semin-egor 0.9.0

data/History.txt

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+== 0.9.0 version
+
+* 5 major enhancement:
+    * --heatmap option has been added to generate heat maps from substitution tables
+    * --heatmap-format option has been added for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
+    * --heatmap-stem option has been added to set a file name for total heat maps figure when --heatmap 1 or 2 is set
+    * --heatmap-columns option has been added to set the number of tables in a row when --heatmap 1 or 2 is set
+    * --heatmap-value option has been added to print values in the cells of heat maps
+
+* 2 minor enhancement:
+    * --noround option has been renamed to --noroundoff
+    * 'simple_memoize' RubyGem package is no longer required
+
+== 0.0.5 2009-1-23
+
+* 4 major enhancement:
+    * Egor warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
+    * --augosigma option was added to avoid excessive influence of background frequencies
+    * a bug in p2 probability calculation of the partial smoothing procedure was fixed
+    * a bug in total probability/log odds ratio calculation was fixed
+
+* 4 minor enhancement:
+    * --noround option was added to get original log odds ratios
+    * --p1smooth option was added to enable p1 probability smoothing when partial smoothing
+    * default verbosity has been changed from ERROR to WARN
+    * codes were refactored to be more human readable and DRY
+
+== 0.0.4 2008-12-15
+
+* 2 major enhancement:
+    * log-odds ratio matrices can be generated with --nosmooth option
+    * safe handling for zero observations or mutations of amino acids
+
+== 0.0.3 2008-12-09
+
+* 2 major enhancement:
+    * An option '--cys (-j) 2' added not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
+    * Masking works for target amino acid, too
+
+== 0.0.2 2008-11-13
+
+* 2 major enhancement:
+    * Constrained environment features are properly handled
+    * Sane log-odds ratio matrices are produced
+
+== 0.0.1 2008-11-07
+
+* 1 major enhancement:
+    * Initial release

data/Manifest.txt

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+History.txt
+Manifest.txt
+PostInstall.txt
+Rakefile
+bin/egor
+config/website.yml
+config/website.yml.sample
+egor.gemspec
+lib/egor.rb
+lib/egor/cli.rb
+lib/egor/environment.rb
+lib/egor/environment_class_hash.rb
+lib/egor/environment_feature.rb
+lib/egor/environment_feature_array.rb
+lib/egor/heatmap_array.rb
+lib/math_extensions.rb
+lib/narray_extensions.rb
+lib/nmatrix_extensions.rb
+lib/string_extensions.rb
+script/console
+script/destroy
+script/generate
+script/txt2html
+test/test_egor.rb
+test/test_egor_cli.rb
+test/test_egor_environment_class_hash.rb
+test/test_egor_environment_feature.rb
+test/test_helper.rb
+test/test_math_extensions.rb
+test/test_narray_extensions.rb
+test/test_nmatrix_extensions.rb
+test/test_string_extensions.rb
+website/index.html
+website/index.txt
+website/javascripts/rounded_corners_lite.inc.js
+website/stylesheets/screen.css
+website/template.html.erb

data/PostInstall.txt

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+HELP/OPTIONS: egor -h
+
+For more information on egor, see http://egor.rubyforge.org
+
+

data/Rakefile

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+%w[rubygems rake rake/clean fileutils newgem rubigen].each { |f| require f }
+require File.dirname(__FILE__) + '/lib/egor'
+
+# Generate all the Rake tasks
+# Run 'rake -T' to see list of generated tasks (from gem root directory)
+$hoe = Hoe.new('egor', Egor::VERSION) do |p|
+  p.developer('Semin Lee', 'seminlee@gmail.com')
+  p.changes               = p.paragraphs_of("History.txt", 0..1).join("\n\n")
+  p.post_install_message  = 'PostInstall.txt' # TODO remove if post-install message not required
+  p.rubyforge_name        = p.name # TODO this is default value
+  p.extra_deps            = [
+    ['narray',  '>= 0.5.9.5'],
+    ['bio',     '>= 1.2.1'],
+    ['facets',  '>= 2.4.5'],
+    ['rmagick', '>= 2.9.1'],
+  ]
+
+  p.extra_dev_deps = [
+    ['newgem', ">= #{::Newgem::VERSION}"]
+  ]
+
+  p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
+  path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
+  p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
+  p.rsync_args = '-av --delete --ignore-errors'
+end
+
+require 'newgem/tasks' # load /tasks/*.rake
+Dir['tasks/**/*.rake'].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# task :default => [:spec, :features]

data/bin/egor

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+#!/usr/bin/env ruby
+#
+#  Created on 2008-11-7.
+#  Copyright (c) 2008. All rights reserved.
+
+require File.expand_path(File.dirname(__FILE__) + "/../lib/egor")
+
+require "egor/cli"
+
+Egor::CLI.execute(ARGV)

data/config/website.yml

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+host: semin@rubyforge.org
+remote_dir: /var/www/gforge-projects/egor

data/config/website.yml.sample

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+host: unknown@rubyforge.org
+remote_dir: /var/www/gforge-projects/egor

data/egor.gemspec

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+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{egor}
+  s.version = "0.9.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Semin Lee"]
+  s.date = %q{2009-02-12}
+  s.default_executable = %q{egor}
+  s.email = ["seminlee@gmail.com"]
+  s.executables = ["egor"]
+  s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "website/index.txt"]
+  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "Rakefile", "bin/egor", "config/website.yml", "config/website.yml.sample", "egor.gemspec", "lib/egor.rb", "lib/egor/cli.rb", "lib/egor/environment.rb", "lib/egor/environment_class_hash.rb", "lib/egor/environment_feature.rb", "lib/egor/environment_feature_array.rb", "lib/egor/heatmap_array.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_egor.rb", "test/test_egor_cli.rb", "test/test_egor_environment_class_hash.rb", "test/test_egor_environment_feature.rb", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
+  s.has_rdoc = true
+  s.post_install_message = %q{PostInstall.txt}
+  s.rdoc_options = ["--main", "README.markdown"]
+  s.require_paths = ["lib"]
+  s.rubyforge_project = %q{egor}
+  s.rubygems_version = %q{1.3.1}
+  s.summary = "A new ESST generator"
+  s.test_files = ["test/test_string_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_egor_cli.rb", "test/test_egor_environment_class_hash.rb", "test/test_math_extensions.rb", "test/test_helper.rb", "test/test_egor_environment_feature.rb", "test/test_narray_extensions.rb", "test/test_egor.rb"]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 2
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_development_dependency(%q<newgem>, [">= 1.2.3"])
+      s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
+    else
+      s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+      s.add_dependency(%q<bio>, [">= 1.2.1"])
+      s.add_dependency(%q<facets>, [">= 2.4.5"])
+      s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_dependency(%q<newgem>, [">= 1.2.3"])
+      s.add_dependency(%q<hoe>, [">= 1.8.0"])
+    end
+  else
+    s.add_dependency(%q<narray>, [">= 0.5.9.5"])
+    s.add_dependency(%q<bio>, [">= 1.2.1"])
+    s.add_dependency(%q<facets>, [">= 2.4.5"])
+    s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+    s.add_dependency(%q<newgem>, [">= 1.2.3"])
+    s.add_dependency(%q<hoe>, [">= 1.8.0"])
+  end
+end