egor 0.0.2 → 0.0.3

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/lib/egor.rb CHANGED
@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
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  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
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  module Egor
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- VERSION = '0.0.2'
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+ VERSION = '0.0.3'
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  end
data/lib/environment.rb CHANGED
@@ -5,26 +5,26 @@ require "facets"
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  class Environment
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- @@amino_acids = "ACDEFGHIKLMNPQRSTVWYJ".split("")
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-
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- attr_accessor :number,
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+ attr_accessor :amino_acids,
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+ :number,
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  :label,
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  :freq_array,
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  :prob_array,
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  :logodd_array,
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  :smooth_prob_array
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- def initialize(number, label)
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+ def initialize(number, label, amino_acids = "ACDEFGHIKLMNPQRSTVWYJ".split(''))
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+ @amino_acids = amino_acids
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  @number = number
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  @label = label
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- @freq_array = $noweight ? NArray.int(21) : NArray.float(21)
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- @prob_array = NArray.float(21)
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- @logodd_array = NArray.float(21)
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- @smooth_prob_array = NArray.float(21)
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+ @freq_array = $noweight ? NArray.int(@amino_acids.size) : NArray.float(@amino_acids.size)
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+ @prob_array = NArray.float(@amino_acids.size)
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+ @logodd_array = NArray.float(@amino_acids.size)
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+ @smooth_prob_array = NArray.float(@amino_acids.size)
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  end
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  def increase_residue_count(a, inc = 1.0)
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- @freq_array[@@amino_acids.index(a.upcase)] += inc
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+ @freq_array[@amino_acids.index(a.upcase)] += inc
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  end
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  def label_set
data/website/index.html CHANGED
@@ -34,13 +34,11 @@
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  <div class="sidebar">
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  <div id="version" class="clickable" onclick='document.location = "http://rubyforge.org/projects/egor"; return false'>
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  <p>Get Version</p>
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- <a href="http://rubyforge.org/projects/egor" class="numbers">0.0.1</a>
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+ <a href="http://rubyforge.org/projects/egor" class="numbers">0.0.3</a>
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  </div>
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  </div>
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  <h2>What</h2>
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  <p>&#8216;egor&#8217; is a program for calculating environment-specific substitution tables</p>
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- <h2>Installation</h2>
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- <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>
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  <h2>Features</h2>
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  <ul>
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  <li>No more segmentation fault</li>
@@ -49,8 +47,10 @@
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  <li>Full smoothing supported</li>
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  <li>In theory, infinite number of environment features can be handled</li>
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  </ul>
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+ <h2>Installation</h2>
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+ <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>
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  <h2>Demonstration of usage</h2>
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- <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>
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+ <p>It&#8217;s pretty much the same as Kenji&#8217;s subst, so in most cases, you can swap &#8216;subst&#8217; with &#8216;egor&#8217;.</p>
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  <pre>$ egor -l TEMLIST-file -c classdef.dat</pre>
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  or
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  <pre>$ egor -l TEM-file -c classdef.dat</pre>
@@ -69,7 +69,7 @@ or
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  <h2>Contact</h2>
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  <p>Comments are welcome, please send an email to me (seminlee at gmail dot com).</p>
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  <p class="coda">
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- Semin Lee, 12th November 2008<br>
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+ Semin Lee, 6th December 2008<br>
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  Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
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  </p>
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  </div>
data/website/index.txt CHANGED
@@ -6,11 +6,6 @@ h2. What
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  'egor' is a program for calculating environment-specific substitution tables
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- h2. Installation
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-
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- <pre syntax="ruby">$ sudo gem install egor</pre>
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-
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-
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  h2. Features
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  * No more segmentation fault
@@ -20,9 +15,14 @@ h2. Features
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  * In theory, infinite number of environment features can be handled
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+ h2. Installation
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+
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+ <pre syntax="ruby">$ sudo gem install egor</pre>
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+
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+
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  h2. Demonstration of usage
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- It's pretty much the same as Kenji's subst, so in most cases, you just need swap 'subst' with 'egor'.
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+ It's pretty much the same as Kenji's subst, so in most cases, you can swap 'subst' with 'egor'.
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  <pre>$ egor -l TEMLIST-file -c classdef.dat</pre>
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  or
@@ -41,10 +41,12 @@ or, You can fetch the source from
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  <pre>$ git clone git://github.com/semin/egor.git</pre>
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+
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  h2. License
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  This code is free to use under the terms of the MIT license.
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+
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  h2. Contact
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  Comments are welcome, please send an email to me (seminlee at gmail dot com).
data.tar.gz.sig ADDED
Binary file
metadata CHANGED
@@ -1,15 +1,36 @@
1
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  --- !ruby/object:Gem::Specification
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  name: egor
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  version: !ruby/object:Gem::Version
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- version: 0.0.2
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+ version: 0.0.3
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  platform: ruby
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  authors:
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  - Semin Lee
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  autorequire:
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  bindir: bin
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- cert_chain: []
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+ cert_chain:
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+ - |
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+ -----BEGIN CERTIFICATE-----
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+ 35w+y1Jd
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+ -----END CERTIFICATE-----
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- date: 2008-11-13 00:00:00 +00:00
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+ date: 2008-12-09 00:00:00 +00:00
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  default_executable:
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  dependencies:
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  - !ruby/object:Gem::Dependency
@@ -146,9 +167,9 @@ signing_key:
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  specification_version: 2
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  summary: "egor: Esst GeneratOR, a program for calculating environment-specific substitution tables"
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  test_files:
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- - test/test_helper.rb
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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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- - test/test_egor_cli.rb
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