17 files changed, 3 insertions, 1839 deletions
diff --git a/.gitignore b/.gitignore
index 00278f4..00c0b86 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
 *.sw?
 .DS_Store
 coverage
+rdoc
 pkg
diff --git a/README.rdoc b/README.rdoc
index f33ef93..e4d8a0e 100644
--- a/README.rdoc
+++ b/README.rdoc
@@ -16,7 +16,7 @@ Install the gem:
 
 - set the environment variables OPENTOX_COMPOUNDS, OPENTOX_FEATURES, OPENTOX_DATASETS, OPENTOX_FMINER to the base URI of the OpenTox REST webservices
 - require 'opentox-ruby-api-wrapper' in your ruby application
-- consult the API documentation for details 
+- consult the rdoc API documentation for details 
 
 == Copyright
 
diff --git a/Rakefile b/Rakefile
index a1b950e..de8e703 100644
--- a/Rakefile
+++ b/Rakefile
@@ -6,7 +6,7 @@ begin
   Jeweler::Tasks.new do |gem|
     gem.name = "opentox-ruby-api-wrapper"
     gem.summary = %Q{Ruby wrapper for the OpenTox REST API}
-    gem.description = %Q{}
+    gem.description = %Q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)}
     gem.email = "helma@in-silico.ch"
     gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper"
     gem.authors = ["Christoph Helma"]
diff --git a/rdoc/classes/OpenTox.html b/rdoc/classes/OpenTox.html
deleted file mode 100644
index 21b7032..0000000
--- a/rdoc/classes/OpenTox.html
+++ /dev/null
@@ -1,115 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html 
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>Module: OpenTox</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-
-    elemStyle = elem.style;
-    
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-
-    return true;
-  }
-  
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  
-  // ]]>
-  </script>
-
-</head>
-<body>
-
-
-
-    <div id="classHeader">
-        <table class="header-table">
-        <tr class="top-aligned-row">
-          <td><strong>Module</strong></td>
-          <td class="class-name-in-header">OpenTox</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <a href="../files/lib/opentox-ruby-api-wrapper_rb.html">
-                lib/opentox-ruby-api-wrapper.rb
-                </a>
-        <br />
-            </td>
-        </tr>
-
-        </table>
-    </div>
-  <!-- banner header -->
-
-  <div id="bodyContent">
-
-
-
-  <div id="contextContent">
-
-
-
-   </div>
-
-
-  </div>
-
-
-    <!-- if includes -->
-
-    <div id="section">
-
-    <div id="class-list">
-      <h3 class="section-bar">Classes and Modules</h3>
-
-      Class <a href="OpenTox/Compound.html" class="link">OpenTox::Compound</a><br />
-Class <a href="OpenTox/Dataset.html" class="link">OpenTox::Dataset</a><br />
-Class <a href="OpenTox/Feature.html" class="link">OpenTox::Feature</a><br />
-Class <a href="OpenTox/Fminer.html" class="link">OpenTox::Fminer</a><br />
-Class <a href="OpenTox/OpenTox.html" class="link">OpenTox::OpenTox</a><br />
-
-    </div>
-
-
-
-
-      
-
-
-    <!-- if method_list -->
-
-
-  </div>
-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/classes/OpenTox/Compound.html b/rdoc/classes/OpenTox/Compound.html
deleted file mode 100644
index c892d0e..0000000
--- a/rdoc/classes/OpenTox/Compound.html
+++ /dev/null
@@ -1,247 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html 
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>Class: OpenTox::Compound</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-
-    elemStyle = elem.style;
-    
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-
-    return true;
-  }
-  
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  
-  // ]]>
-  </script>
-
-</head>
-<body>
-
-
-
-    <div id="classHeader">
-        <table class="header-table">
-        <tr class="top-aligned-row">
-          <td><strong>Class</strong></td>
-          <td class="class-name-in-header">OpenTox::Compound</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html">
-                lib/opentox-ruby-api-wrapper.rb
-                </a>
-        <br />
-            </td>
-        </tr>
-
-        <tr class="top-aligned-row">
-            <td><strong>Parent:</strong></td>
-            <td>
-                <a href="OpenTox.html">
-                OpenTox
-               </a>
-            </td>
-        </tr>
-        </table>
-    </div>
-  <!-- banner header -->
-
-  <div id="bodyContent">
-
-
-
-  <div id="contextContent">
-
-
-
-   </div>
-
-    <div id="method-list">
-      <h3 class="section-bar">Methods</h3>
-
-      <div class="name-list">
-      <a href="#M000004">match</a>&nbsp;&nbsp;
-      <a href="#M000003">match?</a>&nbsp;&nbsp;
-      <a href="#M000001">new</a>&nbsp;&nbsp;
-      <a href="#M000002">smiles</a>&nbsp;&nbsp;
-      </div>
-    </div>
-
-  </div>
-
-
-    <!-- if includes -->
-
-    <div id="section">
-
-
-
-
-
-      
-
-
-    <!-- if method_list -->
-    <div id="methods">
-      <h3 class="section-bar">Public Class methods</h3>
-
-      <div id="method-M000001" class="method-detail">
-        <a name="M000001"></a>
-
-        <div class="method-heading">
-          <a href="#M000001" class="method-signature">
-          <span class="method-name">new</span><span class="method-args">(params)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Initialize with <tt>:uri =&gt; uri</tt>, <tt>:<a
-href="Compound.html#M000002">smiles</a> =&gt; <a
-href="Compound.html#M000002">smiles</a></tt> or <tt>:name =&gt; name</tt>
-(name can be also an InChI/InChiKey, CAS number, etc)
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000001-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000001-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 18</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">params</span>)
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>]
-                                <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>].<span class="ruby-identifier">to_s</span>
