parse_fasta 0.0.5 → 1.0.0

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Files changed (36) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +0 -1
  3. data/COPYING +674 -0
  4. data/README.md +56 -6
  5. data/Rakefile +6 -0
  6. data/doc/FastaFile.html +292 -0
  7. data/doc/File.html +212 -0
  8. data/doc/ParseFasta.html +144 -0
  9. data/doc/Sequence.html +361 -0
  10. data/doc/_index.html +136 -0
  11. data/doc/class_list.html +54 -0
  12. data/doc/css/common.css +1 -0
  13. data/doc/css/full_list.css +57 -0
  14. data/doc/css/style.css +339 -0
  15. data/doc/file.README.html +161 -0
  16. data/doc/file_list.html +56 -0
  17. data/doc/frames.html +26 -0
  18. data/doc/index.html +161 -0
  19. data/doc/js/app.js +219 -0
  20. data/doc/js/full_list.js +178 -0
  21. data/doc/js/jquery.js +4 -0
  22. data/doc/method_list.html +71 -0
  23. data/doc/top-level-namespace.html +114 -0
  24. data/lib/parse_fasta/fasta_file.rb +46 -0
  25. data/lib/parse_fasta/sequence.rb +55 -0
  26. data/lib/parse_fasta/version.rb +19 -1
  27. data/lib/parse_fasta.rb +11 -21
  28. data/parse_fasta.gemspec +3 -0
  29. data/spec/lib/fasta_file_spec.rb +46 -0
  30. data/spec/lib/sequence_spec.rb +52 -0
  31. data/spec/spec_helper.rb +19 -0
  32. data/test_files/benchmark.rb +70 -0
  33. data/test_files/test.fa +9 -0
  34. metadata +75 -5
  35. data/LICENSE.txt +0 -22
  36. data/benchmark.rb +0 -22
data/doc/ParseFasta.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Module: ParseFasta
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+
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+ &mdash; Documentation by YARD 0.8.7.4
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+
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+ </title>
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+
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+ <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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+
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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+
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+ <script type="text/javascript" charset="utf-8">
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+ hasFrames = window.top.frames.main ? true : false;
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+ relpath = '';
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+ framesUrl = "frames.html#!ParseFasta.html";
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+ </script>
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+
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+
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+
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+
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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="_index.html">Index (P)</a> &raquo;
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+
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+
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+ <span class="title">ParseFasta</span>
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+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+
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+ <a class="full_list_link" id="class_list_link"
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+ href="class_list.html">
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+ Class List
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+ </a>
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+
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+ <a class="full_list_link" id="method_list_link"
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+ href="method_list.html">
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+ Method List
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+ </a>
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+
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+ <a class="full_list_link" id="file_list_link"
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+ href="file_list.html">
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+ File List
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+ </a>
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+
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Module: ParseFasta
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+
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+
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+
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+ </h1>
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+
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+ <dl class="box">
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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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+ <dt class="r1 last">Defined in:</dt>
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+ <dd class="r1 last">lib/parse_fasta/version.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>Copyright 2014 Ryan Moore Contact: moorer@udel.edu</p>
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+
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+ <p>This file is part of parse_fasta.</p>
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+
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+ <p>parse_fasta is free software: you can redistribute it and/or modify it
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+ under the terms of the GNU General Public License as published by the Free
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+ Software Foundation, either version 3 of the License, or (at your option)
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+ any later version.</p>
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+
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+ <p>parse_fasta is distributed in the hope that it will be useful, but WITHOUT
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+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
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+ more details.</p>
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+
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+ <p>You should have received a copy of the GNU General Public License along
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+ with parse_fasta. If not, see &lt;<a
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+ href="http://www.gnu.org/licenses">www.gnu.org/licenses</a>/&gt;.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div>
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+ <h2>Constant Summary</h2>
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+
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+ <dl class="constants">
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+
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+ <dt id="VERSION-constant" class="">VERSION =
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+
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+ </dt>
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+ <dd><pre class="code"><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>1.0.0</span><span class='tstring_end'>&quot;</span></span></pre></dd>
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+
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+ </dl>
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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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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Jun 3 22:55:41 2014 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.7.4 (ruby-2.1.1).
