--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+<head>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Base36</title>
+
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+ <ul>
+
+ <li><a href="./base36_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="base36.rb">base36.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
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+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-decode">::decode</a></li>
+
+ <li><a href="#method-c-encode">::encode</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
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+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
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+
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+
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+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Base36</h1>
+
+ <div id="description">
+ <p>
+Class containing methods to encode and decode Base 36. Note that the ALPH
+is [alph + num] and not [num + alph] which prevents us from simply using
+.to_i(36) and .to_s(36).
+</p>
+<p>
+<a
+href="http://en.wikipedia.org/wiki/Base_36">en.wikipedia.org/wiki/Base_36</a>
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="decode-method" class="method-detail ">
+ <a name="method-c-decode"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">decode</span><span
+ class="method-args">(base36)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that decodes a base36 string and returns an integer.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="decode-source">
+<pre>
+ <span class="ruby-comment cmt"># File base36.rb, line 55</span>
+55: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">decode</span>(<span class="ruby-identifier">base36</span>)
+56: <span class="ruby-identifier">raise</span> <span class="ruby-constant">Base36Error</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">base36</span>.<span class="ruby-identifier">empty?</span>
+57:
+58: <span class="ruby-identifier">result</span> = <span class="ruby-value">0</span>
+59: <span class="ruby-identifier">pos</span> = <span class="ruby-value">0</span>
+60:
+61: <span class="ruby-identifier">base36</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">reverse</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
+62: <span class="ruby-identifier">result</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">ALPH</span>.<span class="ruby-identifier">index</span>(<span class="ruby-identifier">char</span>) * (<span class="ruby-constant">BASE36</span> <span class="ruby-operator">**</span> <span class="ruby-identifier">pos</span>)
+63: <span class="ruby-identifier">pos</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+64: <span class="ruby-keyword kw">end</span>
+65:
+66: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">result</span>;
+67: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="encode-method" class="method-detail ">
+ <a name="method-c-encode"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">encode</span><span
+ class="method-args">(num)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that encodes an integer into a base36 string that is returned.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="encode-source">
+<pre>
+ <span class="ruby-comment cmt"># File base36.rb, line 39</span>
+39: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">encode</span>(<span class="ruby-identifier">num</span>)
+40: <span class="ruby-identifier">raise</span> <span class="ruby-constant">Base36Error</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">num</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
+41:
+42: <span class="ruby-identifier">base36</span> = <span class="ruby-value str">""</span>
+43:
+44: <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">num</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
+45: <span class="ruby-identifier">base36</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">ALPH</span>[(<span class="ruby-identifier">num</span> <span class="ruby-operator">%</span> <span class="ruby-constant">BASE36</span>)]
+46: <span class="ruby-identifier">num</span> <span class="ruby-operator">/=</span> <span class="ruby-constant">BASE36</span>
+47: <span class="ruby-keyword kw">end</span>
+48:
+49: <span class="ruby-identifier">base36</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">ALPH</span>[<span class="ruby-value">0</span>] <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">num</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+50:
+51: <span class="ruby-identifier">base36</span>.<span class="ruby-identifier">reverse</span>
+52: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Base36Error</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+
+ <li><a href="./base36_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="base36.rb">base36.rb</a></li>
+
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+
+ </div>
+
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+
+ <!-- Parent Class -->
+
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+ <h3 class="section-header">Parent</h3>
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+
+ <li><a href="./Base36.html">Base36</a></li>
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+ <li><a href="./Base36Error.html">Base36Error</a></li>
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+
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+
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+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
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+
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+
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+
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+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
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+
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+
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+
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+
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+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Base36Error</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a href="Base36.html">Base36</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+<head>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Biopieces</title>
+
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+ <li><a href="./biopieces_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="biopieces.rb">biopieces.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
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+
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+
+
+ <!-- Namespace Contents -->
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+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-each">#each</a></li>
+
+ <li><a href="#method-i-each_record">#each_record</a></li>
+
+ <li><a href="#method-i-mktmpdir">#mktmpdir</a></li>
+
+ <li><a href="#method-i-parse">#parse</a></li>
+
+ <li><a href="#method-i-puts">#puts</a></li>
+
+ <li><a href="#method-i-to_s">#to_s</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ <div id="includes-section" class="section">
+ <h3 class="section-header">Included Modules</h3>
+ <ul class="link-list">
+
+
+ <li><span class="include">Enumerable</span></li>
+
+
+ </ul>
+ </div>
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
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+ class="quicksearch-field" />
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+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
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+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
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+
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+
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+
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+
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+
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+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Biopieces</h1>
+
+ <div id="description">
+ <p>
+<a href="Biopieces.html">Biopieces</a> are command line scripts and uses
+OptionParser to parse command line options according to a list of casts.
+Each cast prescribes the long and short name of the option, the type, if it
+is mandatory, the default value, and allowed and disallowed values. An
+optional list of extra casts can be supplied, and the integrity of the
+casts are checked. Following the command line parsing, the options are
+checked according to the casts. Methods are also included for handling the
+parsing and emitting of Biopiece records, which are ASCII text records
+consisting of lines with a key/value pair separated by a colon and a white
+space ’: ’. Each record is separated by a line with three
+dashes ’—’.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+ <div id="attribute-method-details" class="method-section section">
+ <h3 class="section-header">Attributes</h3>
+
+
+ <div id="out-attribute-method" class="method-detail">
+ <a name="out"></a>
+
+ <a name="out="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">out</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ </div>
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(test=nil, input=STDIN, output=STDOUT)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Initialize a Biopiece and write the status to file. Options are for testing
+purposes only.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 49</span>
+49: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">test</span>=<span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">input</span>=<span class="ruby-constant">STDIN</span>, <span class="ruby-identifier">output</span>=<span class="ruby-constant">STDOUT</span>)
+50: <span class="ruby-ivar">@test</span> = <span class="ruby-identifier">test</span>
+51: <span class="ruby-ivar">@input</span> = <span class="ruby-identifier">input</span>
+52: <span class="ruby-ivar">@output</span> = <span class="ruby-identifier">output</span>
+53: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="each-method" class="method-detail method-alias">
+ <a name="method-i-each"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ </div>
+
+
+
+
+ <div class="aliases">
+ Alias for: <a href="Biopieces.html#method-i-each_record">each_record</a>
+ </div>
+
+ </div>
+
+
+ <div id="each-record-method" class="method-detail ">
+ <a name="method-i-each_record"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each_record</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Open Biopiece input stream if not open and iterate over all Biopiece
+records in the stream.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="each-record-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 66</span>
+66: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each_record</span>
+67: <span class="ruby-ivar">@in</span> = <span class="ruby-constant">Stream</span><span class="ruby-operator">::</span><span class="ruby-identifier">open</span>(<span class="ruby-ivar">@options</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>, <span class="ruby-ivar">@input</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">IO</span>
+68: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">nil?</span>
+69:
+70: <span class="ruby-identifier">record</span> = {}
+71:
+72: <span class="ruby-ivar">@in</span>.<span class="ruby-identifier">each_line</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
+73: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">line</span>
+74: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^([^:]+): (.*)$/</span>
+75: <span class="ruby-identifier">record</span>[<span class="ruby-node">$1</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-node">$2</span>
+76: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^---$/</span>
+77: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">empty?</span>
+78: <span class="ruby-identifier">record</span> = {}
+79: <span class="ruby-keyword kw">else</span>
+80: <span class="ruby-identifier">raise</span> <span class="ruby-node">"Bad record format: #{line}"</span>
+81: <span class="ruby-keyword kw">end</span>
+82: <span class="ruby-keyword kw">end</span>
+83:
+84: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">empty?</span>
+85:
+86: <span class="ruby-keyword kw">self</span> <span class="ruby-comment cmt"># conventionally</span>
+87: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+ <div class="aliases">
+ Also aliased as: <a href="Biopieces.html#method-i-each">each</a>
+ </div>
+
+
+
+ </div>
+
+
+ <div id="mktmpdir-method" class="method-detail ">
+ <a name="method-i-mktmpdir"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">mktmpdir</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Create a temporary directory inside the ENV[“BP_TMP“] dir.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="mktmpdir-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 106</span>
+106: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mktmpdir</span>
+107: <span class="ruby-identifier">time</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">now</span>.<span class="ruby-identifier">to_i</span>
+108: <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
+109: <span class="ruby-identifier">pid</span> = <span class="ruby-identifier">$$</span>
+110: <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_TMP"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/"</span> <span class="ruby-operator">+</span> [<span class="ruby-identifier">user</span>, <span class="ruby-identifier">time</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">pid</span>, <span class="ruby-identifier">pid</span>, <span class="ruby-value str">"bp_tmp"</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"_"</span>)
+111: <span class="ruby-constant">Dir</span>.<span class="ruby-identifier">mkdir</span>(<span class="ruby-identifier">path</span>)
+112: <span class="ruby-constant">Status</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">set_tmpdir</span>(<span class="ruby-identifier">path</span>)
+113: <span class="ruby-identifier">path</span>
+114: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="parse-method" class="method-detail ">
+ <a name="method-i-parse"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">parse</span><span
+ class="method-args">(argv, cast_list=[], script_path=$0)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check the integrity of a list of casts, followed by parsion options from
+argv and finally checking the options according to the casts. Returns nil
+if argv is empty, otherwise an options hash.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="parse-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 58</span>
+58: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">parse</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">cast_list</span>=[], <span class="ruby-identifier">script_path</span>=<span class="ruby-identifier">$0</span>)
+59: <span class="ruby-identifier">casts</span> = <span class="ruby-constant">Casts</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">cast_list</span>)
+60: <span class="ruby-identifier">option_handler</span> = <span class="ruby-constant">OptionHandler</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">casts</span>, <span class="ruby-identifier">script_path</span>, <span class="ruby-ivar">@test</span>)
+61: <span class="ruby-ivar">@options</span> = <span class="ruby-identifier">option_handler</span>.<span class="ruby-identifier">options_parse</span>
+62: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="puts-method" class="method-detail ">
+ <a name="method-i-puts"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">puts</span><span
+ class="method-args">(record)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Open Biopiece output stream if not open and puts record to the stream.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="puts-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 92</span>
+ 92: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">puts</span>(<span class="ruby-identifier">record</span>)
+ 93: <span class="ruby-ivar">@out</span> = <span class="ruby-constant">Stream</span><span class="ruby-operator">::</span><span class="ruby-identifier">open</span>(<span class="ruby-ivar">@options</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>, <span class="ruby-ivar">@output</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">IO</span>
+ 94:
+ 95: <span class="ruby-identifier">record</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">key</span>,<span class="ruby-identifier">value</span><span class="ruby-operator">|</span>
+ 96: <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">"#{key.to_s}: #{value}\n"</span>
+ 97: <span class="ruby-keyword kw">end</span>
+ 98:
+ 99: <span class="ruby-ivar">@out</span>.<span class="ruby-identifier">print</span> <span class="ruby-value str">"---\n"</span>
+100: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-s-method" class="method-detail ">
+ <a name="method-i-to_s"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_s</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="to-s-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 102</span>
+102: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
+103: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: BitArray</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./bitarray_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="bitarray.rb">bitarray.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-%26">#&</a></li>
+
+ <li><a href="#method-i-%5E">#^</a></li>
+
+ <li><a href="#method-i-bit_pos">#bit_pos</a></li>
+
+ <li><a href="#method-i-bit_set">#bit_set</a></li>
+
+ <li><a href="#method-i-bit_set%3F">#bit_set?</a></li>
+
+ <li><a href="#method-i-bits_in_char">#bits_in_char</a></li>
+
+ <li><a href="#method-i-bits_off">#bits_off</a></li>
+
+ <li><a href="#method-i-bits_on">#bits_on</a></li>
+
+ <li><a href="#method-i-byte_pos">#byte_pos</a></li>
+
+ <li><a href="#method-i-init_byte_array">#init_byte_array</a></li>
+
+ <li><a href="#method-i-init_count_array">#init_count_array</a></li>
+
+ <li><a href="#method-i-to_s">#to_s</a></li>
+
+ <li><a href="#method-i-%7C">#|</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">BitArray</h1>
+
+ <div id="description">
+ <p>
+Class containing methods for creating and manipulating a bit array.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+ <div id="attribute-method-details" class="method-section section">
+ <h3 class="section-header">Attributes</h3>
+
+
+ <div id="size-attribute-method" class="method-detail">
+ <a name="size"></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">size</span><span
+ class="attribute-access-type">[R]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="byte-array-attribute-method" class="method-detail">
+ <a name="byte_array"></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">byte_array</span><span
+ class="attribute-access-type">[R]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ </div>
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(size)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to initialize a new bit array of a given size.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 35</span>
+35: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">size</span>)
+36: <span class="ruby-ivar">@size</span> = <span class="ruby-identifier">size</span>
+37: <span class="ruby-ivar">@byte_array</span> = <span class="ruby-identifier">init_byte_array</span>
+38: <span class="ruby-ivar">@count_array</span> = <span class="ruby-identifier">init_count_array</span>
+39: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="--method" class="method-detail ">
+ <a name="method-i-%26"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">&</span><span
+ class="method-args">(ba)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to run bitwise AND (&) on two bit arrays and return the result
+in a new bit array. Bits are copied if they exists in BOTH operands.
+00111100 & 00001101 = 00001100
+</p>
+
+
+
+ <div class="method-source-code"
+ id="--source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 76</span>
+76: <span class="ruby-keyword kw">def</span> &(<span class="ruby-identifier">ba</span>)
+77: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"uneven size of bit arrays: #{self.size} != #{ba.size}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>
+78:
+79: <span class="ruby-identifier">result</span> = <span class="ruby-constant">BitArray</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>)
+80:
+81: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
+82: <span class="ruby-identifier">result</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>] = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span> & <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>).<span class="ruby-identifier">chr</span>
+83: <span class="ruby-keyword kw">end</span>
+84:
+85: <span class="ruby-identifier">result</span>
+86: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="--method" class="method-detail ">
+ <a name="method-i-%5E"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">^</span><span
+ class="method-args">(ba)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to run bitwise XOR (^) on two bit arrays and return the result in a
+new bit array. Bits are copied if they exists in ONE BUT NOT BOTH operands.
+00111100 ^ 00001101 = 00110001
+</p>
+
+
+
+ <div class="method-source-code"
+ id="--source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 106</span>
+106: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">^</span>(<span class="ruby-identifier">ba</span>)
+107: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"uneven size of bit arrays: #{self.size} != #{ba.size}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>
+108:
+109: <span class="ruby-identifier">result</span> = <span class="ruby-constant">BitArray</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>)
+110:
+111: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
+112: <span class="ruby-identifier">result</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>] = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">^</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>).<span class="ruby-identifier">chr</span>
+113: <span class="ruby-keyword kw">end</span>
+114:
+115: <span class="ruby-identifier">result</span>
+116: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="bit-set-method" class="method-detail ">
+ <a name="method-i-bit_set"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">bit_set</span><span
+ class="method-args">(pos)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to set a bit to 1 at a given position in the bit array.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="bit-set-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 42</span>
+42: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bit_set</span>(<span class="ruby-identifier">pos</span>)
+43: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} must be an integer."</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">pos</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
+44: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} outside of range: 0 ... #{@size}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-ivar">@size</span> ).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">pos</span>
+45:
+46: <span class="ruby-ivar">@byte_array</span>[<span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)] = (<span class="ruby-ivar">@byte_array</span>[<span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)].<span class="ruby-identifier">ord</span> <span class="ruby-operator">|</span> <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)).<span class="ruby-identifier">chr</span>
+47: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="bit-set--method" class="method-detail ">
+ <a name="method-i-bit_set%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">bit_set?</span><span
+ class="method-args">(pos)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to check if a bit at a given position in the bit array is set.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="bit-set--source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 50</span>
+50: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bit_set?</span>(<span class="ruby-identifier">pos</span>)
+51: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} must be an integer."</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">pos</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
+52: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Position #{pos} outside of range: 0 ... #{@size}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-ivar">@size</span> ).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">pos</span>
+53:
+54: (<span class="ruby-ivar">@byte_array</span>[<span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)].<span class="ruby-identifier">ord</span> & <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>
+55: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="bits-off-method" class="method-detail ">
+ <a name="method-i-bits_off"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">bits_off</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the number of bits set “off” in a bit
+array.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="bits-off-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 69</span>
+69: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bits_off</span>
+70: <span class="ruby-ivar">@size</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">bits_on</span>
+71: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="bits-on-method" class="method-detail ">
+ <a name="method-i-bits_on"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">bits_on</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the number of bits set “on” in a bit array.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="bits-on-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 58</span>
+58: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bits_on</span>
+59: <span class="ruby-identifier">bits_on</span> = <span class="ruby-value">0</span>
+60:
+61: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
+62: <span class="ruby-identifier">bits_on</span> <span class="ruby-operator">+=</span> <span class="ruby-ivar">@count_array</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>]
+63: <span class="ruby-keyword kw">end</span>
+64:
+65: <span class="ruby-identifier">bits_on</span>
+66: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-s-method" class="method-detail ">
+ <a name="method-i-to_s"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_s</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to convert a bit array to a string.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-s-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 119</span>
+119: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>
+120: <span class="ruby-identifier">string</span> = <span class="ruby-value str">""</span>
+121:
+122: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-ivar">@size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">pos</span><span class="ruby-operator">|</span>
+123: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bit_set?</span> <span class="ruby-identifier">pos</span>
+124: <span class="ruby-identifier">string</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"1"</span>
+125: <span class="ruby-keyword kw">else</span>
+126: <span class="ruby-identifier">string</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"0"</span>
+127: <span class="ruby-keyword kw">end</span>
+128: <span class="ruby-keyword kw">end</span>
+129:
+130: <span class="ruby-identifier">string</span>
+131: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="--method" class="method-detail ">
+ <a name="method-i-%7C"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">|</span><span
+ class="method-args">(ba)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to run bitwise OR (|) on two bit arrays and return the result in a
+new bit array. Bits are copied if they exists in EITHER operands. 00111100
+| 00001101 = 00111101
+</p>
+
+
+
+ <div class="method-source-code"
+ id="--source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 91</span>
+ 91: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">|</span>(<span class="ruby-identifier">ba</span>)
+ 92: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"uneven size of bit arrays: #{self.size} != #{ba.size}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>
+ 93:
+ 94: <span class="ruby-identifier">result</span> = <span class="ruby-constant">BitArray</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ba</span>.<span class="ruby-identifier">size</span>)
+ 95:
+ 96: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>.<span class="ruby-identifier">size</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">byte</span><span class="ruby-operator">|</span>
+ 97: <span class="ruby-identifier">result</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>] = (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">|</span> <span class="ruby-identifier">ba</span>.<span class="ruby-identifier">byte_array</span>[<span class="ruby-identifier">byte</span>].<span class="ruby-identifier">ord</span>).<span class="ruby-identifier">chr</span>
+ 98: <span class="ruby-keyword kw">end</span>
+ 99:
+100: <span class="ruby-identifier">result</span>
+101: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="bit-pos-method" class="method-detail ">
+ <a name="method-i-bit_pos"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">bit_pos</span><span
+ class="method-args">(pos)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the bit position in a byte.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="bit-pos-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 177</span>
+177: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)
+178: <span class="ruby-value">1</span> <span class="ruby-operator"><<</span> (<span class="ruby-constant">BitsInChar</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">-</span> (<span class="ruby-identifier">pos</span> <span class="ruby-operator">%</span> <span class="ruby-constant">BitsInChar</span>))
+179: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="bits-in-char-method" class="method-detail ">
+ <a name="method-i-bits_in_char"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">bits_in_char</span><span
+ class="method-args">(char)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the number of set bits in a char.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="bits-in-char-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 161</span>
+161: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">bits_in_char</span>(<span class="ruby-identifier">char</span>)
+162: <span class="ruby-identifier">bits</span> = <span class="ruby-value">0</span>
+163:
+164: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-constant">BitsInChar</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">pos</span><span class="ruby-operator">|</span>
+165: <span class="ruby-identifier">bits</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span> <span class="ruby-keyword kw">if</span> ((<span class="ruby-identifier">char</span> & <span class="ruby-identifier">bit_pos</span>(<span class="ruby-identifier">pos</span>)) <span class="ruby-operator">!=</span> <span class="ruby-value">0</span>)
+166: <span class="ruby-keyword kw">end</span>
+167:
+168: <span class="ruby-identifier">bits</span>
+169: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="byte-pos-method" class="method-detail ">
+ <a name="method-i-byte_pos"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">byte_pos</span><span
+ class="method-args">(pos)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the byte position in the byte array for a given bit
+position.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="byte-pos-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 172</span>
+172: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">byte_pos</span>(<span class="ruby-identifier">pos</span>)
+173: <span class="ruby-identifier">pos</span> <span class="ruby-operator">/</span> <span class="ruby-constant">BitsInChar</span>
+174: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="init-byte-array-method" class="method-detail ">
+ <a name="method-i-init_byte_array"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">init_byte_array</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to initialize the byte array (string) that constitutes the bit
+array.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="init-byte-array-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 138</span>
+138: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">init_byte_array</span>
+139: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Size must be an integer, not #{@size}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@size</span>.<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Fixnum</span>
+140: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BitArrayError</span>, <span class="ruby-node">"Size must be positive, not #{@size}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@size</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
+141:
+142: <span class="ruby-identifier">byte_array</span> = <span class="ruby-value str">""</span>
+143: <span class="ruby-identifier">byte_array</span> <span class="ruby-operator"><<</span> <span class="ruby-value">0</span>.<span class="ruby-identifier">chr</span> * (((<span class="ruby-ivar">@size</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>) <span class="ruby-operator">/</span> <span class="ruby-constant">BitsInChar</span>) <span class="ruby-operator">+</span> <span class="ruby-value">1</span>)
+144:
+145: <span class="ruby-identifier">byte_array</span>
+146: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="init-count-array-method" class="method-detail ">
+ <a name="method-i-init_count_array"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">init_count_array</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns an array where the element index value is the number of
+bits set for that index value.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="init-count-array-source">
+<pre>
+ <span class="ruby-comment cmt"># File bitarray.rb, line 150</span>
+150: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">init_count_array</span>
+151: <span class="ruby-identifier">count_array</span> = []
+152:
+153: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> (<span class="ruby-value">2</span> <span class="ruby-operator">**</span> <span class="ruby-constant">BitsInChar</span>)).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
+154: <span class="ruby-identifier">count_array</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">bits_in_char</span>(<span class="ruby-identifier">i</span>)
+155: <span class="ruby-keyword kw">end</span>
+156:
+157: <span class="ruby-identifier">count_array</span>
+158: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: BitArrayError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
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+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
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+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./bitarray_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="bitarray.rb">bitarray.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
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+ <!-- Namespace Contents -->
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+ <!-- Method Quickref -->
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+ <!-- Included Modules -->
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+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
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+ <li><a href="./FastaError.html">FastaError</a></li>
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+
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+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">BitArrayError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a
+href="BitArray.html">BitArray</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Boulder</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./boulder_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="boulder.rb">boulder.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link"><a href="Filesys.html">Filesys</a></p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-each">#each</a></li>
+
+ <li><a href="#method-i-to_boulder">#to_boulder</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Boulder</h1>
+
+ <div id="description">
+ <p>
+Class to manipulate boulder records - Lincoln Steins own YAML like format:
+<a
+href="http://stein.cshl.org/boulder/docs/Boulder.html">stein.cshl.org/boulder/docs/Boulder.html</a>
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(input=STDIN, output=STDOUT)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Initialize a <a href="Boulder.html">Boulder</a> object. Options are for
+testing purposes only.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File boulder.rb, line 39</span>
+39: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">input</span>=<span class="ruby-constant">STDIN</span>, <span class="ruby-identifier">output</span>=<span class="ruby-constant">STDOUT</span>)
+40: <span class="ruby-ivar">@input</span> = <span class="ruby-identifier">input</span>
+41: <span class="ruby-ivar">@output</span> = <span class="ruby-identifier">output</span>
+42: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="each-method" class="method-detail ">
+ <a name="method-i-each"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="each-source">
+<pre>
+ <span class="ruby-comment cmt"># File boulder.rb, line 44</span>
+44: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
+45: <span class="ruby-keyword kw">while</span> <span class="ruby-keyword kw">not</span> <span class="ruby-ivar">@input</span>.<span class="ruby-identifier">eof?</span> <span class="ruby-keyword kw">do</span>
+46: <span class="ruby-identifier">block</span> = <span class="ruby-ivar">@input</span>.<span class="ruby-identifier">gets</span>(<span class="ruby-constant">SEP</span>)
+47: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing record seperator"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">block</span> <span class="ruby-operator">=~</span> <span class="ruby-node">/#{SEP}$/</span>
+48:
+49: <span class="ruby-identifier">record</span> = {}
+50:
+51: <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp</span>(<span class="ruby-constant">SEP</span>).<span class="ruby-identifier">each_line</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
+52: <span class="ruby-identifier">key</span>, <span class="ruby-identifier">val</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">'='</span>, <span class="ruby-value">2</span>)
+53:
+54: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing key/value seperator"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">nil?</span>
+55: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing key"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">key</span>.<span class="ruby-identifier">empty?</span>
+56: <span class="ruby-identifier">raise</span> <span class="ruby-constant">BoulderError</span>, <span class="ruby-value str">"Missing value"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">empty?</span>
+57:
+58: <span class="ruby-identifier">record</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">val</span>
+59: <span class="ruby-keyword kw">end</span>
+60:
+61: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span>
+62: <span class="ruby-keyword kw">end</span>
+63: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-boulder-method" class="method-detail ">
+ <a name="method-i-to_boulder"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_boulder</span><span
+ class="method-args">(record)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that converts and returns a hash record as a <a
+href="Boulder.html">Boulder</a> string.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-boulder-source">
+<pre>
+ <span class="ruby-comment cmt"># File boulder.rb, line 67</span>
+67: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_boulder</span>(<span class="ruby-identifier">record</span>)
+68: <span class="ruby-identifier">str</span> = <span class="ruby-value str">""</span>
+69:
+70: <span class="ruby-identifier">record</span>.<span class="ruby-identifier">each_pair</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">key</span>, <span class="ruby-identifier">val</span><span class="ruby-operator">|</span>
+71: <span class="ruby-identifier">str</span> <span class="ruby-operator"><<</span> <span class="ruby-node">"#{key}=#{val}\n"</span>
+72: <span class="ruby-keyword kw">end</span>
+73:
+74: <span class="ruby-identifier">str</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"=\n"</span>
+75:
+76: <span class="ruby-identifier">str</span>
+77: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: BoulderError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
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+
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+ <p>
+Error class for all exceptions to do with option casts.