-                        <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:smiles</span>]
-                                <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_COMPOUNDS'</span>] ,<span class="ruby-identifier">:smiles</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">params</span>[<span class="ruby-identifier">:smiles</span>])
-                        <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>]
-                                <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_COMPOUNDS'</span>] ,<span class="ruby-identifier">:name</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>])
-                        <span class="ruby-keyword kw">end</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <h3 class="section-bar">Public Instance methods</h3>
-
-      <div id="method-M000004" class="method-detail">
-        <a name="M000004"></a>
-
-        <div class="method-heading">
-          <a href="#M000004" class="method-signature">
-          <span class="method-name">match</span><span class="method-args">(smarts_features)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Match an array of smarts features, returns matching features
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000004-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000004-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 43</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">match</span>(<span class="ruby-identifier">smarts_features</span>)
-                        <span class="ruby-identifier">smarts_features</span>.<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">smarts</span><span class="ruby-operator">|</span> <span class="ruby-identifier">smarts</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">match?</span>(<span class="ruby-identifier">smarts</span>.<span class="ruby-identifier">name</span>) }.<span class="ruby-identifier">compact</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000003" class="method-detail">
-        <a name="M000003"></a>
-
-        <div class="method-heading">
-          <a href="#M000003" class="method-signature">
-          <span class="method-name">match?</span><span class="method-args">(smarts)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Matchs a smarts string
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000003-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000003-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 34</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">match?</span>(<span class="ruby-identifier">smarts</span>)
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/match/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">smarts</span>)) <span class="ruby-operator">==</span> <span class="ruby-value str">'true'</span>
-                                <span class="ruby-keyword kw">true</span>
-                        <span class="ruby-keyword kw">else</span>
-                                <span class="ruby-keyword kw">false</span>
-                        <span class="ruby-keyword kw">end</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000002" class="method-detail">
-        <a name="M000002"></a>
-
-        <div class="method-heading">
-          <a href="#M000002" class="method-signature">
-          <span class="method-name">smiles</span><span class="method-args">()</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get the (canonical) <a href="Compound.html#M000002">smiles</a>
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000002-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000002-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 29</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">smiles</span>
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-
-    </div>
-
-
-  </div>
-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/classes/OpenTox/Dataset.html b/rdoc/classes/OpenTox/Dataset.html
deleted file mode 100644
index f6966f7..0000000
--- a/rdoc/classes/OpenTox/Dataset.html
+++ /dev/null
@@ -1,331 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html 
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>Class: OpenTox::Dataset</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-
-    elemStyle = elem.style;
-    
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-
-    return true;
-  }
-  
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  
-  // ]]>
-  </script>
-
-</head>
-<body>
-
-
-
-    <div id="classHeader">
-        <table class="header-table">
-        <tr class="top-aligned-row">
-          <td><strong>Class</strong></td>
-          <td class="class-name-in-header">OpenTox::Dataset</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html">
-                lib/opentox-ruby-api-wrapper.rb
-                </a>
-        <br />
-            </td>
-        </tr>
-
-        <tr class="top-aligned-row">
-            <td><strong>Parent:</strong></td>
-            <td>
-                <a href="OpenTox.html">
-                OpenTox
-               </a>
-            </td>
-        </tr>
-        </table>
-    </div>
-  <!-- banner header -->
-
-  <div id="bodyContent">
-
-
-
-  <div id="contextContent">
-
-
-
-   </div>
-
-    <div id="method-list">
-      <h3 class="section-bar">Methods</h3>
-
-      <div class="name-list">
-      <a href="#M000016">add</a>&nbsp;&nbsp;
-      <a href="#M000013">all_compounds_and_features</a>&nbsp;&nbsp;
-      <a href="#M000014">all_features</a>&nbsp;&nbsp;
-      <a href="#M000012">compounds</a>&nbsp;&nbsp;
-      <a href="#M000015">features</a>&nbsp;&nbsp;
-      <a href="#M000011">name</a>&nbsp;&nbsp;
-      <a href="#M000010">new</a>&nbsp;&nbsp;
-      </div>
-    </div>
-
-  </div>
-
-
-    <!-- if includes -->
-
-    <div id="section">
-
-
-
-
-
-      
-
-
-    <!-- if method_list -->
-    <div id="methods">
