RubyGems - genevalidator - Versions diffs - 1.6.1 → 1.6.2 - Mend

genevalidator 1.6.1 → 1.6.2

Files changed (131) hide show

checksums.yaml +4 -4
data/.gitignore +3 -1
data/.travis.yml +2 -0
data/README.md +78 -30
data/Rakefile +11 -8
data/aux/app_template_footer.erb +1 -6
data/aux/app_template_header.erb +12 -32
data/aux/files/css/style.css +2 -8
data/aux/files/js/plots.js +564 -576
data/aux/files/js/script.js +10 -0
data/aux/json_footer.erb +8 -0
data/aux/json_header.erb +19 -0
data/aux/json_query.erb +14 -0
data/aux/template_footer.erb +9 -58
data/aux/template_header.erb +18 -58
data/aux/template_query.erb +8 -36
data/bin/genevalidator +45 -32
data/genevalidator.gemspec +11 -7
data/lib/genevalidator.rb +75 -455
data/lib/genevalidator/arg_validation.rb +78 -107
data/lib/genevalidator/blast.rb +57 -60
data/lib/genevalidator/clusterization.rb +15 -15
data/lib/genevalidator/exceptions.rb +32 -5
data/lib/genevalidator/get_raw_sequences.rb +70 -33
data/lib/genevalidator/hsp.rb +1 -4
data/lib/genevalidator/json_to_gv_results.rb +109 -0
data/lib/genevalidator/output.rb +177 -185
data/lib/genevalidator/pool.rb +2 -1
data/lib/genevalidator/sequences.rb +3 -3
data/lib/genevalidator/tabular_parser.rb +24 -18
data/lib/genevalidator/validation.rb +279 -0
data/lib/genevalidator/validation_alignment.rb +31 -47
data/lib/genevalidator/validation_blast_reading_frame.rb +19 -18
data/lib/genevalidator/validation_duplication.rb +23 -19
data/lib/genevalidator/validation_gene_merge.rb +30 -65
data/lib/genevalidator/validation_length_cluster.rb +14 -53
data/lib/genevalidator/validation_length_rank.rb +10 -11
data/lib/genevalidator/validation_open_reading_frame.rb +18 -19
data/lib/genevalidator/validation_report.rb +2 -5
data/lib/genevalidator/validation_test.rb +8 -4
data/lib/genevalidator/version.rb +1 -1
data/test/test_all_validations.rb +51 -66
data/test/test_blast.rb +68 -51
data/test/test_clusterization.rb +1 -1
data/test/test_clusterization_2d.rb +19 -13
data/test/test_extended_array_methods.rb +1 -1
data/test/test_files/all_validations_mrna/mrna.blast_tab6 +1806 -0
data/test/test_files/all_validations_mrna/mrna.blast_tab7 +1865 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml → mrna.blast_xml} +18642 -1
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.index → mrna.blast_xml.index} +300 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta → mrna.fa} +0 -0
data/test/test_files/all_validations_mrna/mrna.raw_seq +3970 -0
data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.raw_seq.idx → mrna.raw_seq.idx} +901 -1
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_tab → prot.blast_tab6} +416 -0
data/test/test_files/all_validations_prot/prot.blast_tab7 +2400 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml → prot.blast_xml} +18299 -6723
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.index → prot.blast_xml.index} +408 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta → prot.fa} +0 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq → prot.raw_seq} +2735 -0
data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq.idx → prot.raw_seq.idx} +3032 -1808
data/test/test_sequences.rb +46 -41
data/test/test_validation_open_reading_frame.rb +318 -202
data/test/test_validations.rb +48 -32
