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-rw-r--r--rdoc/classes/OpenTox.html115
-rw-r--r--rdoc/classes/OpenTox/Compound.html247
-rw-r--r--rdoc/classes/OpenTox/Dataset.html331
-rw-r--r--rdoc/classes/OpenTox/Feature.html217
-rw-r--r--rdoc/classes/OpenTox/Fminer.html178
-rw-r--r--rdoc/classes/OpenTox/OpenTox.html162
-rw-r--r--rdoc/created.rid1
-rw-r--r--rdoc/files/README_rdoc.html140
-rw-r--r--rdoc/files/lib/opentox-ruby-api-wrapper_rb.html109
-rw-r--r--rdoc/fr_class_index.html32
-rw-r--r--rdoc/fr_file_index.html28
-rw-r--r--rdoc/fr_method_index.html43
-rw-r--r--rdoc/index.html26
-rw-r--r--rdoc/rdoc-style.css208
14 files changed, 1837 insertions, 0 deletions
diff --git a/rdoc/classes/OpenTox.html b/rdoc/classes/OpenTox.html
new file mode 100644
index 0000000..21b7032
--- /dev/null
+++ b/rdoc/classes/OpenTox.html
@@ -0,0 +1,115 @@
+<?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
new file mode 100644
index 0000000..c892d0e
--- /dev/null
+++ b/rdoc/classes/OpenTox/Compound.html
@@ -0,0 +1,247 @@
+<?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
new file mode 100644
index 0000000..f6966f7
--- /dev/null
+++ b/rdoc/classes/OpenTox/Dataset.html
@@ -0,0 +1,331 @@
+<?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
new file mode 100644
index 0000000..5e53a12
--- /dev/null
+++ b/rdoc/classes/OpenTox/Feature.html
@@ -0,0 +1,217 @@
+<?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
new file mode 100644
index 0000000..6c3b4fe
--- /dev/null
+++ b/rdoc/classes/OpenTox/Fminer.html
@@ -0,0 +1,178 @@
+<?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>
+ <div class="method-source-code" id="M000009-source">
+<pre>
+<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 131</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">dataset</span>
+ <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>
+</div>
+
+</body>
+</html> \ No newline at end of file
diff --git a/rdoc/classes/OpenTox/OpenTox.html b/rdoc/classes/OpenTox/OpenTox.html
new file mode 100644
index 0000000..35611f8
--- /dev/null
+++ b/rdoc/classes/OpenTox/OpenTox.html
@@ -0,0 +1,162 @@
+<?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::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>Class</strong></td>
+ <td class="class-name-in-header">OpenTox::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>
+
+ <tr class="top-aligned-row">
+ <td><strong>Parent:</strong></td>
+ <td>
+ Object
+ </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="#M000017">uri_escape</a>&nbsp;&nbsp;
+ </div>
+ </div>
+
+ </div>
+
+
+ <!-- if includes -->
+
+ <div id="section">
+
+
+
+
+
+ <div id="attribute-list">
+ <h3 class="section-bar">Attributes</h3>
+
+ <div class="name-list">
+ <table>
+ <tr class="top-aligned-row context-row">
+ <td class="context-item-name">uri</td>
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+ <td class="context-item-desc"></td>
+ </tr>
+ </table>
+ </div>
+ </div>
+
+
+
+ <!-- if method_list -->
+ <div id="methods">
+ <h3 class="section-bar">Public Instance methods</h3>
+
+ <div id="method-M000017" class="method-detail">
+ <a name="M000017"></a>
+
+ <div class="method-heading">
+ <a href="#M000017" class="method-signature">
+ <span class="method-name">uri_escape</span><span class="method-args">(string)</span>
+ </a>
+ </div>
+
+ <div class="method-description">
+ <p>
+Escape all nonword characters
+</p>
+ <p><a class="source-toggle" href="#"
+ onclick="toggleCode('M000017-source');return false;">[Source]</a></p>
+ <div class="method-source-code" id="M000017-source">
+<pre>