-      <h3 class="section-bar">Public Class methods</h3>
-
-      <div id="method-M000010" class="method-detail">
-        <a name="M000010"></a>
-
-        <div class="method-heading">
-          <a href="#M000010" class="method-signature">
-          <span class="method-name">new</span><span class="method-args">(params)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Initialize with <tt>:uri =&gt; uri</tt> or <tt>:<a
-href="Dataset.html#M000011">name</a> =&gt; <a
-href="Dataset.html#M000011">name</a></tt> (creates a <a
-href="Dataset.html#M000010">new</a> dataset)
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000010-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000010-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 78</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">params</span>)
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>]
-                                <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>].<span class="ruby-identifier">to_s</span>
-                        <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>] 
-                                <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_DATASETS'</span>], <span class="ruby-identifier">:name</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>]
-                                <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">delete</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/associations'</span>
-                        <span class="ruby-keyword kw">end</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <h3 class="section-bar">Public Instance methods</h3>
-
-      <div id="method-M000016" class="method-detail">
-        <a name="M000016"></a>
-
-        <div class="method-heading">
-          <a href="#M000016" class="method-signature">
-          <span class="method-name">add</span><span class="method-args">(compound,feature)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Add a compound and a feature to a dataset
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000016-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000016-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 118</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">compound</span>,<span class="ruby-identifier">feature</span>)
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">put</span> <span class="ruby-ivar">@uri</span>, <span class="ruby-identifier">:compound_uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">compound</span>.<span class="ruby-identifier">uri</span>, <span class="ruby-identifier">:feature_uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">uri</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000013" class="method-detail">
-        <a name="M000013"></a>
-
-        <div class="method-heading">
-          <a href="#M000013" class="method-signature">
-          <span class="method-name">all_compounds_and_features</span><span class="method-args">()</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get all <a href="Dataset.html#M000012">compounds</a> and <a
-href="Dataset.html#M000015">features</a> from a dataset, returns a hash
-with compound_uris as keys and arrays of <a
-href="Dataset.html#M000015">features</a> as values
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000013-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000013-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 98</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_compounds_and_features</span>
-                        <span class="ruby-identifier">compounds</span> = {}
-                        <span class="ruby-constant">Crack</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compounds/features'</span>)[<span class="ruby-value str">'dataset'</span>][<span class="ruby-value str">'compound'</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span>
-                                <span class="ruby-identifier">features</span> = <span class="ruby-identifier">c</span>[<span class="ruby-value str">'feature_uri'</span>].<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span> <span class="ruby-identifier">:uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">f</span> }
-                                <span class="ruby-identifier">compounds</span>[<span class="ruby-identifier">c</span>[<span class="ruby-value str">'uri'</span>]] = <span class="ruby-identifier">features</span>
-                        <span class="ruby-keyword kw">end</span>
-                        <span class="ruby-identifier">compounds</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000014" class="method-detail">
-        <a name="M000014"></a>
-
-        <div class="method-heading">
-          <a href="#M000014" class="method-signature">
-          <span class="method-name">all_features</span><span class="method-args">()</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get all <a href="Dataset.html#M000015">features</a> from a dataset
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000014-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000014-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 108</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_features</span>
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/features'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">&quot;\n&quot;</span>).<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">f</span>)}
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000012" class="method-detail">
-        <a name="M000012"></a>
-
-        <div class="method-heading">
-          <a href="#M000012" class="method-signature">
-          <span class="method-name">compounds</span><span class="method-args">()</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get all <a href="Dataset.html#M000012">compounds</a> from a dataset