+</p>
+
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+
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+
+
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+
+
+ <!-- Methods -->
+
+
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+
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+
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--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
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+
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+
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+
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+
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+
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+
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+
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+
+ <li><a href="#method-i-check_val_disallowed">#check_val_disallowed</a></li>
+
+ <li><a href="#method-i-check_val_long">#check_val_long</a></li>
+
+ <li><a href="#method-i-check_val_mandatory">#check_val_mandatory</a></li>
+
+ <li><a href="#method-i-check_val_short">#check_val_short</a></li>
+
+ <li><a href="#method-i-check_val_type">#check_val_type</a></li>
+
+ <li><a href="#method-i-check_values">#check_values</a></li>
+
+ <li><a href="#method-i-long_to_sym">#long_to_sym</a></li>
+
+ <li><a href="#method-i-ubiquitous">#ubiquitous</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
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+
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+ </div>
+
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+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Casts</h1>
+
+ <div id="description">
+ <p>
+Class to handle casts of command line options. Each cast prescribes the
+long and short name of the option, the type, if it is mandatory, the
+default value, and allowed and disallowed values. An optional list of extra
+casts can be supplied, and the integrity of the casts are checked.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+ <div id="constants-list" class="section">
+ <h3 class="section-header">Constants</h3>
+ <dl>
+
+ <dt><a name="TYPES">TYPES</a></dt>
+
+ <dd class="description"></dd>
+
+
+ <dt><a name="MANDATORY">MANDATORY</a></dt>
+
+ <dd class="description"></dd>
+
+
+ </dl>
+ </div>
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(cast_list=[])</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Initialize cast object with an optional options cast list to which
+ubiquitous casts are added after which all casts are checked.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 132</span>
+132: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">cast_list</span>=[])
+133: <span class="ruby-ivar">@cast_list</span> = <span class="ruby-identifier">cast_list</span>
+134: <span class="ruby-identifier">ubiquitous</span>
+135: <span class="ruby-identifier">check</span>
+136: <span class="ruby-identifier">long_to_sym</span>
+137: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">push</span> *<span class="ruby-ivar">@cast_list</span>
+138: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="check-method" class="method-detail ">
+ <a name="method-i-check"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check integrity of the casts.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 151</span>
+151: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check</span>
+152: <span class="ruby-identifier">check_keys</span>
+153: <span class="ruby-identifier">check_values</span>
+154: <span class="ruby-identifier">check_duplicates</span>
+155: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-duplicates-method" class="method-detail ">
+ <a name="method-i-check_duplicates"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_duplicates</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check cast for duplicate long or short options names.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-duplicates-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 237</span>
+237: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_duplicates</span>
+238: <span class="ruby-identifier">check_hash</span> = {}
+239: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+240: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Duplicate argument: '--#{cast[:long]}'"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">check_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+241: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Duplicate argument: '-#{cast[:short]}'"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">check_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>]
+242: <span class="ruby-identifier">check_hash</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-keyword kw">true</span>
+243: <span class="ruby-identifier">check_hash</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>]] = <span class="ruby-keyword kw">true</span>
+244: <span class="ruby-keyword kw">end</span>
+245: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-keys-method" class="method-detail ">
+ <a name="method-i-check_keys"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_keys</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if all mandatory keys are present in casts and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-keys-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 158</span>
+158: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_keys</span>
+159: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+160: <span class="ruby-constant">MANDATORY</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">mandatory</span><span class="ruby-operator">|</span>
+161: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Missing symbol in cast: '#{mandatory.to_sym}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">mandatory</span>.<span class="ruby-identifier">to_sym</span>
+162: <span class="ruby-keyword kw">end</span>
+163: <span class="ruby-keyword kw">end</span>
+164: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-val-allowed-method" class="method-detail ">
+ <a name="method-i-check_val_allowed"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_val_allowed</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if values to allowed are legal and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-val-allowed-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 223</span>
+223: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_allowed</span>(<span class="ruby-identifier">cast</span>)
+224: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>].<span class="ruby-identifier">nil?</span>
+225: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of allowed: '#{cast[:allowed]}'"</span>
+226: <span class="ruby-keyword kw">end</span>
+227: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-val-default-method" class="method-detail ">
+ <a name="method-i-check_val_default"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_val_default</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if values to default are legal and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-val-default-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 213</span>
+213: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_default</span>(<span class="ruby-identifier">cast</span>)
+214: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span>
+215: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">or</span>
+216: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span> <span class="ruby-keyword kw">or</span>
+217: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Float</span>
+218: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of default: '#{cast[:default]}'"</span>
+219: <span class="ruby-keyword kw">end</span>
+220: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-val-disallowed-method" class="method-detail ">
+ <a name="method-i-check_val_disallowed"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_val_disallowed</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if values to disallowed are legal and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-val-disallowed-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 230</span>
+230: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_disallowed</span>(<span class="ruby-identifier">cast</span>)
+231: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>].<span class="ruby-identifier">nil?</span>
+232: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of disallowed: '#{cast[:disallowed]}'"</span>
+233: <span class="ruby-keyword kw">end</span>
+234: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-val-long-method" class="method-detail ">
+ <a name="method-i-check_val_long"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_val_long</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if the values to long are legal and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-val-long-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 180</span>
+180: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_long</span>(<span class="ruby-identifier">cast</span>)
+181: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>].<span class="ruby-identifier">length</span> <span class="ruby-operator">></span> <span class="ruby-value">1</span>
+182: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of long: '#{cast[:long]}'"</span>
+183: <span class="ruby-keyword kw">end</span>
+184: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-val-mandatory-method" class="method-detail ">
+ <a name="method-i-check_val_mandatory"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_val_mandatory</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if values to mandatory are legal and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-val-mandatory-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 206</span>
+206: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_mandatory</span>(<span class="ruby-identifier">cast</span>)
+207: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:mandatory</span>] <span class="ruby-operator">==</span> <span class="ruby-keyword kw">true</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:mandatory</span>] <span class="ruby-operator">==</span> <span class="ruby-keyword kw">false</span>
+208: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of mandatory: '#{cast[:mandatory]}'"</span>
+209: <span class="ruby-keyword kw">end</span>
+210: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-val-short-method" class="method-detail ">
+ <a name="method-i-check_val_short"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_val_short</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if the values to short are legal and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-val-short-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 187</span>
+187: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_short</span>(<span class="ruby-identifier">cast</span>)
+188: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">String</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:short</span>].<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
+189: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of short: '#{cast[:short]}'"</span>
+190: <span class="ruby-keyword kw">end</span>
+191: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-val-type-method" class="method-detail ">
+ <a name="method-i-check_val_type"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_val_type</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if values to type are legal and raise if not.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-val-type-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 194</span>
+194: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_val_type</span>(<span class="ruby-identifier">cast</span>)
+195: <span class="ruby-identifier">type_hash</span> = {}
+196: <span class="ruby-constant">TYPES</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">type</span><span class="ruby-operator">|</span>
+197: <span class="ruby-identifier">type_hash</span>[<span class="ruby-identifier">type</span>] = <span class="ruby-keyword kw">true</span>
+198: <span class="ruby-keyword kw">end</span>
+199:
+200: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">type_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>]
+201: <span class="ruby-identifier">raise</span> <span class="ruby-constant">CastError</span>, <span class="ruby-node">"Illegal cast of type: '#{cast[:type]}'"</span>
+202: <span class="ruby-keyword kw">end</span>
+203: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-values-method" class="method-detail ">
+ <a name="method-i-check_values"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_values</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if all values in casts are valid.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-values-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 167</span>
+167: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_values</span>
+168: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+169: <span class="ruby-identifier">check_val_long</span>(<span class="ruby-identifier">cast</span>)
+170: <span class="ruby-identifier">check_val_short</span>(<span class="ruby-identifier">cast</span>)
+171: <span class="ruby-identifier">check_val_type</span>(<span class="ruby-identifier">cast</span>)
+172: <span class="ruby-identifier">check_val_mandatory</span>(<span class="ruby-identifier">cast</span>)
+173: <span class="ruby-identifier">check_val_default</span>(<span class="ruby-identifier">cast</span>)
+174: <span class="ruby-identifier">check_val_allowed</span>(<span class="ruby-identifier">cast</span>)
+175: <span class="ruby-identifier">check_val_disallowed</span>(<span class="ruby-identifier">cast</span>)
+176: <span class="ruby-keyword kw">end</span>
+177: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="long-to-sym-method" class="method-detail ">
+ <a name="method-i-long_to_sym"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">long_to_sym</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Convert values to :long keys to symbols for all casts.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="long-to-sym-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 248</span>
+248: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">long_to_sym</span>
+249: <span class="ruby-ivar">@cast_list</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+250: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>] = <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>].<span class="ruby-identifier">to_sym</span>
+251: <span class="ruby-keyword kw">end</span>
+252: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="ubiquitous-method" class="method-detail ">
+ <a name="method-i-ubiquitous"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">ubiquitous</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Add ubiquitous options casts.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="ubiquitous-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 143</span>
+143: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">ubiquitous</span>
+144: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'help'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'?'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'flag'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
+145: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'stream_in'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'I'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'files!'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
+146: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'stream_out'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'O'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'file'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
+147: <span class="ruby-ivar">@cast_list</span> <span class="ruby-operator"><<</span> {<span class="ruby-value">:long=</span><span class="ruby-operator">></span><span class="ruby-value str">'verbose'</span>, <span class="ruby-value">:short=</span><span class="ruby-operator">></span><span class="ruby-value str">'v'</span>, <span class="ruby-value">:type=</span><span class="ruby-operator">></span><span class="ruby-value str">'flag'</span>, <span class="ruby-value">:mandatory=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">false</span>, <span class="ruby-value">:default=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:allowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>, <span class="ruby-value">:disallowed=</span><span class="ruby-operator">></span><span class="ruby-keyword kw">nil</span>}
+148: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Digest</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
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+ <div class="section-body">
+ <ul>
+
+ <li><a href="./digest_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="digest.rb">digest.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
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+
+
+ <!-- Namespace Contents -->
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+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-disambiguate">#disambiguate</a></li>
+
+ <li><a href="#method-i-each">#each</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ <div id="includes-section" class="section">
+ <h3 class="section-header">Included Modules</h3>
+ <ul class="link-list">
+
+
+ <li><span class="include">Enumerable</span></li>
+
+
+ </ul>
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+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
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+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Digest</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(seq, pattern, cut_pos)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Initialize a digest object with the following arguments:
+</p>
+<ul>
+<li><p>
+seq: A sequence object.
+</p>
+</li>
+<li><p>
+pattern: A restriction enzyme recognition pattern.
+</p>
+</li>
+<li><p>
+cut_pos: Offset from match position where the enzyme cuts.
+</p>
+</li>
+</ul>
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File digest.rb, line 37</span>
+37: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">seq</span>, <span class="ruby-identifier">pattern</span>, <span class="ruby-identifier">cut_pos</span>)
+38: <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">seq</span>
+39: <span class="ruby-ivar">@pattern</span> = <span class="ruby-identifier">disambiguate</span>(<span class="ruby-identifier">pattern</span>)
+40: <span class="ruby-ivar">@cut_pos</span> = <span class="ruby-identifier">cut_pos</span>
+41: <span class="ruby-ivar">@offset</span> = <span class="ruby-value">0</span>
+42: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="each-method" class="method-detail ">
+ <a name="method-i-each"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to get the next digestion product from a sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="each-source">
+<pre>
+ <span class="ruby-comment cmt"># File digest.rb, line 45</span>
+45: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
+46: <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">scan</span> <span class="ruby-ivar">@pattern</span> <span class="ruby-keyword kw">do</span>
+47: <span class="ruby-identifier">pos</span> = <span class="ruby-node">$`</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@cut_pos</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+48:
+49: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">>=</span> <span class="ruby-value">0</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">2</span>
+50: <span class="ruby-identifier">seq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-node">"#{@seq.seq_name}[#{@offset}-#{pos}]"</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-ivar">@offset</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">pos</span>], <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">type</span>)
+51:
+52: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">seq</span>
+53: <span class="ruby-keyword kw">end</span>
+54:
+55: <span class="ruby-ivar">@offset</span> = <span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+56: <span class="ruby-keyword kw">end</span>
+57:
+58: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@offset</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span>
+59: <span class="ruby-ivar">@offset</span> = <span class="ruby-value">0</span>
+60: <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@offset</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">length</span>
+61: <span class="ruby-ivar">@offset</span> = <span class="ruby-value">0</span>
+62: <span class="ruby-keyword kw">end</span>
+63:
+64: <span class="ruby-identifier">seq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-node">"#{@seq.seq_name}[#{@offset}-#{@seq.length - 1}]"</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-ivar">@offset</span> <span class="ruby-operator">..</span> <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">length</span>], <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">type</span>)
+65:
+66: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">seq</span>
+67:
+68: <span class="ruby-keyword kw">self</span> <span class="ruby-comment cmt"># conventionally</span>
+69: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="disambiguate-method" class="method-detail ">
+ <a name="method-i-disambiguate"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">disambiguate</span><span
+ class="method-args">(pattern)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns a regexp object with a restriction enzyme pattern with
+ambiguity codes substituted to the appropriate regexp.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="disambiguate-source">
+<pre>
+ <span class="ruby-comment cmt"># File digest.rb, line 76</span>
+ 76: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">disambiguate</span>(<span class="ruby-identifier">pattern</span>)
+ 77: <span class="ruby-identifier">ambiguity</span> = {
+ 78: <span class="ruby-value str">'A'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"A"</span>,
+ 79: <span class="ruby-value str">'T'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"T"</span>,
+ 80: <span class="ruby-value str">'U'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"T"</span>,
+ 81: <span class="ruby-value str">'C'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"C"</span>,
+ 82: <span class="ruby-value str">'G'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"G"</span>,
+ 83: <span class="ruby-value str">'M'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AC]"</span>,
+ 84: <span class="ruby-value str">'R'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AG]"</span>,
+ 85: <span class="ruby-value str">'W'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AT]"</span>,
+ 86: <span class="ruby-value str">'S'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[CG]"</span>,
+ 87: <span class="ruby-value str">'Y'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[CT]"</span>,
+ 88: <span class="ruby-value str">'K'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[GT]"</span>,
+ 89: <span class="ruby-value str">'V'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[ACG]"</span>,
+ 90: <span class="ruby-value str">'H'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[ACT]"</span>,
+ 91: <span class="ruby-value str">'D'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[AGT]"</span>,
+ 92: <span class="ruby-value str">'B'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[CGT]"</span>,
+ 93: <span class="ruby-value str">'N'</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"[GATC]"</span>
+ 94: }
+ 95:
+ 96: <span class="ruby-identifier">new_pattern</span> = <span class="ruby-value str">""</span>
+ 97:
+ 98: <span class="ruby-identifier">pattern</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
+ 99: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">ambiguity</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">char</span>
+100: <span class="ruby-identifier">new_pattern</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">ambiguity</span>[<span class="ruby-identifier">char</span>]
+101: <span class="ruby-keyword kw">else</span>
+102: <span class="ruby-identifier">raise</span> <span class="ruby-constant">DigestError</span>, <span class="ruby-node">"Could not disambiguate residue: #{char}"</span>
+103: <span class="ruby-keyword kw">end</span>
+104: <span class="ruby-keyword kw">end</span>
+105:
+106: <span class="ruby-constant">Regexp</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">new_pattern</span>)
+107: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: DigestError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./digest_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="digest.rb">digest.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
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+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">DigestError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a href="Digest.html">Digest</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Fasta</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
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+ <h3 class="section-header">In Files</h3>
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+
+ <li><a href="./fasta_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="fasta.rb">fasta.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link"><a href="Filesys.html">Filesys</a></p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-i-get_entry">#get_entry</a></li>
+
+ <li><a href="#method-i-puts">#puts</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Fasta</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="get-entry-method" class="method-detail ">
+ <a name="method-i-get_entry"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">get_entry</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </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 class="method-source-code"
+ id="get-entry-source">
+<pre>
+ <span class="ruby-comment cmt"># File fasta.rb, line 34</span>
+34: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
+35: <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>)
+36: <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>
+37:
+38: <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp!</span>(<span class="ruby-identifier">$/</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'>'</span>)
+39:
+40: (<span class="ruby-identifier">seq_name</span>, <span class="ruby-identifier">seq</span>) = <span class="ruby-identifier">block</span>.<span class="ruby-identifier">split</span>(<span class="ruby-identifier">$/</span>, <span class="ruby-value">2</span>)
+41:
+42: <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>
+43:
+44: <span class="ruby-identifier">entry</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>
+45: <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-operator">?</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>
+46: <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>)
+47: <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>
+48:
+49: <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>
+50: <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>
+51:
+52: <span class="ruby-identifier">entry</span>
+53: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="puts-method" class="method-detail ">
+ <a name="method-i-puts"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">puts</span><span
+ class="method-args">(record)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+TODO - this should be some custom to_s method instead.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="puts-source">
+<pre>
+ <span class="ruby-comment cmt"># File fasta.rb, line 56</span>
+56: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">puts</span>(<span class="ruby-identifier">record</span>)
+57: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ_NAME</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ</span>
+58: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">">#{record[:SEQ_NAME]}\n"</span>
+59: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">"#{record[:SEQ]}\n"</span>
+60: <span class="ruby-keyword kw">end</span>
+61: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: FastaError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+
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+
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+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./fasta_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="fasta.rb">fasta.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">FastaError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with FASTA.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Fastq</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./fastq_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="fastq.rb">fastq.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link"><a href="Filesys.html">Filesys</a></p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-i-get_entry">#get_entry</a></li>
+
+ <li><a href="#method-i-puts">#puts</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Fastq</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="get-entry-method" class="method-detail ">
+ <a name="method-i-get_entry"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">get_entry</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to get the next FASTQ 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 class="method-source-code"
+ id="get-entry-source">
+<pre>
+ <span class="ruby-comment cmt"># File fastq.rb, line 34</span>
+34: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
+35: <span class="ruby-keyword kw">begin</span>
+36: <span class="ruby-identifier">seq_name</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
+37: <span class="ruby-identifier">seq</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
+38: <span class="ruby-identifier">qual_name</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
+39: <span class="ruby-identifier">qual</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>.<span class="ruby-identifier">chomp!</span>
+40:
+41: <span class="ruby-identifier">entry</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>
+42: <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-operator">?</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>
+43: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq</span>
+44: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">seq_name</span> = <span class="ruby-identifier">seq_name</span>[<span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">seq_name</span>.<span class="ruby-identifier">length</span>]
+45: <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-identifier">qual</span>
+46:
+47: <span class="ruby-identifier">entry</span>
+48: <span class="ruby-keyword kw">rescue</span>
+49: <span class="ruby-keyword kw">nil</span>
+50: <span class="ruby-keyword kw">end</span>
+51: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="puts-method" class="method-detail ">
+ <a name="method-i-puts"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">puts</span><span
+ class="method-args">(record)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+TODO - this should be some custom to_s method instead.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="puts-source">
+<pre>
+ <span class="ruby-comment cmt"># File fastq.rb, line 54</span>
+54: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">puts</span>(<span class="ruby-identifier">record</span>)
+55: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ_NAME</span> <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">record</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-value">:SEQ</span>
+56: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">">#{record[:SEQ_NAME]}\n"</span>
+57: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">print</span> <span class="ruby-node">"#{record[:SEQ]}\n"</span>
+58: <span class="ruby-keyword kw">end</span>
+59: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: FastqError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./fastq_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="fastq.rb">fastq.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">FastqError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with FASTQ.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Filesys</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./filesys_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="filesys.rb">filesys.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-c-open">::open</a></li>
+
+ <li><a href="#method-c-zopen">::zopen</a></li>
+
+ <li><a href="#method-i-close">#close</a></li>
+
+ <li><a href="#method-i-each">#each</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ <div id="includes-section" class="section">
+ <h3 class="section-header">Included Modules</h3>
+ <ul class="link-list">
+
+
+ <li><span class="include">Enumerable</span></li>
+
+
+ </ul>
+ </div>
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Filesys</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(io, type=nil)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File filesys.rb, line 58</span>
+58: <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>)
+59: <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
+60: <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">type</span>
+61: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="open-method" class="method-detail ">
+ <a name="method-c-open"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">open</span><span
+ class="method-args">(*args)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Class method allowing open to be used on (zipped) files. See File.open.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="open-source">
+<pre>
+ <span class="ruby-comment cmt"># File filesys.rb, line 35</span>
+35: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
+36: <span class="ruby-identifier">args</span> = *<span class="ruby-identifier">args</span>
+37: <span class="ruby-identifier">file</span> = <span class="ruby-identifier">args</span>.<span class="ruby-identifier">first</span>
+38:
+39: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">file</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"-"</span>
+40: <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-constant">STDIN</span>)
+41: <span class="ruby-keyword kw">elsif</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">pipe?</span> <span class="ruby-identifier">file</span>
+42: <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>))
+43: <span class="ruby-keyword kw">else</span>
+44: <span class="ruby-identifier">ios</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zopen</span>(*<span class="ruby-identifier">args</span>)
+45: <span class="ruby-keyword kw">end</span>
+46:
+47: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
+48: <span class="ruby-keyword kw">begin</span>
+49: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">ios</span>
+50: <span class="ruby-keyword kw">ensure</span>
+51: <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">close</span>
+52: <span class="ruby-keyword kw">end</span>
+53: <span class="ruby-keyword kw">else</span>
+54: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">ios</span>
+55: <span class="ruby-keyword kw">end</span>
+56: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-class-method-details" class="method-section section">
+ <h3 class="section-header">Private Class Methods</h3>
+
+
+ <div id="zopen-method" class="method-detail ">
+ <a name="method-c-zopen"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">zopen</span><span
+ class="method-args">(*args)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Helper method to return an ios to a file that may be zipped in which case
+the ios is unzipped on the fly. See File.open.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="zopen-source">
+<pre>
+ <span class="ruby-comment cmt"># File filesys.rb, line 79</span>
+79: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zopen</span>(*<span class="ruby-identifier">args</span>)
+80: <span class="ruby-identifier">ios</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
+81:
+82: <span class="ruby-keyword kw">begin</span>
+83: <span class="ruby-identifier">ios</span> = <span class="ruby-constant">Zlib</span><span class="ruby-operator">::</span><span class="ruby-constant">GzipReader</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
+84: <span class="ruby-keyword kw">rescue</span>
+85: <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">rewind</span>
+86: <span class="ruby-keyword kw">end</span>
+87:
+88: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
+89: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="close-method" class="method-detail ">
+ <a name="method-i-close"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">close</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to close ios.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="close-source">
+<pre>
+ <span class="ruby-comment cmt"># File filesys.rb, line 64</span>
+64: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>
+65: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">close</span>
+66: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="each-method" class="method-detail ">
+ <a name="method-i-each"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Iterator method for parsing entries.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="each-source">
+<pre>
+ <span class="ruby-comment cmt"># File filesys.rb, line 69</span>
+69: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
+70: <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>
+71: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">entry</span>
+72: <span class="ruby-keyword kw">end</span>
+73: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: FilesysError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./filesys_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="filesys.rb">filesys.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">FilesysError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a