+<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 10</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">string</span>)
+ <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>
+</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/created.rid b/rdoc/created.rid
new file mode 100644
index 0000000..8dc2058
--- /dev/null
+++ b/rdoc/created.rid
@@ -0,0 +1 @@
+Thu, 13 Aug 2009 11:01:58 +0200
diff --git a/rdoc/files/README_rdoc.html b/rdoc/files/README_rdoc.html
new file mode 100644
index 0000000..3342971
--- /dev/null
+++ b/rdoc/files/README_rdoc.html
@@ -0,0 +1,140 @@
+<?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>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[
+
+ 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="fileHeader">
+ <h1>README.rdoc</h1>
+ <table class="header-table">
+ <tr class="top-aligned-row">
+ <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>
+ </tr>
+ </table>
+ </div>
+ <!-- banner header -->
+
+ <div id="bodyContent">
+
+
+
+ <div id="contextContent">
+
+ <div id="description">
+ <h1>opentox-ruby-api-wrapper</h1>
+<p>
+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>
+
+
+ </div>
+
+
+ <!-- if includes -->
+
+ <div id="section">
+
+
+
+
+
+
+
+
+ <!-- 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/files/lib/opentox-ruby-api-wrapper_rb.html b/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html
new file mode 100644
index 0000000..be6ca28
--- /dev/null
+++ b/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html
@@ -0,0 +1,109 @@
+<?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>File: opentox-ruby-api-wrapper.rb</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="fileHeader">
+ <h1>opentox-ruby-api-wrapper.rb</h1>
+ <table class="header-table">
+ <tr class="top-aligned-row">
+ <td><strong>Path:</strong></td>
+ <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>
+ </tr>
+ </table>
+ </div>
+ <!-- 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 -->
+
+ <div id="section">
+
+
+
+
+
+
+
+
+ <!-- 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/fr_class_index.html b/rdoc/fr_class_index.html
new file mode 100644
index 0000000..7242f18
--- /dev/null
+++ b/rdoc/fr_class_index.html
@@ -0,0 +1,32 @@
+
+<?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">
+
+<!--
+
+ Classes
+
+ -->
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Classes</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+ <link rel="stylesheet" href="rdoc-style.css" type="text/css" />
+ <base target="docwin" />
+</head>
+<body>
+<div id="index">
+ <h1 class="section-bar">Classes</h1>
+ <div id="index-entries">
+ <a href="classes/OpenTox.html">OpenTox</a><br />
+ <a href="classes/OpenTox/Compound.html">OpenTox::Compound</a><br />
+ <a href="classes/OpenTox/Dataset.html">OpenTox::Dataset</a><br />
+ <a href="classes/OpenTox/Feature.html">OpenTox::Feature</a><br />
+ <a href="classes/OpenTox/Fminer.html">OpenTox::Fminer</a><br />
+ <a href="classes/OpenTox/OpenTox.html">OpenTox::OpenTox</a><br />
+ </div>
+</div>
+</body>
+</html> \ No newline at end of file
diff --git a/rdoc/fr_file_index.html b/rdoc/fr_file_index.html
new file mode 100644
index 0000000..eac1d09
--- /dev/null
+++ b/rdoc/fr_file_index.html
@@ -0,0 +1,28 @@
+
+<?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">
+
+<!--
+
+ Files
+
+ -->
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Files</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+ <link rel="stylesheet" href="rdoc-style.css" type="text/css" />
+ <base target="docwin" />
+</head>
+<body>
+<div id="index">
+ <h1 class="section-bar">Files</h1>