metadata +76 -102
data/doc/AliasDuplicationError.html +0 -134
data/doc/AlignmentValidation.html +0 -1687
data/doc/AlignmentValidationOutput.html +0 -659
data/doc/Blast.html +0 -1905
data/doc/BlastRFValidationOutput.html +0 -545
data/doc/BlastReadingFrameValidation.html +0 -370
data/doc/BlastUtils.html +0 -875
data/doc/ClasspathError.html +0 -134
data/doc/Cluster.html +0 -1316
data/doc/DuplciationValidationOutput.html +0 -564
data/doc/DuplicationValidation.html +0 -920
data/doc/DuplicationValidationOutput.html +0 -564
data/doc/FileNotFoundException.html +0 -134
data/doc/GeneMergeValidation.html +0 -935
data/doc/GeneMergeValidationOutput.html +0 -652
data/doc/HierarchicalClusterization.html +0 -994
data/doc/Hsp.html +0 -1485
data/doc/InconsistentTabularFormat.html +0 -135
data/doc/LengthClusterValidation.html +0 -982
data/doc/LengthClusterValidationOutput.html +0 -515
data/doc/LengthRankValidation.html +0 -496
data/doc/LengthRankValidationOutput.html +0 -517
data/doc/NoInternetError.html +0 -135
data/doc/NoMafftInstallationError.html +0 -134
data/doc/NoPIdentError.html +0 -134
data/doc/NoValidationError.html +0 -134
data/doc/NotEnoughHitsError.html +0 -135
data/doc/ORFValidationOutput.html +0 -593
data/doc/OpenReadingFrameValidation.html +0 -1107
data/doc/OtherError.html +0 -123
data/doc/Output.html +0 -1540
data/doc/Pair.html +0 -309
data/doc/PairCluster.html +0 -767
data/doc/Plot.html +0 -837
data/doc/QueryError.html +0 -134
data/doc/ReportClassError.html +0 -135
data/doc/Sequence.html +0 -1299
data/doc/SequenceTypeError.html +0 -135
data/doc/TabularEntry.html +0 -837
data/doc/TabularParser.html +0 -1104
data/doc/Validation.html +0 -2147
data/doc/ValidationClassError.html +0 -134
data/doc/ValidationOutput.html +0 -460
data/doc/ValidationReport.html +0 -940
data/doc/ValidationTest.html +0 -939
data/doc/_index.html +0 -449
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 -338
data/doc/file.README.html +0 -151
data/doc/file_list.html +0 -56
data/doc/frames.html +0 -26
data/doc/index.html +0 -151
data/doc/js/app.js +0 -214
data/doc/js/full_list.js +0 -178
data/doc/js/jquery.js +0 -4
data/doc/method_list.html +0 -1505
data/doc/top-level-namespace.html +0 -112
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index +0 -967
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq +0 -4929
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx +0 -1006
data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq +0 -2075
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index +0 -1864
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq +0 -42411
data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx +0 -3751

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-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
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-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">Exception</li>
-            <li class="next">OtherError</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/exceptions.rb</dd>
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-<div class="clear"></div>
-</div>
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:32 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.2 (ruby-1.9.3).
