egor 0.0.1

data/lib/egor.rb

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+$:.unshift(File.dirname(__FILE__)) unless
+  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+
+module Egor
+  VERSION = '0.0.1'
+end

data/lib/enumerable_extensions.rb

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+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

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+require "rubygems"
+require "set"
+require "narray"
+require "facets"
+
+class Environment
+
+  @@amino_acids  = "ACDEFGHIKLMNPQRSTVWYJ".split("")
+
+  attr_accessor :number,
+                :label,
+                :freq_array,
+                :prob_array,
+                :logodd_array,
+                :smooth_prob_array
+
+  def initialize(number, label)
+    @number             = number
+    @label              = label
+    @freq_array         = $noweight ? NArray.int(21) : NArray.float(21)
+    @prob_array         = NArray.float(21)
+    @logodd_array       = NArray.float(21)
+    @smooth_prob_array  = NArray.float(21)
+  end
+
+  def add_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_feature.rb

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+class EnvironmentFeature < Struct.new(:name, :symbols, :labels, :constrained, :silent)
+
+  def to_s
+    values.join(";")
+  end
+
+  def constrained?
+    constrained == "T"
+  end
+
+  def silent?
+    silent == "T"
+  end
+end

data/lib/math_extensions.rb

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+module MathExtensions
+  def log2(val)
+    log(val) / log(2)
+  end
+end
+
+Math.extend(MathExtensions)

data/lib/narray_extensions.rb

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+require "rubygems"
+require "facets"
+
+module NArrayExtensions
+
+  def pretty_string(opts={})
+    { :col_header   => nil,
+      :row_header   => nil }.merge!(opts)
+
+    ("%-3s" % "#") + opts[:col_header].inject("") { |s, a| s + ("%7s" % a) } + "\n" +
+      self.to_a.inject("%-3s" % opts[:row_header]) { |s, v|
+      if v.is_a? Float
+        s + ("%7.2f" % v)
+      else
+        s + ("%7d" % v)
+      end
+    }
+  end
+end
+
+NArray.send(:include, NArrayExtensions)

data/lib/nmatrix_extensions.rb

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+require "rubygems"
+require "facets"
+require "narray"
+
+module NMatrixExtensions
+  def pretty_string(opts={})
+    { :col_header   => nil,
+      :row_header   => nil }.merge!(opts)
+
+    ("%-3s" % "#") + opts[:col_header].inject("") { |s, a|
+      s + ("%7s" % a)
+    } + "\n" + self.to_a.map_with_index { |a, i|
+      ("%-3s" % opts[:row_header][i]) + a.inject("") { |s, v|
+        if v.is_a? Float
+          s + ("%7.2f" % v)
+        else
+          s + ("%7d" % v)
+        end
+      }
+    }.join("\n")
+  end
+end
+
+NMatrix.send(:include, NMatrixExtensions)

data/script/console

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+#!/usr/bin/env ruby
+# File: script/console
+irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
+
+libs =  " -r irb/completion"
+# Perhaps use a console_lib to store any extra methods I may want available in the cosole
+# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/egor.rb'}"
+puts "Loading egor gem"
+exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

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+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/destroy'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

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+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/generate'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Generate.new.run(ARGV)

data/script/txt2html

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+#!/usr/bin/env ruby
+
+load File.dirname(__FILE__) + "/../Rakefile"
+require 'rubyforge'
+require 'redcloth'
+require 'syntax/convertors/html'
+require 'erb'
+
+download = "http://rubyforge.org/projects/#{$hoe.rubyforge_name}"
+version  = $hoe.version
+
+def rubyforge_project_id
+  RubyForge.new.configure.autoconfig["group_ids"][$hoe.rubyforge_name]
+end
+
+class Fixnum
+  def ordinal
+    # teens
+    return 'th' if (10..19).include?(self % 100)
+    # others
+    case self % 10
+    when 1: return 'st'
+    when 2: return 'nd'
+    when 3: return 'rd'
+    else    return 'th'
+    end
+  end
+end
+
+class Time
+  def pretty
+    return "#{mday}#{mday.ordinal} #{strftime('%B')} #{year}"
+  end
+end
+
+def convert_syntax(syntax, source)
+  return Syntax::Convertors::HTML.for_syntax(syntax).convert(source).gsub(%r!^<pre>|</pre>$!,'')
+end
+
+if ARGV.length >= 1
+  src, template = ARGV
+  template ||= File.join(File.dirname(__FILE__), '/../website/template.html.erb')
+else
+  puts("Usage: #{File.split($0).last} source.txt [template.html.erb] > output.html")
+  exit!
+end
+
+template = ERB.new(File.open(template).read)
+
+title = nil
+body = nil
+File.open(src) do |fsrc|
+  title_text = fsrc.readline
+  body_text_template = fsrc.read
+  body_text = ERB.new(body_text_template).result(binding)
+  syntax_items = []
+  body_text.gsub!(%r!<(pre|code)[^>]*?syntax=['"]([^'"]+)[^>]*>(.*?)</\1>!m){
+    ident = syntax_items.length
+    element, syntax, source = $1, $2, $3
+    syntax_items << "<#{element} class='syntax'>#{convert_syntax(syntax, source)}</#{element}>"
+    "syntax-temp-#{ident}"
+  }
+  title = RedCloth.new(title_text).to_html.gsub(%r!<.*?>!,'').strip
+  body = RedCloth.new(body_text).to_html
+  body.gsub!(%r!(?:<pre><code>)?syntax-temp-(\d+)(?:</code></pre>)?!){ syntax_items[$1.to_i] }
+end
+stat = File.stat(src)
+created = stat.ctime
+modified = stat.mtime
+
+$stdout << template.result(binding)

data/test/test_egor.rb

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+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class TestEgor < Test::Unit::TestCase
+
+  def setup
+  end
+  
+  def test_truth
+    assert true
+  end
+end

data/test/test_egor_cli.rb

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+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