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/Sequence.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Class: Sequence
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+
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+ &mdash; Documentation by YARD 0.8.7.4
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+
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+ </title>
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+
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+ <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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+
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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+
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+ <script type="text/javascript" charset="utf-8">
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+ hasFrames = window.top.frames.main ? true : false;
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+ relpath = '';
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+ framesUrl = "frames.html#!Sequence.html";
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+ </script>
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+
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+
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+
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+
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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="_index.html">Index (S)</a> &raquo;
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+
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+
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+ <span class="title">Sequence</span>
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+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+
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+ <a class="full_list_link" id="class_list_link"
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+ href="class_list.html">
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+ Class List
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+ </a>
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+
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+ <a class="full_list_link" id="method_list_link"
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+ href="method_list.html">
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+ Method List
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+ </a>
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+
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+ <a class="full_list_link" id="file_list_link"
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+ href="file_list.html">
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+ File List
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+ </a>
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+
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1>Class: Sequence
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+
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+
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+
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+ </h1>
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+
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+ <dl class="box">
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+
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+ <dt class="r1">Inherits:</dt>
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+ <dd class="r1">
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+ <span class="inheritName">String</span>
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+
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+ <ul class="fullTree">
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+ <li>Object</li>
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+
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+ <li class="next">String</li>
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+
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+ <li class="next">Sequence</li>
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+
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+
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+ </dd>
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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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+ <dt class="r2 last">Defined in:</dt>
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+ <dd class="r2 last">lib/parse_fasta/sequence.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+ <h2>Overview</h2><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>Provide some methods for dealing with common tasks regarding nucleotide
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+ sequences.</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div>
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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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+ <h2>
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+ Instance Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#gc-instance_method" title="#gc (instance method)">- (0, Float) <strong>gc</strong> </a>
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+
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+
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+
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+ </span>
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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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+ <span class="summary_desc"><div class='inline'>
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+ <p>Returns GC content for self.</p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#initialize-instance_method" title="#initialize (instance method)">- (Sequence) <strong>initialize</strong>(str) </a>
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+
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+
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+
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+ </span>
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+
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+
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+ <span class="note title constructor">constructor</span>
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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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+ <span class="summary_desc"><div class='inline'>
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+ <p>A new instance of Sequence.</p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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+ <div id="constructor_details" class="method_details_list">
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+ <h2>Constructor Details</h2>
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="initialize-instance_method">
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+
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+ - (<tt><span class='object_link'><a href="" title="Sequence (class)">Sequence</a></span></tt>) <strong>initialize</strong>(str)
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>Returns a new instance of Sequence</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 22
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+ 23
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+ 24</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/parse_fasta/sequence.rb', line 22</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_str'>str</span><span class='rparen'>)</span>
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+ <span class='kw'>super</span><span class='lparen'>(</span><span class='id identifier rubyid_str'>str</span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+
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+ <div id="instance_method_details" class="method_details_list">
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+ <h2>Instance Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <h3 class="signature first" id="gc-instance_method">
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+
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+ - (<tt>0</tt>, <tt>Float</tt>) <strong>gc</strong>
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+
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+
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+
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+
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+
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+ </h3><div class="docstring">
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+ <div class="discussion">
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+
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+ <p>Returns GC content for self</p>
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+
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+ <p>Calculates GC content by dividing count of G + C divided by count of G + C
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+ + T + A +U. If there are both T&#39;s and U&#39;s in the Sequence, things
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+ will get weird, but then again, that wouldn&#39;t happen, now would it!</p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+
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+ <div class="examples">
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+ <p class="tag_title">Examples:</p>
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+
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+
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+ <p class="example_title"><div class='inline'>
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+ <p>Get GC of a Sequence</p>
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+ </div></p>
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+
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+ <pre class="example code"><code><span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>ACTg</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_gc'>gc</span> <span class='comment'>#=&gt; 0.5</span></code></pre>
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+
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+
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+ <p class="example_title"><div class='inline'>
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+ <p>Using with FastaFile#each_record</p>
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+ </div></p>
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+
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+ <pre class="example code"><code><span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>reads.fna</span><span class='tstring_end'>&#39;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
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+ <span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_gc'>gc</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></code></pre>
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+
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+ </div>
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+
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+ <p class="tag_title">Returns:</p>
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+ <ul class="return">
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+
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+ <li>
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+
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+
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+ <span class='type'>(<tt>0</tt>)</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'>
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+ <p>if the Sequence is empty or there are no A, C, T, G or U present</p>
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+ </div>
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+
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+ </li>
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+
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+ <li>
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+
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+
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+ <span class='type'>(<tt>Float</tt>)</span>
