RubyGems - parse_fasta - Versions diffs - 1.0.0 → 1.0.1 - Mend

parse_fasta 1.0.0 → 1.0.1

Files changed (22) hide show

checksums.yaml +4 -4
data/.gitignore +1 -0
data/lib/parse_fasta/version.rb +1 -1
metadata +1 -19
data/doc/FastaFile.html +0 -292
data/doc/File.html +0 -212
data/doc/ParseFasta.html +0 -144
data/doc/Sequence.html +0 -361
data/doc/_index.html +0 -136
data/doc/class_list.html +0 -54
data/doc/css/common.css +0 -1
data/doc/css/full_list.css +0 -57
data/doc/css/style.css +0 -339
data/doc/file.README.html +0 -161
data/doc/file_list.html +0 -56
data/doc/frames.html +0 -26
data/doc/index.html +0 -161
data/doc/js/app.js +0 -219
data/doc/js/full_list.js +0 -178
data/doc/js/jquery.js +0 -4
data/doc/method_list.html +0 -71
data/doc/top-level-namespace.html +0 -114

checksums.yaml CHANGED Viewed

@@ -1,7 +1,7 @@
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-  data.tar.gz: 4dffe3d99bf98969205b1a10fc5650b701676e67
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data/.gitignore CHANGED Viewed

@@ -6,6 +6,7 @@
 Gemfile.lock
 InstalledFiles
 _yardoc
+doc/
 coverage
 lib/bundler/man
 pkg

data/lib/parse_fasta/version.rb CHANGED Viewed

@@ -17,5 +17,5 @@
 # along with parse_fasta.  If not, see <http://www.gnu.org/licenses/>.
 module ParseFasta
-  VERSION = "1.0.0"
+  VERSION = "1.0.1"
 end

metadata CHANGED Viewed

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: parse_fasta
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Ryan Moore
@@ -92,24 +92,6 @@ files:
 - Gemfile
 - README.md
 - Rakefile
-- doc/FastaFile.html
-- doc/File.html
-- doc/ParseFasta.html
-- doc/Sequence.html
-- doc/_index.html
-- doc/class_list.html
-- doc/css/common.css
-- doc/css/full_list.css
-- doc/css/style.css
-- doc/file.README.html
-- doc/file_list.html
-- doc/frames.html
-- doc/index.html
-- doc/js/app.js
-- doc/js/full_list.js
-- doc/js/jquery.js
-- doc/method_list.html
-- doc/top-level-namespace.html
 - lib/parse_fasta.rb
 - lib/parse_fasta/fasta_file.rb
 - lib/parse_fasta/sequence.rb

data/doc/FastaFile.html DELETED Viewed

@@ -1,292 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: FastaFile
-    &mdash; Documentation by YARD 0.8.7.4
-</title>
-  <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
-  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '';
-  framesUrl = "frames.html#!FastaFile.html";
-</script>
-  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="_index.html">Index (F)</a> &raquo;
-    <span class="title">FastaFile</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: FastaFile
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">File</span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">File</li>
-            <li class="next">FastaFile</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/parse_fasta/fasta_file.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<p>Provides simple interface for parsing fasta format files.</p>
-  </div>
-</div>
-<div class="tags">
-</div>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#each_record-instance_method" title="#each_record (instance method)">- (Object) <strong>each_record</strong> {|header, sequence| ... }</a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Analagous to File#each_line, #each_record is used to go through a fasta
-file record by record.</p>
-</div></span>
-</li>
-    </ul>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="each_record-instance_method">
-    - (<tt>Object</tt>) <strong>each_record</strong> {|header, sequence| ... }
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Analagous to File#each_line, #each_record is used to go through a fasta
-file record by record.</p>
-  </div>
-</div>
-<div class="tags">
-  <div class="examples">
-    <p class="tag_title">Examples:</p>
-        <p class="example_title"><div class='inline'>
-<p>Parsing a fasta file</p>
-</div></p>
-      <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>
-  <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>
-<span class='kw'>end</span></code></pre>
-  </div>
-<p class="tag_title">Yields:</p>
-<ul class="yield">
-    <li>
-        <span class='type'></span>
-        <div class='inline'>
-<p>The header and sequence for each record in the fasta file to the block</p>
-</div>
-    </li>
-</ul>
-<p class="tag_title">Yield Parameters:</p>
-<ul class="yieldparam">
-    <li>
-        <span class='name'>header</span>
-        <span class='type'>(<tt>String</tt>)</span>
-        &mdash;
-        <div class='inline'>
-<p>The header of the fasta record without the leading &#39;&gt;&#39;</p>
-</div>
-    </li>
-    <li>
-        <span class='name'>sequence</span>
-        <span class='type'>(<tt><span class='object_link'><a href="Sequence.html" title="Sequence (class)">Sequence</a></span></tt>)</span>
-        &mdash;
-        <div class='inline'>
-<p>The sequence of the fasta record</p>
-</div>
-    </li>
-</ul>
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-35
-36
-37
-38
-39
-40</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/parse_fasta/fasta_file.rb', line 35</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_each_record'>each_record</span>
-  <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n&gt;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</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> <span class='id identifier rubyid_parse_line'>parse_line</span><span class='lparen'>(</span><span class='id identifier rubyid_line'>line</span><span class='rparen'>)</span>
-    <span class='kw'>yield</span><span class='lparen'>(</span><span class='id identifier rubyid_header'>header</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='comma'>,</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_sequence'>sequence</span><span class='rparen'>)</span><span class='rparen'>)</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Tue Jun  3 22:55:41 2014 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.4 (ruby-2.1.1).
-</div>
-  </body>
-</html>

data/doc/File.html DELETED Viewed

@@ -1,212 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: File
-    &mdash; Documentation by YARD 0.8.7.4
-</title>
-  <link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
-  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '';
-  framesUrl = "frames.html#!File.html";
-</script>
-  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="_index.html">Index (F)</a> &raquo;
-    <span class="title">File</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: File
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">Object</span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">File</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/parse_fasta/file.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<p>You should have received a copy of the GNU General Public License along
-with parse_fasta.  If not, see &lt;<a
-href="http://www.gnu.org/licenses">www.gnu.org/licenses</a>/&gt;.</p>
-  </div>
-</div>
-<div class="tags">
-</div><div id="subclasses">
-  <h2>Direct Known Subclasses</h2>
-  <p class="children"><span class='object_link'><a href="FastaFile.html" title="FastaFile (class)">FastaFile</a></span></p>
-</div>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#each_record-instance_method" title="#each_record (instance method)">- (Object) <strong>each_record</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-    </ul>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="each_record-instance_method">
-    - (<tt>Object</tt>) <strong>each_record</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-20
-21
-22
-23
-24
-25</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/parse_fasta/file.rb', line 20</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_each_record'>each_record</span>
-  <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n&gt;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_line'>line</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> <span class='id identifier rubyid_parse_line'>parse_line</span><span class='lparen'>(</span><span class='id identifier rubyid_line'>line</span><span class='rparen'>)</span>
-    <span class='kw'>yield</span> <span class='id identifier rubyid_header'>header</span><span class='period'>.</span><span class='id identifier rubyid_strip'>strip</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Tue Jun  3 22:41:14 2014 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.4 (ruby-2.1.1).
-</div>
-  </body>
-</html>