--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Class: Fasta [RDoc Documentation]</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <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">Fasta</td>
+ </tr>
+ <tr class="top-aligned-row">
+ <td><strong>In:</strong></td>
+ <td>
+
+
+ <a href="../files/fasta_rb.html">
+
+ fasta.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="#M000033">each</a>
+
+ <a href="#M000034">get_entry</a>
+
+ <a href="#M000032">new</a>
+
+ <a href="#M000031">open</a>
+
+ </div>
+ </div>
+
+ </div>
+
+ <!-- if includes -->
+
+ <div id="includes">
+ <h3 class="section-bar">Included Modules</h3>
+
+ <div id="includes-list">
+
+ <span class="include-name">Enumerable</span>
+
+ </div>
+ </div>
+
+ <div id="section">
+
+
+
+
+ <!-- if method_list -->
+
+ <div id="methods">
+
+ <h3 class="section-bar">Public Class methods</h3>
+
+
+ <div id="method-M000032" class="method-detail">
+ <a name="M000032"></a>
+
+ <div class="method-heading">
+
+ <a href="Fasta.src/M000032.html" target="Code" class="method-signature"
+ onclick="popupCode('Fasta.src/M000032.html');return false;">
+
+ <span class="method-name">new</span><span class="method-args">(io, type=nil)</span>
+
+ </a>
+
+ </div>
+
+ <div class="method-description">
+
+ </div>
+ </div>
+
+
+ <div id="method-M000031" class="method-detail">
+ <a name="M000031"></a>
+
+ <div class="method-heading">
+
+ <a href="Fasta.src/M000031.html" target="Code" class="method-signature"
+ onclick="popupCode('Fasta.src/M000031.html');return false;">
+
+ <span class="method-name">open</span><span class="method-args">(*args) {|fasta| ...}</span>
+
+ </a>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Class method allowing open to be used on files. See File.open.
+</p>
+
+ </div>
+ </div>
+
+
+ <h3 class="section-bar">Public Instance methods</h3>
+
+
+ <div id="method-M000033" class="method-detail">
+ <a name="M000033"></a>
+
+ <div class="method-heading">
+
+ <a href="Fasta.src/M000033.html" target="Code" class="method-signature"
+ onclick="popupCode('Fasta.src/M000033.html');return false;">
+
+ <span class="method-name">each</span><span class="method-args">() {|entry| ...}</span>
+
+ </a>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Iterator method for parsing FASTA enries.
+</p>
+
+ </div>
+ </div>
+
+
+ <div id="method-M000034" class="method-detail">
+ <a name="M000034"></a>
+
+ <div class="method-heading">
+
+ <a href="Fasta.src/M000034.html" target="Code" class="method-signature"
+ onclick="popupCode('Fasta.src/M000034.html');return false;">
+
+ <span class="method-name">get_entry</span><span class="method-args">()</span>
+
+ </a>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to get the next FASTA entry form an ios and return this as a <a
+href="Seq.html">Seq</a> object. If no entry is found or eof then nil is
+returned.