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000012-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000012-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 93</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">compounds</span>
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compounds'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">&quot;\n&quot;</span>).<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span> <span class="ruby-constant">Compound</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">c</span>) }
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000015" class="method-detail">
-        <a name="M000015"></a>
-
-        <div class="method-heading">
-          <a href="#M000015" class="method-signature">
-          <span class="method-name">features</span><span class="method-args">(compound)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get all <a href="Dataset.html#M000015">features</a> for a compound
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000015-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000015-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 113</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">features</span>(<span class="ruby-identifier">compound</span>)
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compound/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">compound</span>.<span class="ruby-identifier">uri</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/features'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">&quot;\n&quot;</span>).<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">f</span>) }
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000011" class="method-detail">
-        <a name="M000011"></a>
-
-        <div class="method-heading">
-          <a href="#M000011" class="method-signature">
-          <span class="method-name">name</span><span class="method-args">()</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get the dataset <a href="Dataset.html#M000011">name</a>
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000011-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000011-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 88</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">name</span>
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/name'</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-
-    </div>
-
-
-  </div>
-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/classes/OpenTox/Feature.html b/rdoc/classes/OpenTox/Feature.html
deleted file mode 100644
index 5e53a12..0000000
--- a/rdoc/classes/OpenTox/Feature.html
+++ /dev/null
@@ -1,217 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html 
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>Class: OpenTox::Feature</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-
-    elemStyle = elem.style;
-    
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-
-    return true;
-  }
-  
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  
-  // ]]>
-  </script>
-
-</head>
-<body>
-
-
-
-    <div id="classHeader">
-        <table class="header-table">
-        <tr class="top-aligned-row">
-          <td><strong>Class</strong></td>
-          <td class="class-name-in-header">OpenTox::Feature</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html">
-                lib/opentox-ruby-api-wrapper.rb
-                </a>
-        <br />
-            </td>
-        </tr>
-
-        <tr class="top-aligned-row">
-            <td><strong>Parent:</strong></td>
-            <td>
-                <a href="OpenTox.html">
-                OpenTox
-               </a>
-            </td>
-        </tr>
-        </table>
-    </div>
-  <!-- banner header -->
-
-  <div id="bodyContent">
-
-
-
-  <div id="contextContent">
-
-
-
-   </div>
-
-    <div id="method-list">
-      <h3 class="section-bar">Methods</h3>
-
-      <div class="name-list">
-      <a href="#M000007">name</a>&nbsp;&nbsp;
-      <a href="#M000005">new</a>&nbsp;&nbsp;
-      <a href="#M000006">value</a>&nbsp;&nbsp;
-      </div>
-    </div>
-
-  </div>
-
-
-    <!-- if includes -->
-
-    <div id="section">
-
-
-
-
-
-      
-
-
-    <!-- if method_list -->
-    <div id="methods">
-      <h3 class="section-bar">Public Class methods</h3>
-
-      <div id="method-M000005" class="method-detail">
-        <a name="M000005"></a>
-
-        <div class="method-heading">
-          <a href="#M000005" class="method-signature">
-          <span class="method-name">new</span><span class="method-args">(params)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Initialize with <tt>:uri =&gt; uri</tt>, or <tt>:<a
-href="Feature.html#M000007">name</a> =&gt; <a
-href="Feature.html#M000007">name</a>, :values =&gt;
-hash_of_property_names_and_values</tt>
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000005-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000005-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 52</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">params</span>)
-                        <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>]
-                                <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>].<span class="ruby-identifier">to_s</span>
-                        <span class="ruby-keyword kw">else</span>
-                                <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_FEATURES'</span>] <span class="ruby-operator">+</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>]) 
-                                <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:values</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
-                                        <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span>
-                                <span class="ruby-keyword kw">end</span>