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data/doc/Output.html DELETED

@@ -1,1540 +0,0 @@
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-  "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: Output
-    &mdash; Documentation by YARD 0.8.7.2
-</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">
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-  framesUrl = "frames.html#!" + escape(window.location.href);
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-  <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 (O)</a> &raquo;
-    <span class="title">Output</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"
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-      Class List
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-    <a class="full_list_link" id="method_list_link"
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-      Method List
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-    <a class="full_list_link" id="file_list_link"
-        href="file_list.html">
-      File List
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-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: Output
-</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">Output</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/output.rb</dd>
-</dl>
-<div class="clear"></div>
-  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
-  <ul class="summary">
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#filename-instance_method" title="#filename (instance method)">- (Object) <strong>filename</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute filename.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#html_path-instance_method" title="#html_path (instance method)">- (Object) <strong>html_path</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute html_path.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#idx-instance_method" title="#idx (instance method)">- (Object) <strong>idx</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute idx.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#nr_hits-instance_method" title="#nr_hits (instance method)">- (Object) <strong>nr_hits</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute nr_hits.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#prediction_def-instance_method" title="#prediction_def (instance method)">- (Object) <strong>prediction_def</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute prediction_def.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#prediction_len-instance_method" title="#prediction_len (instance method)">- (Object) <strong>prediction_len</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute prediction_len.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#start_idx-instance_method" title="#start_idx (instance method)">- (Object) <strong>start_idx</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute start_idx.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#validations-instance_method" title="#validations (instance method)">- (Object) <strong>validations</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>list of <tt>ValidationReport</tt> objects.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#yaml_path-instance_method" title="#yaml_path (instance method)">- (Object) <strong>yaml_path</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute yaml_path.</p>
-</div></span>
-</li>
-  </ul>
-    <h2>
-      Class Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#overall_evaluation-class_method" title="overall_evaluation (class method)">+ (Object) <strong>overall_evaluation</strong>(all_query_outputs) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Calculates an overall evaluation of the output Params:
-<tt>all_query_outputs</tt>: Array of <tt>ValidationTest</tt> objects Output
-Array of Strigs with the reports.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#print_footer-class_method" title="print_footer (class method)">+ (Object) <strong>print_footer</strong>(all_query_outputs, html_path) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Class that closes the gas in the html file and writes the overall
-evaluation Param: <tt>all_query_outputs</tt>: array with
-<tt>ValidationTest</tt> objects <tt>html_path</tt>: path of the html
-folder.</p>
-</div></span>
-</li>
-    </ul>
-    <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="#generate_html-instance_method" title="#generate_html (instance method)">- (Object) <strong>generate_html</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (Output) <strong>initialize</strong>(filename, html_path, yaml_path, idx = 0, start_idx = 0) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Initilizes the object Params: <tt>filename</tt>: name of the fasta input
-file <tt>html_path</tt>: path of the html folder <tt>yaml_path</tt>: path
-where the yaml output wil be saved <tt>idx</tt>: idnex of the current query
-<tt>start_idx</tt>: number of the sequence from the file to start with.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#print_output_console-instance_method" title="#print_output_console (instance method)">- (Object) <strong>print_output_console</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#print_output_file_yaml-instance_method" title="#print_output_file_yaml (instance method)">- (Object) <strong>print_output_file_yaml</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-    </ul>
-<div id="constructor_details" class="method_details_list">
-  <h2>Constructor Details</h2>
-    <div class="method_details first">
-  <h3 class="signature first" id="initialize-instance_method">
-    - (<tt><span class='object_link'><a href="" title="Output (class)">Output</a></span></tt>) <strong>initialize</strong>(filename, html_path, yaml_path, idx = 0, start_idx = 0)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Initilizes the object Params: <tt>filename</tt>: name of the fasta input
-file <tt>html_path</tt>: path of the html folder <tt>yaml_path</tt>: path
-where the yaml output wil be saved <tt>idx</tt>: idnex of the current query
-<tt>start_idx</tt>: number of the sequence from the file to start with</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-28
-29