+</p>
+
+ </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>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>open (Fasta)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File fasta.rb, line 33</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(<span class="ruby-operator">*</span><span class="ruby-identifier">args</span>)
+ <span class="ruby-identifier">ios</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-operator">*</span><span class="ruby-identifier">args</span>)
+ <span class="ruby-identifier">fasta</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
+
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
+ <span class="ruby-keyword kw">begin</span>
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">fasta</span>
+ <span class="ruby-keyword kw">ensure</span>
+ <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">close</span>
+ <span class="ruby-keyword kw">end</span>
+
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+ <span class="ruby-keyword kw">else</span>
+ <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">fasta</span>
+ <span class="ruby-keyword kw">end</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>new (Fasta)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File fasta.rb, line 50</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>, <span class="ruby-identifier">type</span>=<span class="ruby-keyword kw">nil</span>)
+ <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
+ <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">type</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>each (Fasta)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File fasta.rb, line 56</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
+ <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">entry</span> = <span class="ruby-identifier">get_entry</span> <span class="ruby-keyword kw">do</span>
+ <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">entry</span>
+ <span class="ruby-keyword kw">end</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>get_entry (Fasta)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File fasta.rb, line 64</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
+ <span class="ruby-identifier">block</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>(<span class="ruby-identifier">$/</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'>'</span>)
+ <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block</span>.<span class="ruby-identifier">nil?</span>
+
+ <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp!</span>(<span class="ruby-identifier">$/</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'>'</span>)
+
+ (<span class="ruby-identifier">seq_name</span>, <span class="ruby-identifier">seq</span>) = <span class="ruby-identifier">block</span>.<span class="ruby-identifier">split</span>(<span class="ruby-identifier">$/</span>, <span class="ruby-value">2</span>)
+
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
+
+ <span class="ruby-identifier">entry</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>
+ <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">type</span> = <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-value">? </span><span class="ruby-keyword kw">nil</span> <span class="ruby-operator">:</span> <span class="ruby-ivar">@type</span>.<span class="ruby-identifier">downcase</span>
+ <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-regexp re">/\s/</span>, <span class="ruby-value str">''</span>)
+ <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span> = <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">sub</span>(<span class="ruby-regexp re">/^>/</span>, <span class="ruby-value str">''</span>).<span class="ruby-identifier">rstrip</span>
+
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">empty?</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">FastaError</span>, <span class="ruby-value str">"Bad FASTA format"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">empty?</span>
+
+ <span class="ruby-identifier">entry</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Class: FastaError [RDoc Documentation]</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <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">FastaError</td>
+ </tr>
+ <tr class="top-aligned-row">
+ <td><strong>In:</strong></td>
+ <td>
+
+
+ <a href="../files/fasta_rb.html">
+
+ fasta.rb
+
+ </a>
+
+
+ <br />
+
+ </td>
+ </tr>
+
+
+ <tr class="top-aligned-row">
+ <td><strong>Parent:</strong></td>
+ <td>
+
+ StandardError
+
+ </td>
+ </tr>
+
+ </table>
+ </div>
+ <!-- banner header -->
+
+ <div id="bodyContent">
+
+ <div id="contextContent">
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with FASTA.
+</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>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>length (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 11</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">length</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-value">? </span><span class="ruby-value">0</span> <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">length</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>is_dna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 18</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_dna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'dna'</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>is_rna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 22</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_rna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'rna'</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>is_protein (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 26</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_protein</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'protein'</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>to_rna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 31</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_rna</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'rna'</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Tt'</span>,<span class="ruby-value str">'Uu'</span>)
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>to_dna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 39</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_dna</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot reverse-transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot reverse-transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'dna'</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Uu'</span>,<span class="ruby-value str">'Tt'</span>)
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>complement (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 47</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot complement 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn'</span> )
+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn'</span> )
+ <span class="ruby-keyword kw">else</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot complement sequence type: #{self.type}"</span>
+ <span class="ruby-keyword kw">end</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>generate (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 60</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate</span>(<span class="ruby-identifier">length</span>,<span class="ruby-identifier">type</span>)
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate negative sequence length: #{length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
+
+ <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
+ <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"dna"</span>
+ <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