+href="Filesys.html">Filesys</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Genbank</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="genbank.rb">genbank.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link"><a href="Filesys.html">Filesys</a></p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-each">#each</a></li>
+
+ <li><a href="#method-i-get_entry">#get_entry</a></li>
+
+ <li><a href="#method-i-get_keys">#get_keys</a></li>
+
+ <li><a href="#method-i-get_seq">#get_seq</a></li>
+
+ <li><a href="#method-i-want_key%3F">#want_key?</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Genbank</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(io)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 32</span>
+32: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>)
+33: <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
+34: <span class="ruby-ivar">@entry</span> = []
+35: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="each-method" class="method-detail ">
+ <a name="method-i-each"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each</span><span
+ class="method-args">(hash_keys, hash_feats, hash_quals)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Iterator method for parsing <a href="Genbank.html">Genbank</a> entries.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="each-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 38</span>
+38: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>(<span class="ruby-identifier">hash_keys</span>, <span class="ruby-identifier">hash_feats</span>, <span class="ruby-identifier">hash_quals</span>)
+39: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span> = <span class="ruby-identifier">get_entry</span> <span class="ruby-keyword kw">do</span>
+40: <span class="ruby-identifier">keys</span> = <span class="ruby-identifier">get_keys</span>(<span class="ruby-identifier">hash_keys</span>)
+41: <span class="ruby-identifier">seq</span> = <span class="ruby-identifier">get_seq</span>
+42:
+43: <span class="ruby-identifier">features</span> = <span class="ruby-constant">GenbankFeatures</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@entry</span>, <span class="ruby-identifier">hash_feats</span>, <span class="ruby-identifier">hash_quals</span>)
+44:
+45: <span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">record</span><span class="ruby-operator">|</span>
+46: <span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each_pair</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">key</span>,<span class="ruby-identifier">val</span><span class="ruby-operator">|</span> <span class="ruby-identifier">record</span>[<span class="ruby-identifier">key</span>] = <span class="ruby-identifier">val</span> }
+47:
+48: <span class="ruby-identifier">loc</span> = <span class="ruby-constant">Locator</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">record</span>[<span class="ruby-value">:LOCATOR</span>], <span class="ruby-identifier">seq</span>)
+49: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">subseq</span>.<span class="ruby-identifier">seq</span>
+50: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ_LEN</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">subseq</span>.<span class="ruby-identifier">length</span>
+51: <span class="ruby-identifier">record</span>[<span class="ruby-value">:STRAND</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">strand</span>
+52: <span class="ruby-identifier">record</span>[<span class="ruby-value">:S_BEG</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">s_beg</span>
+53: <span class="ruby-identifier">record</span>[<span class="ruby-value">:S_END</span>] = <span class="ruby-identifier">loc</span>.<span class="ruby-identifier">s_end</span>
+54:
+55: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span>
+56: <span class="ruby-keyword kw">end</span>
+57: <span class="ruby-keyword kw">end</span>
+58: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="get-entry-method" class="method-detail ">
+ <a name="method-i-get_entry"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">get_entry</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to get the next <a href="Genbank.html">Genbank</a> entry form an ios
+and return this.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="get-entry-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 63</span>
+63: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_entry</span>
+64: <span class="ruby-identifier">block</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">gets</span>(<span class="ruby-value str">"//"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">$/</span>)
+65: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block</span>.<span class="ruby-identifier">nil?</span>
+66:
+67: <span class="ruby-identifier">block</span>.<span class="ruby-identifier">chomp!</span>(<span class="ruby-value str">"//"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">$/</span> )
+68:
+69: <span class="ruby-identifier">entry</span> = <span class="ruby-identifier">block</span>.<span class="ruby-identifier">split</span> <span class="ruby-identifier">$/</span>
+70:
+71: <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">entry</span>.<span class="ruby-identifier">empty?</span>
+72:
+73: <span class="ruby-identifier">entry</span>
+74: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="get-keys-method" class="method-detail ">
+ <a name="method-i-get_keys"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">get_keys</span><span
+ class="method-args">(hash_keys)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to get the base keys from <a href="Genbank.html">Genbank</a> entry
+and return these in a hash.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="get-keys-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 93</span>
+ 93: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_keys</span>(<span class="ruby-identifier">hash_keys</span>)
+ 94: <span class="ruby-identifier">keys</span> = {}
+ 95: <span class="ruby-identifier">i</span> = <span class="ruby-value">0</span>
+ 96: <span class="ruby-identifier">j</span> = <span class="ruby-value">0</span>
+ 97:
+ 98: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^FEATURES/</span>
+ 99: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^\s{0,3}([A-Z]{2})/</span>
+100: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">want_key?</span>(<span class="ruby-identifier">hash_keys</span>, <span class="ruby-node">$1</span>)
+101: <span class="ruby-identifier">j</span> = <span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+102:
+103: <span class="ruby-identifier">key</span>, <span class="ruby-identifier">val</span> = <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">lstrip</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\s+/</span>, <span class="ruby-value">2</span>)
+104:
+105: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^\s{0,3}[A-Z]/</span>
+106: <span class="ruby-identifier">val</span> <span class="ruby-operator"><<</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>].<span class="ruby-identifier">lstrip</span>
+107: <span class="ruby-identifier">j</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+108: <span class="ruby-keyword kw">end</span>
+109:
+110: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>]
+111: <span class="ruby-identifier">keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>] <span class="ruby-operator"><<</span> <span class="ruby-value str">";"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">val</span>
+112: <span class="ruby-keyword kw">else</span>
+113: <span class="ruby-identifier">keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">val</span>
+114: <span class="ruby-keyword kw">end</span>
+115: <span class="ruby-keyword kw">end</span>
+116: <span class="ruby-keyword kw">end</span>
+117:
+118: <span class="ruby-identifier">j</span> <span class="ruby-operator">></span> <span class="ruby-identifier">i</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">i</span> = <span class="ruby-identifier">j</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+119: <span class="ruby-keyword kw">end</span>
+120:
+121: <span class="ruby-identifier">keys</span>
+122: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="get-seq-method" class="method-detail ">
+ <a name="method-i-get_seq"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">get_seq</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to get the DNA sequence from a <a href="Genbank.html">Genbank</a>
+entry and return this as a <a href="Seq.html">Seq</a> object.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="get-seq-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 78</span>
+78: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_seq</span>
+79: <span class="ruby-identifier">i</span> = <span class="ruby-ivar">@entry</span>.<span class="ruby-identifier">size</span>
+80: <span class="ruby-identifier">j</span> = <span class="ruby-identifier">i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+81:
+82: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^[A-Z]/</span>
+83: <span class="ruby-identifier">j</span> <span class="ruby-operator">-=</span> <span class="ruby-value">1</span>
+84: <span class="ruby-keyword kw">end</span>
+85:
+86: <span class="ruby-identifier">seq</span> = <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">j</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">i</span>].<span class="ruby-identifier">join</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value str">" 0123456789"</span>)
+87:
+88: <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">seq</span>, <span class="ruby-value str">"dna"</span>) <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">seq</span>
+89: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="want-key--method" class="method-detail ">
+ <a name="method-i-want_key%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">want_key?</span><span
+ class="method-args">(hash_keys, key)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="want-key--source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 124</span>
+124: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">want_key?</span>(<span class="ruby-identifier">hash_keys</span>, <span class="ruby-identifier">key</span>)
+125: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hash_keys</span>
+126: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hash_keys</span>[<span class="ruby-identifier">key</span>.<span class="ruby-identifier">to_sym</span>]
+127: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+128: <span class="ruby-keyword kw">else</span>
+129: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+130: <span class="ruby-keyword kw">end</span>
+131: <span class="ruby-keyword kw">else</span>
+132: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+133: <span class="ruby-keyword kw">end</span>
+134: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: GenbankError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="genbank.rb">genbank.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">GenbankError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a
+href="Genbank.html">Genbank</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: GenbankFeatures</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="genbank.rb">genbank.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-each">#each</a></li>
+
+ <li><a href="#method-i-get_quals">#get_quals</a></li>
+
+ <li><a href="#method-i-want_feat%3F">#want_feat?</a></li>
+
+ <li><a href="#method-i-want_qual%3F">#want_qual?</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">GenbankFeatures</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(entry, hash_feats, hash_quals)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 141</span>
+141: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">entry</span>, <span class="ruby-identifier">hash_feats</span>, <span class="ruby-identifier">hash_quals</span>)
+142: <span class="ruby-ivar">@entry</span> = <span class="ruby-identifier">entry</span>
+143: <span class="ruby-ivar">@hash_feats</span> = <span class="ruby-identifier">hash_feats</span>
+144: <span class="ruby-ivar">@hash_quals</span> = <span class="ruby-identifier">hash_quals</span>
+145: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="each-method" class="method-detail ">
+ <a name="method-i-each"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="each-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 147</span>
+147: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
+148: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^ORIGIN/</span>
+149: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>] <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^\s{5}([A-Za-z_-]+)/</span>
+150: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">want_feat?</span> <span class="ruby-node">$1</span>
+151: <span class="ruby-identifier">record</span> = {}
+152:
+153: <span class="ruby-identifier">feat</span>, <span class="ruby-identifier">loc</span> = <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@i</span>].<span class="ruby-identifier">lstrip</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\s+/</span>, <span class="ruby-value">2</span>)
+154:
+155: <span class="ruby-identifier">@@j</span> = <span class="ruby-identifier">@@i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+156:
+157: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/</span>
+158: <span class="ruby-identifier">loc</span> <span class="ruby-operator"><<</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>].<span class="ruby-identifier">lstrip</span>
+159: <span class="ruby-identifier">@@j</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+160: <span class="ruby-keyword kw">end</span>
+161:
+162: <span class="ruby-identifier">get_quals</span>.<span class="ruby-identifier">each_pair</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
+163: <span class="ruby-identifier">record</span>[<span class="ruby-identifier">k</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">v</span>
+164: }
+165:
+166: <span class="ruby-identifier">record</span>[<span class="ruby-value">:FEATURE</span>] = <span class="ruby-identifier">feat</span>
+167: <span class="ruby-identifier">record</span>[<span class="ruby-value">:LOCATOR</span>] = <span class="ruby-identifier">loc</span>
+168:
+169: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">record</span>
+170: <span class="ruby-keyword kw">end</span>
+171: <span class="ruby-keyword kw">end</span>
+172:
+173: <span class="ruby-identifier">@@j</span> <span class="ruby-operator">></span> <span class="ruby-identifier">@@i</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">@@i</span> = <span class="ruby-identifier">@@j</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">@@i</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+174: <span class="ruby-keyword kw">end</span>
+175: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="get-quals-method" class="method-detail ">
+ <a name="method-i-get_quals"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">get_quals</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="get-quals-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 179</span>
+179: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_quals</span>
+180: <span class="ruby-identifier">quals</span> = {}
+181: <span class="ruby-identifier">k</span> = <span class="ruby-value">0</span>
+182:
+183: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^\s{5}[A-Za-z_-]|^[A-Z]/</span>
+184: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">@@j</span>] <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^\s{21}\/([^=]+)="([^"]+)/</span>
+185: <span class="ruby-identifier">qual</span> = <span class="ruby-node">$1</span>
+186: <span class="ruby-identifier">val</span> = <span class="ruby-node">$2</span>
+187:
+188: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">want_qual?</span> <span class="ruby-identifier">qual</span>
+189: <span class="ruby-identifier">k</span> = <span class="ruby-identifier">@@j</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
+190:
+191: <span class="ruby-keyword kw">while</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">k</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">k</span>] <span class="ruby-operator">!~</span> <span class="ruby-regexp re">/^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/</span>
+192: <span class="ruby-identifier">val</span> <span class="ruby-operator"><<</span> <span class="ruby-ivar">@entry</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">lstrip</span>.<span class="ruby-identifier">chomp</span>(<span class="ruby-value str">'"'</span>)
+193: <span class="ruby-identifier">k</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+194: <span class="ruby-keyword kw">end</span>
+195:
+196: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">quals</span>[<span class="ruby-identifier">qual</span>]
+197: <span class="ruby-identifier">quals</span>[<span class="ruby-identifier">qual</span>] <span class="ruby-operator"><<</span> <span class="ruby-value str">";"</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">val</span>
+198: <span class="ruby-keyword kw">else</span>
+199: <span class="ruby-identifier">quals</span>[<span class="ruby-identifier">qual</span>] = <span class="ruby-identifier">val</span>
+200: <span class="ruby-keyword kw">end</span>
+201: <span class="ruby-keyword kw">end</span>
+202: <span class="ruby-keyword kw">end</span>
+203:
+204: <span class="ruby-identifier">k</span> <span class="ruby-operator">></span> <span class="ruby-identifier">@@j</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">@@j</span> = <span class="ruby-identifier">k</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">@@j</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+205: <span class="ruby-keyword kw">end</span>
+206:
+207: <span class="ruby-identifier">quals</span>
+208: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="want-feat--method" class="method-detail ">
+ <a name="method-i-want_feat%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">want_feat?</span><span
+ class="method-args">(feat)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="want-feat--source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 210</span>
+210: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">want_feat?</span>(<span class="ruby-identifier">feat</span>)
+211: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_feats</span>
+212: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_feats</span>[<span class="ruby-identifier">feat</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">to_sym</span>]
+213: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+214: <span class="ruby-keyword kw">else</span>
+215: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+216: <span class="ruby-keyword kw">end</span>
+217: <span class="ruby-keyword kw">else</span>
+218: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+219: <span class="ruby-keyword kw">end</span>
+220: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="want-qual--method" class="method-detail ">
+ <a name="method-i-want_qual%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">want_qual?</span><span
+ class="method-args">(qual)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="want-qual--source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 222</span>
+222: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">want_qual?</span>(<span class="ruby-identifier">qual</span>)
+223: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_quals</span>
+224: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@hash_quals</span>[<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">to_sym</span>]
+225: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+226: <span class="ruby-keyword kw">else</span>
+227: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+228: <span class="ruby-keyword kw">end</span>
+229: <span class="ruby-keyword kw">else</span>
+230: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+231: <span class="ruby-keyword kw">end</span>
+232: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Locator</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="genbank.rb">genbank.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-balance_parens%3F">#balance_parens?</a></li>
+
+ <li><a href="#method-i-parse_locator">#parse_locator</a></li>
+
+ <li><a href="#method-i-s_beg">#s_beg</a></li>
+
+ <li><a href="#method-i-s_end">#s_end</a></li>
+
+ <li><a href="#method-i-strand">#strand</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Locator</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+ <div id="attribute-method-details" class="method-section section">
+ <h3 class="section-header">Attributes</h3>
+
+
+ <div id="locator-attribute-method" class="method-detail">
+ <a name="locator"></a>
+
+ <a name="locator="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">locator</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="seq-attribute-method" class="method-detail">
+ <a name="seq"></a>
+
+ <a name="seq="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">seq</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="subseq-attribute-method" class="method-detail">
+ <a name="subseq"></a>
+
+ <a name="subseq="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">subseq</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ </div>
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(locator, seq)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 242</span>
+242: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">seq</span>)
+243: <span class="ruby-ivar">@locator</span> = <span class="ruby-identifier">locator</span>
+244: <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">seq</span>
+245: <span class="ruby-ivar">@subseq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-value str">""</span>, <span class="ruby-value str">"dna"</span>)
+246: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>)
+247: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="s-beg-method" class="method-detail ">
+ <a name="method-i-s_beg"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">s_beg</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="s-beg-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 257</span>
+257: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">s_beg</span>
+258: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@locator</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/(\d+)/</span>
+259: <span class="ruby-keyword kw">return</span> <span class="ruby-node">$1</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+260: <span class="ruby-keyword kw">end</span>
+261: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="s-end-method" class="method-detail ">
+ <a name="method-i-s_end"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">s_end</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="s-end-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 263</span>
+263: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">s_end</span>
+264: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@locator</span>.<span class="ruby-identifier">reverse</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/(\d+)/</span>
+265: <span class="ruby-keyword kw">return</span> <span class="ruby-node">$1</span>.<span class="ruby-identifier">reverse</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+266: <span class="ruby-keyword kw">end</span>
+267: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="strand-method" class="method-detail ">
+ <a name="method-i-strand"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">strand</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="strand-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 249</span>
+249: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">strand</span>
+250: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@locator</span>.<span class="ruby-identifier">match</span>(<span class="ruby-value str">"complement"</span>)
+251: <span class="ruby-keyword kw">return</span> <span class="ruby-value str">"-"</span>
+252: <span class="ruby-keyword kw">else</span>
+253: <span class="ruby-keyword kw">return</span> <span class="ruby-value str">"+"</span>
+254: <span class="ruby-keyword kw">end</span>
+255: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="balance-parens--method" class="method-detail ">
+ <a name="method-i-balance_parens%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">balance_parens?</span><span
+ class="method-args">(locator)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="balance-parens--source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 342</span>
+342: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">balance_parens?</span>(<span class="ruby-identifier">locator</span>)
+343: <span class="ruby-identifier">parens</span> = <span class="ruby-value">0</span>
+344:
+345: <span class="ruby-identifier">locator</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
+346: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">char</span>
+347: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'('</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">parens</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+348: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">')'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">parens</span> <span class="ruby-operator">-=</span> <span class="ruby-value">1</span>
+349: <span class="ruby-keyword kw">end</span>
+350: <span class="ruby-keyword kw">end</span>
+351:
+352: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">parens</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+353: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+354: <span class="ruby-keyword kw">else</span>
+355: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+356: <span class="ruby-keyword kw">end</span>
+357: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="parse-locator-method" class="method-detail ">
+ <a name="method-i-parse_locator"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">parse_locator</span><span
+ class="method-args">(locator, join = nil, comp = nil, order = nil)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that uses recursion to parse a locator string from a feature table
+and fetches the appropriate subsequence. the operators join(),
+complement(), and order() are handled. the locator string is broken into a
+comma separated lists, and modified if the parens donnot balance. otherwise
+the comma separated list of ranges are stripped from operators, and the
+subsequence are fetched and handled according to the operators. SNP
+locators are also dealt with (single positions).
+</p>
+
+
+
+ <div class="method-source-code"
+ id="parse-locator-source">
+<pre>
+ <span class="ruby-comment cmt"># File genbank.rb, line 279</span>
+279: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">comp</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">order</span> = <span class="ruby-keyword kw">nil</span>)
+280: <span class="ruby-identifier">intervals</span> = <span class="ruby-identifier">locator</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">","</span>)
+281:
+282: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">balance_parens?</span>(<span class="ruby-identifier">intervals</span>.<span class="ruby-identifier">first</span>) <span class="ruby-comment cmt"># locator includes a join/comp/order of several ranges</span>
+283: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">locator</span>
+284: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^join\((.*)\)$/</span>
+285: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
+286: <span class="ruby-identifier">join</span> = <span class="ruby-keyword kw">true</span>
+287: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^complement\((.*)\)$/</span>
+288: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
+289: <span class="ruby-identifier">comp</span> = <span class="ruby-keyword kw">true</span>
+290: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^order\((.*)\)$/</span>
+291: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
+292: <span class="ruby-identifier">order</span> = <span class="ruby-keyword kw">true</span>
+293: <span class="ruby-keyword kw">end</span>
+294:
+295: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
+296: <span class="ruby-keyword kw">else</span>
+297: <span class="ruby-identifier">intervals</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">interval</span><span class="ruby-operator">|</span>
+298: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">interval</span>
+299: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^join\((.*)\)$/</span>
+300: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
+301: <span class="ruby-identifier">join</span> = <span class="ruby-keyword kw">true</span>
+302: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
+303: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^complement\((.*)\)$/</span>
+304: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
+305: <span class="ruby-identifier">comp</span> = <span class="ruby-keyword kw">true</span>
+306: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
+307: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^order\((.*)\)$/</span>
+308: <span class="ruby-identifier">locator</span> = <span class="ruby-node">$1</span>
+309: <span class="ruby-identifier">order</span> = <span class="ruby-keyword kw">true</span>
+310: <span class="ruby-identifier">parse_locator</span>(<span class="ruby-identifier">locator</span>, <span class="ruby-identifier">join</span>, <span class="ruby-identifier">comp</span>, <span class="ruby-identifier">order</span>)
+311: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^[<>]?(\d+)[^\d]+(\d+)$/</span>
+312: <span class="ruby-identifier">int_beg</span> = <span class="ruby-node">$1</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+313: <span class="ruby-identifier">int_end</span> = <span class="ruby-node">$2</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+314:
+315: <span class="ruby-identifier">newseq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">int_beg</span><span class="ruby-operator">...</span><span class="ruby-identifier">int_end</span>], <span class="ruby-value str">"dna"</span>)
+316:
+317: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
+318: <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">revcomp</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">comp</span>
+319:
+320: <span class="ruby-ivar">@subseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator"><<</span> (<span class="ruby-identifier">order</span> <span class="ruby-operator">?</span> <span class="ruby-value str">" "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>)
+321: <span class="ruby-keyword kw">end</span>
+322: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/^(\d+)$/</span>
+323: <span class="ruby-identifier">pos</span> = <span class="ruby-node">$1</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+324:
+325: <span class="ruby-identifier">newseq</span> = <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">nil</span>, <span class="ruby-ivar">@seq</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">pos</span>], <span class="ruby-value str">"dna"</span>)
+326:
+327: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span>
+328: <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">revcomp</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">comp</span>
+329:
+330: <span class="ruby-ivar">@subseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator"><<</span> (<span class="ruby-identifier">order</span> <span class="ruby-operator">?</span> <span class="ruby-value str">" "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">newseq</span>.<span class="ruby-identifier">seq</span>)
+331: <span class="ruby-keyword kw">end</span>
+332: <span class="ruby-keyword kw">else</span>
+333: <span class="ruby-identifier">$stderr</span>.<span class="ruby-identifier">puts</span> <span class="ruby-node">"WARNING: Could not match locator -> #{locator}"</span>;
+334: <span class="ruby-ivar">@subseq</span>.<span class="ruby-identifier">seq</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">""</span>
+335: <span class="ruby-keyword kw">end</span>
+336: <span class="ruby-keyword kw">end</span>
+337: <span class="ruby-keyword kw">end</span>
+338:
+339: <span class="ruby-keyword kw">return</span> <span class="ruby-ivar">@subseq</span>
+340: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: LocatorError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./genbank_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="genbank.rb">genbank.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
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+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
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+
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+
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+
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+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
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+
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+
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+
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+
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+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">LocatorError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with Genbank/EMBL/DDBJ feature table
+locators.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+<head>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: OptionHandler</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
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+ charset="utf-8"></script>
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+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./biopieces_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="biopieces.rb">biopieces.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-options_check">#options_check</a></li>
+
+ <li><a href="#method-i-options_check_allowed">#options_check_allowed</a></li>
+
+ <li><a href="#method-i-options_check_dir">#options_check_dir</a></li>
+
+ <li><a href="#method-i-options_check_disallowed">#options_check_disallowed</a></li>
+
+ <li><a href="#method-i-options_check_file">#options_check_file</a></li>
+
+ <li><a href="#method-i-options_check_files">#options_check_files</a></li>
+
+ <li><a href="#method-i-options_check_int">#options_check_int</a></li>
+
+ <li><a href="#method-i-options_check_mandatory">#options_check_mandatory</a></li>
+
+ <li><a href="#method-i-options_check_uint">#options_check_uint</a></li>
+
+ <li><a href="#method-i-options_default">#options_default</a></li>
+
+ <li><a href="#method-i-options_glob">#options_glob</a></li>
+
+ <li><a href="#method-i-options_parse">#options_parse</a></li>
+
+ <li><a href="#method-i-print_usage_and_exit">#print_usage_and_exit</a></li>
+
+ <li><a href="#method-i-print_usage_full%3F">#print_usage_full?</a></li>
+
+ <li><a href="#method-i-print_usage_short%3F">#print_usage_short?</a></li>
+
+ <li><a href="#method-i-wiki_path">#wiki_path</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">OptionHandler</h1>
+
+ <div id="description">
+ <p>
+Class for parsing argv using OptionParser according to given casts. Default
+options are set, file glob expressions expanded, and options are checked
+according to the casts. Usage information is printed and exit called if
+required.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+ <div id="constants-list" class="section">
+ <h3 class="section-header">Constants</h3>
+ <dl>
+
+ <dt><a name="REGEX_LIST">REGEX_LIST</a></dt>
+
+ <dd class="description"></dd>
+
+
+ <dt><a name="REGEX_INT">REGEX_INT</a></dt>
+
+ <dd class="description"></dd>
+
+
+ <dt><a name="REGEX_STRING">REGEX_STRING</a></dt>
+
+ <dd class="description"></dd>
+
+
+ </dl>
+ </div>
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(argv, casts, script_path, test=nil)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 266</span>
+266: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">argv</span>, <span class="ruby-identifier">casts</span>, <span class="ruby-identifier">script_path</span>, <span class="ruby-identifier">test</span>=<span class="ruby-keyword kw">nil</span>)
+267: <span class="ruby-ivar">@argv</span> = <span class="ruby-identifier">argv</span>
+268: <span class="ruby-ivar">@casts</span> = <span class="ruby-identifier">casts</span>
+269: <span class="ruby-ivar">@script_path</span> = <span class="ruby-identifier">script_path</span>
+270: <span class="ruby-ivar">@test</span> = <span class="ruby-identifier">test</span>
+271: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="options-check-method" class="method-detail ">
+ <a name="method-i-options_check"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check all options according to casts.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 407</span>
+407: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check</span>
+408: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+409: <span class="ruby-identifier">options_check_mandatory</span>(<span class="ruby-identifier">cast</span>)
+410: <span class="ruby-identifier">options_check_int</span>(<span class="ruby-identifier">cast</span>)
+411: <span class="ruby-identifier">options_check_uint</span>(<span class="ruby-identifier">cast</span>)
+412: <span class="ruby-identifier">options_check_file</span>(<span class="ruby-identifier">cast</span>)
+413: <span class="ruby-identifier">options_check_files</span>(<span class="ruby-identifier">cast</span>)
+414: <span class="ruby-identifier">options_check_dir</span>(<span class="ruby-identifier">cast</span>)
+415: <span class="ruby-identifier">options_check_allowed</span>(<span class="ruby-identifier">cast</span>)
+416: <span class="ruby-identifier">options_check_disallowed</span>(<span class="ruby-identifier">cast</span>)
+417: <span class="ruby-keyword kw">end</span>
+418: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-allowed-method" class="method-detail ">
