ! # Shortcuts for the methods of Bio::Fasta::Report::Hit::Target ! def target_len ! @target.length ! end ! def query_seq ! @query.sequence ! end ! def target_seq ! @target.sequence ! end ! def query_type ! @query.moltype ! end ! def target_type ! @target.moltype ! end ! # Information on matching region ! def query_start ! @query.start ! end + def query_end + @query.stop + end ! def target_start ! @target.start ! end ! def target_end ! @target.stop ! end ! def lap_at ! [ query_start, query_end, target_start, target_end ] ! end ! class Query ! def initialize(data) ! @definition, *data = data.split(/\n/) ! @data = {} ! @sequence = '' ! pat = /;\s+([^:]+):\s+(.*)/ ! data.each do |x| ! if pat.match(x) ! @data[$1] = $2 ! else ! @sequence += x end + end + end ! # Returns the definition of the entry as a String. ! # You can access this value by Report::Hit#query_def method. ! attr_reader :definition ! # Returns a Hash containing 'sq_len', 'sq_offset', 'sq_type', ! # 'al_start', 'al_stop', and 'al_display_start' values. ! # You can access most of these values by Report::Hit#query_* methods. ! attr_reader :data ! # Returns the sequence (with gaps) as a String. ! # You can access this value by the Report::Hit#query_seq method. ! attr_reader :sequence ! ! # Returns the first word in the definition as a String. ! # You can get this value by Report::Hit#query_id method. ! def entry_id ! @definition[/\S+/] ! end ! ! # Returns the sequence length. ! # You can access this value by the Report::Hit#query_len method. ! def length ! @data['sq_len'].to_i ! end ! ! # Returns 'p' for protein sequence, 'D' for nucleotide sequence. ! def moltype ! @data['sq_type'] ! end ! ! # Returns alignment start position. You can also access this value ! # by Report::Hit#query_start method for shortcut. ! def start ! @data['al_start'].to_i ! end ! ! # Returns alignment end position. You can access this value ! # by Report::Hit#query_end method for shortcut. ! def stop ! @data['al_stop'].to_i end end + # Same as Bio::Fasta::Report::Hit::Query but for Target. + class Target < Query; end end ! ! end # Report ! ! end # Fasta ! end # Bio *************** *** 279,428 **** - =begin - - = Bio::Fasta::Report - - Summarized results of the fasta execution hits. - - --- Bio::Fasta::Report.new(data) - --- Bio::Fasta::Report#each - - Iterates on each Bio::Fasta::Report::Hit object. - - --- Bio::Fasta::Report#hits - - Returns an Array of Bio::Fasta::Report::Hit objects. - - --- Bio::Fasta::Report#threshold(evalue_max = 0.1) - - Returns an Array of Bio::Fasta::Report::Hit objects having - better evalue than 'evalue_max'. - - --- Bio::Fasta::Report#lap_over(length_min = 0) - - Returns an Array of Bio::Fasta::Report::Hit objects having - longer overlap length than 'length_min'. - - --- Bio::Fasta::Report#program - - Returns a Bio::Fasta::Report::Program object. - - --- Bio::Fasta::Report#list - - Returns the 'The best scores are' lines as a String. - - --- Bio::Fasta::Report#log - - Returns the trailing lines including library size, execution date, - fasta function used, and fasta versions as a String. - - - == Bio::Fasta::Report::Program - - Log of the fasta execution environments. - - --- Bio::Fasta::Report::Program#definition - - Returns a String containing query and library filenames. - - --- Bio::Fasta::Report::Program#program - - Accessor for a Hash containing 'mp_name', 'mp_ver', 'mp_argv', - 'pg_name', 'pg_ver, 'pg_matrix', 'pg_gap-pen', 'pg_ktup', - 'pg_optcut', 'pg_cgap', 'mp_extrap', 'mp_stats', and 'mp_KS' values. - - - == Bio::Fasta::Report::Hit - - --- Bio::Fasta::Report::Hit#definition - --- Bio::Fasta::Report::Hit#score - --- Bio::Fasta::Report::Hit#query - --- Bio::Fasta::Report::Hit#target - - Accessors for the internal structures. - - --- Bio::Fasta::Report::Hit#evalue - --- Bio::Fasta::Report::Hit#bit_score - --- Bio::Fasta::Report::Hit#sw - --- Bio::Fasta::Report::Hit#identity - - Matching scores. - - --- Bio::Fasta::Report::Hit#query_id - --- Bio::Fasta::Report::Hit#query_def - --- Bio::Fasta::Report::Hit#query_len - --- Bio::Fasta::Report::Hit#query_seq - --- Bio::Fasta::Report::Hit#query_type - --- Bio::Fasta::Report::Hit#target_id - --- Bio::Fasta::Report::Hit#target_def - --- Bio::Fasta::Report::Hit#target_len - --- Bio::Fasta::Report::Hit#target_seq - --- Bio::Fasta::Report::Hit#target_type - - Matching subjects. - Shortcuts for the methods of Hit::Query and the Hit::Target. - - --- Bio::Fasta::Report::Hit#query_start - --- Bio::Fasta::Report::Hit#query_end - --- Bio::Fasta::Report::Hit#target_start - --- Bio::Fasta::Report::Hit#target_end - --- Bio::Fasta::Report::Hit#overlap - --- Bio::Fasta::Report::Hit#lap_at - --- Bio::Fasta::Report::Hit#direction - - Matching regions. - - - == Bio::Fasta::Report::Hit::Query - - --- Bio::Fasta::Report::Hit::Query#entry_id - - Returns the first word in the definition as a String. - You can get this value by Report::Hit#query_id method. - - --- Bio::Fasta::Report::Hit::Query#definition - - Returns the definition of the entry as a String. - You can access this value by Report::Hit#query_def method. - - --- Bio::Fasta::Report::Hit::Query#sequence - - Returns the sequence (with gaps) as a String. - You can access this value by the Report::Hit#query_seq method. - - --- Bio::Fasta::Report::Hit::Query#length - - Returns the sequence length. - You can access this value by the Report::Hit#query_len method. - - --- Bio::Fasta::Report::Hit::Query#moltype - - Returns 'p' for protein sequence, 'D' for nucleotide sequence. - - --- Bio::Fasta::Report::Hit::Query#start - --- Bio::Fasta::Report::Hit::Query#stop - - Returns alignment start and stop position. - You can access these values by Report::Hit#query_start and - Report::Hit#query_end methods. - - --- Bio::Fasta::Report::Hit::Query#data - - Returns a Hash containing 'sq_len', 'sq_offset', 'sq_type', - 'al_start', 'al_stop', and 'al_display_start' values. - You can access most of these values by Report::Hit#query_* methods. - - - == Bio::Fasta::Report::Hit::Target - - --- Bio::Fasta::Report::Hit::Target#entry_id - --- Bio::Fasta::Report::Hit::Target#definition - --- Bio::Fasta::Report::Hit::Target#data - --- Bio::Fasta::Report::Hit::Target#sequence - --- Bio::Fasta::Report::Hit::Target#length - --- Bio::Fasta::Report::Hit::Target#start - --- Bio::Fasta::Report::Hit::Target#stop - - Same as Bio::Fasta::Report::Hit::Query but for Target. - - =end --- 324,325 ---- From k at dev.open-bio.org Fri Apr 6 13:13:39 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Fri, 06 Apr 2007 13:13:39 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/fasta format6.rb,1.2,NONE Message-ID: <200704061313.l36DDdTd022257@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/fasta In directory dev.open-bio.org:/tmp/cvs-serv22253 Removed Files: format6.rb Log Message: * deprecated --- format6.rb DELETED --- From aerts at dev.open-bio.org Thu Apr 12 12:19:18 2007 From: aerts at dev.open-bio.org (Jan Aerts) Date: Thu, 12 Apr 2007 12:19:18 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio map.rb,1.10,1.11 Message-ID: <200704121219.l3CCJIDQ032222@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio In directory dev.open-bio.org:/tmp/cvs-serv32200/lib/bio Modified Files: map.rb Log Message: * Added mappings_on method to Bio::Map::ActsLikeMarker. * Extended unit tests to get 100% coverage. Index: map.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/map.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** map.rb 5 Apr 2007 23:45:10 -0000 1.10 --- map.rb 12 Apr 2007 12:19:16 -0000 1.11 *************** *** 263,266 **** --- 263,286 ---- return positions end + + # Return all mappings of this marker on a given map. + # --- + # *Arguments*: + # * _map_: an object that mixes in Bio::Map::ActsLikeMap + # *Returns*:: array of Bio::Map::Mapping objects + def mappings_on(map) + unless map.class.include?(Bio::Map::ActsLikeMap) + raise "[Error] map is not object that implements Bio::Map::ActsLikeMap" + end + + m = Array.new + self.mappings_as_marker.each do |mapping| + if mapping.map == map + m.push(mapping) + end + end + + return m + end *************** *** 304,308 **** end ! return self.location.<=>(other.location) end end # Mapping --- 324,328 ---- end ! return self.location[0].<=>(other.location[0]) end end # Mapping From aerts at dev.open-bio.org Thu Apr 12 12:19:19 2007 From: aerts at dev.open-bio.org (Jan Aerts) Date: Thu, 12 Apr 2007 12:19:19 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio test_map.rb,1.5,1.6 Message-ID: <200704121219.l3CCJJxi032225@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio In directory dev.open-bio.org:/tmp/cvs-serv32200/test/unit/bio Modified Files: test_map.rb Log Message: * Added mappings_on method to Bio::Map::ActsLikeMarker. * Extended unit tests to get 100% coverage. Index: test_map.