diff options
author | Christoph Helma <helma@in-silico.de> | 2009-08-13 11:12:40 +0200 |
---|---|---|
committer | Christoph Helma <helma@in-silico.de> | 2009-08-13 11:12:40 +0200 |
commit | b5d23150591cd29accf3ec818389e30d5812d7ef (patch) | |
tree | 4ebe99e5cd297467ec1d0be1877074257b6739fc | |
parent | 6683afffc7f9b2f1d58a6ebbf8e9b2f4213437ef (diff) |
description added, rdoc removed
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | README.rdoc | 2 | ||||
-rw-r--r-- | Rakefile | 2 | ||||
-rw-r--r-- | rdoc/classes/OpenTox.html | 115 | ||||
-rw-r--r-- | rdoc/classes/OpenTox/Compound.html | 247 | ||||
-rw-r--r-- | rdoc/classes/OpenTox/Dataset.html | 331 | ||||
-rw-r--r-- | rdoc/classes/OpenTox/Feature.html | 217 | ||||
-rw-r--r-- | rdoc/classes/OpenTox/Fminer.html | 178 | ||||
-rw-r--r-- | rdoc/classes/OpenTox/OpenTox.html | 162 | ||||
-rw-r--r-- | rdoc/created.rid | 1 | ||||
-rw-r--r-- | rdoc/files/README_rdoc.html | 140 | ||||
-rw-r--r-- | rdoc/files/lib/opentox-ruby-api-wrapper_rb.html | 109 | ||||
-rw-r--r-- | rdoc/fr_class_index.html | 32 | ||||
-rw-r--r-- | rdoc/fr_file_index.html | 28 | ||||
-rw-r--r-- | rdoc/fr_method_index.html | 43 | ||||
-rw-r--r-- | rdoc/index.html | 26 | ||||
-rw-r--r-- | rdoc/rdoc-style.css | 208 |
17 files changed, 3 insertions, 1839 deletions
@@ -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 @@ -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> - <a href="#M000003">match?</a> - <a href="#M000001">new</a> - <a href="#M000002">smiles</a> - </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 => uri</tt>, <tt>:<a -href="Compound.html#M000002">smiles</a> => <a -href="Compound.html#M000002">smiles</a></tt> or <tt>:name => 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">></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">></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> - <a href="#M000013">all_compounds_and_features</a> - <a href="#M000014">all_features</a> - <a href="#M000012">compounds</a> - <a href="#M000015">features</a> - <a href="#M000011">name</a> - <a href="#M000010">new</a> - </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 => uri</tt> or <tt>:<a -href="Dataset.html#M000011">name</a> => <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">></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">></span> <span class="ruby-identifier">compound</span>.<span class="ruby-identifier">uri</span>, <span class="ruby-identifier">:feature_uri</span> =<span class="ruby-operator">></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">></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">"\n"</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">></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">"\n"</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">></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">"\n"</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">></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> - <a href="#M000005">new</a> - <a href="#M000006">value</a> - </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 => uri</tt>, or <tt>:<a -href="Feature.html#M000007">name</a> => <a -href="Feature.html#M000007">name</a>, :values => -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> - <a href="#M000008">new</a> - </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">></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">></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 deleted file mode 100644 index 35611f8..0000000 --- a/rdoc/classes/OpenTox/OpenTox.html +++ /dev/null @@ -1,162 +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::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> - </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"> [R] </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 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 +++ /dev/null @@ -1,140 +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>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‘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 ‘opentox-ruby-api-wrapper’ 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 deleted file mode 100644 index be6ca28..0000000 --- a/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html +++ /dev/null @@ -1,109 +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>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 - crack/xml - </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 deleted file mode 100644 index 7242f18..0000000 --- a/rdoc/fr_class_index.html +++ /dev/null @@ -1,32 +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"> - -<!-- - - 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 deleted file mode 100644 index eac1d09..0000000 --- a/rdoc/fr_file_index.html +++ /dev/null @@ -1,28 +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"> - -<!-- - - 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 deleted file mode 100644 index 63abf5e..0000000 --- a/rdoc/fr_method_index.html +++ /dev/null @@ -1,43 +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"> - -<!-- - - 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 deleted file mode 100644 index bb24624..0000000 --- a/rdoc/index.html +++ /dev/null @@ -1,26 +0,0 @@ -<?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 deleted file mode 100644 index 44c7b3d..0000000 --- a/rdoc/rdoc-style.css +++ /dev/null @@ -1,208 +0,0 @@ - -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; }
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