+ <a name="method-i-options_check_allowed"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_allowed</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check options and raise unless allowed.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-allowed-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 470</span>
+470: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_allowed</span>(<span class="ruby-identifier">cast</span>)
+471: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+472: <span class="ruby-identifier">allowed_hash</span> = {}
+473: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:allowed</span>].<span class="ruby-identifier">split</span>(<span class="ruby-value str">','</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">allowed_hash</span>[<span class="ruby-identifier">a</span>.<span class="ruby-identifier">to_s</span>] = <span class="ruby-value">1</span> }
+474:
+475: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument '#{@options[cast[:long]]}' to --#{cast[:long]} not allowed"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">allowed_hash</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">to_s</span>
+476: <span class="ruby-keyword kw">end</span>
+477: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-dir-method" class="method-detail ">
+ <a name="method-i-options_check_dir"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_dir</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check dir! type argument and raise if directory don’t exist.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-dir-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 463</span>
+463: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_dir</span>(<span class="ruby-identifier">cast</span>)
+464: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'dir!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+465: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"No such directory: '#{@options[cast[:long]]}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">directory?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]]
+466: <span class="ruby-keyword kw">end</span>
+467: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-disallowed-method" class="method-detail ">
+ <a name="method-i-options_check_disallowed"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_disallowed</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check disallowed argument values and raise if disallowed.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-disallowed-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 480</span>
+480: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_disallowed</span>(<span class="ruby-identifier">cast</span>)
+481: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+482: <span class="ruby-identifier">cast</span>[<span class="ruby-value">:disallowed</span>].<span class="ruby-identifier">split</span>(<span class="ruby-value str">','</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">val</span><span class="ruby-operator">|</span>
+483: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument '#{@options[cast[:long]]}' to --#{cast[:long]} is disallowed"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">==</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">to_s</span>
+484: <span class="ruby-keyword kw">end</span>
+485: <span class="ruby-keyword kw">end</span>
+486: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-file-method" class="method-detail ">
+ <a name="method-i-options_check_file"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_file</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check file! type argument and raise if file don’t exists.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-file-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 446</span>
+446: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_file</span>(<span class="ruby-identifier">cast</span>)
+447: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'file!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+448: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"No such file: '#{@options[cast[:long]]}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]]
+449: <span class="ruby-keyword kw">end</span>
+450: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-files-method" class="method-detail ">
+ <a name="method-i-options_check_files"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_files</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check files! type argument and raise if files don’t exists.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-files-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 453</span>
+453: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_files</span>(<span class="ruby-identifier">cast</span>)
+454: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files!'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+455: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">path</span><span class="ruby-operator">|</span>
+456: <span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">path</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"-"</span>
+457: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"File not readable: '#{path}'"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">readable?</span> <span class="ruby-identifier">path</span>
+458: <span class="ruby-keyword kw">end</span>
+459: <span class="ruby-keyword kw">end</span>
+460: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-int-method" class="method-detail ">
+ <a name="method-i-options_check_int"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_int</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check int type option and raise if not an integer.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-int-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 428</span>
+428: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_int</span>(<span class="ruby-identifier">cast</span>)
+429: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'int'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+430: <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span>
+431: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument to --#{cast[:long]} must be an integer, not '#{@options[cast[:long]]}'"</span>
+432: <span class="ruby-keyword kw">end</span>
+433: <span class="ruby-keyword kw">end</span>
+434: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-mandatory-method" class="method-detail ">
+ <a name="method-i-options_check_mandatory"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_mandatory</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if a mandatory option is set and raise if it isn’t.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-mandatory-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 421</span>
+421: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_mandatory</span>(<span class="ruby-identifier">cast</span>)
+422: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:mandatory</span>]
+423: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Mandatory argument: --#{cast[:long]}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+424: <span class="ruby-keyword kw">end</span>
+425: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-check-uint-method" class="method-detail ">
+ <a name="method-i-options_check_uint"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_check_uint</span><span
+ class="method-args">(cast)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check uint type option and raise if not an unsinged integer.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-check-uint-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 437</span>
+437: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_check_uint</span>(<span class="ruby-identifier">cast</span>)
+438: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'uint'</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+439: <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">is_a?</span> <span class="ruby-constant">Integer</span> <span class="ruby-keyword kw">and</span> <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] <span class="ruby-operator">>=</span> <span class="ruby-value">0</span>
+440: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Argument to --#{cast[:long]} must be an unsigned integer, not '#{@options[cast[:long]]}'"</span>
+441: <span class="ruby-keyword kw">end</span>
+442: <span class="ruby-keyword kw">end</span>
+443: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-default-method" class="method-detail ">
+ <a name="method-i-options_default"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_default</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Set default options value from cast unless a value is set.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-default-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 374</span>
+374: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_default</span>
+375: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+376: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>]
+377: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">cast</span>[<span class="ruby-value">:default</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+378: <span class="ruby-keyword kw">end</span>
+379: <span class="ruby-keyword kw">end</span>
+380: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-glob-method" class="method-detail ">
+ <a name="method-i-options_glob"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_glob</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Expands glob expressions to a full list of paths. Examples:
+“*.fna” or “foo.fna,*.fna” or
+“foo.fna,/bar/*.fna“
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-glob-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 384</span>
+384: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_glob</span>
+385: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+386: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files'</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'files!'</span>
+387: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@options</span>.<span class="ruby-identifier">has_key?</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]
+388: <span class="ruby-identifier">files</span> = []
+389:
+390: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">path</span><span class="ruby-operator">|</span>
+391: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">path</span>.<span class="ruby-identifier">include?</span> <span class="ruby-value str">"*"</span>
+392: <span class="ruby-constant">Dir</span>.<span class="ruby-identifier">glob</span>(<span class="ruby-identifier">path</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
+393: <span class="ruby-identifier">files</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">file</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-identifier">file</span>
+394: <span class="ruby-keyword kw">end</span>
+395: <span class="ruby-keyword kw">else</span>
+396: <span class="ruby-identifier">files</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">path</span>
+397: <span class="ruby-keyword kw">end</span>
+398: <span class="ruby-keyword kw">end</span>
+399:
+400: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">files</span>
+401: <span class="ruby-keyword kw">end</span>
+402: <span class="ruby-keyword kw">end</span>
+403: <span class="ruby-keyword kw">end</span>
+404: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="options-parse-method" class="method-detail ">
+ <a name="method-i-options_parse"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">options_parse</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Parse options from argv using OptionParser and casts denoting long and
+short option names. Usage information is printed and exit called. A hash
+with options is returned.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="options-parse-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 276</span>
+276: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">options_parse</span>
+277: <span class="ruby-ivar">@options</span> = {}
+278:
+279: <span class="ruby-identifier">option_parser</span> = <span class="ruby-constant">OptionParser</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">option</span><span class="ruby-operator">|</span>
+280: <span class="ruby-ivar">@casts</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">cast</span><span class="ruby-operator">|</span>
+281: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">cast</span>[<span class="ruby-value">:type</span>]
+282: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'flag'</span>
+283: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]}"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">o</span><span class="ruby-operator">|</span>
+284: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">o</span>
+285: <span class="ruby-keyword kw">end</span>
+286: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'float'</span>
+287: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} F"</span>, <span class="ruby-constant">Float</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span>
+288: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">f</span>
+289: <span class="ruby-keyword kw">end</span>
+290: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'string'</span>
+291: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} S"</span>, <span class="ruby-constant">String</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
+292: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">s</span>.<span class="ruby-identifier">to_sym</span>
+293: <span class="ruby-keyword kw">end</span>
+294: <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_LIST</span>
+295: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>( <span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} A"</span>, <span class="ruby-constant">Array</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span>
+296: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">a</span>
+297: <span class="ruby-keyword kw">end</span>
+298: <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_INT</span>
+299: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} I"</span>, <span class="ruby-constant">Integer</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
+300: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">i</span>
+301: <span class="ruby-keyword kw">end</span>
+302: <span class="ruby-keyword kw">when</span> <span class="ruby-constant">REGEX_STRING</span>
+303: <span class="ruby-identifier">option</span>.<span class="ruby-identifier">on</span>(<span class="ruby-node">"-#{cast[:short]}"</span>, <span class="ruby-node">"--#{cast[:long]} S"</span>, <span class="ruby-constant">String</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
+304: <span class="ruby-ivar">@options</span>[<span class="ruby-identifier">cast</span>[<span class="ruby-value">:long</span>]] = <span class="ruby-identifier">s</span>
+305: <span class="ruby-keyword kw">end</span>
+306: <span class="ruby-keyword kw">else</span>
+307: <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-node">"Unknown option type: '#{cast[:type]}'"</span>
+308: <span class="ruby-keyword kw">end</span>
+309: <span class="ruby-keyword kw">end</span>
+310: <span class="ruby-keyword kw">end</span>
+311:
+312: <span class="ruby-identifier">option_parser</span>.<span class="ruby-identifier">parse!</span>(<span class="ruby-ivar">@argv</span>)
+313:
+314: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">print_usage_full?</span>
+315: <span class="ruby-identifier">print_usage_and_exit</span>(<span class="ruby-keyword kw">true</span>)
+316: <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">print_usage_short?</span>
+317: <span class="ruby-identifier">print_usage_and_exit</span>
+318: <span class="ruby-keyword kw">end</span>
+319:
+320: <span class="ruby-identifier">options_default</span>
+321: <span class="ruby-identifier">options_glob</span>
+322: <span class="ruby-identifier">options_check</span>
+323:
+324: <span class="ruby-ivar">@options</span>
+325: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="print-usage-and-exit-method" class="method-detail ">
+ <a name="method-i-print_usage_and_exit"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">print_usage_and_exit</span><span
+ class="method-args">(full=nil)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Print usage info by Calling an external script ‘print_wiki’
+using a system() call and exit. An optional ‘full’ flag outputs
+the full usage info.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="print-usage-and-exit-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 357</span>
+357: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_and_exit</span>(<span class="ruby-identifier">full</span>=<span class="ruby-keyword kw">nil</span>)
+358: <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@test</span>
+359: <span class="ruby-keyword kw">return</span>
+360: <span class="ruby-keyword kw">else</span>
+361: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">full</span>
+362: <span class="ruby-identifier">system</span>(<span class="ruby-node">"print_wiki --data_in #{wiki_path} --help"</span>)
+363: <span class="ruby-keyword kw">else</span>
+364: <span class="ruby-identifier">system</span>(<span class="ruby-node">"print_wiki --data_in #{wiki_path}"</span>)
+365: <span class="ruby-keyword kw">end</span>
+366:
+367: <span class="ruby-identifier">raise</span> <span class="ruby-node">"Failed printing wiki: #{wiki_path}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">$?</span>.<span class="ruby-identifier">success?</span>
+368:
+369: <span class="ruby-identifier">exit</span>
+370: <span class="ruby-keyword kw">end</span>
+371: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="print-usage-full--method" class="method-detail ">
+ <a name="method-i-print_usage_full%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">print_usage_full?</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if full “usage info” should be printed.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="print-usage-full--source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 335</span>
+335: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_full?</span>
+336: <span class="ruby-ivar">@options</span>[<span class="ruby-value">:help</span>]
+337: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="print-usage-short--method" class="method-detail ">
+ <a name="method-i-print_usage_short%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">print_usage_short?</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Check if short “usage info” should be printed.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="print-usage-short--source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 340</span>
+340: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">print_usage_short?</span>
+341: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">$stdin</span>.<span class="ruby-identifier">tty?</span>
+342: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+343: <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@options</span>[<span class="ruby-value">:stream_in</span>]
+344: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+345: <span class="ruby-keyword kw">elsif</span> <span class="ruby-ivar">@options</span>[<span class="ruby-value">:data_in</span>]
+346: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+347: <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">wiki_path</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/</span> <span class="ruby-comment cmt"># TODO get rid of this!</span>
+348: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">false</span>
+349: <span class="ruby-keyword kw">else</span>
+350: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">true</span>
+351: <span class="ruby-keyword kw">end</span>
+352: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="wiki-path-method" class="method-detail ">
+ <a name="method-i-wiki_path"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">wiki_path</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Given the script name determine the path of the wiki file with the usage
+info.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="wiki-path-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 328</span>
+328: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">wiki_path</span>
+329: <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_DIR"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/bp_usage/"</span> <span class="ruby-operator">+</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-ivar">@script_path</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">".wiki"</span>
+330: <span class="ruby-identifier">raise</span> <span class="ruby-node">"No such wiki file: #{path}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">file?</span> <span class="ruby-identifier">path</span>
+331: <span class="ruby-identifier">path</span>
+332: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
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+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-i-clip">#clip</a></li>
+
+ <li><a href="#method-i-coordinates_get">#coordinates_get</a></li>
+
+ <li><a href="#method-i-mask">#mask</a></li>
+
+ <li><a href="#method-i-to_bp">#to_bp</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Read</h1>
+
+ <div id="description">
+ <p>
+Class containing data accessor methods for an <a href="SFF.html">SFF</a>
+entry and methods for manipulating this entry.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+ <div id="attribute-method-details" class="method-section section">
+ <h3 class="section-header">Attributes</h3>
+
+
+ <div id="read-header-length-attribute-method" class="method-detail">
+ <a name="read_header_length"></a>
+
+ <a name="read_header_length="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">read_header_length</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="name-length-attribute-method" class="method-detail">
+ <a name="name_length"></a>
+
+ <a name="name_length="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">name_length</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="number-of-bases-attribute-method" class="method-detail">
+ <a name="number_of_bases"></a>
+
+ <a name="number_of_bases="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">number_of_bases</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="clip-qual-left-attribute-method" class="method-detail">
+ <a name="clip_qual_left"></a>
+
+ <a name="clip_qual_left="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">clip_qual_left</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="clip-qual-right-attribute-method" class="method-detail">
+ <a name="clip_qual_right"></a>
+
+ <a name="clip_qual_right="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">clip_qual_right</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="clip-adapter-left-attribute-method" class="method-detail">
+ <a name="clip_adapter_left"></a>
+
+ <a name="clip_adapter_left="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">clip_adapter_left</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="clip-adaptor-right-attribute-method" class="method-detail">
+ <a name="clip_adaptor_right"></a>
+
+ <a name="clip_adaptor_right="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">clip_adaptor_right</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="name-attribute-method" class="method-detail">
+ <a name="name"></a>
+
+ <a name="name="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">name</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="flowgram-values-attribute-method" class="method-detail">
+ <a name="flowgram_values"></a>
+
+ <a name="flowgram_values="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">flowgram_values</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="flow-index-per-base-attribute-method" class="method-detail">
+ <a name="flow_index_per_base"></a>
+
+ <a name="flow_index_per_base="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">flow_index_per_base</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="bases-attribute-method" class="method-detail">
+ <a name="bases"></a>
+
+ <a name="bases="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">bases</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="quality-scores-attribute-method" class="method-detail">
+ <a name="quality_scores"></a>
+
+ <a name="quality_scores="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">quality_scores</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="x-pos-attribute-method" class="method-detail">
+ <a name="x_pos"></a>
+
+ <a name="x_pos="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">x_pos</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="y-pos-attribute-method" class="method-detail">
+ <a name="y_pos"></a>
+
+ <a name="y_pos="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">y_pos</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ </div>
+
+
+ <!-- Methods -->
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="clip-method" class="method-detail ">
+ <a name="method-i-clip"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">clip</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that clips sequence (i.e. trims) according to <a
+href="Read.html#clip_qual_left">clip_qual_left</a> and <a
+href="Read.html#clip_qual_right">clip_qual_right</a> information.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="clip-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 228</span>
+228: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">clip</span>
+229: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
+230: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
+231: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="mask-method" class="method-detail ">
+ <a name="method-i-mask"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">mask</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that soft masks the sequence (i.e. lowercases sequence) according to
+<a href="Read.html#clip_qual_left">clip_qual_left</a> and <a
+href="Read.html#clip_qual_right">clip_qual_right</a> information.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="mask-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 218</span>
+218: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">mask</span>
+219: <span class="ruby-identifier">left</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">downcase</span>
+220: <span class="ruby-identifier">middle</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span>]
+221: <span class="ruby-identifier">right</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>[<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">downcase</span>
+222:
+223: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span> = <span class="ruby-identifier">left</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">middle</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">right</span>
+224: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-bp-method" class="method-detail ">
+ <a name="method-i-to_bp"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_bp</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that converts a <a href="Read.html">Read</a> object’s data to
+a Biopiece record (a hash).
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-bp-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 197</span>
+197: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_bp</span>
+198: <span class="ruby-identifier">coordinates_get</span>
+199:
+200: <span class="ruby-identifier">hash</span> = {}
+201:
+202: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ_NAME</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>
+203: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>
+204: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SEQ_LEN</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bases</span>.<span class="ruby-identifier">length</span>
+205: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_QUAL_LEFT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+206: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_QUAL_RIGHT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_qual_right</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+207: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_ADAPTOR_LEFT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_adapter_left</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+208: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:CLIP_ADAPTOR_RIGHT</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">clip_adaptor_right</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+209: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:SCORES</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">quality_scores</span>.<span class="ruby-identifier">map</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> (<span class="ruby-identifier">i</span> <span class="ruby-operator">+=</span> <span class="ruby-value">64</span>).<span class="ruby-identifier">chr</span> }.<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
+210: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:X_POS</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">x_pos</span>
+211: <span class="ruby-identifier">hash</span>[<span class="ruby-value">:Y_POS</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">y_pos</span>
+212:
+213: <span class="ruby-identifier">hash</span>
+214: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="coordinates-get-method" class="method-detail ">
+ <a name="method-i-coordinates_get"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">coordinates_get</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that extracts the X/Y coordinates from an <a href="SFF.html">SFF</a>
+read name encoded with base36.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="coordinates-get-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 237</span>
+237: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">coordinates_get</span>
+238: <span class="ruby-identifier">base36</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">name</span>[<span class="ruby-value">5</span>, <span class="ruby-value">5</span>]
+239: <span class="ruby-identifier">num</span> = <span class="ruby-constant">Base36</span>.<span class="ruby-identifier">decode</span>(<span class="ruby-identifier">base36</span>)
+240:
+241: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">x_pos</span> = <span class="ruby-identifier">num</span> <span class="ruby-operator">>></span> <span class="ruby-constant">BIT_SHIFT</span>
+242: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">y_pos</span> = <span class="ruby-identifier">num</span> & <span class="ruby-constant">BIT_MASK</span>
+243: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: SFF</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./sff_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="sff.rb">sff.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-c-open">::open</a></li>
+
+ <li><a href="#method-i-check_header_length">#check_header_length</a></li>
+
+ <li><a href="#method-i-check_magic_number">#check_magic_number</a></li>
+
+ <li><a href="#method-i-check_version">#check_version</a></li>
+
+ <li><a href="#method-i-close">#close</a></li>
+
+ <li><a href="#method-i-each">#each</a></li>
+
+ <li><a href="#method-i-fast_forward">#fast_forward</a></li>
+
+ <li><a href="#method-i-header_parse">#header_parse</a></li>
+
+ <li><a href="#method-i-read_parse">#read_parse</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ <div id="includes-section" class="section">
+ <h3 class="section-header">Included Modules</h3>
+ <ul class="link-list">
+
+
+ <li><span class="include">Enumerable</span></li>
+
+
+ </ul>
+ </div>
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">SFF</h1>
+
+ <div id="description">
+ <p>
+Class containing methods to parse <a href="SFF.html">SFF</a> files: <a
+href="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff">www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff</a>
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(io)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to initialize an <a href="SFF.html">SFF</a> object along with
+instance variables pertaining to the <a href="SFF.html">SFF</a> header
+section.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 58</span>
+58: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">io</span>)
+59: <span class="ruby-ivar">@io</span> = <span class="ruby-identifier">io</span>
+60: <span class="ruby-ivar">@magic_number</span> = <span class="ruby-value">0</span>
+61: <span class="ruby-ivar">@version</span> = <span class="ruby-value str">""</span>
+62: <span class="ruby-ivar">@index_offset</span> = <span class="ruby-value">0</span>
+63: <span class="ruby-ivar">@index_length</span> = <span class="ruby-value">0</span>
+64: <span class="ruby-ivar">@number_of_reads</span> = <span class="ruby-value">0</span>
+65: <span class="ruby-ivar">@header_length</span> = <span class="ruby-value">0</span>
+66: <span class="ruby-ivar">@key_length</span> = <span class="ruby-value">0</span>
+67: <span class="ruby-ivar">@number_of_flows_per_read</span> = <span class="ruby-value">0</span>
+68: <span class="ruby-ivar">@flowgram_format_code</span> = <span class="ruby-value">0</span>
+69: <span class="ruby-ivar">@flow_chars</span> = <span class="ruby-value str">""</span>
+70: <span class="ruby-ivar">@key_sequence</span> = <span class="ruby-value str">""</span>
+71: <span class="ruby-ivar">@eight_byte_padding</span> = <span class="ruby-value">0</span>
+72:
+73: <span class="ruby-identifier">header_parse</span>
+74: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="open-method" class="method-detail ">
+ <a name="method-c-open"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">open</span><span
+ class="method-args">(*args)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Class method for opening <a href="SFF.html">SFF</a> files.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="open-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 41</span>
+41: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
+42: <span class="ruby-identifier">ios</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(*<span class="ruby-identifier">args</span>)
+43:
+44: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">block_given?</span>
+45: <span class="ruby-keyword kw">begin</span>
+46: <span class="ruby-keyword kw">yield</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
+47: <span class="ruby-keyword kw">ensure</span>
+48: <span class="ruby-identifier">ios</span>.<span class="ruby-identifier">close</span>
+49: <span class="ruby-keyword kw">end</span>
+50: <span class="ruby-keyword kw">else</span>
+51: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">ios</span>)
+52: <span class="ruby-keyword kw">end</span>
+53: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="close-method" class="method-detail ">
+ <a name="method-i-close"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">close</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to close ios.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="close-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 77</span>
+77: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>
+78: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">close</span>
+79: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="each-method" class="method-detail ">
+ <a name="method-i-each"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">each</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to iterate over each <a href="SFF.html">SFF</a> entry.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="each-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 82</span>
+82: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">each</span>
+83: <span class="ruby-keyword kw">while</span> (<span class="ruby-identifier">read</span> = <span class="ruby-identifier">read_parse</span>) <span class="ruby-keyword kw">do</span>
+84: <span class="ruby-keyword kw">yield</span> <span class="ruby-identifier">read</span>
+85: <span class="ruby-keyword kw">end</span>
+86:
+87: <span class="ruby-keyword kw">self</span> <span class="ruby-comment cmt"># conventionally</span>
+88: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="check-header-length-method" class="method-detail ">
+ <a name="method-i-check_header_length"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_header_length</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to check the header length of an <a href="SFF.html">SFF</a> file.
+Raises an error if the header length don’t match the file position
+after reading the header section.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-header-length-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 183</span>
+183: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_header_length</span>
+184: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SFFError</span>, <span class="ruby-node">"Bad header length: #{header_length}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">pos</span> <span class="ruby-operator">==</span> <span class="ruby-ivar">@header_length</span>
+185: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-magic-number-method" class="method-detail ">
+ <a name="method-i-check_magic_number"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_magic_number</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to check the magic number of an <a href="SFF.html">SFF</a> file.
+Raises an error if the magic number don’t match.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-magic-number-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 170</span>
+170: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_magic_number</span>
+171: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SFFError</span>, <span class="ruby-value str">"Badly formatted SFF file."</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@magic_number</span> <span class="ruby-operator">==</span> <span class="ruby-value">779314790</span>
+172: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="check-version-method" class="method-detail ">
+ <a name="method-i-check_version"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">check_version</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to check the version number of an <a href="SFF.html">SFF</a> file.