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_map.rb,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** test_map.rb 5 Apr 2007 23:35:42 -0000 1.5 --- test_map.rb 12 Apr 2007 12:19:16 -0000 1.6 *************** *** 41,44 **** --- 41,45 ---- @marker3 = Bio::Map::Marker.new('marker3') @map1 = Bio::Map::SimpleMap.new('map1', 'some_type', 'some_unit') + @map2 = Bio::Map::SimpleMap.new('map2', 'some_other_type', 'some_other_unit') end *************** *** 101,104 **** --- 102,108 ---- @marker1.add_mapping_as_marker(@map1, '53') # This mapping should _not_ be added, because it's already defined. assert_equal(3, @marker1.mappings_as_marker.length) + + @map1.add_mapping_as_map(@marker1, '53') + assert_equal(3, @marker1.mappings_as_marker.length) end *************** *** 110,113 **** --- 114,159 ---- assert_equal('5,37', @marker1.positions_on(@map1).collect{|p| p.first.from.to_s}.sort{|a,b| a.to_i <=> b.to_i}.join(',')) # FIXME: Test is not correct (uses Location.first) end + + def test_mappings_on + @map1.add_mapping_as_map(@marker1, '5') + @map1.add_mapping_as_map(@marker1, '37') + assert_equal('5,37', @marker1.mappings_on(@map1).sort{|a,b| a.location[0].from.to_i <=> b.location[0].from.to_i}.collect{|m| m.location[0].from}.join(',')) # FIXME: Test is not correct (uses Location.first) + end + + def test_mapping_location_comparison + @map1.add_mapping_as_map(@marker1, '5') + @map1.add_mapping_as_map(@marker2, '5') + @map1.add_mapping_as_map(@marker3, '17') + + mapping1 = @marker1.mappings_on(@map1)[0] + mapping2 = @marker2.mappings_on(@map1)[0] + mapping3 = @marker3.mappings_on(@map1)[0] + assert_equal(true, mapping1 == mapping2) + assert_equal(false, mapping1 < mapping2) + assert_equal(false, mapping1 > mapping2) + assert_equal(false, mapping1 == mapping3) + assert_equal(true, mapping1 < mapping3) + assert_equal(false, mapping1 > mapping3) + + @map2.add_mapping_as_map(@marker1, '23') + mapping4 = @marker1.mappings_on(@map2)[0] + assert_raise(RuntimeError) { mapping2 < mapping4 } + end + + def test_raise_error_kind_of + marker_without_class = 'marker1' + assert_raise(RuntimeError) { @map1.add_mapping_as_map(marker_without_class, '5') } + assert_raise(RuntimeError) { @map1.contains_marker?(marker_without_class) } + + map_without_class = 'map1' + assert_raise(RuntimeError) { @marker1.add_mapping_as_marker(map_without_class, '5') } + assert_raise(RuntimeError) { @marker1.mapped_to?(map_without_class) } + assert_raise(RuntimeError) { @marker1.positions_on(map_without_class) } + assert_raise(RuntimeError) { @marker1.mappings_on(map_without_class) } + + @map1.add_mapping_as_map(@marker1, '5') + mapping1 = @marker1.mappings_on(@map1)[0] + assert_raise(RuntimeError) { mapping1 > 'some_mapping' } + end end From k at dev.open-bio.org Sat Apr 14 02:29:47 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Sat, 14 Apr 2007 02:29:47 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.58,1.59 Message-ID: <200704140229.l3E2Tl8w004766@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/io In directory dev.open-bio.org:/tmp/cvs-serv4757/lib/bio/io Modified Files: flatfile.rb Log Message: * KEGG::ORTHOLOG is renamed to KEGG::ORTHOLOGY Index: flatfile.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile.rb,v retrieving revision 1.58 retrieving revision 1.59 diff -C2 -d -r1.58 -r1.59 *** flatfile.rb 5 Apr 2007 23:35:41 -0000 1.58 --- flatfile.rb 14 Apr 2007 02:29:45 -0000 1.59 *************** *** 1146,1150 **** brite = RuleRegexp[ 'Bio::KEGG::BRITE', /^Entry [A-Z0-9]+/ ], ! ortholog = RuleRegexp[ 'Bio::KEGG::ORTHOLOG', /^ENTRY .+ KO\s*/ ], drug = RuleRegexp[ 'Bio::KEGG::DRUG', --- 1146,1150 ---- brite = RuleRegexp[ 'Bio::KEGG::BRITE', /^Entry [A-Z0-9]+/ ], ! orthology = RuleRegexp[ 'Bio::KEGG::ORTHOLOGY', /^ENTRY .+ KO\s*/ ], drug = RuleRegexp[ 'Bio::KEGG::DRUG', *************** *** 1250,1255 **** #aaindex.is_prior_to litdb #litdb.is_prior_to brite ! brite.is_prior_to ortholog ! ortholog.is_prior_to drug drug.is_prior_to glycan glycan.is_prior_to enzyme --- 1250,1255 ---- #aaindex.is_prior_to litdb #litdb.is_prior_to brite ! brite.is_prior_to orthology ! orthology.is_prior_to drug drug.is_prior_to glycan glycan.is_prior_to enzyme From k at dev.open-bio.org Sat Apr 14 05:09:25 2007 From: k at dev.open-bio.org (Katayama Toshiaki) Date: Sat, 14 Apr 2007 05:09:25 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio/sequence test_aa.rb,1.3,1.4 Message-ID: <200704140509.l3E59Px2005968@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv5963/test/unit/bio/sequence Modified Files: test_aa.rb Log Message: * follow the change in to_re method that the regexp includes ambiguous amino acid itself Index: test_aa.