egor 0.0.1

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data/History.txt ADDED
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+ == 0.0.1 2008-11-07
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+
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+ * 1 major enhancement:
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+ * Initial release
data/Manifest.txt ADDED
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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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+ Rakefile
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+ bin/egor
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+ config/website.yml
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+ config/website.yml.sample
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+ egor.gemspec
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+ lib/egor.rb
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+ lib/egor/cli.rb
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+ lib/enumerable_extensions.rb
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+ lib/environment.rb
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+ lib/environment_feature.rb
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+ lib/math_extensions.rb
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+ lib/narray_extensions.rb
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+ lib/nmatrix_extensions.rb
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+ script/console
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+ script/destroy
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+ script/generate
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+ script/txt2html
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+ test/test_egor.rb
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+ test/test_egor_cli.rb
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+ test/test_enumerable_extensions.rb
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+ test/test_environment_feature.rb
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+ test/test_helper.rb
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+ test/test_nmatrix_extensions.rb
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+ website/index.html
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+ website/index.txt
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+ website/javascripts/rounded_corners_lite.inc.js
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+ website/stylesheets/screen.css
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+ website/template.html.erb
data/PostInstall.txt ADDED
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+ HELP/OPTIONS: egor -h
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+
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+ For more information on egor, see http://egor.rubyforge.org
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+
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+
data/README.rdoc ADDED
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+ = egor
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+
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+ * http://egor.rubyforge.org
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+
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+ == DESCRIPTION:
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+
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+ egor: Esst GeneratOR, a program for calculating environment-specific substitution tables
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+
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+ == FEATURES/PROBLEMS:
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+
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+ * No more segmentation fault
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+ * Full smoothing supported
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+ * Infinite number of environment features can be handled (in theory)
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+
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+ == BASIC USAGE:
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+
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+ $ egor -l TEMLIST-file -c classdef.dat
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+ or
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+ $ egor -f TEM-file -c classdef.dat
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+
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+ == OPTIONS:
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+ --tem-file (-f) STRING: a tem file
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+ --tem-list (-l) STRING: a list for tem files
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+ --classdef (-c) STRING: a file for the defintion of environments (default: 'classdef.dat')
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+ --outfile (-o) STRING: output filename ("allmat.dat" if not specified)
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+ --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (not supported yet)
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+ --noweight: calculate substitution counts with no weights (default)
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+ --smooth (-s) INTEGER:
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+ 0 for parial smoothing (default)
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+ 1 for full smoothing
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+ --nosmooth: perform no smoothing operation
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+ --cys (-y) INTEGER: (!!!not implemented yet!!!)
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+ 0 for using C and J only for structure
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+ 1 for both structure and sequence (default)
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+ --output INTEGER:
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+ 0 for raw counts (no-smoothing performed)
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+ 1 for probabilities
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+ 2 for log-odds (default)
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+ --scale INTEGER: log-odds matrices in 1/n bit units (default 3)
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+ --sigma DOUBLE: change the sigma value for smoothing (default 5)
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+ --add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 1/#classes)
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+ --penv: use environment-dependent frequencies for log-odds calculation (default false) (!!!not implemented yet!!!)
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+ --pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
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+ --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
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+ --verbose (-v) INTEGER
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+ 0 for ERROR level (default)
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+ 1 for WARN or above level
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+ 2 for INFO or above level
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+ 3 for DEBUG or above level
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+ --version: print version
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+ --help (-h): show help
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+
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+ == REQUIREMENTS:
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+
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+ * ruby 1.8.6 or above (http://www.ruby-lang.org)
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+ * rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
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+ * narray (http://narray.rubyforge.org/)
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+ * facets (http://facets.rubyforge.org/)
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+ * bio (http://bioruby.open-bio.org/)
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+
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+ == INSTALL:
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+
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+ $ sudo gem install egor
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+
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+ == LICENSE:
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+
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+ (The MIT License)
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+
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+ Copyright (c) 2008 Semin Lee
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ 'Software'), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
data/Rakefile ADDED
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+ %w[rubygems rake rake/clean fileutils newgem rubigen].each { |f| require f }
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+ require File.dirname(__FILE__) + '/lib/egor'
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+
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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.new('egor', Egor::VERSION) do |p|
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+ p.developer('Semin Lee', 'seminlee@gmail.com')
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+ p.changes = p.paragraphs_of("History.txt", 0..1).join("\n\n")
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+ p.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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+ p.rubyforge_name = p.name # TODO this is default value
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+ p.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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+ ['simple_memoize', '>= 1.0.0'],
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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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+
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+ p.clean_globs |= %w[**/.DS_Store tmp *.log]
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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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+
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+ require 'newgem/tasks' # load /tasks/*.rake
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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]
data/bin/egor ADDED
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+ #!/usr/bin/env ruby
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+ #
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+ # Created on 2008-11-7.
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+ # Copyright (c) 2008. All rights reserved.
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+
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+ require File.expand_path(File.dirname(__FILE__) + "/../lib/egor")
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+
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+ require "egor/cli"
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+
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+ Egor::CLI.execute(ARGV)
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+ host: semin@rubyforge.org
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+ remote_dir: /var/www/gforge-projects/egor
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+ host: unknown@rubyforge.org
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+ remote_dir: /var/www/gforge-projects/egor
data/egor.gemspec ADDED
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+ # -*- encoding: utf-8 -*-
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+
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+ Gem::Specification.new do |s|
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+ s.name = %q{egor}
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+ s.version = "0.0.1"
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+
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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{2008-11-10}
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+ s.default_executable = %q{egor}
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+ s.description = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
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+ s.email = ["seminlee@gmail.com"]
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+ s.executables = ["egor"]
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+ s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
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+ s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/egor", "config/website.yml", "config/website.yml.sample", "egor.gemspec", "lib/egor.rb", "lib/egor/cli.rb", "lib/enumerable_extensions.rb", "lib/environment.rb", "lib/environment_feature.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_egor.rb", "test/test_egor_cli.rb", "test/test_enumerable_extensions.rb", "test/test_environment_feature.rb", "test/test_helper.rb", "test/test_nmatrix_extensions.rb", "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.has_rdoc = true
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+ s.homepage = %q{http://egor.rubyforge.org}
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+ s.post_install_message = %q{PostInstall.txt}
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+ s.rdoc_options = ["--main", "README.rdoc"]
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+ s.require_paths = ["lib"]
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+ s.rubyforge_project = %q{egor}
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+ s.rubygems_version = %q{1.3.1}
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+ s.summary = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
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+ s.test_files = ["test/test_helper.rb", "test/test_egor.rb", "test/test_enumerable_extensions.rb", "test/test_environment_feature.rb", "test/test_nmatrix_extensions.rb", "test/test_egor_cli.rb"]
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+
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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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+ s.specification_version = 2
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+
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+ if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
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+ s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
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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<simple_memoize>, [">= 1.0.0"])
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+ s.add_development_dependency(%q<newgem>, [">= 1.0.7"])
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+ s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
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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<simple_memoize>, [">= 1.0.0"])
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+ s.add_dependency(%q<newgem>, [">= 1.0.7"])
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+ s.add_dependency(%q<hoe>, [">= 1.8.0"])
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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<simple_memoize>, [">= 1.0.0"])
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+ s.add_dependency(%q<newgem>, [">= 1.0.7"])
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+ s.add_dependency(%q<hoe>, [">= 1.8.0"])
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+ end
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+ end