-                        <span class="ruby-keyword kw">end</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <h3 class="section-bar">Public Instance methods</h3>
-
-      <div id="method-M000007" class="method-detail">
-        <a name="M000007"></a>
-
-        <div class="method-heading">
-          <a href="#M000007" class="method-signature">
-          <span class="method-name">name</span><span class="method-args">()</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get the <a href="Feature.html#M000007">name</a> of the feature
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000007-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000007-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 69</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">name</span>
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/name'</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <div id="method-M000006" class="method-detail">
-        <a name="M000006"></a>
-
-        <div class="method-heading">
-          <a href="#M000006" class="method-signature">
-          <span class="method-name">value</span><span class="method-args">(property)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Get the <a href="Feature.html#M000006">value</a> of a property
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000006-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000006-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 64</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">value</span>(<span class="ruby-identifier">property</span>)
-                        <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">property</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-
-    </div>
-
-
-  </div>
-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/classes/OpenTox/Fminer.html b/rdoc/classes/OpenTox/Fminer.html
deleted file mode 100644
index 6c3b4fe..0000000
--- a/rdoc/classes/OpenTox/Fminer.html
+++ /dev/null
@@ -1,178 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html 
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>Class: OpenTox::Fminer</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-
-    elemStyle = elem.style;
-    
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-
-    return true;
-  }
-  
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  
-  // ]]>
-  </script>
-
-</head>
-<body>
-
-
-
-    <div id="classHeader">
-        <table class="header-table">
-        <tr class="top-aligned-row">
-          <td><strong>Class</strong></td>
-          <td class="class-name-in-header">OpenTox::Fminer</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html">
-                lib/opentox-ruby-api-wrapper.rb
-                </a>
-        <br />
-            </td>
-        </tr>
-
-        <tr class="top-aligned-row">
-            <td><strong>Parent:</strong></td>
-            <td>
-                <a href="OpenTox.html">
-                OpenTox
-               </a>
-            </td>
-        </tr>
-        </table>
-    </div>
-  <!-- banner header -->
-
-  <div id="bodyContent">
-
-
-
-  <div id="contextContent">
-
-
-
-   </div>
-
-    <div id="method-list">
-      <h3 class="section-bar">Methods</h3>
-
-      <div class="name-list">
-      <a href="#M000009">dataset</a>&nbsp;&nbsp;
-      <a href="#M000008">new</a>&nbsp;&nbsp;
-      </div>
-    </div>
-
-  </div>
-
-
-    <!-- if includes -->
-
-    <div id="section">
-
-
-
-
-
-      
-
-
-    <!-- if method_list -->
-    <div id="methods">
-      <h3 class="section-bar">Public Class methods</h3>
-
-      <div id="method-M000008" class="method-detail">
-        <a name="M000008"></a>
-
-        <div class="method-heading">
-          <a href="#M000008" class="method-signature">
-          <span class="method-name">new</span><span class="method-args">(training_dataset)</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p>
-Create a <a href="Fminer.html#M000008">new</a> <a
-href="Fminer.html#M000009">dataset</a> with BBRC features
-</p>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000008-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000008-source">
-<pre>
-<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 127</span>
-                <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">training_dataset</span>)
-                        <span class="ruby-ivar">@dataset_uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_FMINER'</span>], <span class="ruby-identifier">:dataset_uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">training_dataset</span>.<span class="ruby-identifier">uri</span>
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-      <h3 class="section-bar">Public Instance methods</h3>
-
-      <div id="method-M000009" class="method-detail">
-        <a name="M000009"></a>
-
-        <div class="method-heading">
-          <a href="#M000009" class="method-signature">
-          <span class="method-name">dataset</span><span class="method-args">()</span>
-          </a>
-        </div>
-      
-        <div class="method-description">
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000009-source');return false;">[Source]</a></p>
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-                        <span class="ruby-constant">Dataset</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-ivar">@dataset_uri</span>)
-                <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-
-
-    </div>
-
-
-  </div>
-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/classes/OpenTox/OpenTox.html b/rdoc/classes/OpenTox/OpenTox.html
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index 35611f8..0000000
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+++ /dev/null
@@ -1,162 +0,0 @@
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-<!DOCTYPE html 