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/sequence/test_aa.rb,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** test_aa.rb 5 Apr 2007 23:35:44 -0000 1.3 --- test_aa.rb 14 Apr 2007 05:09:23 -0000 1.4 *************** *** 68,72 **** assert_equal(re, @obj.to_re) @obj[1, 1] = 'B' ! re = /R[DN]LEHTFVFLRNFSLMLLRY/ assert_equal(re, @obj.to_re) end --- 68,72 ---- assert_equal(re, @obj.to_re) @obj[1, 1] = 'B' ! re = /R[DNB]LEHTFVFLRNFSLMLLRY/ assert_equal(re, @obj.to_re) end From ngoto at dev.open-bio.org Thu Apr 19 13:59:31 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Thu, 19 Apr 2007 13:59:31 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.21,1.22 Message-ID: <200704191359.l3JDxV0e017218@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv17198/lib/bio/db/pdb Modified Files: pdb.rb Log Message: BUG: When parsing a pdb file with many models, but only one chain per model, all atoms are added to residues in the first Bio::PDB::Model of the Bio::PDB structure. ([BioRuby] bug in pdb.rb bio-1.0.0) reported by Mikael Borg. Index: pdb.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -d -r1.21 -r1.22 *** pdb.rb 5 Apr 2007 23:35:41 -0000 1.21 --- pdb.rb 19 Apr 2007 13:59:29 -0000 1.22 *************** *** 1536,1539 **** --- 1536,1540 ---- when 'MODEL' c_atom = nil + cChain = nil if cModel.model_serial or cModel.chains.size > 0 then self.addModel(cModel) From ngoto at dev.open-bio.org Sat Apr 21 08:25:15 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Sat, 21 Apr 2007 08:25:15 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.20, 1.21 wublast.rb, 1.9, 1.10 Message-ID: <200704210825.l3L8PF8k021508@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv21488/lib/bio/appl/blast Modified Files: format0.rb wublast.rb Log Message: * Incompatible Changes: In Bio::BLAST::Default::Report#expect and and Bio::BLAST::WU::Report#expect are changed to return a Float or nil instead of a String or nil. * Incompatible Changes: In Bio::BLAST::Default::Report::Hit, Bio::BLAST::Default::Report::HSP, Bio::BLAST::WU::Report::Hit, and Bio::BLAST::WU::Report::HSP, following methods are changed to return a Float object instead of a String object: evalue, pvalue (note that pvalue is only available in WU-BLAST). Index: wublast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -d -r1.9 -r1.10 *** wublast.rb 5 Apr 2007 23:35:39 -0000 1.9 --- wublast.rb 21 Apr 2007 08:25:13 -0000 1.10 *************** *** 138,141 **** --- 138,145 ---- end end + if ev = @parameters['E'] then + ev = '1' + ev if ev[0] == ?e + @parameters['E'] = ev.to_f + end @parse_parameters = true end *************** *** 251,256 **** scr = z.pop.to_s pval = z.pop.to_s nnum = z.pop.to_i - #ev = '1' + ev if ev[0] == ?e h.instance_eval { @score = scr --- 255,261 ---- scr = z.pop.to_s pval = z.pop.to_s + pval = '1' + pval if pval[0] == ?e + pval = (pval.empty? ? (1.0/0.0) : pval.to_f) nnum = z.pop.to_i h.instance_eval { @score = scr Index: format0.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** format0.rb 5 Apr 2007 23:35:39 -0000 1.20 --- format0.rb 21 Apr 2007 08:25:13 -0000 1.21 *************** *** 328,332 **** while sc.rest? if sc.match?(/Number of sequences better than +([e\-\.\d]+) *\: *(.+)/) then ! @expect = sc[1] @num_hits = sc[2].tr(',', '').to_i end --- 328,334 ---- while sc.rest? if sc.match?(/Number of sequences better than +([e\-\.\d]+) *\: *(.+)/) then ! ev = sc[1] ! ev = '1' + ev if ev[0] == ?e ! @expect = ev.to_f @num_hits = sc[2].tr(',', '').to_i end *************** *** 659,663 **** bs = z.pop.to_s ev = z.pop.to_s ! #ev = '1' + ev if ev[0] == ?e h.instance_eval { @bit_score = bs; @evalue = ev } @hits << h --- 661,666 ---- bs = z.pop.to_s ev = z.pop.to_s ! ev = '1' + ev if ev[0] == ?e ! ev = (ev.empty? ? (1.0/0.0) : ev.to_f) h.instance_eval { @bit_score = bs; @evalue = ev } @hits << h *************** *** 950,955 **** sc.skip(/\s*/) if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then ! @evalue = sc[1] ! #@evalue = '1' + @evalue if @evalue[0] == ?e elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then @bit_score = sc[1] --- 953,959 ---- sc.skip(/\s*/) if sc.skip(/Expect(?:\(\d\))? *\= *([e\-\.\d]+)/) then ! ev = sc[1].to_s ! ev = '1' + ev if ev[0] == ?e ! @evalue = ev.to_f elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then @bit_score = sc[1] *************** *** 1001,1009 **** #WU-BLAST @p_sum_n = nil ! @pvalue = sc[1] elsif sc.skip(/Sum +P *\( *(\d+) *\) *\= *([e\-\.\d]+)/) then #WU-BLAST @p_sum_n = sc[1].to_i ! @pvalue = sc[2] else raise ScanError --- 1005,1017 ---- #WU-BLAST @p_sum_n = nil ! pv = sc[1] ! pv = '1' + pv if pv[0] == ?e ! @pvalue = pv.to_f elsif sc.skip(/Sum +P *\( *(\d+) *\) *\= *([e\-\.