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-40</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 28</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_filename'>filename</span><span class='comma'>,</span> <span class='id identifier rubyid_html_path'>html_path</span><span class='comma'>,</span> <span class='id identifier rubyid_yaml_path'>yaml_path</span><span class='comma'>,</span> <span class='id identifier rubyid_idx'>idx</span> <span class='op'>=</span> <span class='int'>0</span><span class='comma'>,</span> <span class='id identifier rubyid_start_idx'>start_idx</span> <span class='op'>=</span> <span class='int'>0</span><span class='rparen'>)</span>
-  <span class='ivar'>@prediction_len</span> <span class='op'>=</span> <span class='int'>0</span>
-  <span class='ivar'>@prediction_def</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>no_definition</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@nr_hits</span> <span class='op'>=</span> <span class='int'>0</span>
-  <span class='ivar'>@filename</span> <span class='op'>=</span> <span class='id identifier rubyid_filename'>filename</span>
-  <span class='ivar'>@html_path</span> <span class='op'>=</span> <span class='id identifier rubyid_html_path'>html_path</span>
-  <span class='ivar'>@yaml_path</span> <span class='op'>=</span> <span class='id identifier rubyid_yaml_path'>yaml_path</span>
-  <span class='ivar'>@idx</span> <span class='op'>=</span> <span class='id identifier rubyid_idx'>idx</span>
-  <span class='ivar'>@start_idx</span> <span class='op'>=</span> <span class='id identifier rubyid_start_idx'>start_idx</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-</div>
-  <div id="instance_attr_details" class="attr_details">
-    <h2>Instance Attribute Details</h2>
-      <span id="filename=-instance_method"></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="filename-instance_method">
-    - (<tt>Object</tt>) <strong>filename</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute filename</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-14
-15
-16</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 14</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_filename'>filename</span>
-  <span class='ivar'>@filename</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="html_path=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="html_path-instance_method">
-    - (<tt>Object</tt>) <strong>html_path</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute html_path</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 15</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_html_path'>html_path</span>
-  <span class='ivar'>@html_path</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="idx=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="idx-instance_method">
-    - (<tt>Object</tt>) <strong>idx</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute idx</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 17</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_idx'>idx</span>
-  <span class='ivar'>@idx</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="nr_hits=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="nr_hits-instance_method">
-    - (<tt>Object</tt>) <strong>nr_hits</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute nr_hits</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 9</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_nr_hits'>nr_hits</span>
-  <span class='ivar'>@nr_hits</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="prediction_def=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="prediction_def-instance_method">
-    - (<tt>Object</tt>) <strong>prediction_def</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute prediction_def</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 8</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_prediction_def'>prediction_def</span>
-  <span class='ivar'>@prediction_def</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="prediction_len=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="prediction_len-instance_method">
-    - (<tt>Object</tt>) <strong>prediction_len</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute prediction_len</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-7
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 7</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_prediction_len'>prediction_len</span>
-  <span class='ivar'>@prediction_len</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="start_idx=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="start_idx-instance_method">
-    - (<tt>Object</tt>) <strong>start_idx</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute start_idx</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 18</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_start_idx'>start_idx</span>
-  <span class='ivar'>@start_idx</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="validations=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="validations-instance_method">
-    - (<tt>Object</tt>) <strong>validations</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>list of <tt>ValidationReport</tt> objects</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-12
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 12</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_validations'>validations</span>
-  <span class='ivar'>@validations</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="yaml_path=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="yaml_path-instance_method">
-    - (<tt>Object</tt>) <strong>yaml_path</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute yaml_path</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 16</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_yaml_path'>yaml_path</span>
-  <span class='ivar'>@yaml_path</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="class_method_details" class="method_details_list">
-    <h2>Class Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="overall_evaluation-class_method">
-    + (<tt>Object</tt>) <strong>overall_evaluation</strong>(all_query_outputs)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Calculates an overall evaluation of the output Params:
-<tt>all_query_outputs</tt>: Array of <tt>ValidationTest</tt> objects Output
-Array of Strigs with the reports</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 148</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Query score evaluation:</span><span class='tstring_end'>&quot;</span></span>