+ <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"rna"</span>
+ <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
+ <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"protein"</span>
+ <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
+ <span class="ruby-keyword kw">else</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
+ <span class="ruby-keyword kw">end</span>
+
+ <span class="ruby-identifier">seq_new</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">length</span>) { <span class="ruby-identifier">alph</span>[<span class="ruby-identifier">rand</span>(<span class="ruby-identifier">alph</span>.<span class="ruby-identifier">size</span>)] }.<span class="ruby-identifier">join</span>(<span class="ruby-value str">""</span>)
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq_new</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
+
+ <span class="ruby-identifier">seq_new</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>is_dna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 18</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_dna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'dna'</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>is_rna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 22</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_rna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'rna'</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>is_protein (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 26</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_protein</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value str">'protein'</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>to_rna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 31</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_rna</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'rna'</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Tt'</span>,<span class="ruby-value str">'Uu'</span>)
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>to_dna (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 39</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_dna</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot reverse-transcribe 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot reverse-transcribe sequence type: #{self.type}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'dna'</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>(<span class="ruby-value str">'Uu'</span>,<span class="ruby-value str">'Tt'</span>)
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>to_bp (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 47</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_bp</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq_name"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">nil?</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Missing seq"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
+ <span class="ruby-identifier">record</span> = {}
+ <span class="ruby-identifier">record</span>[<span class="ruby-value str">'SEQ_NAME'</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>
+ <span class="ruby-identifier">record</span>[<span class="ruby-value str">'SEQ'</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>
+ <span class="ruby-identifier">record</span>[<span class="ruby-value str">'SEQ_LEN'</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
+ <span class="ruby-identifier">record</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>complement (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 58</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-value str">"Cannot complement 0 length sequence"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+
+ <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn'</span> )
+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">tr!</span>( <span class="ruby-value str">'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn'</span>, <span class="ruby-value str">'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn'</span> )
+ <span class="ruby-keyword kw">else</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot complement sequence type: #{self.type}"</span>
+ <span class="ruby-keyword kw">end</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>generate (Seq)</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+ <pre><span class="ruby-comment cmt"># File seq.rb, line 71</span>
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate</span>(<span class="ruby-identifier">length</span>,<span class="ruby-identifier">type</span>)
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate negative sequence length: #{length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">length</span> <span class="ruby-operator"><=</span> <span class="ruby-value">0</span>
+
+ <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
+ <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"dna"</span>
+ <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
+ <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"rna"</span>
+ <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
+ <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"protein"</span>
+ <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
+ <span class="ruby-keyword kw">else</span>
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
+ <span class="ruby-keyword kw">end</span>
+
+ <span class="ruby-identifier">seq_new</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">length</span>) { <span class="ruby-identifier">alph</span>[<span class="ruby-identifier">rand</span>(<span class="ruby-identifier">alph</span>.<span class="ruby-identifier">size</span>)] }.<span class="ruby-identifier">join</span>(<span class="ruby-value str">""</span>)
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq_new</span>
+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
+ <span class="ruby-identifier">seq_new</span>
+ <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>Class: SeqError [RDoc Documentation]</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <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">SeqError</td>
+ </tr>
+ <tr class="top-aligned-row">
+ <td><strong>In:</strong></td>
+ <td>
+
+
+ <a href="../files/seq_rb.html">
+
+ seq.rb
+
+ </a>
+
+
+ <br />
+
+ </td>
+ </tr>
+
+
+ <tr class="top-aligned-row">
+ <td><strong>Parent:</strong></td>
+ <td>
+
+ StandardError
+
+ </td>
+ </tr>
+
+ </table>
+ </div>
+ <!-- banner header -->
+
+ <div id="bodyContent">
+
+ <div id="contextContent">
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a href="Seq.html">Seq</a>.
+</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>
--- /dev/null
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+<head>
+ <title>File: fasta.rb [RDoc Documentation]</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <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>fasta.rb</h1>
+ <table class="header-table">
+ <tr class="top-aligned-row">
+ <td><strong>Path:</strong></td>
+ <td>fasta.rb
+
+ </td>
+ </tr>
+ <tr class="top-aligned-row">
+ <td><strong>Last Update:</strong></td>
+ <td>2010-08-17 15:43:01 +0200</td>
+ </tr>
+ </table>
+ </div>
+ <!-- banner header -->
+
+ <div id="bodyContent">
+
+ <div id="contextContent">
+
+ <div id="description">
+ <p>
+This program is free software; you can redistribute it and/or modify it
+under the terms of the GNU General Public License as published by the Free
+Software Foundation; either version 2 of the License, or (at your option)
+any later version.
+</p>
+
+ </div>
+
+ <div id="requires-list">
+ <h3 class="section-bar">Required files</h3>
+
+ <div class="name-list">
+
+ <a href="seq_rb.html">seq</a>
+
+ </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>
projects / biopieces.git / commitdiff