\d]+)/) then #WU-BLAST @p_sum_n = sc[1].to_i ! pv = sc[2] ! pv = '1' + pv if pv[0] == ?e ! @pvalue = pv.to_f else raise ScanError From ngoto at dev.open-bio.org Sat Apr 21 08:58:19 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Sat, 21 Apr 2007 08:58:19 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.21, 1.22 wublast.rb, 1.10, 1.11 Message-ID: <200704210858.l3L8wJn9021602@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast In directory dev.open-bio.org:/tmp/cvs-serv21582/lib/bio/appl/blast Modified Files: format0.rb wublast.rb Log Message: * Incompatible changes: Hit#bit_score, and HSP#bit_score are changed to return a Float object or nil instead of a String object or nil. * Incompatible changes: Following methods are changed to return an integer value or nil instead of a String object or nil: score, percent_identity, percent_positive, percent_gaps. Index: wublast.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** wublast.rb 21 Apr 2007 08:25:13 -0000 1.10 --- wublast.rb 21 Apr 2007 08:58:17 -0000 1.11 *************** *** 253,257 **** end z.pop if flag_tblast #ignore Reading Frame ! scr = z.pop.to_s pval = z.pop.to_s pval = '1' + pval if pval[0] == ?e --- 253,258 ---- end z.pop if flag_tblast #ignore Reading Frame ! scr = z.pop ! scr = (scr ? scr.to_i : nil) pval = z.pop.to_s pval = '1' + pval if pval[0] == ?e Index: format0.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/format0.rb,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -d -r1.21 -r1.22 *** format0.rb 21 Apr 2007 08:25:13 -0000 1.21 --- format0.rb 21 Apr 2007 08:58:17 -0000 1.22 *************** *** 660,663 **** --- 660,665 ---- h = Hit.new([ z.pop.to_s.sub(/\.+\z/, '') ]) bs = z.pop.to_s + bs = '1' + bs if bs[0] == ?e + bs = (bs.empty? ? nil : bs.to_f) ev = z.pop.to_s ev = '1' + ev if ev[0] == ?e *************** *** 957,962 **** @evalue = ev.to_f elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then ! @bit_score = sc[1] ! @score = sc[2] elsif sc.skip(/(Identities|Positives|Gaps) *\= (\d+) *\/ *(\d+) *\(([\.\d]+) *\% *\)/) then alen = sc[3].to_i --- 959,966 ---- @evalue = ev.to_f elsif sc.skip(/Score *\= *([e\-\.\d]+) *bits *\( *([e\-\.\d]+) *\)/) then ! bs = sc[1] ! bs = '1' + bs if bs[0] == ?e ! @bit_score = bs.to_f ! @score = sc[2].to_i elsif sc.skip(/(Identities|Positives|Gaps) *\= (\d+) *\/ *(\d+) *\(([\.\d]+) *\% *\)/) then alen = sc[3].to_i *************** *** 966,976 **** when 'Identities' @identity = sc[2].to_i ! @percent_identity = sc[4] when 'Positives' @positive = sc[2].to_i ! @percent_positive = sc[4] when 'Gaps' @gaps = sc[2].to_i ! @percent_gaps = sc[4] else raise ScanError --- 970,980 ---- when 'Identities' @identity = sc[2].to_i ! @percent_identity = sc[4].to_i when 'Positives' @positive = sc[2].to_i ! @percent_positive = sc[4].to_i when 'Gaps' @gaps = sc[2].to_i ! @percent_gaps = sc[4].to_i else raise ScanError *************** *** 1000,1005 **** elsif sc.skip(/Score *\= *([e\-\.\d]+) +\(([e\-\.\d]+) *bits *\)/) then #WU-BLAST ! @score = sc[1] ! @bit_score = sc[2] elsif sc.skip(/P *\= * ([e\-\.\d]+)/) then #WU-BLAST --- 1004,1011 ---- elsif sc.skip(/Score *\= *([e\-\.\d]+) +\(([e\-\.\d]+) *bits *\)/) then #WU-BLAST ! @score = sc[1].to_i ! bs = sc[2] ! bs = '1' + bs if bs[0] == ?e ! @bit_score = bs.to_f elsif sc.skip(/P *\= * ([e\-\.\d]+)/) then #WU-BLAST From ngoto at dev.open-bio.org Sat Apr 21 08:59:47 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Sat, 21 Apr 2007 08:59:47 +0000 Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.19,1.20 Message-ID: <200704210859.l3L8xlXC021652@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/doc In directory dev.open-bio.org:/tmp/cvs-serv21632/doc Modified Files: Changes-0.7.rd Log Message: incompatible changes in Bio::BLAST::Default and Bio::BLAST::WU are added. Index: Changes-0.7.rd =================================================================== RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v retrieving revision 1.19 retrieving revision 1.20 diff -C2 -d -r1.19 -r1.20 *** Changes-0.7.rd 2 Apr 2007 12:55:26 -0000 1.19 --- Changes-0.7.rd 21 Apr 2007 08:59:45 -0000 1.20 *************** *** 308,311 **** --- 308,325 ---- formmatted text instead of Array. + --- Bio::BLAST::Default::Report, Bio::BLAST::Default::Report::Hit, + Bio::BLAST::Default::Report::HSP, Bio::BLAST::WU::Report, + Bio::BLAST::WU::Report::Hit, Bio::BLAST::WU::Report::HSP + + In 1.1.0: + + * Hit#evalue, HSP#evalue, WU::Hit#pvalue, and WU::HSP#pvalue are + changed to return a Float object instead of a String object. + * Report#expect, Hit#bit_score, and HSP#bit_score are changed to return + a Float object or nil instead of a String object or nil. + * Following methods are changed to