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+$:.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

@@ -0,0 +1,11 @@
+$:.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

data/test/test_helper.rb

@@ -0,0 +1,2 @@
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/egor'

data/test/test_nmatrix_extensions.rb

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+$:.unshift File.join(File.dirname(__FILE__), "..", "lib")
+
+require "test/unit"
+require "nmatrix_extensions"
+
+class TestNmatrixExtensions < Test::Unit::TestCase
+
+  def test_pretty_string(opts={})
+    m = NMatrix.float(3,3).indgen
+    result ="#        A      B      C\n" +
+            "VAL   0.00   1.00   2.00\n" +
+            "      3.00   4.00   5.00\n" +
+            "      6.00   7.00   8.00"
+    assert_equal(result, m.pretty_string(:col_header => %w[A B C], :row_header => %w[VAL]))
+  end
+end

data/website/index.html

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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+  <link rel="stylesheet" href="stylesheets/screen.css" type="text/css" media="screen" />
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+  <title>
+      egor: Environment-specific substitution table GeneratOR
+  </title>
+  <script src="javascripts/rounded_corners_lite.inc.js" type="text/javascript"></script>
+<style>
+
+</style>
+  <script type="text/javascript">
+    window.onload = function() {
+      settings = {
+          tl: { radius: 10 },
+          tr: { radius: 10 },
+          bl: { radius: 10 },
+          br: { radius: 10 },
+          antiAlias: true,
+          autoPad: true,
+          validTags: ["div"]
+      }
+      var versionBox = new curvyCorners(settings, document.getElementById("version"));
+      versionBox.applyCornersToAll();
+    }
+  </script>
+</head>
+<body>
+<div id="main">
+
+    <h1>egor: Environment-specific substitution table GeneratOR</h1>
+    <div class="sidebar">
+      <div id="version" class="clickable" onclick='document.location = "http://rubyforge.org/projects/egor"; return false'>
+        <p>Get Version</p>
+        <a href="http://rubyforge.org/projects/egor" class="numbers">0.0.1</a>
+      </div>
+    </div>
+    <h2>What</h2>
+<p>&#8216;egor&#8217; is a program for calculating environment-specific substitution tables</p>
+<h2>Installation</h2>
+<p><pre class='syntax'><span class="global">$ </span><span class="ident">sudo</span> <span class="ident">gem</span> <span class="ident">install</span> <span class="ident">egor</span></pre></p>
+<h2>Features</h2>
+<ul>
+	<li>No more segmentation fault</li>
+	<li>Full smoothing supported</li>
+	<li>In theory, infinite number of environment features can be handled</li>
+</ul>
+<h2>Demonstration of usage</h2>
+<p>It&#8217;s pretty much the same as Kenji&#8217;s subst, so in most cases, you just need swap &#8216;subst&#8217; with &#8216;egor&#8217;.</p>
+<pre>$ egor -l TEMLIST-file -c classdef.dat</pre>
+or
+<pre>$ egor -l TEM-file -c classdef.dat</pre>
+<h2>Repository</h2>
+<p>You can download a pre-built RubyGem package from</p>
+<ul>
+	<li>rubyforge: <a href="http://rubyforge.org/projects/egor">http://rubyforge.org/projects/egor</a></li>
+</ul>
+<p>or, You can fetch the source from</p>
+<ul>
+	<li>github: <a href="http://github.com/semin/egor/tree/master">http://github.com/semin/egor/tree/master</a></li>
+</ul>
+<pre>$ git clone git://github.com/semin/egor.git</pre>
+<h2>License</h2>
+<p>This code is free to use under the terms of the <span class="caps">MIT</span> license.</p>
+<h2>Contact</h2>
+<p>Comments are welcome, please send an email to me (seminlee at gmail dot com).</p>
+    <p class="coda">
+      <a href="FIXME email">Semin Lee</a>, 10th November 2008<br>
+      Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
+    </p>
+</div>
+
+<!-- insert site tracking codes here, like Google Urchin -->
+
+</body>
+</html>

data/website/index.txt

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+h1. egor: Environment-specific substitution table GeneratOR
+
+
+h2. What
+
+'egor' is a program for calculating environment-specific substitution tables
+
+
+h2. Installation
+
+<pre syntax="ruby">$ sudo gem install egor</pre>
+
+
+h2. Features
+
+* No more segmentation fault
+* Full smoothing supported
+* In theory, infinite number of environment features can be handled
+
+
+h2. Demonstration of usage
+
+It's pretty much the same as Kenji's subst, so in most cases, you just need swap 'subst' with 'egor'.
+
+<pre>$ egor -l TEMLIST-file -c classdef.dat</pre>
+    or
+<pre>$ egor -l TEM-file -c classdef.dat</pre>
+
+
+h2. Repository
+
+You can download a pre-built RubyGem package from
+
+* rubyforge: "http://rubyforge.org/projects/egor":http://rubyforge.org/projects/egor
+
+or, You can fetch the source from
+
+* github: "http://github.com/semin/egor/tree/master":http://github.com/semin/egor/tree/master
+
+<pre>$ git clone git://github.com/semin/egor.git</pre>
+
+h2. License
+
+This code is free to use under the terms of the MIT license. 
+
+h2. Contact
+
+Comments are welcome, please send an email to me (seminlee at gmail dot com).