-    <span class='comment'># count the cases of &quot;not enough evidence&quot;
-</span>    <span class='id identifier rubyid_no_evidence'>no_evidence</span> <span class='op'>=</span> <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_report'>report</span><span class='op'>|</span>
-      <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span> <span class='symbol'>:unapplicable</span> <span class='kw'>or</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span> <span class='symbol'>:warning</span><span class='rbrace'>}</span> <span class='op'>==</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-    <span class='rbrace'>}</span>
-    <span class='comment'># print at the console
-</span>    <span class='id identifier rubyid_scores'>scores</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-    <span class='id identifier rubyid_no_mafft'>no_mafft</span> <span class='op'>=</span> <span class='int'>0</span>
-    <span class='id identifier rubyid_no_internet'>no_internet</span> <span class='op'>=</span> <span class='int'>0</span>
-    <span class='comment'># how many genes are good
-</span>    <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_report'>report</span><span class='op'>|</span>
-      <span class='id identifier rubyid_successes'>successes</span> <span class='op'>=</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_fails'>fails</span> <span class='op'>=</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:unapplicable</span> <span class='kw'>and</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:error</span> <span class='kw'>and</span>
-        <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>!=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_overall_score'>overall_score</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span><span class='op'>*</span><span class='int'>100</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span> <span class='op'>+</span> <span class='id identifier rubyid_fails'>fails</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_scores'>scores</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='id identifier rubyid_overall_score'>overall_score</span>
-      <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span> <span class='op'>!=</span> <span class='kw'>nil</span>
-          <span class='id identifier rubyid_no_mafft'>no_mafft</span> <span class='op'>+=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_e'>e</span> <span class='op'>==</span> <span class='const'>NoMafftInstallationError</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-      <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span> <span class='op'>!=</span> <span class='kw'>nil</span>
-          <span class='id identifier rubyid_no_internet'>no_internet</span> <span class='op'>+=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_e'>e</span> <span class='op'>==</span> <span class='const'>NoInternetError</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_good_scores'>good_scores</span> <span class='op'>=</span> <span class='id identifier rubyid_scores'>scores</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span> <span class='op'>&gt;</span> <span class='int'>75</span><span class='rbrace'>}</span>
-    <span class='id identifier rubyid_bad_scores'>bad_scores</span> <span class='op'>=</span> <span class='id identifier rubyid_scores'>scores</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_good_scores'>good_scores</span>
-    <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nThere were validated </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbrace'>}</span><span class='tstring_content'> predictions from which:</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_good_scores'>good_scores</span> <span class='op'>==</span> <span class='int'>1</span>
-      <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nOne good prediction</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_good_scores'>good_scores</span><span class='rbrace'>}</span><span class='tstring_content'> are good predictions</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_bad_scores'>bad_scores</span> <span class='op'>==</span> <span class='int'>1</span>
-      <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nOne possibly weak prediction</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_bad_scores'>bad_scores</span><span class='rbrace'>}</span><span class='tstring_content'> are possibly weak predictions</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_no_evidence'>no_evidence</span> <span class='op'>!=</span> <span class='int'>0</span>
-      <span class='id identifier rubyid_score_evaluation'>score_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_no_evidence'>no_evidence</span><span class='rbrace'>}</span><span class='tstring_content'> of them couldn't be evaluated because of low evidence</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
-    <span class='comment'># errors per validation
-</span>    <span class='id identifier rubyid_validations'>validations</span> <span class='op'>=</span> <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='comma'>,</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-      <span class='id identifier rubyid_no_errors'>no_errors</span> <span class='op'>=</span> <span class='int'>0</span>
-      <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_report'>report</span><span class='op'>|</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>==</span> <span class='symbol'>:error</span>
-          <span class='id identifier rubyid_no_errors'>no_errors</span> <span class='op'>+=</span> <span class='int'>1</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_no_errors'>no_errors</span> <span class='op'>!=</span> <span class='int'>0</span>
-        <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>&lt;&lt;</span>  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nWe couldn't run </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbrace'>}</span><span class='tstring_content'> Validation for </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_no_errors'>no_errors</span><span class='rbrace'>}</span><span class='tstring_content'> queries</span><span class='tstring_end'>&quot;</span></span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_no_mafft'>no_mafft</span> <span class='op'>&gt;=</span>  <span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_no_evidence'>no_evidence</span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nWe couldn't run MAFFT multiple alignment</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_no_internet'>no_internet</span> <span class='op'>&gt;=</span>  <span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_no_evidence'>no_evidence</span><span class='rparen'>)</span>