return an integer value or nil + instead of a string or nil: score, percent_identity, percent_positive, + percent_gaps. + === Deleted files From ngoto at dev.open-bio.org Mon Apr 23 16:03:27 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Mon, 23 Apr 2007 16:03:27 +0000 Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.20,1.21 Message-ID: <200704231603.l3NG3RZh023014@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/doc In directory dev.open-bio.org:/tmp/cvs-serv22990/doc Modified Files: Changes-0.7.rd Log Message: Bio::PDB::Residue#[] (and Bio::PDB::Heterogen#[]) are changed to use the name field for selecting atoms, because the element field is not useful for selecting atoms and is not used in many pdb files. (reported by Alex Gutteridge in [BioRuby] Bio::PDB::Residue patch) Index: Changes-0.7.rd =================================================================== RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -d -r1.20 -r1.21 *** Changes-0.7.rd 21 Apr 2007 08:59:45 -0000 1.20 --- Changes-0.7.rd 23 Apr 2007 16:03:24 -0000 1.21 *************** *** 256,259 **** --- 256,262 ---- are also subject to the above changes, because Bio::PDB::HETATM inherits Bio::PDB::ATOM. + * Bio::PDB::Residue#[] and Bio::PDB::Heterogen#[] are changed to use the + name field for selecting atoms, because the element field is not useful + for selecting atoms and is not used in many pdb files. --- Bio::FlatFile From ngoto at dev.open-bio.org Mon Apr 23 16:03:27 2007 From: ngoto at dev.open-bio.org (Naohisa Goto) Date: Mon, 23 Apr 2007 16:03:27 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb residue.rb,1.12,1.13 Message-ID: <200704231603.l3NG3RIa023017@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb In directory dev.open-bio.org:/tmp/cvs-serv22990/lib/bio/db/pdb Modified Files: residue.rb Log Message: Bio::PDB::Residue#[] (and Bio::PDB::Heterogen#[]) are changed to use the name field for selecting atoms, because the element field is not useful for selecting atoms and is not used in many pdb files. (reported by Alex Gutteridge in [BioRuby] Bio::PDB::Residue patch) Index: residue.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** residue.rb 5 Apr 2007 23:35:41 -0000 1.12 --- residue.rb 23 Apr 2007 16:03:25 -0000 1.13 *************** *** 66,72 **** alias id residue_id ! #Keyed access to atoms based on element e.g. ["CA"] def [](key) ! atom = @atoms.find{ |atom| key == atom.element } end --- 66,72 ---- alias id residue_id ! #Keyed access to atoms based on atom name e.g. ["CA"] def [](key) ! atom = @atoms.find{ |atom| key == atom.name } end From trevor at dev.open-bio.org Mon Apr 23 16:43:53 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 16:43:53 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/sequence na.rb,1.6,1.7 Message-ID: <200704231643.l3NGhr9r023198@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/sequence In directory dev.open-bio.org:/tmp/cvs-serv23176/bio/sequence Modified Files: na.rb Log Message: Move cut_with_enzyme to Bio::Sequence::NA Index: na.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/na.rb,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** na.rb 5 Apr 2007 23:35:41 -0000 1.6 --- na.rb 23 Apr 2007 16:43:51 -0000 1.7 *************** *** 468,471 **** --- 468,487 ---- protected :rna? + # Example: + # + # seq = Bio::Sequence::NA.new('gaattc') + # cuts = seq.cut_with_enzyme('EcoRI') + # + # _or_ + # + # seq = Bio::Sequence::NA.new('gaattc') + # cuts = seq.cut_with_enzyme('g^aattc') + # --- + # See Bio::RestrictionEnzyme::Analysis.cut + def cut_with_enzyme(*args) + Bio::RestrictionEnzyme::Analysis.cut(self, *args) + end + alias cut_with_enzymes cut_with_enzyme + end # NA From trevor at dev.open-bio.org Mon Apr 23 16:43:53 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 16:43:53 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis_basic.rb, 1.12, 1.13 Message-ID: <200704231643.l3NGhrs5023203@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23176/bio/util/restriction_enzyme Modified Files: analysis_basic.rb Log Message: Move cut_with_enzyme to Bio::Sequence::NA Index: analysis_basic.