+Raises an error if the version don’t match.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="check-version-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 176</span>
+176: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">check_version</span>
+177: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SFFError</span>, <span class="ruby-node">"Wrong version: #{@version}"</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@version</span>.<span class="ruby-identifier">to_i</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
+178: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="fast-forward-method" class="method-detail ">
+ <a name="method-i-fast_forward"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">fast_forward</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that reads the eight_byte_padding field found at the end of the data
+section and fast forwards, i.e. move the file read pointer, so that the
+length of the section is divisible by 8.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="fast-forward-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 122</span>
+122: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">fast_forward</span>
+123: <span class="ruby-identifier">eight_byte_padding</span> = <span class="ruby-value">8</span> <span class="ruby-operator">-</span> (<span class="ruby-ivar">@io</span>.<span class="ruby-identifier">pos</span> <span class="ruby-operator">%</span> <span class="ruby-value">8</span>)
+124:
+125: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">eight_byte_padding</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">eight_byte_padding</span> <span class="ruby-operator">==</span> <span class="ruby-value">8</span>
+126: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="header-parse-method" class="method-detail ">
+ <a name="method-i-header_parse"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">header_parse</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to parse the <a href="SFF.html">SFF</a> file’s header section
+and load the information into the instance variables.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="header-parse-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 94</span>
+ 94: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">header_parse</span>
+ 95: <span class="ruby-identifier">template</span> = <span class="ruby-value str">"NC4N2NNnnnC"</span>
+ 96: <span class="ruby-identifier">bits_in_uint</span> = <span class="ruby-value">32</span>
+ 97:
+ 98: <span class="ruby-identifier">data</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-value">31</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-identifier">template</span>)
+ 99:
+100: <span class="ruby-ivar">@magic_number</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">0</span>]
+101: <span class="ruby-ivar">@version</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-value">4</span>].<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
+102: <span class="ruby-ivar">@index_offset</span> = (<span class="ruby-identifier">data</span>[<span class="ruby-value">5</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">bits_in_uint</span>) <span class="ruby-operator">|</span> <span class="ruby-identifier">data</span>[<span class="ruby-value">6</span>]
+103: <span class="ruby-ivar">@index_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">7</span>]
+104: <span class="ruby-ivar">@number_of_reads</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">8</span>]
+105: <span class="ruby-ivar">@header_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">9</span>]
+106: <span class="ruby-ivar">@key_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">10</span>]
+107: <span class="ruby-ivar">@number_of_flows_per_read</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">11</span>]
+108: <span class="ruby-ivar">@flowgram_format_code</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">12</span>]
+109: <span class="ruby-ivar">@flow_chars</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-ivar">@number_of_flows_per_read</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
+110: <span class="ruby-ivar">@key_sequence</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-ivar">@key_length</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
+111:
+112: <span class="ruby-identifier">fast_forward</span>
+113:
+114: <span class="ruby-identifier">check_magic_number</span>
+115: <span class="ruby-identifier">check_version</span>
+116: <span class="ruby-identifier">check_header_length</span>
+117: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="read-parse-method" class="method-detail ">
+ <a name="method-i-read_parse"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">read_parse</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to parse a read section of an <a href="SFF.html">SFF</a> file.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="read-parse-source">
+<pre>
+ <span class="ruby-comment cmt"># File sff.rb, line 129</span>
+129: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">read_parse</span>
+130: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@number_of_reads</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">@@count</span>
+131:
+132: <span class="ruby-identifier">template</span> = <span class="ruby-value str">"nnNnnnn"</span>
+133:
+134: <span class="ruby-identifier">read</span> = <span class="ruby-constant">Read</span>.<span class="ruby-identifier">new</span>()
+135:
+136: <span class="ruby-identifier">data</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-value">16</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-identifier">template</span>)
+137:
+138: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">read_header_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">0</span>]
+139: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">name_length</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">1</span>]
+140: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">2</span>]
+141: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_qual_left</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">3</span>]
+142: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_qual_right</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">4</span>]
+143: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_adapter_left</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">5</span>]
+144: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">clip_adaptor_right</span> = <span class="ruby-identifier">data</span>[<span class="ruby-value">6</span>]
+145: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">name</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">name_length</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
+146:
+147: <span class="ruby-identifier">fast_forward</span>
+148:
+149: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-value">2</span> * <span class="ruby-ivar">@number_of_flows_per_read</span>) <span class="ruby-comment cmt"># skip through flowgram_values</span>
+150: <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span>) <span class="ruby-comment cmt"># skip through flow_index_per_base</span>
+151:
+152: <span class="ruby-comment cmt"># NB! Parsing of flowgram_values and flow_index_per_base is currently disabled since these are not needed.</span>
+153: <span class="ruby-comment cmt"># read.flowgram_values = @io.read(2 * @number_of_flows_per_read).unpack("n*").map { |val| val = sprintf("%.2f", val * 0.01) }</span>
+154: <span class="ruby-comment cmt"># flow_index_per_base = @io.read(read.number_of_bases).unpack("C*")</span>
+155: <span class="ruby-comment cmt"># (1 ... flow_index_per_base.length).each { |i| flow_index_per_base[i] += flow_index_per_base[i - 1] }</span>
+156: <span class="ruby-comment cmt"># read.flow_index_per_base = flow_index_per_base</span>
+157:
+158: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">bases</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"A*"</span>).<span class="ruby-identifier">join</span> <span class="ruby-value str">""</span>
+159: <span class="ruby-identifier">read</span>.<span class="ruby-identifier">quality_scores</span> = <span class="ruby-ivar">@io</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">read</span>.<span class="ruby-identifier">number_of_bases</span>).<span class="ruby-identifier">unpack</span>(<span class="ruby-value str">"C*"</span>)
+160:
+161: <span class="ruby-identifier">fast_forward</span>
+162:
+163: <span class="ruby-identifier">@@count</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+164:
+165: <span class="ruby-identifier">read</span>
+166: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+
+ <title>Class: SFFError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
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+ <!-- Parent Class -->
+
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+ <h3 class="section-header">Class Index
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+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
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+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
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+
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+ <li><a href="./FastqError.html">FastqError</a></li>
+
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+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">SFFError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a href="SFF.html">SFF</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Seq</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
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+ charset="utf-8"></script>
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+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./seq_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="seq.rb">seq.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-generate_oligos">::generate_oligos</a></li>
+
+ <li><a href="#method-c-new">::new</a></li>
+
+ <li><a href="#method-i-adaptor_clip_left">#adaptor_clip_left</a></li>
+
+ <li><a href="#method-i-adaptor_clip_right">#adaptor_clip_right</a></li>
+
+ <li><a href="#method-i-adaptor_locate_left">#adaptor_locate_left</a></li>
+
+ <li><a href="#method-i-adaptor_locate_right">#adaptor_locate_right</a></li>
+
+ <li><a href="#method-i-complement">#complement</a></li>
+
+ <li><a href="#method-i-composition">#composition</a></li>
+
+ <li><a href="#method-i-convert_phred2illumina%21">#convert_phred2illumina!</a></li>
+
+ <li><a href="#method-i-convert_solexa2illumina%21">#convert_solexa2illumina!</a></li>
+
+ <li><a href="#method-i-generate">#generate</a></li>
+
+ <li><a href="#method-i-hard_mask">#hard_mask</a></li>
+
+ <li><a href="#method-i-homopol_max">#homopol_max</a></li>
+
+ <li><a href="#method-i-indels">#indels</a></li>
+
+ <li><a href="#method-i-is_dna%3F">#is_dna?</a></li>
+
+ <li><a href="#method-i-is_protein%3F">#is_protein?</a></li>
+
+ <li><a href="#method-i-is_rna%3F">#is_rna?</a></li>
+
+ <li><a href="#method-i-len">#len</a></li>
+
+ <li><a href="#method-i-length">#length</a></li>
+
+ <li><a href="#method-i-match">#match</a></li>
+
+ <li><a href="#method-i-revcomp">#revcomp</a></li>
+
+ <li><a href="#method-i-reverse">#reverse</a></li>
+
+ <li><a href="#method-i-reverse_complement">#reverse_complement</a></li>
+
+ <li><a href="#method-i-soft_mask">#soft_mask</a></li>
+
+ <li><a href="#method-i-solexa2phred">#solexa2phred</a></li>
+
+ <li><a href="#method-i-solexa_char2illumina_char">#solexa_char2illumina_char</a></li>
+
+ <li><a href="#method-i-subseq">#subseq</a></li>
+
+ <li><a href="#method-i-subseq%21">#subseq!</a></li>
+
+ <li><a href="#method-i-subseq_rand">#subseq_rand</a></li>
+
+ <li><a href="#method-i-to_bp">#to_bp</a></li>
+
+ <li><a href="#method-i-to_dna">#to_dna</a></li>
+
+ <li><a href="#method-i-to_fasta">#to_fasta</a></li>
+
+ <li><a href="#method-i-to_key">#to_key</a></li>
+
+ <li><a href="#method-i-to_rna">#to_rna</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ <div id="includes-section" class="section">
+ <h3 class="section-header">Included Modules</h3>
+ <ul class="link-list">
+
+
+ <li><span class="include">Amatch</span></li>
+
+
+ </ul>
+ </div>
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
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+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Seq</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+ <div id="attribute-method-details" class="method-section section">
+ <h3 class="section-header">Attributes</h3>
+
+
+ <div id="seq-name-attribute-method" class="method-detail">
+ <a name="seq_name"></a>
+
+ <a name="seq_name="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">seq_name</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="seq-attribute-method" class="method-detail">
+ <a name="seq"></a>
+
+ <a name="seq="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">seq</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="type-attribute-method" class="method-detail">
+ <a name="type"></a>
+
+ <a name="type="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">type</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ <div id="qual-attribute-method" class="method-detail">
+ <a name="qual"></a>
+
+ <a name="qual="></a>
+
+ <div class="method-heading attribute-method-heading">
+ <span class="method-name">qual</span><span
+ class="attribute-access-type">[RW]</span>
+ </div>
+
+ <div class="method-description">
+
+
+
+ </div>
+ </div>
+
+ </div>
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="generate-oligos-method" class="method-detail ">
+ <a name="method-c-generate_oligos"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">generate_oligos</span><span
+ class="method-args">(length, type)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that generates all possible oligos of a specifed length and type.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="generate-oligos-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 47</span>
+47: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">generate_oligos</span>(<span class="ruby-identifier">length</span>, <span class="ruby-identifier">type</span>)
+48: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate negative oligo 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>
+49:
+50: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
+51: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/dna/</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
+52: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/rna/</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
+53: <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/protein/</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
+54: <span class="ruby-keyword kw">else</span>
+55: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
+56: <span class="ruby-keyword kw">end</span>
+57:
+58: <span class="ruby-identifier">oligos</span> = [<span class="ruby-value str">""</span>]
+59:
+60: (<span class="ruby-value">1</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">length</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span>
+61: <span class="ruby-identifier">list</span> = []
+62:
+63: <span class="ruby-identifier">oligos</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">oligo</span><span class="ruby-operator">|</span>
+64: <span class="ruby-identifier">alph</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
+65: <span class="ruby-identifier">list</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">oligo</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">char</span>
+66: <span class="ruby-keyword kw">end</span>
+67: <span class="ruby-keyword kw">end</span>
+68:
+69: <span class="ruby-identifier">oligos</span> = <span class="ruby-identifier">list</span>
+70: <span class="ruby-keyword kw">end</span>
+71:
+72: <span class="ruby-identifier">oligos</span>
+73: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="new-method" class="method-detail ">
+ <a name="method-c-new"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">new</span><span
+ class="method-args">(seq_name = nil, seq = nil, type = nil, qual = nil)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Initialize a sequence object with the following arguments:
+</p>
+<ul>
+<li><p>
+<a href="Seq.html#seq_name">seq_name</a>: Name of the sequence.
+</p>
+</li>
+<li><p>
+seq: The sequence.
+</p>
+</li>
+<li><p>
+type: The sequence type - DNA, RNA, or protein
+</p>
+</li>
+<li><p>
+qual: An Illumina type quality scores string.
+</p>
+</li>
+</ul>
+
+
+
+ <div class="method-source-code"
+ id="new-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 80</span>
+80: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">seq_name</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">type</span> = <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">nil</span>)
+81: <span class="ruby-ivar">@seq_name</span> = <span class="ruby-identifier">seq_name</span>
+82: <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">seq</span>
+83: <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">type</span>
+84: <span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">qual</span>
+85: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="adaptor-clip-left-method" class="method-detail ">
+ <a name="method-i-adaptor_clip_left"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">adaptor_clip_left</span><span
+ class="method-args">(adaptor, hd_percent = 0)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that locates an adaptor or part thereof in the sequence of a <a
+href="Seq.html">Seq</a> object beginning from the left and removes the
+adaptor sequence if found. The hd_percent is used to calculate the maximum
+hamming distance allowed for all possible overlaps.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="adaptor-clip-left-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 377</span>
+377: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_clip_left</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
+378: <span class="ruby-identifier">pos</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">adaptor_locate_left</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span>)
+379:
+380: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
+381: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>]
+382: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">length</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
+383: <span class="ruby-keyword kw">end</span>
+384: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="adaptor-clip-right-method" class="method-detail ">
+ <a name="method-i-adaptor_clip_right"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">adaptor_clip_right</span><span
+ class="method-args">(adaptor, hd_percent = 0)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that locates an adaptor or part thereof in the sequence of a <a
+href="Seq.html">Seq</a> object beginning from the right and removes the
+adaptor sequence if found. The hd_percent is used to calculate the maximum
+hamming distance allowed for all possible overlaps.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="adaptor-clip-right-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 364</span>
+364: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_clip_right</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
+365: <span class="ruby-identifier">pos</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">adaptor_locate_right</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span>)
+366:
+367: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
+368: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">pos</span>]
+369: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">pos</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
+370: <span class="ruby-keyword kw">end</span>
+371: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="adaptor-locate-left-method" class="method-detail ">
+ <a name="method-i-adaptor_locate_left"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">adaptor_locate_left</span><span
+ class="method-args">(adaptor, hd_percent = 0)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that locates an adaptor or part thereof in the sequence of a <a
+href="Seq.html">Seq</a> object beginning from the left. Returns the
+location in the sequence that overlaps with the adaptor or -1 if the
+adaptor was not found. The hd_percent is used to calculate the maximum
+hamming distance allowed for all possible overlaps.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="adaptor-locate-left-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 340</span>
+340: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_locate_left</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
+341: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Hamming distance percent out of range #{hd_percent}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">..</span> <span class="ruby-value">100</span>).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">hd_percent</span>
+342: <span class="ruby-identifier">pos</span> = <span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span>
+343:
+344: <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
+345: <span class="ruby-identifier">len</span> = <span class="ruby-identifier">pos</span>
+346: <span class="ruby-identifier">subseq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">len</span>].<span class="ruby-identifier">upcase</span>
+347: <span class="ruby-identifier">subadaptor</span> = <span class="ruby-identifier">adaptor</span>[<span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">len</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">upcase</span>
+348: <span class="ruby-identifier">m</span> = <span class="ruby-constant">Hamming</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">subseq</span>)
+349: <span class="ruby-identifier">hamming_dist</span> = <span class="ruby-identifier">m</span>.<span class="ruby-identifier">match</span>(<span class="ruby-identifier">subadaptor</span>)
+350: <span class="ruby-identifier">hamming_max</span> = (<span class="ruby-identifier">len</span> * <span class="ruby-identifier">hd_percent</span> * <span class="ruby-value">0.01</span>).<span class="ruby-identifier">round</span>
+351:
+352: <span class="ruby-identifier">pos</span> <span class="ruby-operator">-=</span> <span class="ruby-value">1</span>
+353:
+354: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">pos</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hamming_dist</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">hamming_max</span>
+355: <span class="ruby-keyword kw">end</span>
+356:
+357: <span class="ruby-value">1</span>
+358: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="adaptor-locate-right-method" class="method-detail ">
+ <a name="method-i-adaptor_locate_right"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">adaptor_locate_right</span><span
+ class="method-args">(adaptor, hd_percent = 0)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that locates an adaptor or part thereof in the sequence of a <a
+href="Seq.html">Seq</a> object beginning from the right. Returns the
+location in the sequence that overlaps with the adaptor or -1 if the
+adaptor was not found. The hd_percent is used to calculate the maximum
+hamming distance allowed for all possible overlaps.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="adaptor-locate-right-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 316</span>
+316: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">adaptor_locate_right</span>(<span class="ruby-identifier">adaptor</span>, <span class="ruby-identifier">hd_percent</span> = <span class="ruby-value">0</span>)
+317: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Hamming distance percent out of range #{hd_percent}"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">..</span> <span class="ruby-value">100</span>).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">hd_percent</span>
+318: <span class="ruby-identifier">pos</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">adaptor</span>.<span class="ruby-identifier">length</span>
+319:
+320: <span class="ruby-keyword kw">while</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator"><</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
+321: <span class="ruby-identifier">len</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">pos</span>
+322: <span class="ruby-identifier">subseq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">pos</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">len</span>].<span class="ruby-identifier">upcase</span>
+323: <span class="ruby-identifier">subadaptor</span> = <span class="ruby-identifier">adaptor</span>[<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">len</span>].<span class="ruby-identifier">upcase</span>
+324: <span class="ruby-identifier">m</span> = <span class="ruby-constant">Hamming</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">subseq</span>)
+325: <span class="ruby-identifier">hamming_dist</span> = <span class="ruby-identifier">m</span>.<span class="ruby-identifier">match</span>(<span class="ruby-identifier">subadaptor</span>)
+326: <span class="ruby-identifier">hamming_max</span> = (<span class="ruby-identifier">len</span> * <span class="ruby-identifier">hd_percent</span> * <span class="ruby-value">0.01</span>).<span class="ruby-identifier">round</span>
+327: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">pos</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">hamming_dist</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">hamming_max</span>
+328:
+329: <span class="ruby-identifier">pos</span> <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+330: <span class="ruby-keyword kw">end</span>
+331:
+332: <span class="ruby-value">1</span>
+333: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="complement-method" class="method-detail ">
+ <a name="method-i-complement"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">complement</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that complements sequence including ambiguity codes.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="complement-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 196</span>
+196: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">complement</span>
+197: <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>
+198:
+199: <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_dna?</span>
+200: <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> )
+201: <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">is_rna?</span>
+202: <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> )
+203: <span class="ruby-keyword kw">else</span>
+204: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot complement sequence type: #{self.type}"</span>
+205: <span class="ruby-keyword kw">end</span>
+206: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="composition-method" class="method-detail ">
+ <a name="method-i-composition"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">composition</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the residue compositions of a sequence in a hash where
+the key is the residue and the value is the residue count.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="composition-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 272</span>
+272: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">composition</span>
+273: <span class="ruby-identifier">comp</span> = <span class="ruby-constant">Hash</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">0</span>);
+274:
+275: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
+276: <span class="ruby-identifier">comp</span>[<span class="ruby-identifier">char</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
+277: <span class="ruby-keyword kw">end</span>
+278:
+279: <span class="ruby-identifier">comp</span>
+280: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="convert-phred-illumina--method" class="method-detail ">
+ <a name="method-i-convert_phred2illumina%21"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">convert_phred2illumina!</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to convert the quality scores from a specified base to another base.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="convert-phred-illumina--source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 388</span>
+388: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">convert_phred2illumina!</span>
+389: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">gsub!</span> <span class="ruby-regexp re">/./</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">score</span><span class="ruby-operator">|</span>
+390: <span class="ruby-identifier">score_phred</span> = <span class="ruby-identifier">score</span>.<span class="ruby-identifier">ord</span> <span class="ruby-operator">-</span> <span class="ruby-constant">SCORE_PHRED</span>
+391: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Bad Phred score: #{score} (#{score_phred})"</span> <span class="ruby-keyword kw">unless</span> (<span class="ruby-value">0</span> <span class="ruby-operator">..</span> <span class="ruby-value">40</span>).<span class="ruby-identifier">include?</span> <span class="ruby-identifier">score_phred</span>
+392: <span class="ruby-identifier">score_illumina</span> = <span class="ruby-identifier">score_phred</span> <span class="ruby-operator">+</span> <span class="ruby-constant">SCORE_ILLUMINA</span>
+393: <span class="ruby-identifier">score</span> = <span class="ruby-identifier">score_illumina</span>.<span class="ruby-identifier">chr</span>
+394: <span class="ruby-keyword kw">end</span>
+395: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="convert-solexa-illumina--method" class="method-detail ">
+ <a name="method-i-convert_solexa2illumina%21"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">convert_solexa2illumina!</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to convert the quality scores from Solexa odd/ratio to Illumina
+format.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="convert-solexa-illumina--source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 399</span>
+399: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">convert_solexa2illumina!</span>
+400: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">gsub!</span> <span class="ruby-regexp re">/./</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">score</span><span class="ruby-operator">|</span>
+401: <span class="ruby-identifier">score</span> = <span class="ruby-identifier">solexa_char2illumina_char</span>(<span class="ruby-identifier">score</span>)
+402: <span class="ruby-keyword kw">end</span>
+403: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="generate-method" class="method-detail ">
+ <a name="method-i-generate"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">generate</span><span
+ class="method-args">(length, type)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that generates a random sequence of a given length and type.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="generate-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 209</span>
+209: <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>)
+210: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Cannot generate sequence length < 1: #{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>
+211:
+212: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>.<span class="ruby-identifier">downcase</span>
+213: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"dna"</span>
+214: <span class="ruby-identifier">alph</span> = <span class="ruby-constant">DNA</span>
+215: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"rna"</span>
+216: <span class="ruby-identifier">alph</span> = <span class="ruby-constant">RNA</span>
+217: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">"protein"</span>
+218: <span class="ruby-identifier">alph</span> = <span class="ruby-constant">PROTEIN</span>
+219: <span class="ruby-keyword kw">else</span>
+220: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Unknown sequence type: #{type}"</span>
+221: <span class="ruby-keyword kw">end</span>
+222:
+223: <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>)
+224: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq_new</span>
+225: <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>
+226: <span class="ruby-identifier">seq_new</span>
+227: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="hard-mask-method" class="method-detail ">
+ <a name="method-i-hard_mask"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">hard_mask</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the percentage of hard masked residues or N’s in
+a sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="hard-mask-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 301</span>
+301: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">hard_mask</span>
+302: ((<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-value str">"N"</span>).<span class="ruby-identifier">size</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">len</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">indels</span>).<span class="ruby-identifier">to_f</span>) * <span class="ruby-value">100</span>).<span class="ruby-identifier">round</span>(<span class="ruby-value">2</span>)
+303: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="homopol-max-method" class="method-detail ">
+ <a name="method-i-homopol_max"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">homopol_max</span><span
+ class="method-args">(min = 1)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the length of the longest homopolymeric stretch found
+in a sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="homopol-max-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 284</span>
+284: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">homopol_max</span>(<span class="ruby-identifier">min</span> = <span class="ruby-value">1</span>)
+285: <span class="ruby-keyword kw">return</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">seq</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword kw">or</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">empty?</span>
+286:
+287: <span class="ruby-identifier">found</span> = <span class="ruby-keyword kw">false</span>
+288:
+289: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-node">/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">match</span><span class="ruby-operator">|</span>
+290: <span class="ruby-identifier">found</span> = <span class="ruby-keyword kw">true</span>
+291: <span class="ruby-identifier">min</span> = <span class="ruby-identifier">match</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">></span> <span class="ruby-identifier">min</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">match</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">min</span>
+292: <span class="ruby-keyword kw">end</span>
+293:
+294: <span class="ruby-keyword kw">return</span> <span class="ruby-value">0</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">found</span>
+295:
+296: <span class="ruby-identifier">min</span>
+297: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="indels-method" class="method-detail ">
+ <a name="method-i-indels"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">indels</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Return the number indels in a sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="indels-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 95</span>
+95: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">indels</span>
+96: <span class="ruby-identifier">regex</span> = <span class="ruby-constant">Regexp</span>.<span class="ruby-identifier">new</span>(<span class="ruby-node">/[#{Regexp.escape(INDELS.join(""))}]/</span>)
+97: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-identifier">regex</span>).<span class="ruby-identifier">size</span>
+98: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="is-dna--method" class="method-detail ">
+ <a name="method-i-is_dna%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">is_dna?</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns true is a given sequence type is DNA.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="is-dna--source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 101</span>
+101: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_dna?</span>
+102: <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>
+103: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="is-protein--method" class="method-detail ">
+ <a name="method-i-is_protein%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">is_protein?</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns true is a given sequence type is protein.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="is-protein--source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 111</span>
+111: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_protein?</span>
+112: <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>
+113: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="is-rna--method" class="method-detail ">
+ <a name="method-i-is_rna%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">is_rna?</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns true is a given sequence type is RNA.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="is-rna--source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 106</span>
+106: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">is_rna?</span>
+107: <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>
+108: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="len-method" class="method-detail method-alias">
+ <a name="method-i-len"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">len</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ </div>
+
+
+
+
+ <div class="aliases">
+ Alias for: <a href="Seq.html#method-i-length">length</a>
+ </div>
+
+ </div>
+
+
+ <div id="length-method" class="method-detail ">
+ <a name="method-i-length"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">length</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Returns the length of a sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="length-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 88</span>
+88: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">length</span>
+89: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">?</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>
+90: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+ <div class="aliases">
+ Also aliased as: <a href="Seq.html#method-i-len">len</a>
+ </div>
+
+
+
+ </div>
+
+
+ <div id="match-method" class="method-detail ">
+ <a name="method-i-match"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">match</span><span
+ class="method-args">(patter, pos)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <hr style="height: 10px"></hr><pre>
+ seq.match(pattern[, pos ] [, hd=max] [, ed=max]) -> matchdata or nil
+</pre>
+<hr style="height: 10px"></hr><p>
+Method to locate a pattern in a sequence and return the position of the
+match or nil if no match was found. Optional maximum Hamming and Edit
+distance can be specified.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="match-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 411</span>
+411: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">match</span>(<span class="ruby-identifier">patter</span>, <span class="ruby-identifier">pos</span>)
+412: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="revcomp-method" class="method-detail method-alias">
+ <a name="method-i-revcomp"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">revcomp</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+
+
+
+
+ </div>
+
+
+
+
+ <div class="aliases">
+ Alias for: <a href="Seq.html#method-i-reverse_complement">reverse_complement</a>
+ </div>
+
+ </div>
+
+
+ <div id="reverse-method" class="method-detail ">
+ <a name="method-i-reverse"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">reverse</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to reverse the sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="reverse-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 191</span>
+191: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">reverse</span>
+192: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">reverse!</span>
+193: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="reverse-complement-method" class="method-detail ">
+ <a name="method-i-reverse_complement"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">reverse_complement</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to reverse complement sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="reverse-complement-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 183</span>
+183: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">reverse_complement</span>
+184: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">reverse</span>
+185: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">complement</span>
+186: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+ <div class="aliases">
+ Also aliased as: <a href="Seq.html#method-i-revcomp">revcomp</a>
+ </div>
+
+
+
+ </div>
+
+
+ <div id="soft-mask-method" class="method-detail ">
+ <a name="method-i-soft_mask"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">soft_mask</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns the percentage of soft masked residues or lower cased
+residues in a sequence.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="soft-mask-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 307</span>
+307: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">soft_mask</span>
+308: ((<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">scan</span>(<span class="ruby-regexp re">/[a-z]/</span>).<span class="ruby-identifier">size</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">len</span> <span class="ruby-operator">-</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">indels</span>).<span class="ruby-identifier">to_f</span>) * <span class="ruby-value">100</span>).<span class="ruby-identifier">round</span>(<span class="ruby-value">2</span>)
+309: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="subseq-method" class="method-detail ">
+ <a name="method-i-subseq"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">subseq</span><span
+ class="method-args">(start, length = self.length - start)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns a subsequence of from a given start position and of a
+given length.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="subseq-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 231</span>
+231: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">subseq</span>(<span class="ruby-identifier">start</span>, <span class="ruby-identifier">length</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">start</span>)
+232: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start: #{start} < 0"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span>
+233: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence length: #{length} < 1"</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>
+234: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
+235:
+236: <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+237:
+238: <span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>]
+239: <span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
+240:
+241: <span class="ruby-constant">Seq</span>.<span class="ruby-identifier">new</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>, <span class="ruby-identifier">seq</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span>, <span class="ruby-identifier">qual</span>)
+242: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="subseq--method" class="method-detail ">
+ <a name="method-i-subseq%21"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">subseq!</span><span
+ class="method-args">(start, length = self.length - start)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that replaces a sequence with a subsequence from a given start
+position and of a given length.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="subseq--source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 246</span>
+246: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">subseq!</span>(<span class="ruby-identifier">start</span>, <span class="ruby-identifier">length</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">start</span>)
+247: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start: #{start} < 0"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator"><</span> <span class="ruby-value">0</span>
+248: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence length: #{length} < 1"</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>
+249: <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">></span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
+250:
+251: <span class="ruby-identifier">stop</span> = <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>
+252:
+253: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>]
+254: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>[<span class="ruby-identifier">start</span> <span class="ruby-operator">..</span> <span class="ruby-identifier">stop</span>] <span class="ruby-keyword kw">unless</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>.<span class="ruby-identifier">nil?</span>
+255: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="subseq-rand-method" class="method-detail ">
+ <a name="method-i-subseq_rand"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">subseq_rand</span><span
+ class="method-args">(length)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that returns a subsequence of a given length beginning at a random
+position.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="subseq-rand-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 259</span>
+259: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">subseq_rand</span>(<span class="ruby-identifier">length</span>)
+260: <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-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
+261: <span class="ruby-identifier">start</span> = <span class="ruby-value">0</span>
+262: <span class="ruby-keyword kw">else</span>
+263: <span class="ruby-identifier">start</span> = <span class="ruby-identifier">rand</span>(<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>)
+264: <span class="ruby-keyword kw">end</span>
+265:
+266: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">subseq</span>(<span class="ruby-identifier">start</span>, <span class="ruby-identifier">length</span>)
+267: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-bp-method" class="method-detail ">
+ <a name="method-i-to_bp"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_bp</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that given a <a href="Seq.html">Seq</a> entry returns a <a
+href="Biopieces.html">Biopieces</a> record (a hash).
