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1 parent 6eaeeb7 commit d355d98830bb236fbfd8355be3151c0f1de15495 @trevor committed Sep 10, 2011
Showing with 4,541 additions and 57 deletions.
  1. +121 −0 COPYING.txt
  2. +2 −6 Gemfile
  3. +4 −17 LICENSE.txt
  4. +16 −13 README.rdoc
  5. +7 −7 Rakefile
  6. +1 −1 VERSION
  7. +57 −0 bio-restriction_enzyme.gemspec
  8. +1 −10 lib/bio-restriction_enzyme.rb
  9. +218 −0 lib/bio/util/restriction_enzyme.rb
  10. +241 −0 lib/bio/util/restriction_enzyme/analysis.rb
  11. +209 −0 lib/bio/util/restriction_enzyme/analysis_basic.rb
  12. +99 −0 lib/bio/util/restriction_enzyme/cut_symbol.rb
  13. +313 −0 lib/bio/util/restriction_enzyme/double_stranded.rb
  14. +127 −0 lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
  15. +95 −0 lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
  16. +30 −0 lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
  17. +68 −0 lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
  18. +99 −0 lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
  19. +16 −0 lib/bio/util/restriction_enzyme/range/cut_range.rb
  20. +39 −0 lib/bio/util/restriction_enzyme/range/cut_ranges.rb
  21. +59 −0 lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
  22. +249 −0 lib/bio/util/restriction_enzyme/range/sequence_range.rb
  23. +236 −0 lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
  24. +43 −0 lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
  25. +33 −0 lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
  26. +69 −0 lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
  27. +193 −0 lib/bio/util/restriction_enzyme/single_strand.rb
  28. +127 −0 lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
  29. +15 −0 lib/bio/util/restriction_enzyme/single_strand_complement.rb
  30. +103 −0 lib/bio/util/restriction_enzyme/string_formatting.rb
  31. +281 −0 test/bio-restriction_enzyme/analysis/test_calculated_cuts.rb
  32. +87 −0 test/bio-restriction_enzyme/analysis/test_cut_ranges.rb
  33. +223 −0 test/bio-restriction_enzyme/analysis/test_sequence_range.rb
  34. +84 −0 test/bio-restriction_enzyme/double_stranded/test_aligned_strands.rb
  35. +58 −0 test/bio-restriction_enzyme/double_stranded/test_cut_location_pair.rb
  36. +56 −0 test/bio-restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb
  37. +35 −0 test/bio-restriction_enzyme/double_stranded/test_cut_locations.rb
  38. +87 −0 test/bio-restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
  39. +66 −0 test/bio-restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
  40. +228 −0 test/bio-restriction_enzyme/test_analysis.rb
  41. +27 −0 test/bio-restriction_enzyme/test_cut_symbol.rb
  42. +98 −0 test/bio-restriction_enzyme/test_double_stranded.rb
  43. +131 −0 test/bio-restriction_enzyme/test_single_strand.rb
  44. +131 −0 test/bio-restriction_enzyme/test_single_strand_complement.rb
  45. +43 −0 test/bio-restriction_enzyme/test_string_formatting.rb
  46. +0 −1 test/helper.rb
  47. +16 −2 test/test_bio-restriction_enzyme.rb
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@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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+4. Limitations and Disclaimers.
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View
@@ -1,12 +1,8 @@
source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-# gem "activesupport", ">= 2.3.5"
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
+gem 'bio-data-restriction_enzyme'
+
group :development do
- gem "shoulda", ">= 0"
gem "bundler", "~> 1.0.0"
gem "jeweler", "~> 1.6.4"
gem "rcov", ">= 0"
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@@ -1,20 +1,7 @@
-Copyright (c) 2011 Trevor Wennblom
+Bio::RestrictionEnzyme
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
+Written in 2005-2011 by Trevor Wennblom <trevor@well.com>
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <http://creativecommons.org/publicdomain/zero/1.0/>.