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v retrieving revision 1.12 retrieving revision 1.13 diff -C2 -d -r1.12 -r1.13 *** analysis_basic.rb 5 Apr 2007 23:35:42 -0000 1.12 --- analysis_basic.rb 23 Apr 2007 16:43:51 -0000 1.13 *************** *** 10,32 **** require 'bio' - class Bio::Sequence::NA - # Example: - # - # seq = Bio::Sequence::NA.new('gaattc') - # cuts = seq.cut_with_enzyme('EcoRI') - # - # _or_ - # - # seq = Bio::Sequence::NA.new('gaattc') - # cuts = seq.cut_with_enzyme('g^aattc') - # --- - # See Bio::RestrictionEnzyme::Analysis.cut - # - # NOTE: move this into Bio::Sequence::NA - def cut_with_enzyme(*args) - Bio::RestrictionEnzyme::Analysis.cut(self, *args) - end - alias cut_with_enzymes cut_with_enzyme - end require 'set' # for method create_enzyme_actions --- 10,13 ---- From trevor at dev.open-bio.org Mon Apr 23 17:11:13 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 17:11:13 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis_basic.rb, 1.13, 1.14 Message-ID: <200704231711.l3NHBD7F023254@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23234/lib/bio/util/restriction_enzyme Modified Files: analysis_basic.rb Log Message: Index: analysis_basic.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis_basic.rb,v retrieving revision 1.13 retrieving revision 1.14 diff -C2 -d -r1.13 -r1.14 *** analysis_basic.rb 23 Apr 2007 16:43:51 -0000 1.13 --- analysis_basic.rb 23 Apr 2007 17:11:11 -0000 1.14 *************** *** 9,14 **** # - require 'bio' - require 'set' # for method create_enzyme_actions require 'bio/util/restriction_enzyme' --- 9,12 ---- From trevor at dev.open-bio.org Mon Apr 23 19:42:57 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 19:42:57 +0000 Subject: [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_analysis.rb, 1.10, 1.11 Message-ID: <200704231943.l3NJgvm6023491@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23466/test/unit/bio/util/restriction_enzyme Modified Files: test_analysis.rb Log Message: Support user specification of maximum allowable permutations. It's becoming apparent that we need some sort of standardized logging mechanism for warnings. Index: test_analysis.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/restriction_enzyme/test_analysis.rb,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -d -r1.10 -r1.11 *** test_analysis.rb 5 Apr 2007 23:35:44 -0000 1.10 --- test_analysis.rb 23 Apr 2007 19:42:55 -0000 1.11 *************** *** 160,164 **** assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary ) assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag').primary ) ! assert_equal([], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('EcoRII').primary ) assert_equal(["ag", "ag", "cag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag', 'EcoRII').primary ) --- 160,164 ---- assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag', 'EcoRII').primary ) assert_equal(["ag", "agccagg", "cag"], Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('ag^ag').primary ) ! assert_equal(:no_cuts_found, Bio::Sequence::NA.new('cagagagccagg').cut_with_enzymes('EcoRII') ) assert_equal(["ag", "ag", "cag", "ccaggt"], Bio::Sequence::NA.new('cagagagccaggt').cut_with_enzymes('ag^ag', 'EcoRII').primary ) *************** *** 170,172 **** end ! end \ No newline at end of file --- 170,172 ---- end ! end From trevor at dev.open-bio.org Mon Apr 23 19:42:57 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 19:42:57 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.17, 1.18 Message-ID: <200704231943.l3NJgvhU023488@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23466/lib/bio/util/restriction_enzyme Modified Files: analysis.rb Log Message: Support user specification of maximum allowable permutations. It's becoming apparent that we need some sort of standardized logging mechanism for warnings. Index: analysis.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/analysis.rb,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 *** analysis.rb 5 Apr 2007 23:35:42 -0000 1.17 --- analysis.rb 23 Apr 2007 19:42:55 -0000 1.18 *************** *** 47,55 **** # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. ! # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments) def cut( sequence, *args ) ! return fragments_for_display( {} ) if !sequence.kind_of?(String) or sequence.empty? # Format the fragments for the user ! fragments_for_display( cut_and_return_by_permutations( sequence, *args ) ) end --- 47,56 ---- # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. ! # *Returns*:: Bio::RestrictionEnzyme::Fragments object populated with Bio::RestrictionEnzyme::Fragment objects. (Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments) or a +Symbol+ containing an error code def cut( sequence, *args ) ! res = cut_and_return_by_permutations( sequence, *args ) ! return res if res.class == Symbol # Format the fragments for the user ! fragments_for_display( res ) end *************** *** 64,76 **** # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. # *Returns*:: +Hash+ Keys are a permutation ID, values are SequenceRange objects that have cuts applied. def cut_and_return_by_permutations( sequence, *args ) my_hash = {} ! return my_hash if !sequence.kind_of?