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-bp-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 132</span>
+132: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_bp</span>
+133: <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>
+134: <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>
+135: <span class="ruby-identifier">record</span> = {}
+136: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ_NAME</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>
+137: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>
+138: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SEQ_LEN</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>
+139: <span class="ruby-identifier">record</span>[<span class="ruby-value">:SCORES</span>] = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span>
+140: <span class="ruby-identifier">record</span>
+141: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-dna-method" class="method-detail ">
+ <a name="method-i-to_dna"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_dna</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to reverse-transcribe RNA to DNA.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-dna-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 124</span>
+124: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_dna</span>
+125: <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>
+126: <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>
+127: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'dna'</span>
+128: <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>)
+129: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-fasta-method" class="method-detail ">
+ <a name="method-i-to_fasta"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_fasta</span><span
+ class="method-args">(wrap = nil)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that given a <a href="Seq.html">Seq</a> entry returns a FASTA entry
+(a string).
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-fasta-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 144</span>
+144: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_fasta</span>(<span class="ruby-identifier">wrap</span> = <span class="ruby-keyword kw">nil</span>)
+145: <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>
+146: <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>
+147:
+148: <span class="ruby-identifier">seq_name</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq_name</span>
+149: <span class="ruby-identifier">seq</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>
+150:
+151: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">wrap</span>.<span class="ruby-identifier">nil?</span>
+152: <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">gsub!</span> <span class="ruby-node">/(.{#{wrap}})/</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">match</span><span class="ruby-operator">|</span>
+153: <span class="ruby-identifier">match</span> <span class="ruby-operator"><<</span> <span class="ruby-value str">"\n"</span>
+154: <span class="ruby-keyword kw">end</span>
+155:
+156: <span class="ruby-identifier">seq</span>.<span class="ruby-identifier">chomp!</span>
+157: <span class="ruby-keyword kw">end</span>
+158:
+159: <span class="ruby-node">">#{seq_name}\n#{seq}\n"</span>
+160: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-key-method" class="method-detail ">
+ <a name="method-i-to_key"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_key</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that generates a unique key for a DNA sequence and return this key
+as a Fixnum.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-key-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 164</span>
+164: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_key</span>
+165: <span class="ruby-identifier">key</span> = <span class="ruby-value">0</span>
+166:
+167: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span>.<span class="ruby-identifier">upcase</span>.<span class="ruby-identifier">each_char</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">char</span><span class="ruby-operator">|</span>
+168: <span class="ruby-identifier">key</span> <span class="ruby-operator"><<=</span> <span class="ruby-value">2</span>
+169:
+170: <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">char</span>
+171: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'A'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">0</span>
+172: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'C'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">1</span>
+173: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'G'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">2</span>
+174: <span class="ruby-keyword kw">when</span> <span class="ruby-value str">'T'</span> <span class="ruby-keyword kw">then</span> <span class="ruby-identifier">key</span> <span class="ruby-operator">|=</span> <span class="ruby-value">3</span>
+175: <span class="ruby-keyword kw">else</span> <span class="ruby-identifier">raise</span> <span class="ruby-constant">SeqError</span>, <span class="ruby-node">"Bad residue: #{char}"</span>
+176: <span class="ruby-keyword kw">end</span>
+177: <span class="ruby-keyword kw">end</span>
+178:
+179: <span class="ruby-identifier">key</span>
+180: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="to-rna-method" class="method-detail ">
+ <a name="method-i-to_rna"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">to_rna</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to transcribe DNA to RNA.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="to-rna-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 116</span>
+116: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_rna</span>
+117: <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>
+118: <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>
+119: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">type</span> = <span class="ruby-value str">'rna'</span>
+120: <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>)
+121: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="solexa-phred-method" class="method-detail ">
+ <a name="method-i-solexa2phred"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">solexa2phred</span><span
+ class="method-args">(score)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to convert a Solexa score (odd ratio) to a phred (probability)
+integer score.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="solexa-phred-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 418</span>
+418: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">solexa2phred</span>(<span class="ruby-identifier">score</span>)
+419: (<span class="ruby-value">10.0</span> * <span class="ruby-constant">Math</span>.<span class="ruby-identifier">log</span>(<span class="ruby-value">10.0</span> <span class="ruby-operator">**</span> (<span class="ruby-identifier">score</span> <span class="ruby-operator">/</span> <span class="ruby-value">10.0</span>) <span class="ruby-operator">+</span> <span class="ruby-value">1.0</span>, <span class="ruby-value">10</span>)).<span class="ruby-identifier">to_i</span>
+420: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="solexa-char-illumina-char-method" class="method-detail ">
+ <a name="method-i-solexa_char2illumina_char"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">solexa_char2illumina_char</span><span
+ class="method-args">(char)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to convert a Solexa score encoded using base 64 ASCII to a Phred
+score encoded using base 64 ASCII.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="solexa-char-illumina-char-source">
+<pre>
+ <span class="ruby-comment cmt"># File seq.rb, line 424</span>
+424: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">solexa_char2illumina_char</span>(<span class="ruby-identifier">char</span>)
+425: <span class="ruby-identifier">score_solexa</span> = <span class="ruby-identifier">char</span>.<span class="ruby-identifier">ord</span> <span class="ruby-operator">-</span> <span class="ruby-value">64</span>
+426: <span class="ruby-identifier">score_phred</span> = <span class="ruby-identifier">solexa2phred</span>(<span class="ruby-identifier">score_solexa</span>)
+427: (<span class="ruby-identifier">score_phred</span> <span class="ruby-operator">+</span> <span class="ruby-value">64</span>).<span class="ruby-identifier">chr</span>
+428: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: SeqError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
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+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./seq_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="seq.rb">seq.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
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+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
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+
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+ <li><a href="./FastaError.html">FastaError</a></li>
+
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+
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+
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+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
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+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
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+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
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+
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+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">SeqError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a href="Seq.html">Seq</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
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+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Status</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
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+ </h3>
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+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./biopieces_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="biopieces.rb">biopieces.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-i-delete">#delete</a></li>
+
+ <li><a href="#method-i-get_tmpdir">#get_tmpdir</a></li>
+
+ <li><a href="#method-i-log">#log</a></li>
+
+ <li><a href="#method-i-path">#path</a></li>
+
+ <li><a href="#method-i-set">#set</a></li>
+
+ <li><a href="#method-i-set_tmpdir">#set_tmpdir</a></li>
+
+ <li><a href="#method-i-time_diff">#time_diff</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
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+
+ <li><a href="./Base36.html">Base36</a></li>
+
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+
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+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
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+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
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+
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+
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+
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+
+ <li><a href="./SFF.html">SFF</a></li>
+
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+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Status</h1>
+
+ <div id="description">
+ <p>
+Class for manipulating the execution status of <a
+href="Biopieces.html">Biopieces</a> by setting a status file with a time
+stamp, process id, and command arguments. The status file is used for
+creating log entries and for displaying the runtime status of <a
+href="Biopieces.html">Biopieces</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="delete-method" class="method-detail ">
+ <a name="method-i-delete"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">delete</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Delete status file.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="delete-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 547</span>
+547: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">delete</span>
+548: <span class="ruby-constant">File</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">path</span>)
+549: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="get-tmpdir-method" class="method-detail ">
+ <a name="method-i-get_tmpdir"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">get_tmpdir</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Extract the temporary directory path from the status file, and return this
+or nil if not found.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="get-tmpdir-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 520</span>
+520: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_tmpdir</span>
+521: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
+522: <span class="ruby-identifier">tmpdir_path</span> = <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">read</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">";"</span>).<span class="ruby-identifier">last</span>
+523: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">tmpdir_path</span> <span class="ruby-keyword kw">if</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">directory?</span>(<span class="ruby-identifier">tmpdir_path</span>)
+524: <span class="ruby-keyword kw">end</span>
+525:
+526: <span class="ruby-keyword kw">nil</span>
+527: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="log-method" class="method-detail ">
+ <a name="method-i-log"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">log</span><span
+ class="method-args">(exit_status)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Write the Biopiece status to the log file.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="log-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 530</span>
+530: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">log</span>(<span class="ruby-identifier">exit_status</span>)
+531: <span class="ruby-identifier">time1</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">"%Y-%m-%d %X"</span>)
+532: <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
+533: <span class="ruby-identifier">script</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-identifier">$0</span>)
+534:
+535: <span class="ruby-identifier">stream</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>)
+536: <span class="ruby-identifier">time0</span>, <span class="ruby-identifier">args</span>, <span class="ruby-identifier">tmp_dir</span> = <span class="ruby-identifier">stream</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">";"</span>)
+537: <span class="ruby-identifier">stream</span>.<span class="ruby-identifier">close</span>
+538:
+539: <span class="ruby-identifier">elap</span> = <span class="ruby-identifier">time_diff</span>(<span class="ruby-identifier">time0</span>, <span class="ruby-identifier">time1</span>)
+540: <span class="ruby-identifier">command</span> = [<span class="ruby-identifier">script</span>, <span class="ruby-identifier">args</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">" "</span>)
+541: <span class="ruby-identifier">log_file</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_LOG"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/biopieces.log"</span>
+542:
+543: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">log_file</span>, <span class="ruby-identifier">mode</span> = <span class="ruby-value str">"a"</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span> <span class="ruby-identifier">file</span>.<span class="ruby-identifier">puts</span> [<span class="ruby-identifier">time0</span>, <span class="ruby-identifier">time1</span>, <span class="ruby-identifier">elap</span>, <span class="ruby-identifier">user</span>, <span class="ruby-identifier">exit_status</span>, <span class="ruby-identifier">command</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"\t"</span>) }
+544: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="set-method" class="method-detail ">
+ <a name="method-i-set"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">set</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Write the status to a status file.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="set-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 495</span>
+495: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">set</span>
+496: <span class="ruby-identifier">time0</span> = <span class="ruby-constant">Time</span>.<span class="ruby-identifier">new</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">"%Y-%m-%d %X"</span>)
+497:
+498: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
+499: <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">puts</span> [<span class="ruby-identifier">time0</span>, <span class="ruby-constant">ARGV</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">" "</span>)].<span class="ruby-identifier">join</span>(<span class="ruby-value str">";"</span>)
+500: <span class="ruby-keyword kw">end</span>
+501: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="set-tmpdir-method" class="method-detail ">
+ <a name="method-i-set_tmpdir"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">set_tmpdir</span><span
+ class="method-args">(tmpdir_path)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Append the a temporary directory path to the status file.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="set-tmpdir-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 504</span>
+504: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">set_tmpdir</span>(<span class="ruby-identifier">tmpdir_path</span>)
+505: <span class="ruby-identifier">status</span> = <span class="ruby-value str">""</span>
+506:
+507: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"r"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
+508: <span class="ruby-identifier">status</span> = <span class="ruby-identifier">fh</span>.<span class="ruby-identifier">read</span>.<span class="ruby-identifier">chomp</span>
+509: <span class="ruby-keyword kw">end</span>
+510:
+511: <span class="ruby-identifier">status</span> = <span class="ruby-node">"#{status};#{tmpdir_path}\n"</span>
+512:
+513: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>) <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">fh</span><span class="ruby-operator">|</span>
+514: <span class="ruby-identifier">fh</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">status</span>
+515: <span class="ruby-keyword kw">end</span>
+516: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-instance-method-details" class="method-section section">
+ <h3 class="section-header">Private Instance Methods</h3>
+
+
+ <div id="path-method" class="method-detail ">
+ <a name="method-i-path"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">path</span><span
+ class="method-args">()</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Path to status file
+</p>
+
+
+
+ <div class="method-source-code"
+ id="path-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 554</span>
+554: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">path</span>
+555: <span class="ruby-identifier">user</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"USER"</span>]
+556: <span class="ruby-identifier">script</span> = <span class="ruby-constant">File</span>.<span class="ruby-identifier">basename</span>(<span class="ruby-identifier">$0</span>)
+557: <span class="ruby-identifier">pid</span> = <span class="ruby-identifier">$$</span>
+558: <span class="ruby-identifier">path</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">"BP_TMP"</span>] <span class="ruby-operator">+</span> <span class="ruby-value str">"/"</span> <span class="ruby-operator">+</span> [<span class="ruby-identifier">user</span>, <span class="ruby-identifier">script</span>, <span class="ruby-identifier">pid</span>, <span class="ruby-value str">"status"</span>].<span class="ruby-identifier">join</span>(<span class="ruby-value str">"."</span>)
+559: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="time-diff-method" class="method-detail ">
+ <a name="method-i-time_diff"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">time_diff</span><span
+ class="method-args">(t0, t1)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Get the elapsed time from the difference between two time stamps.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="time-diff-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 562</span>
+562: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">time_diff</span>(<span class="ruby-identifier">t0</span>, <span class="ruby-identifier">t1</span>)
+563: <span class="ruby-constant">Time</span>.<span class="ruby-identifier">at</span>((<span class="ruby-constant">DateTime</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-identifier">t1</span>).<span class="ruby-identifier">to_time</span> <span class="ruby-operator">-</span> <span class="ruby-constant">DateTime</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-identifier">t0</span>).<span class="ruby-identifier">to_time</span>).<span class="ruby-identifier">to_i</span>).<span class="ruby-identifier">gmtime</span>.<span class="ruby-identifier">strftime</span>(<span class="ruby-value str">'%X'</span>)
+564: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: Stream</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./biopieces_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="biopieces.rb">biopieces.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">IO</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-nread">::nread</a></li>
+
+ <li><a href="#method-c-nwrite">::nwrite</a></li>
+
+ <li><a href="#method-c-open">::open</a></li>
+
+ <li><a href="#method-c-read">::read</a></li>
+
+ <li><a href="#method-c-write">::write</a></li>
+
+ <li><a href="#method-c-zipped%3F">::zipped?</a></li>
+
+ <li><a href="#method-c-zread">::zread</a></li>
+
+ <li><a href="#method-c-zwrite">::zwrite</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">Stream</h1>
+
+ <div id="description">
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="open-method" class="method-detail ">
+ <a name="method-c-open"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">open</span><span
+ class="method-args">(options, mode, stdio)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Open <a href="Biopieces.html">Biopieces</a> output data stream for reading
+from stdin or a file specified in options[:stream_in] OR writing to stdout
+or a file specified in options[:stream_out] or options[:data_out].
+</p>
+
+
+
+ <div class="method-source-code"
+ id="open-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 572</span>
+572: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">options</span>, <span class="ruby-identifier">mode</span>, <span class="ruby-identifier">stdio</span>)
+573: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">mode</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"r"</span>
+574: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:data_in</span>] <span class="ruby-keyword kw">and</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:data_in</span>].<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"-"</span>
+575: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nread</span>([<span class="ruby-value str">"-"</span>])
+576: <span class="ruby-keyword kw">else</span>
+577: <span class="ruby-identifier">$stdin</span>.<span class="ruby-identifier">tty?</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">options</span>[<span class="ruby-value">:stream_in</span>]) <span class="ruby-operator">:</span> <span class="ruby-identifier">stdio</span>
+578: <span class="ruby-keyword kw">end</span>
+579: <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">mode</span> <span class="ruby-operator">==</span> <span class="ruby-value str">"w"</span>
+580: <span class="ruby-identifier">options</span>[<span class="ruby-value">:stream_out</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">options</span>[<span class="ruby-value">:stream_out</span>], <span class="ruby-identifier">options</span>[<span class="ruby-value">:compress</span>]) <span class="ruby-operator">:</span> <span class="ruby-identifier">stdio</span>
+581: <span class="ruby-keyword kw">else</span>
+582: <span class="ruby-identifier">raise</span> <span class="ruby-node">"Bad mode #{mode}"</span>
+583: <span class="ruby-keyword kw">end</span>
+584: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="private-class-method-details" class="method-section section">
+ <h3 class="section-header">Private Class Methods</h3>
+
+
+ <div id="nread-method" class="method-detail ">
+ <a name="method-c-nread"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">nread</span><span
+ class="method-args">(files)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Opens a list of files for reading and return an <em>io</em> object.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="nread-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 616</span>
+616: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nread</span>(<span class="ruby-identifier">files</span>)
+617: <span class="ruby-identifier">stdin</span>, <span class="ruby-identifier">stdout</span>, <span class="ruby-identifier">stderr</span> = <span class="ruby-constant">Open3</span>.<span class="ruby-identifier">popen3</span>(<span class="ruby-value str">"cat "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">files</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">' '</span>));
+618: <span class="ruby-identifier">stdin</span>.<span class="ruby-identifier">close</span>
+619: <span class="ruby-identifier">stderr</span>.<span class="ruby-identifier">close</span>
+620: <span class="ruby-identifier">stdout</span>
+621: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="nwrite-method" class="method-detail ">
+ <a name="method-c-nwrite"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">nwrite</span><span
+ class="method-args">(file)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Opens a file for writing and return an <em>io</em> object.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="nwrite-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 624</span>
+624: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nwrite</span>(<span class="ruby-identifier">file</span>)
+625: <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>, <span class="ruby-identifier">mode</span>=<span class="ruby-value str">"w"</span>)
+626: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="read-method" class="method-detail ">
+ <a name="method-c-read"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">read</span><span
+ class="method-args">(files)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Opens a reads stream to a list of files.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="read-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 589</span>
+589: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read</span>(<span class="ruby-identifier">files</span>)
+590: <span class="ruby-keyword kw">return</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">files</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-comment cmt">#TODO case/when</span>
+591: <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zipped?</span>(<span class="ruby-identifier">files</span>) <span class="ruby-operator">?</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zread</span>(<span class="ruby-identifier">files</span>) <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nread</span>(<span class="ruby-identifier">files</span>)
+592: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="write-method" class="method-detail ">
+ <a name="method-c-write"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">write</span><span
+ class="method-args">(file, zip=nil)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Opens a write stream to a file and returns a <em>io</em> object.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="write-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 595</span>
+595: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">file</span>, <span class="ruby-identifier">zip</span>=<span class="ruby-keyword kw">nil</span>)
+596: <span class="ruby-identifier">zip</span> <span class="ruby-operator">?</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zwrite</span>(<span class="ruby-identifier">file</span>) <span class="ruby-operator">:</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">nwrite</span>(<span class="ruby-identifier">file</span>)
+597: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="zipped--method" class="method-detail ">
+ <a name="method-c-zipped%3F"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">zipped?</span><span
+ class="method-args">(files)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Test if a list of files are gzipped or not. Raises if files are mixed
+zipped and unzipped.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="zipped--source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 630</span>
+630: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zipped?</span>(<span class="ruby-identifier">files</span>)
+631: <span class="ruby-identifier">type_hash</span> = {}
+632:
+633: <span class="ruby-identifier">files</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
+634: <span class="ruby-identifier">type</span> = <span class="ruby-node">`file #{file}`</span>
+635:
+636: <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp re">/gzip compressed/</span>
+637: <span class="ruby-identifier">type_hash</span>[<span class="ruby-value">:gzip</span>] = <span class="ruby-keyword kw">true</span>
+638: <span class="ruby-keyword kw">else</span>
+639: <span class="ruby-identifier">type_hash</span>[<span class="ruby-value">:ascii</span>] = <span class="ruby-keyword kw">true</span>
+640: <span class="ruby-keyword kw">end</span>
+641: <span class="ruby-keyword kw">end</span>
+642:
+643: <span class="ruby-identifier">raise</span> <span class="ruby-value str">"Mixture of zipped and unzipped files"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">type_hash</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">2</span>
+644:
+645: <span class="ruby-identifier">type_hash</span>[<span class="ruby-value">:gzip</span>]
+646: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="zread-method" class="method-detail ">
+ <a name="method-c-zread"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">zread</span><span
+ class="method-args">(files)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Opens a list of gzipped files for reading and return an <em>io</em> object.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="zread-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 600</span>
+600: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zread</span>(<span class="ruby-identifier">files</span>)
+601: <span class="ruby-identifier">stdin</span>, <span class="ruby-identifier">stdout</span>, <span class="ruby-identifier">stderr</span> = <span class="ruby-constant">Open3</span>.<span class="ruby-identifier">popen3</span>(<span class="ruby-value str">"zcat "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">files</span>.<span class="ruby-identifier">join</span>(<span class="ruby-value str">' '</span>));
+602: <span class="ruby-identifier">stdin</span>.<span class="ruby-identifier">close</span>
+603: <span class="ruby-identifier">stderr</span>.<span class="ruby-identifier">close</span>
+604: <span class="ruby-identifier">stdout</span>
+605: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="zwrite-method" class="method-detail ">
+ <a name="method-c-zwrite"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">zwrite</span><span
+ class="method-args">(file)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Opens a file for gzipped writing and return an <em>io</em> object.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="zwrite-source">
+<pre>
+ <span class="ruby-comment cmt"># File biopieces.rb, line 608</span>
+608: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zwrite</span>(<span class="ruby-identifier">file</span>)
+609: <span class="ruby-identifier">stdin</span>, <span class="ruby-identifier">stdout</span>, <span class="ruby-identifier">stderr</span> = <span class="ruby-constant">Open3</span>.<span class="ruby-identifier">popen3</span>(<span class="ruby-node">"gzip -f > #{file}"</span>)
+610: <span class="ruby-identifier">stderr</span>.<span class="ruby-identifier">close</span>
+611: <span class="ruby-identifier">stdout</span>.<span class="ruby-identifier">close</span>
+612: <span class="ruby-identifier">stdin</span>
+613: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: String</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./bits_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="bits.rb">bits.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">Object</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+ <div id="method-list-section" class="section">
+ <h3 class="section-header">Methods</h3>
+ <ul class="link-list">
+
+ <li><a href="#method-c-hamming_dist">::hamming_dist</a></li>
+
+ <li><a href="#method-i-%26">#&</a></li>
+
+ <li><a href="#method-i-%5E">#^</a></li>
+
+ <li><a href="#method-i-%7C">#|</a></li>
+
+ </ul>
+ </div>
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">String</h1>
+
+ <div id="description">
+ <p>
+Monkey patching Class <a href="String.html">String</a> to add bitwise
+operators. Behaviour matching Perl’s: <a
+href="http://perldoc.perl.org/perlop.html#Bitwise-String-Operators">perldoc.perl.org/perlop.html#Bitwise-String-Operators</a>
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+ <div id="public-class-method-details" class="method-section section">
+ <h3 class="section-header">Public Class Methods</h3>
+
+
+ <div id="hamming-dist-method" class="method-detail ">
+ <a name="method-c-hamming_dist"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">hamming_dist</span><span
+ class="method-args">(str1, str2)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method to that returns the case senstive Hamming Distance between two
+strings. <a
+href="http://en.wikipedia.org/wiki/Hamming_distance">en.wikipedia.org/wiki/Hamming_distance</a>
+</p>
+
+
+
+ <div class="method-source-code"
+ id="hamming-dist-source">
+<pre>
+ <span class="ruby-comment cmt"># File bits.rb, line 34</span>
+34: <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">hamming_dist</span>(<span class="ruby-identifier">str1</span>, <span class="ruby-identifier">str2</span>)
+35: <span class="ruby-identifier">raise</span> <span class="ruby-constant">StringError</span>, <span class="ruby-node">"Uneven string lengths: #{str1.length} != #{str2.length}"</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">str1</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">str2</span>.<span class="ruby-identifier">length</span>
+36: (<span class="ruby-identifier">str1</span> <span class="ruby-operator">^</span> <span class="ruby-identifier">str2</span> ).<span class="ruby-identifier">count</span>(<span class="ruby-value str">"\x01-\xff"</span>)
+37: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+ <div id="public-instance-method-details" class="method-section section">
+ <h3 class="section-header">Public Instance Methods</h3>
+
+
+ <div id="--method" class="method-detail ">
+ <a name="method-i-%26"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">&</span><span
+ class="method-args">(str)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that performs bitwise AND operation where bits are copied if they
+exists in BOTH operands. If the operand sizes are different, the &
+operator methods acts as though the longer operand were truncated to the
+length of the shorter.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="--source">
+<pre>
+ <span class="ruby-comment cmt"># File bits.rb, line 43</span>
+43: <span class="ruby-keyword kw">def</span> &(<span class="ruby-identifier">str</span>)
+44: <span class="ruby-identifier">new</span> = <span class="ruby-value str">""</span>
+45:
+46: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> [<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">min</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
+47: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> (<span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span> & <span class="ruby-identifier">str</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span>)
+48: <span class="ruby-keyword kw">end</span>
+49:
+50: <span class="ruby-identifier">new</span>
+51: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="--method" class="method-detail ">
+ <a name="method-i-%5E"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">^</span><span
+ class="method-args">(str)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that performs bitwise XOR operation where bits are copied if they
+exists in ONE BUT NOT BOTH operands.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="--source">
+<pre>
+ <span class="ruby-comment cmt"># File bits.rb, line 77</span>
+77: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">^</span>(<span class="ruby-identifier">str</span>)
+78: <span class="ruby-identifier">new</span> = <span class="ruby-value str">""</span>
+79:
+80: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> [<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">min</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
+81: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> (<span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">^</span> <span class="ruby-identifier">str</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span>)
+82: <span class="ruby-keyword kw">end</span>
+83:
+84: <span class="ruby-identifier">new</span>
+85: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ <div id="--method" class="method-detail ">
+ <a name="method-i-%7C"></a>
+
+ <div class="method-heading">
+
+ <span class="method-name">|</span><span
+ class="method-args">(str)</span>
+ <span class="method-click-advice">click to toggle source</span>
+
+ </div>
+
+ <div class="method-description">
+
+ <p>
+Method that performs bitwise OR operation where bits are copied if they
+exists in EITHER operands. If the operand sizes differ, the shorter operand
+is extended with the terminal part of the longer operand.