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+
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+
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+
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+ &mdash;
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+ <div class='inline'>
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+ <p>if the GC content is defined for the Sequence</p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+
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+
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+ 43
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+ 44
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+ 45
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+ 46
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+ 47
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+ 48
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+ 49
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+ 50
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+ 51
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+ 52
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+ 53</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/parse_fasta/sequence.rb', line 43</span>
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+
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+ <span class='kw'>def</span> <span class='id identifier rubyid_gc'>gc</span>
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+ <span class='id identifier rubyid_s'>s</span> <span class='op'>=</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_downcase'>downcase</span>
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+ <span class='id identifier rubyid_c'>c</span> <span class='op'>=</span> <span class='id identifier rubyid_s'>s</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>c</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_g'>g</span> <span class='op'>=</span> <span class='id identifier rubyid_s'>s</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>g</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_t'>t</span> <span class='op'>=</span> <span class='id identifier rubyid_s'>s</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>t</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_a'>a</span> <span class='op'>=</span> <span class='id identifier rubyid_s'>s</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>a</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
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+ <span class='id identifier rubyid_u'>u</span> <span class='op'>=</span> <span class='id identifier rubyid_s'>s</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>u</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span>
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+
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+ <span class='kw'>return</span> <span class='int'>0</span> <span class='kw'>if</span> <span class='id identifier rubyid_c'>c</span> <span class='op'>+</span> <span class='id identifier rubyid_g'>g</span> <span class='op'>+</span> <span class='id identifier rubyid_t'>t</span> <span class='op'>+</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>+</span> <span class='id identifier rubyid_u'>u</span> <span class='op'>==</span> <span class='int'>0</span>
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+ <span class='kw'>return</span> <span class='lparen'>(</span><span class='id identifier rubyid_c'>c</span> <span class='op'>+</span> <span class='id identifier rubyid_g'>g</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_quo'>quo</span><span class='lparen'>(</span><span class='id identifier rubyid_c'>c</span> <span class='op'>+</span> <span class='id identifier rubyid_g'>g</span> <span class='op'>+</span> <span class='id identifier rubyid_t'>t</span> <span class='op'>+</span> <span class='id identifier rubyid_a'>a</span> <span class='op'>+</span> <span class='id identifier rubyid_u'>u</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Tue Jun 3 22:55:41 2014 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.7.4 (ruby-2.1.1).
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/_index.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <head>
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+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+ <title>
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+ Documentation by YARD 0.8.7.4
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+
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+ </title>
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+
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+ <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
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+
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+ <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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+
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+ <script type="text/javascript" charset="utf-8">
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+ hasFrames = window.top.frames.main ? true : false;
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+ relpath = '';
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+ framesUrl = "frames.html#!_index.html";
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+ </script>
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+
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+
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+ <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
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+
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+ <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
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+
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+
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+ </head>
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+ <body>
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+ <div id="header">
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+ <div id="menu">
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+
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+
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+ <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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+ </div>
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+
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+ <div id="search">
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+
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+ <a class="full_list_link" id="class_list_link"
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+ href="class_list.html">
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+ Class List
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+ </a>
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+
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+ <a class="full_list_link" id="method_list_link"
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+ href="method_list.html">
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+ Method List
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+ </a>
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+
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+ <a class="full_list_link" id="file_list_link"
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+ href="file_list.html">
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+ File List
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+ </a>
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+
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+ </div>
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+ <div class="clear"></div>
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+ </div>
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+
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><h1 class="noborder title">Documentation by YARD 0.8.7.4</h1>
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+ <div id="listing">
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+ <h1 class="alphaindex">Alphabetic Index</h1>
62
+
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+ <h2>File Listing</h2>
64
+ <ul id="files" class="index_inline_list">
65
+
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+
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+ <li class="r1"><a href="index.html" title="README">README</a></li>
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+
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+
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+ </ul>
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+
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+ <div class="clear"></div>
73
+ <h2>Namespace Listing A-Z</h2>
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+
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+
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+
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+
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+ <table>
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+ <tr>
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+ <td valign='top' width="33%">
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+
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+
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+ <ul id="alpha_F" class="alpha">
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+ <li>
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+ </li>
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+
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+ </ul>
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+ </ul>
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+
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+
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+ <ul id="alpha_P" class="alpha">
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+ <li class="letter">P</li>
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+ <ul>
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+
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+ <li>
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+ <span class='object_link'><a href="ParseFasta.html" title="ParseFasta (module)">ParseFasta</a></span>
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+
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+ </li>
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+
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+ </ul>
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+ </ul>
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+
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+
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+ <ul id="alpha_S" class="alpha">
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+ <li class="letter">S</li>
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+ <ul>
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+
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+ <li>
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+ <span class='object_link'><a href="Sequence.html" title="Sequence (class)">Sequence</a></span>
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+
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+ </li>
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+
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+ </ul>
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+ </ul>
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+
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+ </td>
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+ </tr>
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+ </table>
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+
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+ </div>
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+
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+ </div>
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+
129
+ <div id="footer">
130
+ Generated on Tue Jun 3 22:55:41 2014 by
131
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
132
+ 0.8.7.4 (ruby-2.1.1).
133
+ </div>
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+
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+ </body>
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+ </html>