-      <span class='id identifier rubyid_error_evaluation'>error_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nWe couldn't make use of your internet connection</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='comment'># Running time statistics
-</span>    <span class='id identifier rubyid_running_times'>running_times</span> <span class='op'>=</span> <span class='lbrace'>{</span><span class='rbrace'>}</span>
-    <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-      <span class='id identifier rubyid_running_times'>running_times</span><span class='lbracket'>[</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_output'>output</span><span class='op'>|</span>
-      <span class='id identifier rubyid_output'>output</span><span class='period'>.</span><span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_running_time'>running_time</span> <span class='op'>!=</span> <span class='int'>0</span> <span class='kw'>and</span>
-           <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_running_time'>running_time</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span>
-           <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:unapplicable</span> <span class='kw'>and</span>
-           <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:error</span>
-          <span class='id identifier rubyid_running_times'>running_times</span><span class='lbracket'>[</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_running_time'>running_time</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_time_evaluation'>time_evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_time_evaluation'>time_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nRunning Time:</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_running_times'>running_times</span> <span class='op'>=</span> <span class='id identifier rubyid_running_times'>running_times</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>!=</span><span class='int'>0</span><span class='rbrace'>}</span>
-    <span class='id identifier rubyid_running_times'>running_times</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_key'>key</span><span class='comma'>,</span> <span class='id identifier rubyid_array'>array</span><span class='op'>|</span>
-      <span class='id identifier rubyid_average_time'>average_time</span> <span class='op'>=</span> <span class='id identifier rubyid_array'>array</span><span class='period'>.</span><span class='id identifier rubyid_inject'>inject</span><span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_el'>el</span><span class='op'>|</span> <span class='id identifier rubyid_sum'>sum</span> <span class='op'>+</span> <span class='id identifier rubyid_el'>el</span> <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span> <span class='op'>/</span> <span class='id identifier rubyid_array'>array</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span>
-      <span class='id identifier rubyid_time_evaluation'>time_evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\nAverage running time for </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_key'>key</span><span class='rbrace'>}</span><span class='tstring_content'> Validation: </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_average_time'>average_time</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>3</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='tstring_content'>s per validation</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='id identifier rubyid_score_evaluation'>score_evaluation</span><span class='comma'>,</span> <span class='id identifier rubyid_error_evaluation'>error_evaluation</span><span class='comma'>,</span> <span class='id identifier rubyid_time_evaluation'>time_evaluation</span><span class='rbracket'>]</span>
-    <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span> <span class='op'>=</span> <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_e'>e</span><span class='op'>!=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="print_footer-class_method">
-    + (<tt>Object</tt>) <strong>print_footer</strong>(all_query_outputs, html_path)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Class that closes the gas in the html file and writes the overall
-evaluation Param: <tt>all_query_outputs</tt>: array with
-<tt>ValidationTest</tt> objects <tt>html_path</tt>: path of the html folder</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 126</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_print_footer'>print_footer</span><span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='comma'>,</span> <span class='id identifier rubyid_html_path'>html_path</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span> <span class='op'>=</span> <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='lparen'>(</span><span class='id identifier rubyid_all_query_outputs'>all_query_outputs</span><span class='rparen'>)</span>
-  <span class='comment'># print to console
-</span>  <span class='id identifier rubyid_evaluation'>evaluation</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
-  <span class='id identifier rubyid_overall_evaluation'>overall_evaluation</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_e'>e</span><span class='op'>|</span> <span class='id identifier rubyid_evaluation'>evaluation</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_e'>e</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span>
-  <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_evaluation'>evaluation</span>
-  <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
-  <span class='id identifier rubyid_evaluation'>evaluation</span> <span class='op'>=</span> <span class='id identifier rubyid_evaluation'>evaluation</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>&lt;br&gt;</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-  <span class='comment'># print to html