View
@@ -1,19 +1,22 @@
= bio-restriction_enzyme
-Description goes here.
+Bio::RestrictionEnzyme
-== Contributing to bio-restriction_enzyme
-
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
-* Fork the project
-* Start a feature/bugfix branch
-* Commit and push until you are happy with your contribution
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+Digests DNA based on restriction enzyme cut patterns
-== Copyright
-Copyright (c) 2011 Trevor Wennblom. See LICENSE.txt for
-further details.
+== notes
+Re-implementation of Bio::RestrictionEnzyme as a BioGem.
+
+This BioGem does not include changes found in BioRuby 1.4.2. These will be added if resubmitted under a compatible license.
+
+
+== contribution
+
+Improvements encouraged, send pull requests.
+
+
+== license
+
+CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
View
@@ -14,13 +14,13 @@ require 'rake'
require 'jeweler'
Jeweler::Tasks.new do |gem|
# gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
- gem.name = "bio-restriction_enzyme"
- gem.homepage = "http://github.com/trevor/bioruby-restriction_enzyme"
- gem.license = "MIT"
- gem.summary = %Q{TODO: one-line summary of your gem}
- gem.description = %Q{TODO: longer description of your gem}
- gem.email = "trevor@well.com"
- gem.authors = ["Trevor Wennblom"]
+ gem.name = 'bio-restriction_enzyme'
+ gem.homepage = 'http://github.com/trevor/bioruby-restriction_enzyme'
+ gem.license = 'CC0'
+ gem.summary = %Q{Digests DNA based on restriction enzyme cut patterns}
+ gem.description = %Q{Digests DNA based on restriction enzyme cut patterns}
+ gem.email = 'trevor@well.com'
+ gem.authors = ['Trevor Wennblom']
# dependencies defined in Gemfile
end
Jeweler::RubygemsDotOrgTasks.new
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@@ -1 +1 @@
-0.0.0
+1.0.0
@@ -0,0 +1,57 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+ s.name = "bio-restriction_enzyme"
+ s.version = "1.0.0"
+
+ s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+ s.authors = ["Trevor Wennblom"]
+ s.date = "2011-09-10"
+ s.description = "Digests DNA based on restriction enzyme cut patterns"
+ s.email = "trevor@well.com"
+ s.extra_rdoc_files = [
+ "LICENSE.txt",
+ "README.rdoc"
+ ]
+ s.files = [
+ ".document",
+ "Gemfile",
+ "LICENSE.txt",
+ "README.rdoc",
+ "Rakefile",
+ "VERSION",
+ "lib/bio-restriction_enzyme.rb",
+ "test/helper.rb",
+ "test/test_bio-restriction_enzyme.rb"
+ ]
+ s.homepage = "http://github.com/trevor/bioruby-restriction_enzyme"
+ s.licenses = ["CC0"]
+ s.require_paths = ["lib"]
+ s.rubygems_version = "1.8.10"
+ s.summary = "Digests DNA based on restriction enzyme cut patterns"
+
+ if s.respond_to? :specification_version then
+ s.specification_version = 3
+
+ if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+ s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+ s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+ s.add_development_dependency(%q<rcov>, [">= 0"])
+ s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+ else
+ s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+ s.add_dependency(%q<rcov>, [">= 0"])
+ s.add_dependency(%q<bio>, [">= 1.4.1"])
+ end
+ else
+ s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+ s.add_dependency(%q<rcov>, [">= 0"])
+ s.add_dependency(%q<bio>, [">= 1.4.1"])
+ end
+end
+
@@ -1,10 +1 @@
-# Please require your code below, respecting the bioruby directory tree.
-# For instance, perhaps the only uncommented line in this file might
-# be something like this:
-#
-# require 'bio/sequence/awesome_sequence_plugin_thingy'
-#
-# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
-# and put your plugin's code there. It is bad practice to write other code
-# directly into this file, because doing so causes confusion if this biogem
-# was ever to get merged into the main bioruby tree.
+require 'bio/util/restriction_enzyme'
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