+</p>
+
+
+
+ <div class="method-source-code"
+ id="--source">
+<pre>
+ <span class="ruby-comment cmt"># File bits.rb, line 57</span>
+57: <span class="ruby-keyword kw">def</span> <span class="ruby-operator">|</span>(<span class="ruby-identifier">str</span>)
+58: <span class="ruby-identifier">new</span> = <span class="ruby-value str">""</span>
+59:
+60: <span class="ruby-identifier">min</span> = [<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>].<span class="ruby-identifier">min</span>
+61:
+62: (<span class="ruby-value">0</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">min</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
+63: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> (<span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span> <span class="ruby-operator">|</span> <span class="ruby-identifier">str</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">ord</span>)
+64: <span class="ruby-keyword kw">end</span>
+65:
+66: <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-identifier">str</span>.<span class="ruby-identifier">length</span>
+67: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> <span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">min</span> <span class="ruby-operator">...</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span>]
+68: <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>
+69: <span class="ruby-identifier">new</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">str</span>[<span class="ruby-identifier">min</span> <span class="ruby-operator">...</span> <span class="ruby-identifier">str</span>.<span class="ruby-identifier">length</span>]
+70: <span class="ruby-keyword kw">end</span>
+71:
+72: <span class="ruby-identifier">new</span>
+73: <span class="ruby-keyword kw">end</span></pre>
+ </div>
+
+ </div>
+
+
+
+
+ </div>
+
+
+ </div>
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>Class: StringError</title>
+
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
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+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+
+</head>
+<body class="class">
+
+ <div id="metadata">
+ <div id="home-metadata">
+ <div id="home-section" class="section">
+ <h3 class="section-header">
+ <a href="./index.html">Home</a>
+ <a href="./index.html#classes">Classes</a>
+ <a href="./index.html#methods">Methods</a>
+ </h3>
+ </div>
+ </div>
+
+ <div id="file-metadata">
+ <div id="file-list-section" class="section">
+ <h3 class="section-header">In Files</h3>
+ <div class="section-body">
+ <ul>
+
+ <li><a href="./bits_rb.html?TB_iframe=true&height=550&width=785"
+ class="thickbox" title="bits.rb">bits.rb</a></li>
+
+ </ul>
+ </div>
+ </div>
+
+
+ </div>
+
+ <div id="class-metadata">
+
+ <!-- Parent Class -->
+
+ <div id="parent-class-section" class="section">
+ <h3 class="section-header">Parent</h3>
+
+ <p class="link">StandardError</p>
+
+ </div>
+
+
+ <!-- Namespace Contents -->
+
+
+ <!-- Method Quickref -->
+
+
+ <!-- Included Modules -->
+
+ </div>
+
+ <div id="project-metadata">
+
+
+
+ <div id="classindex-section" class="section project-section">
+ <h3 class="section-header">Class Index
+ <span class="search-toggle"><img src="./images/find.png"
+ height="16" width="16" alt="[+]"
+ title="show/hide quicksearch" /></span></h3>
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
+ <fieldset>
+ <legend>Quicksearch</legend>
+ <input type="text" name="quicksearch" value=""
+ class="quicksearch-field" />
+ </fieldset>
+ </form>
+
+ <ul class="link-list">
+
+ <li><a href="./Base36.html">Base36</a></li>
+
+ <li><a href="./Base36Error.html">Base36Error</a></li>
+
+ <li><a href="./Biopieces.html">Biopieces</a></li>
+
+ <li><a href="./BitArray.html">BitArray</a></li>
+
+ <li><a href="./BitArrayError.html">BitArrayError</a></li>
+
+ <li><a href="./Boulder.html">Boulder</a></li>
+
+ <li><a href="./BoulderError.html">BoulderError</a></li>
+
+ <li><a href="./CastError.html">CastError</a></li>
+
+ <li><a href="./Casts.html">Casts</a></li>
+
+ <li><a href="./Digest.html">Digest</a></li>
+
+ <li><a href="./DigestError.html">DigestError</a></li>
+
+ <li><a href="./Fasta.html">Fasta</a></li>
+
+ <li><a href="./FastaError.html">FastaError</a></li>
+
+ <li><a href="./Fastq.html">Fastq</a></li>
+
+ <li><a href="./FastqError.html">FastqError</a></li>
+
+ <li><a href="./Filesys.html">Filesys</a></li>
+
+ <li><a href="./FilesysError.html">FilesysError</a></li>
+
+ <li><a href="./Genbank.html">Genbank</a></li>
+
+ <li><a href="./GenbankError.html">GenbankError</a></li>
+
+ <li><a href="./GenbankFeatures.html">GenbankFeatures</a></li>
+
+ <li><a href="./Locator.html">Locator</a></li>
+
+ <li><a href="./LocatorError.html">LocatorError</a></li>
+
+ <li><a href="./OptionHandler.html">OptionHandler</a></li>
+
+ <li><a href="./Read.html">Read</a></li>
+
+ <li><a href="./SFF.html">SFF</a></li>
+
+ <li><a href="./SFFError.html">SFFError</a></li>
+
+ <li><a href="./Seq.html">Seq</a></li>
+
+ <li><a href="./SeqError.html">SeqError</a></li>
+
+ <li><a href="./Status.html">Status</a></li>
+
+ <li><a href="./Stream.html">Stream</a></li>
+
+ <li><a href="./String.html">String</a></li>
+
+ <li><a href="./StringError.html">StringError</a></li>
+
+ </ul>
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
+ </div>
+
+
+ </div>
+ </div>
+
+ <div id="documentation">
+ <h1 class="class">StringError</h1>
+
+ <div id="description">
+ <p>
+Error class for all exceptions to do with <a href="String.html">String</a>.
+</p>
+
+ </div>
+
+ <!-- Constants -->
+
+
+ <!-- Attributes -->
+
+
+ <!-- Methods -->
+
+
+ </div>
+
+
+ <div id="rdoc-debugging-section-dump" class="debugging-section">
+
+ <p>Disabled; run with --debug to generate this.</p>
+
+ </div>
+
+ <div id="validator-badges">
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
+ Rdoc Generator</a> 1.1.6</small>.</p>
+ </div>
+
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: base36.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-02-11 19:42:32 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: biopieces.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
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+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-19 09:14:44 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>fileutils</li>
+
+ <li>date</li>
+
+ <li>optparse</li>
+
+ <li>open3</li>
+
+ <li>pp</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: bitarray.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-17 15:02:03 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: bits.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-08 11:37:57 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: boulder.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-19 09:17:13 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>filesys</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: digest.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-19 15:41:06 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>seq</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: fasta.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-19 09:11:06 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>seq</li>
+
+ <li>filesys</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: fastq.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-19 09:09:52 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>seq</li>
+
+ <li>filesys</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: filesys.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-18 22:13:22 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>zlib</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: genbank.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-19 09:19:25 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>seq</li>
+
+ <li>filesys</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2010 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+/**
+ *
+ * Darkfish Page Functions
+ * $Id: darkfish.js 53 2009-01-07 02:52:03Z deveiant $
+ *
+ * Author: Michael Granger <mgranger@laika.com>
+ *
+ */
+
+/* Provide console simulation for firebug-less environments */
+if (!("console" in window) || !("firebug" in console)) {
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
+ "group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"];
+
+ window.console = {};
+ for (var i = 0; i < names.length; ++i)
+ window.console[names[i]] = function() {};
+};
+
+
+/**
+ * Unwrap the first element that matches the given @expr@ from the targets and return them.
+ */
+$.fn.unwrap = function( expr ) {
+ return this.each( function() {
+ $(this).parents( expr ).eq( 0 ).after( this ).remove();
+ });
+};
+
+
+function showSource( e ) {
+ var target = e.target;
+ var codeSections = $(target).
+ parents('.method-detail').
+ find('.method-source-code');
+
+ $(target).
+ parents('.method-detail').
+ find('.method-source-code').
+ slideToggle();
+};
+
+function hookSourceViews() {
+ $('.method-description,.method-heading').click( showSource );
+};
+
+function toggleDebuggingSection() {
+ $('.debugging-section').slideToggle();
+};
+
+function hookDebuggingToggle() {
+ $('#debugging-toggle img').click( toggleDebuggingSection );
+};
+
+function hookQuickSearch() {
+ $('.quicksearch-field').each( function() {
+ var searchElems = $(this).parents('.section').find( 'li' );
+ var toggle = $(this).parents('.section').find('h3 .search-toggle');
+ // console.debug( "Toggle is: %o", toggle );
+ var qsbox = $(this).parents('form').get( 0 );
+
+ $(this).quicksearch( this, searchElems, {
+ noSearchResultsIndicator: 'no-class-search-results',
+ focusOnLoad: false
+ });
+ $(toggle).click( function() {
+ // console.debug( "Toggling qsbox: %o", qsbox );
+ $(qsbox).toggle();
+ });
+ });
+};
+
+function highlightTarget( anchor ) {
+ console.debug( "Highlighting target '%s'.", anchor );
+
+ $("a[name=" + anchor + "]").each( function() {
+ if ( !$(this).parent().parent().hasClass('target-section') ) {
+ console.debug( "Wrapping the target-section" );
+ $('div.method-detail').unwrap( 'div.target-section' );
+ $(this).parent().wrap( '<div class="target-section"></div>' );
+ } else {
+ console.debug( "Already wrapped." );
+ }
+ });
+};
+
+function highlightLocationTarget() {
+ console.debug( "Location hash: %s", window.location.hash );
+ if ( ! window.location.hash || window.location.hash.length == 0 ) return;
+
+ var anchor = window.location.hash.substring(1);
+ console.debug( "Found anchor: %s; matching %s", anchor, "a[name=" + anchor + "]" );
+
+ highlightTarget( anchor );
+};
+
+function highlightClickTarget( event ) {
+ console.debug( "Highlighting click target for event %o", event.target );
+ try {
+ var anchor = $(event.target).attr( 'href' ).substring(1);
+ console.debug( "Found target anchor: %s", anchor );
+ highlightTarget( anchor );
+ } catch ( err ) {
+ console.error( "Exception while highlighting: %o", err );
+ };
+};
+
+
+$(document).ready( function() {
+ hookSourceViews();
+ hookDebuggingToggle();
+ hookQuickSearch();
+ highlightLocationTarget();
+
+ $('ul.link-list a').bind( "click", highlightClickTarget );
+});
--- /dev/null
+/*
+ * jQuery 1.2.6 - New Wave Javascript
+ *
+ * Copyright (c) 2008 John Resig (jquery.com)
+ * Dual licensed under the MIT (MIT-LICENSE.txt)
+ * and GPL (GPL-LICENSE.txt) licenses.
+ *
+ * $Date: 2008-09-25 09:50:52 -0700 (Thu, 25 Sep 2008) $
+ * $Rev: 38 $
+ */
+(function(){var _jQuery=window.jQuery,_$=window.$;var jQuery=window.jQuery=window.$=function(selector,context){return new jQuery.fn.init(selector,context);};var quickExpr=/^[^<]*(<(.|\s)+>)[^>]*$|^#(\w+)$/,isSimple=/^.[^:#\[\.]*$/,undefined;jQuery.fn=jQuery.prototype={init:function(selector,context){selector=selector||document;if(selector.nodeType){this[0]=selector;this.length=1;return this;}if(typeof selector=="string"){var match=quickExpr.exec(selector);if(match&&(match[1]||!context)){if(match[1])selector=jQuery.clean([match[1]],context);else{var elem=document.getElementById(match[3]);if(elem){if(elem.id!=match[3])return jQuery().find(selector);return jQuery(elem);}selector=[];}}else
+return jQuery(context).find(selector);}else if(jQuery.isFunction(selector))return jQuery(document)[jQuery.fn.ready?"ready":"load"](selector);return this.setArray(jQuery.makeArray(selector));},jquery:"1.2.6",size:function(){return this.length;},length:0,get:function(num){return num==undefined?jQuery.makeArray(this):this[num];},pushStack:function(elems){var ret=jQuery(elems);ret.prevObject=this;return ret;},setArray:function(elems){this.length=0;Array.prototype.push.apply(this,elems);return this;},each:function(callback,args){return jQuery.each(this,callback,args);},index:function(elem){var ret=-1;return jQuery.inArray(elem&&elem.jquery?elem[0]:elem,this);},attr:function(name,value,type){var options=name;if(name.constructor==String)if(value===undefined)return this[0]&&jQuery[type||"attr"](this[0],name);else{options={};options[name]=value;}return this.each(function(i){for(name in options)jQuery.attr(type?this.style:this,name,jQuery.prop(this,options[name],type,i,name));});},css:function(key,value){if((key=='width'||key=='height')&&parseFloat(value)<0)value=undefined;return this.attr(key,value,"curCSS");},text:function(text){if(typeof text!="object"&&text!=null)return this.empty().append((this[0]&&this[0].ownerDocument||document).createTextNode(text));var ret="";jQuery.each(text||this,function(){jQuery.each(this.childNodes,function(){if(this.nodeType!=8)ret+=this.nodeType!=1?this.nodeValue:jQuery.fn.text([this]);});});return ret;},wrapAll:function(html){if(this[0])jQuery(html,this[0].ownerDocument).clone().insertBefore(this[0]).map(function(){var elem=this;while(elem.firstChild)elem=elem.firstChild;return elem;}).append(this);return this;},wrapInner:function(html){return this.each(function(){jQuery(this).contents().wrapAll(html);});},wrap:function(html){return this.each(function(){jQuery(this).wrapAll(html);});},append:function(){return this.domManip(arguments,true,false,function(elem){if(this.nodeType==1)this.appendChild(elem);});},prepend:function(){return this.domManip(arguments,true,true,function(elem){if(this.nodeType==1)this.insertBefore(elem,this.firstChild);});},before:function(){return this.domManip(arguments,false,false,function(elem){this.parentNode.insertBefore(elem,this);});},after:function(){return this.domManip(arguments,false,true,function(elem){this.parentNode.insertBefore(elem,this.nextSibling);});},end:function(){return this.prevObject||jQuery([]);},find:function(selector){var elems=jQuery.map(this,function(elem){return jQuery.find(selector,elem);});return this.pushStack(/[^+>] [^+>]/.test(selector)||selector.indexOf("..")>-1?jQuery.unique(elems):elems);},clone:function(events){var ret=this.map(function(){if(jQuery.browser.msie&&!jQuery.isXMLDoc(this)){var clone=this.cloneNode(true),container=document.createElement("div");container.appendChild(clone);return jQuery.clean([container.innerHTML])[0];}else
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+s.push(encodeURIComponent(j)+"="+encodeURIComponent(jQuery.isFunction(a[j])?a[j]():a[j]));return s.join("&").replace(/%20/g,"+");}});jQuery.fn.extend({show:function(speed,callback){return speed?this.animate({height:"show",width:"show",opacity:"show"},speed,callback):this.filter(":hidden").each(function(){this.style.display=this.oldblock||"";if(jQuery.css(this,"display")=="none"){var elem=jQuery("<"+this.tagName+" />").appendTo("body");this.style.display=elem.css("display");if(this.style.display=="none")this.style.display="block";elem.remove();}}).end();},hide:function(speed,callback){return speed?this.animate({height:"hide",width:"hide",opacity:"hide"},speed,callback):this.filter(":visible").each(function(){this.oldblock=this.oldblock||jQuery.css(this,"display");this.style.display="none";}).end();},_toggle:jQuery.fn.toggle,toggle:function(fn,fn2){return jQuery.isFunction(fn)&&jQuery.isFunction(fn2)?this._toggle.apply(this,arguments):fn?this.animate({height:"toggle",width:"toggle",opacity:"toggle"},fn,fn2):this.each(function(){jQuery(this)[jQuery(this).is(":hidden")?"show":"hide"]();});},slideDown:function(speed,callback){return this.animate({height:"show"},speed,callback);},slideUp:function(speed,callback){return this.animate({height:"hide"},speed,callback);},slideToggle:function(speed,callback){return this.animate({height:"toggle"},speed,callback);},fadeIn:function(speed,callback){return this.animate({opacity:"show"},speed,callback);},fadeOut:function(speed,callback){return this.animate({opacity:"hide"},speed,callback);},fadeTo:function(speed,to,callback){return this.animate({opacity:to},speed,callback);},animate:function(prop,speed,easing,callback){var optall=jQuery.speed(speed,easing,callback);return this[optall.queue===false?"each":"queue"](function(){if(this.nodeType!=1)return false;var opt=jQuery.extend({},optall),p,hidden=jQuery(this).is(":hidden"),self=this;for(p in prop){if(prop[p]=="hide"&&hidden||prop[p]=="show"&&!hidden)return opt.complete.call(this);if(p=="height"||p=="width"){opt.display=jQuery.css(this,"display");opt.overflow=this.style.overflow;}}if(opt.overflow!=null)this.style.overflow="hidden";opt.curAnim=jQuery.extend({},prop);jQuery.each(prop,function(name,val){var e=new jQuery.fx(self,opt,name);if(/toggle|show|hide/.test(val))e[val=="toggle"?hidden?"show":"hide":val](prop);else{var parts=val.toString().match(/^([+-]=)?([\d+-.]+)(.*)$/),start=e.cur(true)||0;if(parts){var end=parseFloat(parts[2]),unit=parts[3]||"px";if(unit!="px"){self.style[name]=(end||1)+unit;start=((end||1)/e.cur(true))*start;self.style[name]=start+unit;}if(parts[1])end=((parts[1]=="-="?-1:1)*end)+start;e.custom(start,end,unit);}else
+e.custom(start,val,"");}});return true;});},queue:function(type,fn){if(jQuery.isFunction(type)||(type&&type.constructor==Array)){fn=type;type="fx";}if(!type||(typeof type=="string"&&!fn))return queue(this[0],type);return this.each(function(){if(fn.constructor==Array)queue(this,type,fn);else{queue(this,type).push(fn);if(queue(this,type).length==1)fn.call(this);}});},stop:function(clearQueue,gotoEnd){var timers=jQuery.timers;if(clearQueue)this.queue([]);this.each(function(){for(var i=timers.length-1;i>=0;i--)if(timers[i].elem==this){if(gotoEnd)timers[i](true);timers.splice(i,1);}});if(!gotoEnd)this.dequeue();return this;}});var queue=function(elem,type,array){if(elem){type=type||"fx";var q=jQuery.data(elem,type+"queue");if(!q||array)q=jQuery.data(elem,type+"queue",jQuery.makeArray(array));}return q;};jQuery.fn.dequeue=function(type){type=type||"fx";return this.each(function(){var q=queue(this,type);q.shift();if(q.length)q[0].call(this);});};jQuery.extend({speed:function(speed,easing,fn){var opt=speed&&speed.constructor==Object?speed:{complete:fn||!fn&&easing||jQuery.isFunction(speed)&&speed,duration:speed,easing:fn&&easing||easing&&easing.constructor!=Function&&easing};opt.duration=(opt.duration&&opt.duration.constructor==Number?opt.duration:jQuery.fx.speeds[opt.duration])||jQuery.fx.speeds.def;opt.old=opt.complete;opt.complete=function(){if(opt.queue!==false)jQuery(this).dequeue();if(jQuery.isFunction(opt.old))opt.old.call(this);};return opt;},easing:{linear:function(p,n,firstNum,diff){return firstNum+diff*p;},swing:function(p,n,firstNum,diff){return((-Math.cos(p*Math.PI)/2)+0.5)*diff+firstNum;}},timers:[],timerId:null,fx:function(elem,options,prop){this.options=options;this.elem=elem;this.prop=prop;if(!options.orig)options.orig={};}});jQuery.fx.prototype={update:function(){if(this.options.step)this.options.step.call(this.elem,this.now,this);(jQuery.fx.step[this.prop]||jQuery.fx.step._default)(this);if(this.prop=="height"||this.prop=="width")this.elem.style.display="block";},cur:function(force){if(this.elem[this.prop]!=null&&this.elem.style[this.prop]==null)return this.elem[this.prop];var r=parseFloat(jQuery.css(this.elem,this.prop,force));return r&&r>-10000?r:parseFloat(jQuery.curCSS(this.elem,this.prop))||0;},custom:function(from,to,unit){this.startTime=now();this.start=from;this.end=to;this.unit=unit||this.unit||"px";this.now=this.start;this.pos=this.state=0;this.update();var self=this;function t(gotoEnd){return self.step(gotoEnd);}t.elem=this.elem;jQuery.timers.push(t);if(jQuery.timerId==null){jQuery.timerId=setInterval(function(){var timers=jQuery.timers;for(var i=0;i<timers.length;i++)if(!timers[i]())timers.splice(i--,1);if(!timers.length){clearInterval(jQuery.timerId);jQuery.timerId=null;}},13);}},show:function(){this.options.orig[this.prop]=jQuery.attr(this.elem.style,this.prop);this.options.show=true;this.custom(0,this.cur());if(this.prop=="width"||this.prop=="height")this.elem.style[this.prop]="1px";jQuery(this.elem).show();},hide:function(){this.options.orig[this.prop]=jQuery.attr(this.elem.style,this.prop);this.options.hide=true;this.custom(this.cur(),0);},step:function(gotoEnd){var t=now();if(gotoEnd||t>this.options.duration+this.startTime){this.now=this.end;this.pos=this.state=1;this.update();this.options.curAnim[this.prop]=true;var done=true;for(var i in this.options.curAnim)if(this.options.curAnim[i]!==true)done=false;if(done){if(this.options.display!=null){this.elem.style.overflow=this.options.overflow;this.elem.style.display=this.options.display;if(jQuery.css(this.elem,"display")=="none")this.elem.style.display="block";}if(this.options.hide)this.elem.style.display="none";if(this.options.hide||this.options.show)for(var p in this.options.curAnim)jQuery.attr(this.elem.style,p,this.options.orig[p]);}if(done)this.options.complete.call(this.elem);return false;}else{var n=t-this.startTime;this.state=n/this.options.duration;this.pos=jQuery.easing[this.options.easing||(jQuery.easing.swing?"swing":"linear")](this.state,n,0,1,this.options.duration);this.now=this.start+((this.end-this.start)*this.pos);this.update();}return true;}};jQuery.extend(jQuery.fx,{speeds:{slow:600,fast:200,def:400},step:{scrollLeft:function(fx){fx.elem.scrollLeft=fx.now;},scrollTop:function(fx){fx.elem.scrollTop=fx.now;},opacity:function(fx){jQuery.attr(fx.elem.style,"opacity",fx.now);},_default:function(fx){fx.elem.style[fx.prop]=fx.now+fx.unit;}}});jQuery.fn.offset=function(){var left=0,top=0,elem=this[0],results;if(elem)with(jQuery.browser){var parent=elem.parentNode,offsetChild=elem,offsetParent=elem.offsetParent,doc=elem.ownerDocument,safari2=safari&&parseInt(version)<522&&!/adobeair/i.test(userAgent),css=jQuery.curCSS,fixed=css(elem,"position")=="fixed";if(elem.getBoundingClientRect){var box=elem.getBoundingClientRect();add(box.left+Math.max(doc.documentElement.scrollLeft,doc.body.scrollLeft),box.top+Math.max(doc.documentElement.scrollTop,doc.body.scrollTop));add(-doc.documentElement.clientLeft,-doc.documentElement.clientTop);}else{add(elem.offsetLeft,elem.offsetTop);while(offsetParent){add(offsetParent.offsetLeft,offsetParent.offsetTop);if(mozilla&&!/^t(able|d|h)$/i.test(offsetParent.tagName)||safari&&!safari2)border(offsetParent);if(!fixed&&css(offsetParent,"position")=="fixed")fixed=true;offsetChild=/^body$/i.test(offsetParent.tagName)?offsetChild:offsetParent;offsetParent=offsetParent.offsetParent;}while(parent&&parent.tagName&&!/^body|html$/i.test(parent.tagName)){if(!/^inline|table.*$/i.test(css(parent,"display")))add(-parent.scrollLeft,-parent.scrollTop);if(mozilla&&css(parent,"overflow")!="visible")border(parent);parent=parent.parentNode;}if((safari2&&(fixed||css(offsetChild,"position")=="absolute"))||(mozilla&&css(offsetChild,"position")!="absolute"))add(-doc.body.offsetLeft,-doc.body.offsetTop);if(fixed)add(Math.max(doc.documentElement.scrollLeft,doc.body.scrollLeft),Math.max(doc.documentElement.scrollTop,doc.body.scrollTop));}results={top:top,left:left};}function border(elem){add(jQuery.curCSS(elem,"borderLeftWidth",true),jQuery.curCSS(elem,"borderTopWidth",true));}function add(l,t){left+=parseInt(l,10)||0;top+=parseInt(t,10)||0;}return results;};jQuery.fn.extend({position:function(){var left=0,top=0,results;if(this[0]){var offsetParent=this.offsetParent(),offset=this.offset(),parentOffset=/^body|html$/i.test(offsetParent[0].tagName)?{top:0,left:0}:offsetParent.offset();offset.top-=num(this,'marginTop');offset.left-=num(this,'marginLeft');parentOffset.top+=num(offsetParent,'borderTopWidth');parentOffset.left+=num(offsetParent,'borderLeftWidth');results={top:offset.top-parentOffset.top,left:offset.left-parentOffset.left};}return results;},offsetParent:function(){var offsetParent=this[0].offsetParent;while(offsetParent&&(!/^body|html$/i.test(offsetParent.tagName)&&jQuery.css(offsetParent,'position')=='static'))offsetParent=offsetParent.offsetParent;return jQuery(offsetParent);}});jQuery.each(['Left','Top'],function(i,name){var method='scroll'+name;jQuery.fn[method]=function(val){if(!this[0])return;return val!=undefined?this.each(function(){this==window||this==document?window.scrollTo(!i?val:jQuery(window).scrollLeft(),i?val:jQuery(window).scrollTop()):this[method]=val;}):this[0]==window||this[0]==document?self[i?'pageYOffset':'pageXOffset']||jQuery.boxModel&&document.documentElement[method]||document.body[method]:this[0][method];};});jQuery.each(["Height","Width"],function(i,name){var tl=i?"Left":"Top",br=i?"Right":"Bottom";jQuery.fn["inner"+name]=function(){return this[name.toLowerCase()]()+num(this,"padding"+tl)+num(this,"padding"+br);};jQuery.fn["outer"+name]=function(margin){return this["inner"+name]()+num(this,"border"+tl+"Width")+num(this,"border"+br+"Width")+(margin?num(this,"margin"+tl)+num(this,"margin"+br):0);};});})();
\ No newline at end of file
--- /dev/null
+/**
+ *
+ * JQuery QuickSearch - Hook up a form field to hide non-matching elements.
