semin-ulla 0.9.7 → 0.9.8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/History.txt +4 -0
- data/Rakefile +14 -21
- data/lib/ulla/cli.rb +4 -4
- data/lib/ulla.rb +1 -1
- data/ulla.gemspec +7 -10
- data/website/index.html +1 -1
- metadata +5 -16
data/History.txt
CHANGED
data/Rakefile
CHANGED
@@ -1,32 +1,25 @@
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-
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require 'rubygems'
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gem 'hoe', '>= 2.1.0'
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require 'hoe'
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require 'fileutils'
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Hoe.plugin :newgem
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# Hoe.plugin :website
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# Hoe.plugin :cucumberfeatures
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# Generate all the Rake tasks
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# Run 'rake -T' to see list of generated tasks (from gem root directory)
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$hoe = Hoe.
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p.extra_deps = [
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$hoe = Hoe.spec 'ulla' do
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self.developer 'Semin Lee', 'seminlee@gmail.com'
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self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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self.rubyforge_name = self.name # TODO this is default value
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self.extra_deps = [
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['narray', '>= 0.5.9.5'],
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['bio', '>= 1.2.1'],
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['facets', '>= 2.4.5'],
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['rmagick', '>= 2.9.1'],
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]
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-
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p.extra_dev_deps = [
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['newgem', ">= #{::Newgem::VERSION}"]
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]
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p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
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path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
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p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
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p.rsync_args = '-av --delete --ignore-errors'
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end
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require 'newgem/tasks'
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require 'newgem/tasks'
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Dir['tasks/**/*.rake'].each { |t| load t }
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-
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# TODO - want other tests/tasks run by default? Add them to the list
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# task :default => [:spec, :features]
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data/lib/ulla/cli.rb
CHANGED
@@ -384,7 +384,7 @@ Options:
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# if --cys option 2, then we don't care about 'J' (for both Cystine and Cystine)
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if $cys == 2
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$amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J')
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$amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J').split('')
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end
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# create an EnvironmentFeatureArray object for storing all environment
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@@ -709,11 +709,11 @@ Options:
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env_label2 = $environment == 1 ? aa2 + '-' + aa1[1..-1] : env_labels[id2][pos]
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if $cst_features.empty?
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$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
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$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
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$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
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$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
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elsif (env_labels[id1][pos].split('').values_at(*$cst_features) == env_labels[id2][pos].split('').values_at(*$cst_features))
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$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
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$env_classes[env_label2].increase_residue_count(aa1[
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$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
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else
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$logger.debug "Skipped #{id1}-#{pos}-#{aa1[0].chr} and #{id2}-#{pos}-#{aa2[0].chr} having different symbols for constrained environment features each other."
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next
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data/lib/ulla.rb
CHANGED
data/ulla.gemspec
CHANGED
@@ -2,16 +2,16 @@
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Gem::Specification.new do |s|
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s.name = %q{ulla}
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s.version = "0.9.
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s.version = "0.9.8"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Semin Lee"]
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s.date = %q{2009-
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s.date = %q{2009-07-21}
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s.default_executable = %q{ulla}
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s.description = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
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s.email = ["seminlee@gmail.com"]
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s.executables = ["ulla"]
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s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "
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s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
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s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
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s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
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s.post_install_message = %q{PostInstall.txt}
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@@ -20,7 +20,7 @@ Gem::Specification.new do |s|
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s.rubyforge_project = %q{ulla}
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s.rubygems_version = %q{1.3.4}
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s.summary = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
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s.test_files = ["test/
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s.test_files = ["test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "test/test_helper.rb", "test/test_ulla.rb"]
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if s.respond_to? :specification_version then
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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@@ -31,22 +31,19 @@ Gem::Specification.new do |s|
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s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
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s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
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s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
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s.add_development_dependency(%q<
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s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
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s.add_development_dependency(%q<hoe>, [">= 2.3.2"])
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else
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s.add_dependency(%q<narray>, [">= 0.5.9.5"])
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s.add_dependency(%q<bio>, [">= 1.2.1"])
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s.add_dependency(%q<facets>, [">= 2.4.5"])
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s.add_dependency(%q<rmagick>, [">= 2.9.1"])
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s.add_dependency(%q<
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s.add_dependency(%q<hoe>, [">= 1.8.0"])
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s.add_dependency(%q<hoe>, [">= 2.3.2"])
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end
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else
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s.add_dependency(%q<narray>, [">= 0.5.9.5"])
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s.add_dependency(%q<bio>, [">= 1.2.1"])
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s.add_dependency(%q<facets>, [">= 2.4.5"])
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s.add_dependency(%q<rmagick>, [">= 2.9.1"])
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s.add_dependency(%q<
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s.add_dependency(%q<hoe>, [">= 1.8.0"])
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s.add_dependency(%q<hoe>, [">= 2.3.2"])
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end
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end
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data/website/index.html
CHANGED
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<head>
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<meta http-equiv="Refresh" content="5; URL=http://github.com/semin/ulla">
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<title>
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-
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Ulla: a program for calculating environment-specific substitution tables
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</title>
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</head>
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<body>
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metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: semin-ulla
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version: !ruby/object:Gem::Version
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version: 0.9.
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version: 0.9.8
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platform: ruby
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authors:
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- Semin Lee
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@@ -9,7 +9,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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date: 2009-
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date: 2009-07-21 00:00:00 -07:00
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default_executable: ulla
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dependencies:
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- !ruby/object:Gem::Dependency
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- !ruby/object:Gem::Version
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version: 2.9.1
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version:
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- !ruby/object:Gem::Dependency
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name: newgem
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type: :development
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version_requirement:
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: 1.4.1
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version:
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- !ruby/object:Gem::Dependency
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name: hoe
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type: :development
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version:
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version: 2.3.2
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version:
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description: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
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email:
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@@ -83,7 +73,6 @@ extra_rdoc_files:
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- History.txt
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- Manifest.txt
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- PostInstall.txt
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- README.rdoc
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- website/index.txt
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files:
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- History.txt
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@@ -152,12 +141,12 @@ signing_key:
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specification_version: 3
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summary: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
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test_files:
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- test/test_helper.rb
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- test/test_math_extensions.rb
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- test/test_narray_extensions.rb
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- test/test_nmatrix_extensions.rb
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- test/test_string_extensions.rb
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- test/test_ulla.rb
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- test/ulla/test_cli.rb
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- test/ulla/test_environment_class_hash.rb
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- test/ulla/test_environment_feature.rb
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- test/test_helper.rb
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- test/test_ulla.rb
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