-</span>  <span class='id identifier rubyid_index_file'>index_file</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_html_path'>html_path</span><span class='rbrace'>}</span><span class='tstring_content'>/index.html</span><span class='tstring_end'>&quot;</span></span>
-  <span class='id identifier rubyid_template_file'>template_file</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/template_footer.htm.erb</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>r</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_read'>read</span>
-  <span class='id identifier rubyid_erb'>erb</span> <span class='op'>=</span> <span class='const'>ERB</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_template_file'>template_file</span><span class='rparen'>)</span>
-  <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file'>index_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>a+</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_file'>file</span><span class='op'>|</span> <span class='id identifier rubyid_file'>file</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_erb'>erb</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span><span class='lparen'>(</span><span class='id identifier rubyid_binding'>binding</span><span class='rparen'>)</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="generate_html-instance_method">
-    - (<tt>Object</tt>) <strong>generate_html</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 88</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_generate_html'>generate_html</span>
-  <span class='id identifier rubyid_successes'>successes</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>==</span>
-    <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_fails'>fails</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:unapplicable</span> <span class='kw'>and</span>
-    <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_validation'>validation</span> <span class='op'>!=</span> <span class='symbol'>:error</span> <span class='kw'>and</span>
-    <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span> <span class='op'>!=</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_expected'>expected</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_count'>count</span><span class='lparen'>(</span><span class='kw'>true</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_unknown'>unknown</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_successes'>successes</span> <span class='op'>-</span> <span class='id identifier rubyid_fails'>fails</span>
-  <span class='id identifier rubyid_overall_score'>overall_score</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span><span class='op'>*</span><span class='int'>100</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_successes'>successes</span> <span class='op'>+</span> <span class='id identifier rubyid_fails'>fails</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_round'>round</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_fails'>fails</span> <span class='op'>==</span> <span class='int'>0</span>
-    <span class='id identifier rubyid_bg_icon'>bg_icon</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>success</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>else</span>
-    <span class='id identifier rubyid_bg_icon'>bg_icon</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>danger</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_index_file'>index_file</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@html_path</span><span class='rbrace'>}</span><span class='tstring_content'>/index.html</span><span class='tstring_end'>&quot;</span></span>
-  <span class='comment'># if it's the first time I write in the html file
-</span>  <span class='kw'>if</span> <span class='ivar'>@idx</span> <span class='op'>==</span> <span class='ivar'>@start_idx</span>
-    <span class='id identifier rubyid_template_file'>template_file</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/template_header.htm.erb</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>r</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_read'>read</span>
-    <span class='id identifier rubyid_erb'>erb</span> <span class='op'>=</span> <span class='const'>ERB</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_template_file'>template_file</span><span class='rparen'>)</span>
-    <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file'>index_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>w+</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_file'>file</span><span class='op'>|</span> <span class='id identifier rubyid_file'>file</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_erb'>erb</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span><span class='lparen'>(</span><span class='id identifier rubyid_binding'>binding</span><span class='rparen'>)</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_toggle'>toggle</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>toggle</span><span class='embexpr_beg'>#{</span><span class='ivar'>@idx</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-  <span class='id identifier rubyid_template_file'>template_file</span> <span class='op'>=</span> <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>aux/template_query.htm.erb</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>r</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_read'>read</span>
-  <span class='id identifier rubyid_erb'>erb</span> <span class='op'>=</span> <span class='const'>ERB</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_template_file'>template_file</span><span class='rparen'>)</span>
-  <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_index_file'>index_file</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>a</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_file'>file</span><span class='op'>|</span> <span class='id identifier rubyid_file'>file</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_erb'>erb</span><span class='period'>.</span><span class='id identifier rubyid_result'>result</span><span class='lparen'>(</span><span class='id identifier rubyid_binding'>binding</span><span class='rparen'>)</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="print_output_console-instance_method">