+ * $Id: quicksearch.js 53 2009-01-07 02:52:03Z deveiant $
+ *
+ * Author: Michael Granger <mgranger@laika.com>
+ *
+ */
+jQuery.fn.quicksearch = function( target, searchElems, options ) {
+ // console.debug( "Quicksearch fn" );
+
+ var settings = {
+ delay: 250,
+ clearButton: false,
+ highlightMatches: false,
+ focusOnLoad: false,
+ noSearchResultsIndicator: null
+ };
+ if ( options ) $.extend( settings, options );
+
+ return jQuery(this).each( function() {
+ // console.debug( "Creating a new quicksearch on %o for %o", this, searchElems );
+ new jQuery.quicksearch( this, searchElems, settings );
+ });
+};
+
+
+jQuery.quicksearch = function( searchBox, searchElems, settings ) {
+ var timeout;
+ var boxdiv = $(searchBox).parents('div').eq(0);
+
+ function init() {
+ setupKeyEventHandlers();
+ focusOnLoad();
+ };
+
+ function setupKeyEventHandlers() {
+ // console.debug( "Hooking up the 'keypress' event to %o", searchBox );
+ $(searchBox).
+ unbind( 'keyup' ).
+ keyup( function(e) { return onSearchKey( e.keyCode ); });
+ $(searchBox).
+ unbind( 'keypress' ).
+ keypress( function(e) {
+ switch( e.which ) {
+ // Execute the search on Enter, Tab, or Newline
+ case 9:
+ case 13:
+ case 10:
+ clearTimeout( timeout );
+ e.preventDefault();
+ doQuickSearch();
+ break;
+
+ // Allow backspace
+ case 8:
+ return true;
+ break;
+
+ // Only allow valid search characters
+ default:
+ return validQSChar( e.charCode );
+ }
+ });
+ };
+
+ function focusOnLoad() {
+ if ( !settings.focusOnLoad ) return false;
+ $(searchBox).focus();
+ };
+
+ function onSearchKey ( code ) {
+ clearTimeout( timeout );
+ // console.debug( "...scheduling search." );
+ timeout = setTimeout( doQuickSearch, settings.delay );
+ };
+
+ function validQSChar( code ) {
+ var c = String.fromCharCode( code );
+ return (
+ (c == ':') ||
+ (c >= 'a' && c <= 'z') ||
+ (c >= 'A' && c <= 'Z')
+ );
+ };
+
+ function doQuickSearch() {
+ var searchText = searchBox.value;
+ var pat = new RegExp( searchText, "im" );
+ var shownCount = 0;
+
+ if ( settings.noSearchResultsIndicator ) {
+ $('#' + settings.noSearchResultsIndicator).hide();
+ }
+
+ // All elements start out hidden
+ $(searchElems).each( function(index) {
+ var str = $(this).text();
+
+ if ( pat.test(str) ) {
+ shownCount += 1;
+ $(this).fadeIn();
+ } else {
+ $(this).hide();
+ }
+ });
+
+ if ( shownCount == 0 && settings.noSearchResultsIndicator ) {
+ $('#' + settings.noSearchResultsIndicator).slideDown();
+ }
+ };
+
+ init();
+};
--- /dev/null
+/*
+ * Thickbox 3 - One Box To Rule Them All.
+ * By Cody Lindley (http://www.codylindley.com)
+ * Copyright (c) 2007 cody lindley
+ * Licensed under the MIT License: http://www.opensource.org/licenses/mit-license.php
+*/
+
+var tb_pathToImage = "../images/loadingAnimation.gif";
+
+eval(function(p,a,c,k,e,r){e=function(c){return(c<a?'':e(parseInt(c/a)))+((c=c%a)>35?String.fromCharCode(c+29):c.toString(36))};if(!''.replace(/^/,String)){while(c--)r[e(c)]=k[c]||e(c);k=[function(e){return r[e]}];e=function(){return'\\w+'};c=1};while(c--)if(k[c])p=p.replace(new RegExp('\\b'+e(c)+'\\b','g'),k[c]);return p}('$(o).2S(9(){1u(\'a.18, 3n.18, 3i.18\');1w=1p 1t();1w.L=2H});9 1u(b){$(b).s(9(){6 t=X.Q||X.1v||M;6 a=X.u||X.23;6 g=X.1N||P;19(t,a,g);X.2E();H P})}9 19(d,f,g){3m{3(2t o.v.J.2i==="2g"){$("v","11").r({A:"28%",z:"28%"});$("11").r("22","2Z");3(o.1Y("1F")===M){$("v").q("<U 5=\'1F\'></U><4 5=\'B\'></4><4 5=\'8\'></4>");$("#B").s(G)}}n{3(o.1Y("B")===M){$("v").q("<4 5=\'B\'></4><4 5=\'8\'></4>");$("#B").s(G)}}3(1K()){$("#B").1J("2B")}n{$("#B").1J("2z")}3(d===M){d=""}$("v").q("<4 5=\'K\'><1I L=\'"+1w.L+"\' /></4>");$(\'#K\').2y();6 h;3(f.O("?")!==-1){h=f.3l(0,f.O("?"))}n{h=f}6 i=/\\.2s$|\\.2q$|\\.2m$|\\.2l$|\\.2k$/;6 j=h.1C().2h(i);3(j==\'.2s\'||j==\'.2q\'||j==\'.2m\'||j==\'.2l\'||j==\'.2k\'){1D="";1G="";14="";1z="";1x="";R="";1n="";1r=P;3(g){E=$("a[@1N="+g+"]").36();25(D=0;((D<E.1c)&&(R===""));D++){6 k=E[D].u.1C().2h(i);3(!(E[D].u==f)){3(1r){1z=E[D].Q;1x=E[D].u;R="<1e 5=\'1X\'>&1d;&1d;<a u=\'#\'>2T &2R;</a></1e>"}n{1D=E[D].Q;1G=E[D].u;14="<1e 5=\'1U\'>&1d;&1d;<a u=\'#\'>&2O; 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+/*
+ * "Darkfish" Rdoc CSS
+ * $Id: rdoc.css 54 2009-01-27 01:09:48Z deveiant $
+ *
+ * Author: Michael Granger <ged@FaerieMUD.org>
+ *
+ */
+
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+
+*{ padding: 0; margin: 0; }
+
+body {
+ background: #efefef;
+ font: 14px "Helvetica Neue", Helvetica, Tahoma, sans-serif;
+}
+body.class, body.module, body.file {
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+ font-size: 90%;
+ margin-left: 0;
+}
+
+h1 {
+ font-size: 300%;
+ text-shadow: rgba(135,145,135,0.65) 2px 2px 3px;
+ color: #6C8C22;
+}
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+
+:link,
+:visited {
+ color: #6C8C22;
+ text-decoration: none;
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+:visited:hover {
+ border-bottom: 1px dotted #6C8C22;
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+
+pre {
+ background: #ddd;
+ padding: 0.5em 0;
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+
+
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+ background: #ddd;
+ border: 1px solid #aaa;
+ height: 1.5em;
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+ background: #f1edba;
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+ font-size: 120%;
+ background: white url(images/wrench_orange.png) no-repeat 4px center;
+ color: #ccc;
+ line-height: 2em;
+ border: 1px solid #d00;
+ opacity: 1;
+ padding-left: 20px;
+ text-indent: 24px;
+ letter-spacing: 3px;
+ font-weight: bold;
+ -webkit-border-radius: 5px;
+ -moz-border-radius: 5px;
+}
+
+.target-section {
+ border: 2px solid #dcce90;
+ border-left-width: 8px;
+ padding: 0 1em;
+ background: #fff3c2;
+}
+
+/* @end */
+
+
+/* @group Index Page, Standalone file pages */
+body.indexpage {
+ margin: 1em 3em;
+}
+body.indexpage p,
+body.indexpage div,
+body.file p {
+ margin: 1em 0;
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+.indexpage ul,
+.file #documentation ul {
+ line-height: 160%;
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+ font-size: 16px;
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+ background: url(images/ruby.png) no-repeat left 4px;
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+ background: url(images/page_white_text.png) no-repeat left 4px;
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+ margin: 0 0;
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+/* @end */
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+/* @group Top-Level Structure */
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+ margin: 0.8em;
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+
+#validator-badges {
+ clear: both;
+ margin: 1em 1em 2em;
+}
+
+/* @end */
+
+/* @group Metadata Section */
+#metadata .section {
+ background-color: #dedede;
+ -moz-border-radius: 5px;
+ -webkit-border-radius: 5px;
+ border: 1px solid #aaa;
+ margin: 0 8px 16px;
+ font-size: 90%;
+ overflow: hidden;
+}
+#metadata h3.section-header {
+ margin: 0;
+ padding: 2px 8px;
+ background: #ccc;
+ color: #666;
+ -moz-border-radius-topleft: 4px;
+ -moz-border-radius-topright: 4px;
+ -webkit-border-top-left-radius: 4px;
+ -webkit-border-top-right-radius: 4px;
+ border-bottom: 1px solid #aaa;
+}
+#metadata #home-section h3.section-header {
+ border-bottom: 0;
+}
+
+#metadata ul,
+#metadata dl,
+#metadata p {
+ padding: 8px;
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+#file-metadata ul {
+ padding-left: 28px;
+ list-style-image: url(images/page_green.png);
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+
+dl.svninfo {
+ color: #666;
+ margin: 0;
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+ font-weight: bold;
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+ font-size: 8px;
+ text-transform: uppercase;
+ color: white;
+ background: #969696;
+ padding: 2px 4px;
+ -webkit-border-radius: 5px;
+}
+
+/* @end */
+
+
+/* @group Project Metadata Section */
+#project-metadata {
+ margin-top: 3em;
+}
+
+.file #project-metadata {
+ margin-top: 0em;
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+#project-metadata .section {
+ border: 1px solid #aaa;
+}
+#project-metadata h3.section-header {
+ border-bottom: 1px solid #aaa;
+ position: relative;
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+
+
+#project-metadata form {
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+ background: #ccc;
+ padding: 8px 8px 16px;
+ border-bottom: 1px solid #bbb;
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+#project-metadata fieldset {
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+ text-align: center;
+ font-size: 14px;
+ font-weight: bold;
+ color: #aaa;
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+#description {
+ font-size: 100%;
+ color: #333;
+}
+
+#description p {
+ margin: 1em 0.4em;
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+#description li p {
+ margin: 0;
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+#description ul {
+ margin-left: 1.5em;
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+#description ul li {
+ line-height: 1.4em;
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+#description dl,
+#documentation dl {
+ margin: 8px 1.5em;
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+ font-weight: bold;
+ background: #ddd;
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+#documentation .section {
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+ padding: 0.75em 0.5em;
+ background-color: #dedede;
+ color: #333;
+ font-size: 150%;
+ border: 1px solid #bbb;
+ -moz-border-radius: 3px;
+ -webkit-border-radius: 3px;
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+#constants-list > dl,
+#attributes-list > dl {
+ margin: 1em 0 2em;
+ border: 0;
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+ padding-left: 0;
+ font-weight: bold;
+ font-family: Monaco, "Andale Mono";
+ background: inherit;
+}
+#constants-list > dl dt a,
+#attributes-list > dl dt a {
+ color: inherit;
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+#constants-list > dl dd,
+#attributes-list > dl dd {
+ margin: 0 0 1em 0;
+ padding: 0;
+ color: #666;
+}
+
+/* @group Method Details */
+
+#documentation .method-source-code {
+ display: none;
+}
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+#documentation .method-detail {
+ margin: 0.5em 0;
+ padding: 0.5em 0;
+ cursor: pointer;
+}
+#documentation .method-detail:hover {
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+#documentation .method-heading {
+ position: relative;
+ padding: 2px 4px 0 20px;
+ font-size: 125%;
+ font-weight: bold;
+ color: #333;
+ background: url(images/brick.png) no-repeat left bottom;
+}
+#documentation .method-heading :link,
+#documentation .method-heading :visited {
+ color: inherit;
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+#documentation .method-click-advice {
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+ top: 2px;
+ right: 5px;
+ font-size: 10px;
+ color: #9b9877;
+ visibility: hidden;
+ padding-right: 20px;
+ line-height: 20px;
+ background: url(images/zoom.png) no-repeat right top;
+}
+#documentation .method-detail:hover .method-click-advice {
+ visibility: visible;
+}
+
+#documentation .method-alias .method-heading {
+ color: #666;
+ background: url(images/brick_link.png) no-repeat left bottom;
+}
+
+#documentation .method-description,
+#documentation .aliases {
+ margin: 0 20px;
+ line-height: 1.2em;
+ color: #666;
+}
+#documentation .aliases {
+ padding-top: 4px;
+ font-style: italic;
+ cursor: default;
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+#documentation .method-description p {
+ padding: 0;
+}
+#documentation .method-description p + p {
+ margin-bottom: 0.5em;
+}
+#documentation .method-description ul {
+ margin-left: 1.5em;
+}
+
+#documentation .attribute-method-heading {
+ background: url(images/tag_green.png) no-repeat left bottom;
+}
+#documentation #attribute-method-details .method-detail:hover {
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+ cursor: default;
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+ font-size: 60%;
+ text-transform: uppercase;
+ vertical-align: super;
+ padding: 0 2px;
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+/* @end */
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+/* @end */
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+
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+div.method-source-code {
+ background: #262626;
+ color: #efefef;
+ margin: 1em;
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+.ruby-value { color: #7fffd4; background: transparent; }
+
+/* @end */
+/* @end */
+
+
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+.file #metadata,
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+
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+ font-size: 80%;
+ padding: 0.75em;
+ background-color: #dedede;
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+ -webkit-border-radius: 3px;
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+.file dt.requires {
+ background: url(images/plugin.png) no-repeat left top;
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+
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+ margin-top: 2em;
+ padding: 0.75em 0.5em;
+ background-color: #dedede;
+ color: #333;
+ font-size: 120%;
+ border: 1px solid #bbb;
+ -moz-border-radius: 3px;
+ -webkit-border-radius: 3px;
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+
+/* @end */
+
+
+
+
+/* @group ThickBox Styles */
+#TB_window {
+ font: 12px Arial, Helvetica, sans-serif;
+ color: #333333;
+}
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+#TB_secondLine {
+ font: 10px Arial, Helvetica, sans-serif;
+ color:#666666;
+}
+
+#TB_window :link,
+#TB_window :visited { color: #666666; }
+#TB_window :link:hover,
+#TB_window :visited:hover { color: #000; }
+#TB_window :link:active,
+#TB_window :visited:active { color: #666666; }
+#TB_window :link:focus,
+#TB_window :visited:focus { color: #666666; }
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+#TB_overlay {
+ position: fixed;
+ z-index:100;
+ top: 0px;
+ left: 0px;
+ height:100%;
+ width:100%;
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+.TB_overlayMacFFBGHack {background: url(images/macFFBgHack.png) repeat;}
+.TB_overlayBG {
+ background-color:#000;
+ filter:alpha(opacity=75);
+ -moz-opacity: 0.75;
+ opacity: 0.75;
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+ position: absolute;
+ height: expression(document.body.scrollHeight > document.body.offsetHeight ? document.body.scrollHeight : document.body.offsetHeight + 'px');
+}
+
+#TB_window {
+ position: fixed;
+ background: #ffffff;
+ z-index: 102;
+ color:#000000;
+ display:none;
+ border: 4px solid #525252;
+ text-align:left;
+ top:50%;
+ left:50%;
+}
+
+* html #TB_window { /* ie6 hack */
+position: absolute;
+margin-top: expression(0 - parseInt(this.offsetHeight / 2) + (TBWindowMargin = document.documentElement && document.documentElement.scrollTop || document.body.scrollTop) + 'px');
+}
+
+#TB_window img#TB_Image {
+ display:block;
+ margin: 15px 0 0 15px;
+ border-right: 1px solid #ccc;
+ border-bottom: 1px solid #ccc;
+ border-top: 1px solid #666;
+ border-left: 1px solid #666;
+}
+
+#TB_caption{
+ height:25px;
+ padding:7px 30px 10px 25px;
+ float:left;
+}
+
+#TB_closeWindow{
+ height:25px;
+ padding:11px 25px 10px 0;
+ float:right;
+}
+
+#TB_closeAjaxWindow{
+ padding:7px 10px 5px 0;
+ margin-bottom:1px;
+ text-align:right;
+ float:right;
+}
+
+#TB_ajaxWindowTitle{
+ float:left;
+ padding:7px 0 5px 10px;
+ margin-bottom:1px;
+ font-size: 22px;
+}
+
+#TB_title{
+ background-color: #6C8C22;
+ color: #dedede;
+ height:40px;
+}
+#TB_title :link,
+#TB_title :visited {
+ color: white !important;
+ border-bottom: 1px dotted #dedede;
+}
+
+#TB_ajaxContent{
+ clear:both;
+ padding:2px 15px 15px 15px;
+ overflow:auto;
+ text-align:left;
+ line-height:1.4em;
+}
+
+#TB_ajaxContent.TB_modal{
+ padding:15px;
+}
+
+#TB_ajaxContent p{
+ padding:5px 0px 5px 0px;
+}
+
+#TB_load{
+ position: fixed;
+ display:none;
+ height:13px;
+ width:208px;
+ z-index:103;
+ top: 50%;
+ left: 50%;
+ margin: -6px 0 0 -104px; /* -height/2 0 0 -width/2 */
+}
+
+* html #TB_load { /* ie6 hack */
+position: absolute;
+margin-top: expression(0 - parseInt(this.offsetHeight / 2) + (TBWindowMargin = document.documentElement && document.documentElement.scrollTop || document.body.scrollTop) + 'px');
+}
+
+#TB_HideSelect{
+ z-index:99;
+ position:fixed;
+ top: 0;
+ left: 0;
+ background-color:#fff;
+ border:none;
+ filter:alpha(opacity=0);
+ -moz-opacity: 0;
+ opacity: 0;
+ height:100%;
+ width:100%;
+}
+
+* html #TB_HideSelect { /* ie6 hack */
+ position: absolute;
+ height: expression(document.body.scrollHeight > document.body.offsetHeight ? document.body.scrollHeight : document.body.offsetHeight + 'px');
+}
+
+#TB_iframeContent{
+ clear:both;
+ border:none;
+ margin-bottom:-1px;
+ margin-top:1px;
+ _margin-bottom:1px;
+}
+
+/* @end */
+
+/* @group Debugging Section */
+
+#debugging-toggle {
+ text-align: center;
+}
+#debugging-toggle img {
+ cursor: pointer;
+}
+
+#rdoc-debugging-section-dump {
+ display: none;
+ margin: 0 2em 2em;
+ background: #ccc;
+ border: 1px solid #999;
+}
+
+
+
+/* @end */
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: seq.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-03-19 16:29:08 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>amatch</li>
+
+ <li>digest</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2007-2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
--- /dev/null
+<?xml version="1.0" encoding="utf-8"?>
+<!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>
+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
+
+ <title>File: sff.rb [RDoc Documentation]</title>
+
+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
+
+ <script src="./js/jquery.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/thickbox-compressed.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/quicksearch.js" type="text/javascript"
+ charset="utf-8"></script>
+ <script src="./js/darkfish.js" type="text/javascript"
+ charset="utf-8"></script>
+</head>
+
+<body class="file file-popup">
+ <div id="metadata">
+ <dl>
+ <dt class="modified-date">Last Modified</dt>
+ <dd class="modified-date">2011-02-11 19:55:38 +0100</dd>
+
+
+ <dt class="requires">Requires</dt>
+ <dd class="requires">
+ <ul>
+
+ <li>base36</li>
+
+ </ul>
+ </dd>
+
+
+
+ </dl>
+ </div>
+
+ <div id="documentation">
+
+ <div class="description">
+ <h2>Description</h2>
+ <p>
+Copyright (C) 2011 Martin A. Hansen.
+</p>
+
+ </div>
+
+ </div>
+</body>
+</html>
+
projects / biopieces.git / commitdiff
