jandot-bio 1.2.1

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml

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+[ <%= @class %> ]
+<div id="class_list">
+<%= @classes.map{ |x| reference_link(x) }.join(" > ") %>
+</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml

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+<div id="log_<%= @number %>" class="log">
+<div class="input">
+Input: [<%= link_to_remote @number, :url => {:action => "reload_script", :number => @number} %>]
+<pre class="script">
+<%=h @script %>
+</pre>
+<div class="output">
+Result:
+[<%= link_to_remote "methods", :url => {:action => "list_methods", :number => @number} %>]
+[<%= link_to_remote "classes", :url => {:action => "list_classes", :number => @number} %>]
+[<%= link_to_remote "modules", :url => {:action => "list_modules", :number => @number} %>]
+<div id="methods_<%= @number %>" class="methods"></div>
+<div id="classes_<%= @number %>" class="classes"></div>
+<div id="modules_<%= @number %>" class="modules"></div>
+<pre class="result">
+<%=h @result %>
+</pre>
+<% if @output %>
+Output:
+<pre class="output">
+<%=h @output %>
+</pre>
+<% end %>
+</div>
+</div>
+</div>
+

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml

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+[ <%= @class %> ]
+<div id="method_list">
+<table>
+<tr>
+<%- step = @methods.size / 4 + 1 -%>
+<%- 0.step(@methods.size, step) do |i| -%>
+<td><%= @methods[i, step].join("<br>") %></td>
+<%- end -%>
+</tr>
+</table>
+</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml

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+[ <%= @class %> ]
+<div id="module_list">
+<%= @modules.map {|x| reference_link(x) }.sort.join("<br>") %>
+</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml

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+<div id="variables">
+<ul>
+<% local_variables.each do |var| %>
+<li><%= link_to_remote var, :update => "index", :url => {:action => "evaluate", :script => var} %></li>
+<% end %>
+</ul>
+</div>