-    - (<tt>Object</tt>) <strong>print_output_console</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 43</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_print_output_console'>print_output_console</span>
-  <span class='kw'>if</span> <span class='ivar'>@idx</span> <span class='op'>==</span> <span class='ivar'>@start_idx</span>
-    <span class='id identifier rubyid_header'>header</span> <span class='op'>=</span><span class='id identifier rubyid_sprintf'>sprintf</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>%3s|%20s|%5s</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>No</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Identifier</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>No_Hits</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span>
-      <span class='id identifier rubyid_header'>header</span><span class='op'>&lt;&lt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>|</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_short_header'>short_header</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_header'>header</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_short_def'>short_def</span> <span class='op'>=</span> <span class='ivar'>@prediction_def</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>([^ ]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_short_def'>short_def</span> <span class='op'>=</span> <span class='id identifier rubyid_short_def'>short_def</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='lbracket'>[</span><span class='int'>20</span><span class='comma'>,</span><span class='id identifier rubyid_short_def'>short_def</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_min'>min</span><span class='rbracket'>]</span>
-  <span class='id identifier rubyid_validation_outputs'>validation_outputs</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span><span class='rbrace'>}</span>
-  <span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='id identifier rubyid_sprintf'>sprintf</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>%3s|%20s|%5s|</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='ivar'>@idx</span><span class='comma'>,</span> <span class='id identifier rubyid_short_def'>short_def</span><span class='comma'>,</span> <span class='ivar'>@nr_hits</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_validation_outputs'>validation_outputs</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_item'>item</span><span class='op'>|</span>
-    <span class='id identifier rubyid_item_padd'>item_padd</span> <span class='op'>=</span> <span class='id identifier rubyid_sprintf'>sprintf</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>%17s</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_item'>item</span><span class='rparen'>)</span><span class='semicolon'>;</span>
-    <span class='id identifier rubyid_output'>output</span> <span class='op'>&lt;&lt;</span> <span class='id identifier rubyid_item'>item</span>
-    <span class='id identifier rubyid_output'>output</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>|</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_puts'>puts</span> <span class='id identifier rubyid_output'>output</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="print_output_file_yaml-instance_method">
-    - (<tt>Object</tt>) <strong>print_output_file_yaml</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/output.rb', line 69</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_print_output_file_yaml'>print_output_file_yaml</span>
-  <span class='id identifier rubyid_file_yaml'>file_yaml</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@yaml_path</span><span class='rbrace'>}</span><span class='tstring_content'>/</span><span class='embexpr_beg'>#{</span><span class='ivar'>@filename</span><span class='rbrace'>}</span><span class='tstring_content'>.yaml</span><span class='tstring_end'>&quot;</span></span>
-  <span class='id identifier rubyid_report'>report</span> <span class='op'>=</span> <span class='id identifier rubyid_validations'>validations</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='period'>.</span><span class='id identifier rubyid_validation_report'>validation_report</span><span class='rbrace'>}</span>
-  <span class='kw'>unless</span> <span class='ivar'>@idx</span> <span class='op'>==</span> <span class='ivar'>@start_idx</span>
-    <span class='id identifier rubyid_hsh'>hsh</span> <span class='op'>=</span> <span class='const'>YAML</span><span class='period'>.</span><span class='id identifier rubyid_load_file'>load_file</span><span class='lparen'>(</span><span class='id identifier rubyid_file_yaml'>file_yaml</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_hsh'>hsh</span><span class='lbracket'>[</span><span class='ivar'>@prediction_def</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>([^ ]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_report'>report</span>
-    <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_file_yaml'>file_yaml</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</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_f'>f</span><span class='op'>|</span>
-      <span class='const'>YAML</span><span class='period'>.</span><span class='id identifier rubyid_dump'>dump</span><span class='lparen'>(</span><span class='id identifier rubyid_hsh'>hsh</span><span class='comma'>,</span> <span class='id identifier rubyid_f'>f</span><span class='rparen'>)</span>
-    <span class='kw'>end</span>
-  <span class='kw'>else</span>
-    <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='id identifier rubyid_file_yaml'>file_yaml</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>w</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_f'>f</span><span class='op'>|</span>
-      <span class='const'>YAML</span><span class='period'>.</span><span class='id identifier rubyid_dump'>dump</span><span class='lparen'>(</span><span class='lbrace'>{</span><span class='ivar'>@prediction_def</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>([^ ]+)</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_report'>report</span><span class='rbrace'>}</span><span class='comma'>,</span><span class='id identifier rubyid_f'>f</span><span class='rparen'>)</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:32 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.2 (ruby-1.9.3).
-</div>
-  </body>
-</html>