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-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-  <title>Class: OpenTox::OpenTox</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
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-  function popupCode( url ) {
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-                        <span class="ruby-constant">URI</span>.<span class="ruby-identifier">escape</span>(<span class="ruby-identifier">string</span>, <span class="ruby-regexp re">/[^\w]/</span>)
-                <span class="ruby-keyword kw">end</span>
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-        </div>
-      </div>
-
-
-    </div>
-
-
-  </div>
-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/created.rid b/rdoc/created.rid
deleted file mode 100644
index 8dc2058..0000000
--- a/rdoc/created.rid
+++ /dev/null
@@ -1 +0,0 @@
-Thu, 13 Aug 2009 11:01:58 +0200
diff --git a/rdoc/files/README_rdoc.html b/rdoc/files/README_rdoc.html
deleted file mode 100644
index 3342971..0000000
--- a/rdoc/files/README_rdoc.html
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@@ -1,140 +0,0 @@
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-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-<head>
-  <title>File: README.rdoc</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
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-
-  <div id="fileHeader">
-    <h1>README.rdoc</h1>
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-      <td><strong>Path:</strong></td>
-      <td>README.rdoc
-      </td>
-    </tr>
-    <tr class="top-aligned-row">
-      <td><strong>Last Update:</strong></td>
-      <td>Thu Aug 13 11:00:51 +0200 2009</td>
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-  <!-- banner header -->
-
-  <div id="bodyContent">
-
-
-
-  <div id="contextContent">
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-    <div id="description">
-      <h1>opentox-ruby-api-wrapper</h1>
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-Ruby wrapper for the <a href="../classes/OpenTox.html">OpenTox</a> REST API
-(<a href="http://www.opentox.org">www.opentox.org</a>)
-</p>
-<h2>Installation</h2>
-<p>
-Run the following if you haven&#8216;t already:
-</p>
-<pre>
-        gem sources -a http://gems.github.com
-</pre>
-<p>
-Install the gem:
-</p>
-<pre>
-        sudo gem install helma-opentox-ruby-api-wrapper
-</pre>
-<h2>Usage</h2>
-<ul>
-<li>set the environment variables OPENTOX_COMPOUNDS, OPENTOX_FEATURES,
-OPENTOX_DATASETS, OPENTOX_FMINER to the base URI of the <a
-href="../classes/OpenTox.html">OpenTox</a> REST webservices
-
-</li>
-<li>require &#8216;opentox-ruby-api-wrapper&#8217; in your ruby application
-
-</li>
-<li>consult the API documentation for details
-
-</li>
-</ul>
-<h2>Copyright</h2>
-<p>
-Copyright (c) 2009 Christoph Helma. See LICENSE for details.
-</p>
-
-    </div>
-
-
-   </div>
-
-
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-
-
-  </div>
-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html b/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html
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index be6ca28..0000000
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-  <title>File: opentox-ruby-api-wrapper.rb</title>
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-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
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-  <script type="text/javascript">
-  // <![CDATA[
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-      <td>lib/opentox-ruby-api-wrapper.rb
-      </td>
-    </tr>
-    <tr class="top-aligned-row">
-      <td><strong>Last Update:</strong></td>
-      <td>Thu Aug 13 10:44:46 +0200 2009</td>
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-  <!-- banner header -->
-
-  <div id="bodyContent">
-
-
-
-  <div id="contextContent">
-
-
-    <div id="requires-list">
-      <h3 class="section-bar">Required files</h3>
-
-      <div class="name-list">
-      rest_client&nbsp;&nbsp;
-      crack/xml&nbsp;&nbsp;
-      </div>
-    </div>
-
-   </div>
-
-
-  </div>
-
-
-    <!-- if includes -->
-
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-
-
-
-
-
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-
-
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-
-
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/fr_class_index.html b/rdoc/fr_class_index.html
deleted file mode 100644
index 7242f18..0000000
--- a/rdoc/fr_class_index.html
+++ /dev/null
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-
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html 
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-</body>
-</html>
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deleted file mode 100644
index 63abf5e..0000000
--- a/rdoc/fr_method_index.html
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-    <a href="classes/OpenTox/Compound.html#M000001">new (OpenTox::Compound)</a><br />
-    <a href="classes/OpenTox/Dataset.html#M000010">new (OpenTox::Dataset)</a><br />
-    <a href="classes/OpenTox/Fminer.html#M000008">new (OpenTox::Fminer)</a><br />
-    <a href="classes/OpenTox/Feature.html#M000005">new (OpenTox::Feature)</a><br />
-    <a href="classes/OpenTox/Compound.html#M000002">smiles (OpenTox::Compound)</a><br />
-    <a href="classes/OpenTox/OpenTox.html#M000017">uri_escape (OpenTox::OpenTox)</a><br />
-    <a href="classes/OpenTox/Feature.html#M000006">value (OpenTox::Feature)</a><br />
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-</div>
-</body>
-</html>
-\ No newline at end of file
diff --git a/rdoc/index.html b/rdoc/index.html
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index bb24624..0000000
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index 44c7b3d..0000000
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-\ No newline at end of file