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css

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+/* body */
+
+body {
+	margin: 0;
+	color: #555555;
+	background: url("/images/bioruby/bg.gif") repeat-y center;
+	font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
+	font-size: 12px;
+}
+
+div#content {
+	width: 750px;
+	height: auto;
+	margin: 0 auto 0 auto;
+	text-align: left;
+}
+
+/* title */
+
+div#title {
+	width: 550px;
+	padding-right: 200px;
+	margin-bottom: 20px;
+	text-align: left;
+	background: url("/images/bioruby/gem.png") no-repeat left bottom;
+}
+
+div#title .titletop {
+	color: #736451;
+	font-size: 30px;
+	font-weight: normal;
+	text-align: left;
+	text-indent: 70px;
+	margin: 0;
+	padding: 0;
+	padding-top: 20px;
+	margin-bottom: 10px;
+}
+
+div#title .titlesub {
+	color: #000000;
+	font-size: 15px;
+	font-weight: normal;
+	text-align: left;
+	text-indent: 70px;
+	margin: 0;
+	padding: 0;
+	border-bottom: 1px solid #eeeeee;
+}
+
+/* main */
+
+div#main {
+	width: 550px;
+	background-color: #ffffff;
+	padding-top: 0px;
+	padding-left: 10px;
+}
+
+div#notice {
+	background-color: #fcc;
+	border: 1px solid #f00;
+}
+
+div#notice p {
+	margin: 0;
+	padding: 10px;
+}
+
+pre {
+	color: #6e8377;
+	background-color: #eaedeb;
+	border-color: #6e8377;
+	border-style: dashed;
+	border-width: 1px;
+	padding: 5px;
+	width: 500px;
+	overflow: auto;
+}
+
+div.log {
+	width: 500px;
+	margin-top: 15px;
+	padding-top: 5px;
+	border-top: 1px dotted #333333;
+}
+
+div.log div.input pre.script {
+	background-color: #ffffeb;
+	border-style: solid;
+}
+
+div.log div.output div.methods {
+	padding: 5px;
+	background-color: #ffffdd;
+	border: 1px solid #ffcc00;
+}
+
+div.log div.output div.classes {
+	padding: 5px;
+	background-color: #ccffcc;
+	border: 1px solid #00ff00;
+}
+
+div.log div.output div.modules {
+	padding: 5px;
+	background-color: #ffcccc;
+	border: 1px solid #ff0000;
+}
+
+div.log div.output pre.result {
+	border-style: dashed;
+}
+
+div.log div.output pre.output {
+	border-style: dashed;
+}
+
+div.log hr.log {
+	border-style: dotted none none none;
+	border-top-width: 1px;
+	border-color: #6e8377;
+	width: 200px;
+	height: 1px;
+}
+
+/* side */
+
+div#side {
+	width: 150px;
+	float: right;
+	margin-top: 20px;
+	text-align: left;
+	font-size: 12px;
+	color: #e44268;
+}
+
+div#side div.title {
+	font-weight: normal;
+	color: #e44268;
+	text-align: left;
+	border-width: 0px 0px 1px 0px;
+	border-bottom: 1px solid #e44268;
+}
+
+div#side a:link {
+	color: #ffffff;
+	text-decoration: none;
+}
+
+div#side a:visited {
+	color: #ffffff;
+	text-decoration: none;
+}
+
+div#side a:hover {
+	color: #cccccc;
+	text-decoration: underline;
+}
+
+div#side ol,ul {
+	margin: 10px;
+	padding-left: 10px;
+}
+
+div#side li {
+	color: #e44268;
+}
+
+div#side img {
+	padding: 5px;
+	/* centering */
+	display: block;
+	margin-left: auto;
+	margin-right: auto;
+	border: 0px;
+}
+
+/* history */
+
+div#history {
+	width: 500px;
+}
+
+div#history div.histtime {
+	background-color: #eaedeb;
+	padding: 5px;
+}
+
+div#history div.histline {
+	background-color: #ffffeb;
+	padding: 5px;
+	font-family: monospace;
+	white-space: pre;
+}
+
+/* command */
+
+div#command {
+	width: 500px;
+}
+
+/* image */
+
+img {
+}
+
+/* em */
+
+em {
+	color: #6e8377;
+	font-style: normal;
+}
+
+/* link */
+
+a {
+	text-decoration: none;
+}
+
+a:link {
+	color: #669933;
+}
+
+a:visited {
+	color: #669933;
+}
+
+a:hover {
+	text-decoration: underline;
+}
+
+/* header */
+
+h1 {
+	font-size: 180%;
+	color: #ffffff;
+	background-color: #6e8377;
+	line-height: 64px;
+	text-align: left;
+	padding-left: 20px;
+}
+
+h2 {
+	font-size: 160%;
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: dashed;
+	border-width: 0px 0px 1px 0px;
+}
+
+h3 {
+	font-size: 140%;
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: dotted;
+	border-width: 0px 0px 1px 0px;
+}
+
+h4 {
+	font-size: 130%;
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: solid;
+	border-width: 0px 0px 1px 0px;
+}
+
+h5 {
+	font-size: 120%;
+	color: #6e8377;
+}
+
+h6 {
+	font-size: 110%;
+	color: #6e8377;
+}
+
+/* list */
+
+dt {
+	color: #6e8377;
+	border-color: #b9c3be;
+	border-style: dashed;
+	border-width: 1px;
+	padding: 5px;
+}
+
+ul {
+	color: #6e8377;
+}
+
+/* table */
+
+table {
+	border: 1px solid #cccccc;
+	border-collapse: collapse;
+}
+
+th {
+	vertical-align: top;
+	padding: 5px;
+}
+
+td {
+	vertical-align: top;
+	padding: 5px;
+}
+
+div#method_list table {
+	border: none;
+}
+
+
+/* form */
+
+input {
+	background-color: #FFFFFF;
+	padding: 2px;
+	font-size: 10px;
+	color: #666666;
+	border: 1px solid #611022;
+	margin-bottom: 2px;
+}
+
+input[type=submit] {
+	background-color: #FFFFFF;
+	padding: 2px;
+	font-size: 10px;
+	color: #ffffff;
+	border: 1px solid #611022;
+	background-color: #E44268;
+	margin-bottom: 2px;
+}
+
+/* textarea */
+
+textarea {
+	background-color: #eaedeb;
+	font-family: monospace;
+	font-size: 12px;
+	overflow: auto;
+	width: 500px;
+	padding: 5px;
+}
+
+
+/* blockquote */
+
+blockquote {
+	color: #6e8377;
+	background-color: #eaedeb;
+	border-color: #6e8377;
+	border-style: dashed;
+	border-width: 1px;
+}
+
+/* media */
+
+@media print {
+	div#main	{ margin-left: 0px; }
+	div#side	{ display: none; }
+}
+
+@media screen {
+	div#main	{ margin-left: 0px; }
+	div#side	{ display: block; }
+}
+

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml

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+<!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">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />	
+<title>BioRuby shell on Rails</title>
+<%= stylesheet_link_tag "bioruby.css" %>
+<%= javascript_include_tag :defaults %>
+</head>
+
+<body>
+
+<div id="content">
+
+ <div id="side">
+  <div class="title">Project</div>
+  <ul>
+   <li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
+  </ul>
+
+  <div class="title">Functions</div>
+  <ul>
+    <li><%= link_to "Console", :action => "index" %></li>
+    <li><%= link_to "History", :action => "history" %></li>
+    <li><%= link_to "Commands", :action => "commands" %></li>
+  </ul>
+
+  <div class="title">Local variables</div>
+  <%= render :partial => "variables" %>
+
+  <br>
+  <a href="http://bioruby.org/"><img src="/images/bioruby/link.gif" border=0></a>
+ </div><!-- side -->
+
+ <div id="title">
+  <p class="titletop">BioRuby shell on Rails</p>
+  <p class="titlesub">Web interface for the BioRuby library</p>
+ </div><!-- title -->
+
+ <div id="main">
+<%= yield %>
+ </div><!-- main -->
+
+</div><!-- content -->
+
+</body>
+
+</html>