+ <div id="index-entries">
+ <a href="files/README_rdoc.html">README.rdoc</a><br />
+ <a href="files/lib/opentox-ruby-api-wrapper_rb.html">lib/opentox-ruby-api-wrapper.rb</a><br />
+ </div>
+</div>
+</body>
+</html> \ No newline at end of file
diff --git a/rdoc/fr_method_index.html b/rdoc/fr_method_index.html
new file mode 100644
index 0000000..63abf5e
--- /dev/null
+++ b/rdoc/fr_method_index.html
@@ -0,0 +1,43 @@
+
+<?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">
+
+<!--
+
+ Methods
+
+ -->
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Methods</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+ <link rel="stylesheet" href="rdoc-style.css" type="text/css" />
+ <base target="docwin" />
+</head>
+<body>
+<div id="index">
+ <h1 class="section-bar">Methods</h1>
+ <div id="index-entries">
+ <a href="classes/OpenTox/Dataset.html#M000016">add (OpenTox::Dataset)</a><br />
+ <a href="classes/OpenTox/Dataset.html#M000013">all_compounds_and_features (OpenTox::Dataset)</a><br />
+ <a href="classes/OpenTox/Dataset.html#M000014">all_features (OpenTox::Dataset)</a><br />
+ <a href="classes/OpenTox/Dataset.html#M000012">compounds (OpenTox::Dataset)</a><br />
+ <a href="classes/OpenTox/Fminer.html#M000009">dataset (OpenTox::Fminer)</a><br />
+ <a href="classes/OpenTox/Dataset.html#M000015">features (OpenTox::Dataset)</a><br />
+ <a href="classes/OpenTox/Compound.html#M000004">match (OpenTox::Compound)</a><br />
+ <a href="classes/OpenTox/Compound.html#M000003">match? (OpenTox::Compound)</a><br />
+ <a href="classes/OpenTox/Feature.html#M000007">name (OpenTox::Feature)</a><br />
+ <a href="classes/OpenTox/Dataset.html#M000011">name (OpenTox::Dataset)</a><br />
+ <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 />
+ </div>
+</div>
+</body>
+</html> \ No newline at end of file
diff --git a/rdoc/index.html b/rdoc/index.html
new file mode 100644
index 0000000..bb24624
--- /dev/null
+++ b/rdoc/index.html
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!DOCTYPE html
+ PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
+
+<!--
+
+ opentox-ruby-api-wrapper 0.1.0
+
+
+ -->
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>opentox-ruby-api-wrapper 0.1.0
+</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+</head>
+<frameset rows="20%, 80%">
+ <frameset cols="25%,35%,45%">
+ <frame src="fr_file_index.html" title="Files" name="Files" />
+ <frame src="fr_class_index.html" name="Classes" />
+ <frame src="fr_method_index.html" name="Methods" />
+ </frameset>
+ <frame src="files/README_rdoc.html" name="docwin" />
+</frameset>
+</html> \ No newline at end of file
diff --git a/rdoc/rdoc-style.css b/rdoc/rdoc-style.css
new file mode 100644
index 0000000..44c7b3d
--- /dev/null
+++ b/rdoc/rdoc-style.css
@@ -0,0 +1,208 @@
+
+body {
+ font-family: Verdana,Arial,Helvetica,sans-serif;
+ font-size: 90%;
+ margin: 0;
+ margin-left: 40px;
+ padding: 0;
+ background: white;
+}
+
+h1,h2,h3,h4 { margin: 0; color: #efefef; background: transparent; }
+h1 { font-size: 150%; }
+h2,h3,h4 { margin-top: 1em; }
+
+a { background: #eef; color: #039; text-decoration: none; }
+a:hover { background: #039; color: #eef; }
+
+/* Override the base stylesheet's Anchor inside a table cell */
+td > a {
+ background: transparent;
+ color: #039;
+ text-decoration: none;
+}
+
+/* and inside a section title */
+.section-title > a {
+ background: transparent;
+ color: #eee;
+ text-decoration: none;
+}
+
+/* === Structural elements =================================== */
+
+div#index {
+ margin: 0;
+ margin-left: -40px;
+ padding: 0;
+ font-size: 90%;
+}
