egor 0.0.2 → 0.0.3

data/lib/egor.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Egor
-  VERSION = '0.0.2'
+  VERSION = '0.0.3'
 end

data/lib/environment.rb

@@ -5,26 +5,26 @@ require "facets"
 
 class Environment
 
-  @@amino_acids  = "ACDEFGHIKLMNPQRSTVWYJ".split("")
-
-  attr_accessor :number,
+  attr_accessor :amino_acids,
+                :number,
                 :label,
                 :freq_array,
                 :prob_array,
                 :logodd_array,
                 :smooth_prob_array
 
-  def initialize(number, label)
+  def initialize(number, label, amino_acids = "ACDEFGHIKLMNPQRSTVWYJ".split(''))
+    @amino_acids        = amino_acids
     @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)
+    @freq_array         = $noweight ? NArray.int(@amino_acids.size) : NArray.float(@amino_acids.size)
+    @prob_array         = NArray.float(@amino_acids.size)
+    @logodd_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
+    @freq_array[@amino_acids.index(a.upcase)] += inc
   end
 
   def label_set

data/website/index.html

@@ -34,13 +34,11 @@
     <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>
+        <a href="http://rubyforge.org/projects/egor" class="numbers">0.0.3</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>
@@ -49,8 +47,10 @@
 	<li>Full smoothing supported</li>
 	<li>In theory, infinite number of environment features can be handled</li>
 </ul>
+<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>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>
+<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>
 <pre>$ egor -l TEMLIST-file -c classdef.dat</pre>
 or
 <pre>$ egor -l TEM-file -c classdef.dat</pre>
@@ -69,7 +69,7 @@ or
 <h2>Contact</h2>
 <p>Comments are welcome, please send an email to me (seminlee at gmail dot com).</p>
     <p class="coda">
-      Semin Lee, 12th November 2008<br>
+      Semin Lee, 6th December 2008<br>
       Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
     </p>
 </div>

data/website/index.txt

@@ -6,11 +6,6 @@ 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
@@ -20,9 +15,14 @@ h2. Features
 * In theory, infinite number of environment features can be handled
 
 
+h2. Installation
+
+<pre syntax="ruby">$ sudo gem install egor</pre>
+
+
 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'.
+It's pretty much the same as Kenji's subst, so in most cases, you can swap 'subst' with 'egor'.
 
 <pre>$ egor -l TEMLIST-file -c classdef.dat</pre>
     or
@@ -41,10 +41,12 @@ or, You can fetch the source from
 
 <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). 

metadata

@@ -1,15 +1,36 @@
 --- !ruby/object:Gem::Specification 
 name: egor
 version: !ruby/object:Gem::Version 
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors: 
 - Semin Lee
 autorequire: 
 bindir: bin
-cert_chain: []
+cert_chain: 
+- |
+  -----BEGIN CERTIFICATE-----
+  MIIDMjCCAhqgAwIBAgIBADANBgkqhkiG9w0BAQUFADA/MREwDwYDVQQDDAhzZW1p
+  bmxlZTEVMBMGCgmSJomT8ixkARkWBWdtYWlsMRMwEQYKCZImiZPyLGQBGRYDY29t
+  MB4XDTA4MTEwMzEzMzU1NVoXDTA5MTEwMzEzMzU1NVowPzERMA8GA1UEAwwIc2Vt
+  aW5sZWUxFTATBgoJkiaJk/IsZAEZFgVnbWFpbDETMBEGCgmSJomT8ixkARkWA2Nv
+  bTCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBAM/tZks0aN685ZLCFKkZ
+  XXO3XjcJwojDdHMDb6ywOUJaqhiEG+BkDPZNn0UiD9UvNSoM7JF3SKI7SKxZkFid
+  6gdqKB5r758G7gvdITNgdnILa8EaOm85U7XIq10g6zz89w2qFKPSN4S5yqlqi5Kp
+  va4kpfx0Icc6S0rtc8Q+fwGNuSRX51rE7sPTQs6ON2gXvOILgPIGXoC9SJ8+f0Ho
+  kDQCYDsUzwer2XOCSzmMXPyhRPp58SquO/bY9NZI95WdrLYnslNLpHPn9YVfxXLR
+  R2f5J9bvDavVfPQDC2tGP99Ny/tHMwfxvRXPsp8hvDAdzYZOMnY8LOU7UGoGUXiF
+  348CAwEAAaM5MDcwCQYDVR0TBAIwADALBgNVHQ8EBAMCBLAwHQYDVR0OBBYEFICd
+  NBCbSXmZ9iuRN9h+44ZQMhMjMA0GCSqGSIb3DQEBBQUAA4IBAQAWitWf1IM3GdcN
+  viGNYbBXMs99bK+9/eLSXRDkXzx3mj7tb+sm4KBbT0Hfef9aqrw4dj5lZRM3YYdk
+  xf4imsU+3oXyOomUtZC4YK3Ml1llKxrKy5l0fKjWo8TDPXwTotrJEj6YyNJMgYAP
+  CwFRQzZDX3hnKGIlkCkYxw5DwvoEEvykJmKOQhg8FU8zohc3Mjn5ZZ4iDMh/2t8s
+  lf67mkGlorCFBiqRNa+TCnkJhzqK/Eom824LInCbvviCB+qN1ZW9IippKE9cPxjI
+  3IQH/Zpt1gX4LY6kRrFLj108jus+Cd/srgifylUm2EcHwv2tA1TnqXcm41b5RHyn
+  35w+y1Jd
+  -----END CERTIFICATE-----
 
-date: 2008-11-13 00:00:00 +00:00
+date: 2008-12-09 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -146,9 +167,9 @@ signing_key:
 specification_version: 2
 summary: "egor: Esst GeneratOR, a program for calculating environment-specific substitution tables"
 test_files: 
-- test/test_helper.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_nmatrix_extensions.rb
-- test/test_egor_cli.rb

metadata.gz.sig

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