egor 0.0.5 → 0.9.0

data/website/stylesheets/screen.css

@@ -83,7 +83,6 @@ pre, code {
   line-height: 1.4em;
   color: #ff8;
   background-color: #111;
-  width: 40em;
   padding: 2px 10px 2px 10px;
 }
 .comment { color: #aaa; font-style: italic; }

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: egor
 version: !ruby/object:Gem::Version 
-  version: 0.0.5
+  version: 0.9.0
 platform: ruby
 authors: 
 - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-01-23 00:00:00 +00:00
+date: 2009-02-13 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -43,14 +43,14 @@ dependencies:
         version: 2.4.5
     version: 
 - !ruby/object:Gem::Dependency 
-  name: simple_memoize
+  name: rmagick
   type: :runtime
   version_requirement: 
   version_requirements: !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.0.0
+        version: 2.9.1
     version: 
 - !ruby/object:Gem::Dependency 
   name: newgem
@@ -72,7 +72,7 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: 1.8.0
     version: 
-description: "egor: Esst GeneratOR, a program for calculating environment-specific substitution tables"
+description: "'egor' 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."
 email: 
 - seminlee@gmail.com
 executables: 
@@ -97,31 +97,35 @@ files:
 - egor.gemspec
 - lib/egor.rb
 - lib/egor/cli.rb
-- lib/enumerable_extensions.rb
-- lib/environment.rb
-- lib/environment_class_hash.rb
-- lib/environment_feature.rb
-- lib/environment_feature_array.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/egor/test_cli.rb
+- test/egor/test_environment_class_hash.rb
+- test/egor/test_environment_feature.rb
 - 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_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
 has_rdoc: true
-homepage: http://egor.rubyforge.org
+homepage: http://www-cryst.bioc.cam.ac.uk/egor
 post_install_message: PostInstall.txt
 rdoc_options: 
 - --main
@@ -146,11 +150,14 @@ rubyforge_project: egor
 rubygems_version: 1.3.1
 signing_key: 
 specification_version: 2
-summary: "egor: Esst GeneratOR, a program for calculating environment-specific substitution tables"
+summary: "'egor' 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."
 test_files: 
-- 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_string_extensions.rb
 - test/test_nmatrix_extensions.rb
+- test/test_math_extensions.rb
+- test/test_helper.rb
+- test/test_narray_extensions.rb
+- test/egor/test_environment_feature.rb
+- test/egor/test_cli.rb
+- test/egor/test_environment_class_hash.rb
+- test/test_egor.rb

data/lib/enumerable_extensions.rb

@@ -1,11 +0,0 @@
-module EnumerableExtensions
-  def cart_prod( *args )
-    args.inject([[]]){|old,lst|
-      new = []
-      lst.each{|e| new += old.map{|c| c.dup << e }}
-      new
-    }
-  end
-end
-
-Enumerable.extend(EnumerableExtensions)

data/lib/environment.rb

@@ -1,58 +0,0 @@
-require "rubygems"
-require "set"
-require "narray"
-require "facets"
-
-class Environment
-
-  attr_accessor :amino_acids,
-                :number,
-                :label,
-                :freq_array,
-                :prob_array,
-                :logo_array,
-                :smooth_prob_array
-
-  def initialize(number, label, amino_acids = "ACDEFGHIKLMNPQRSTVWYJ".split(''))
-    @amino_acids        = amino_acids
-    @number             = number
-    @label              = label
-    @freq_array         = $noweight ? NArray.int(@amino_acids.size) : NArray.float(@amino_acids.size)
-    @prob_array         = NArray.float(@amino_acids.size)
-    @logo_array         = NArray.float(@amino_acids.size)
-    @smooth_prob_array  = NArray.float(@amino_acids.size)
-  end
-
-  def increase_residue_count(a, inc = 1.0)
-    @freq_array[@amino_acids.index(a.upcase)] += inc
-  end
-
-  def label_set
-    label.split("").map_with_index { |l, i| "#{i}#{l}" }.to_set
-  end
-
-  def to_s
-    "#{number}-#{label}"
-  end
-end
-
-if $0 == __FILE__
-
-  require "test/unit"
-
-  class TestEnvironment < Test::Unit::TestCase
-
-    def setup
-      @env = Environment.new(1, "AHaSon")
-    end
-
-    def test_label_set
-      assert_equal(%w[0A 1H 2a 3S 4o 5n].to_set, @env.label_set)
-    end
-
-    def test_to_s
-      assert_equal("1-AHaSon", @env.to_s)
-    end
-
-  end
-end

data/lib/environment_class_hash.rb

@@ -1,18 +0,0 @@
-class EnvironmentClassHash < Hash
-
-  def group_by_non_residue_labels
-    self.values.group_by { |env| env.label[1..-1] }
-  end
-
-  def groups_sorted_by_residue_labels
-    group_by_non_residue_labels.to_a.sort_by { |env_group|
-      env_group[0].split('').map_with_index { |l, i|
-        $env_features[i + 1].labels.index(l)
-      }
-    }
-  end
-
-  def group_size
-    group_by_non_residue_labels.size
-  end
-end

data/lib/environment_feature.rb

@@ -1,14 +0,0 @@
-class EnvironmentFeature < Struct.new(:name, :symbols, :labels, :constrained, :silent)
-
-  def to_s
-    [name, symbols.join, labels.join, constrained, silent].join(";")
-  end
-
-  def constrained?
-    constrained == "T"
-  end
-
-  def silent?
-    silent == "T"
-  end
-end

data/lib/environment_feature_array.rb

@@ -1,10 +0,0 @@
-class EnvironmentFeatureArray < Array
-
-  def label_combinations
-    self.inject([]) { |sum, ec|
-      sum << ec.labels
-    }.inject { |pro, lb|
-      pro.product(lb)
-    }
-  end
-end

data/test/test_egor_cli.rb

@@ -1,8 +0,0 @@
-require File.join(File.dirname(__FILE__), "test_helper.rb")
-require 'egor/cli'
-
-class TestEgorCli < Test::Unit::TestCase
-  def test_execute
-    Egor::CLI.execute
-  end
-end

data/test/test_enumerable_extensions.rb

@@ -1,16 +0,0 @@
-$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
-
-require "test/unit"
-require "enumerable_extensions"
-
-class TestEnumerableExtensions < Test::Unit::TestCase
-
-  def test_cart_product
-    a = [1,2]
-    b = [3,4]
-    products = [[1,3], [1,4], [2,3], [2,4]]
-    results = Enumerable.cart_prod(a,b)
-    assert_equal(4, results.size)
-    products.each { |p| assert(results.include? p) }
-  end
-end

data/test/test_environment_feature.rb

@@ -1,11 +0,0 @@
-$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
-
-require "test/unit"
-require "environment_feature"
-
-class TestEnvironmentFeature < Test::Unit::TestCase
-
-  def test_true
-    assert(true)
-  end
-end