+
+
+div#index a {
+ margin-left: 0.7em;
+}
+
+div#index .section-bar {
+ margin-left: 0px;
+ padding-left: 0.7em;
+ background: #ccc;
+ font-size: small;
+}
+
+
+div#classHeader, div#fileHeader {
+ width: auto;
+ color: white;
+ padding: 0.5em 1.5em 0.5em 1.5em;
+ margin: 0;
+ margin-left: -40px;
+ border-bottom: 3px solid #006;
+}
+
+div#classHeader a, div#fileHeader a {
+ background: inherit;
+ color: white;
+}
+
+div#classHeader td, div#fileHeader td {
+ background: inherit;
+ color: white;
+}
+
+
+div#fileHeader {
+ background: #057;
+}
+
+div#classHeader {
+ background: #048;
+}
+
+
+.class-name-in-header {
+ font-size: 180%;
+ font-weight: bold;
+}
+
+
+div#bodyContent {
+ padding: 0 1.5em 0 1.5em;
+}
+
+div#description {
+ padding: 0.5em 1.5em;
+ background: #efefef;
+ border: 1px dotted #999;
+}
+
+div#description h1,h2,h3,h4,h5,h6 {
+ color: #125;;
+ background: transparent;
+}
+
+div#validator-badges {
+ text-align: center;
+}
+div#validator-badges img { border: 0; }
+
+div#copyright {
+ color: #333;
+ background: #efefef;
+ font: 0.75em sans-serif;
+ margin-top: 5em;
+ margin-bottom: 0;
+ padding: 0.5em 2em;
+}
+
+
+/* === Classes =================================== */
+
+table.header-table {
+ color: white;
+ font-size: small;
+}
+
+.type-note {
+ font-size: small;
+ color: #DEDEDE;
+}
+
+.xxsection-bar {
+ background: #eee;
+ color: #333;
+ padding: 3px;
+}
+
+.section-bar {
+ color: #333;
+ border-bottom: 1px solid #999;
+ margin-left: -20px;
+}
+
+
+.section-title {
+ background: #79a;
+ color: #eee;
+ padding: 3px;
+ margin-top: 2em;
+ margin-left: -30px;
+ border: 1px solid #999;
+}
+
+.top-aligned-row { vertical-align: top }
+.bottom-aligned-row { vertical-align: bottom }
+
+/* --- Context section classes ----------------------- */
+
+.context-row { }
+.context-item-name { font-family: monospace; font-weight: bold; color: black; }
+.context-item-value { font-size: small; color: #448; }
+.context-item-desc { color: #333; padding-left: 2em; }
+
+/* --- Method classes -------------------------- */
+.method-detail {
+ background: #efefef;
+ padding: 0;
+ margin-top: 0.5em;
+ margin-bottom: 1em;
+ border: 1px dotted #ccc;
+}
+.method-heading {
+ color: black;
+ background: #ccc;
+ border-bottom: 1px solid #666;
+ padding: 0.2em 0.5em 0 0.5em;
+}
+.method-signature { color: black; background: inherit; }
+.method-name { font-weight: bold; }
+.method-args { font-style: italic; }
+.method-description { padding: 0 0.5em 0 0.5em; }
+
+/* --- Source code sections -------------------- */
+
+a.source-toggle { font-size: 90%; }
+div.method-source-code {
+ background: #262626;
+ color: #ffdead;
+ margin: 1em;
+ padding: 0.5em;
+ border: 1px dashed #999;
+ overflow: hidden;
+}
+
+div.method-source-code pre { color: #ffdead; overflow: hidden; }
+
+/* --- Ruby keyword styles --------------------- */
+
+.standalone-code { background: #221111; color: #ffdead; overflow: hidden; }
+
+.ruby-constant { color: #7fffd4; background: transparent; }
+.ruby-keyword { color: #00ffff; background: transparent; }
+.ruby-ivar { color: #eedd82; background: transparent; }
+.ruby-operator { color: #00ffee; background: transparent; }
+.ruby-identifier { color: #ffdead; background: transparent; }
+.ruby-node { color: #ffa07a; background: transparent; }
+.ruby-comment { color: #b22222; font-weight: bold; background: transparent; }
+.ruby-regexp { color: #ffa07a; background: transparent; }
+.ruby-value { color: #7fffd4; background: transparent; } \ No newline at end of file
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-16 03:18:48 +0000