(String) or sequence.empty? sequence = Bio::Sequence::NA.new( sequence ) enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args ) ! return my_hash if enzyme_actions.empty? and initial_cuts.empty? if enzyme_actions.size > 1 --- 65,113 ---- # * +sequence+: +String+ kind of object that will be used as a nucleic acid sequence. # * +args+: Series of enzyme names, enzymes sequences with cut marks, or RestrictionEnzyme objects. + # May also supply a +Hash+ with the key ":max_permutations" to specificy how many permutations are allowed - a value of 0 indicates no permutations are allowed. # *Returns*:: +Hash+ Keys are a permutation ID, values are SequenceRange objects that have cuts applied. + # _also_ may return the +Symbol+ ':sequence_empty', ':no_cuts_found', or ':too_many_permutations' def cut_and_return_by_permutations( sequence, *args ) my_hash = {} + maximum_permutations = nil + + hashes_in_args = args.select { |i| i.class == Hash } + args.delete_if { |i| i.class == Hash } + hashes_in_args.each do |hsh| + hsh.each do |key, value| + case key + when :max_permutations, 'max_permutations', :maximum_permutations, 'maximum_permutations' + maximum_permutations = value.to_i unless value == nil + else + raise ArgumentError, "Received key #{key.inspect} in argument - I only know the key ':max_permutations' currently. Hash passed: #{hsh.inspect}" + end + end + end ! if !sequence.kind_of?(String) or sequence.empty? ! logger.warn "The supplied sequence is empty." if defined?(logger) ! return :sequence_empty ! end sequence = Bio::Sequence::NA.new( sequence ) enzyme_actions, initial_cuts = create_enzyme_actions( sequence, *args ) ! ! if enzyme_actions.empty? and initial_cuts.empty? ! logger.warn "This enzyme does not make any cuts on this sequence." if defined?(logger) ! return :no_cuts_found ! end ! ! # * When enzyme_actions.size is equal to '1' that means there are no permutations. ! # * If enzyme_actions.size is equal to '2' there is one ! # permutation ("[0, 1]") ! # * If enzyme_actions.size is equal to '3' there are two ! # permutations ("[0, 1, 2]") ! # * and so on.. ! if maximum_permutations and enzyme_actions.size > 1 ! if (enzyme_actions.size - 1) > maximum_permutations.to_i ! logger.warn "More permutations than maximum, skipping. Found: #{enzyme_actions.size-1} Max: #{maximum_permutations.to_i}" if defined?(logger) ! return :too_many_permutations ! end ! end if enzyme_actions.size > 1 From trevor at dev.open-bio.org Mon Apr 23 19:53:36 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 19:53:36 +0000 Subject: [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme enzymes.yaml, 1.2, 1.3 Message-ID: <200704231953.l3NJraJu023521@dev.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme In directory dev.open-bio.org:/tmp/cvs-serv23501/lib/bio/util/restriction_enzyme Modified Files: enzymes.yaml Log Message: Update enzymes.yaml to version 704 Index: enzymes.yaml =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/enzymes.yaml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -d -r1.2 -r1.3 *** enzymes.yaml 31 Dec 2006 20:50:43 -0000 1.2 --- enzymes.yaml 23 Apr 2007 19:53:34 -0000 1.3 *************** *** 1,7001 **** --- TspRI: ! :blunt: "0" ! :c2: "-3" ! :c4: "0" :c1: "7" :pattern: CASTG ! :len: "5" :name: TspRI :c3: "0" [...14033 lines suppressed...] BseMI: ! :len: "6" :c1: "8" + :c4: "0" + :ncuts: "2" :pattern: GCAATG ! :c2: "6" :name: BseMI + :blunt: "0" :c3: "0" EcoRII: ! :len: "5" :c1: "-1" + :c4: "0" + :ncuts: "2" :pattern: CCWGG ! :c2: "5" :name: EcoRII + :blunt: "0" :c3: "0" From trevor at dev.open-bio.org Mon Apr 23 20:05:36 2007 From: trevor at dev.open-bio.org (Trevor Wennblom) Date: Mon, 23 Apr 2007 20:05:36 +0000 Subject: [BioRuby-cvs] bioruby README,1.15,1.16 Message-ID: <200704232005.l3NK5a5C023571@dev.open-bio.org> Update of /home/repository/bioruby/bioruby In directory dev.open-bio.org:/tmp/cvs-serv23551 Modified Files: README Log Message: Index: README =================================================================== RCS file: /home/repository/bioruby/bioruby/README,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** README 5 Apr 2007 15:18:51 -0000 1.15 --- README 23 Apr 2007 20:05:34 -0000 1.16 *************** *** 1,4 **** - =begin - $Id$ --- 1,2 ---- *************** *** 177,182 **** Current staffs of the BioRuby project can be reached by sending e-mail to . - - - =end - --- 175,176 ----