egor 0.0.4 → 0.0.5

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 = '0.0.4'
+  VERSION = '0.0.5'
 end

data/lib/environment.rb

@@ -10,7 +10,7 @@ class Environment
                 :label,
                 :freq_array,
                 :prob_array,
-                :logodd_array,
+                :logo_array,
                 :smooth_prob_array
 
   def initialize(number, label, amino_acids = "ACDEFGHIKLMNPQRSTVWYJ".split(''))
@@ -19,7 +19,7 @@ class Environment
     @label              = label
     @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)
+    @logo_array         = NArray.float(@amino_acids.size)
     @smooth_prob_array  = NArray.float(@amino_acids.size)
   end
 

data/lib/environment_class_hash.rb

@@ -0,0 +1,18 @@
+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_array.rb

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

data/website/index.html

@@ -34,7 +34,7 @@
     <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">0.0.4</a>
+        <a href="http://rubyforge.org/projects/egor" class="numbers">0.0.5</a>
       </div>
     </div>
     <h2>What</h2>
@@ -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, 6th December 2008<br>
+      Semin Lee, 8th December 2008<br>
       Theme extended from <a href="http://rb2js.rubyforge.org/">Paul Battley</a>
     </p>
 </div>

metadata

@@ -1,36 +1,15 @@
 --- !ruby/object:Gem::Specification 
 name: egor
 version: !ruby/object:Gem::Version 
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors: 
 - Semin Lee
 autorequire: 
 bindir: bin
-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-----
+cert_chain: []
 
-date: 2008-12-15 00:00:00 +00:00
+date: 2009-01-23 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -81,7 +60,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.2.1
+        version: 1.2.3
     version: 
 - !ruby/object:Gem::Dependency 
   name: hoe
@@ -120,7 +99,9 @@ files:
 - 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/math_extensions.rb
 - lib/narray_extensions.rb
 - lib/nmatrix_extensions.rb