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

@@ -1,940 +0,0 @@
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-<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: ValidationReport
-    &mdash; Documentation by YARD 0.8.7.2
-</title>
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-  <link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
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-  <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 (V)</a> &raquo;
-    <span class="title">ValidationReport</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
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-    <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"
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-      File List
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-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: ValidationReport
-</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">ValidationReport</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/validation_output.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<p>This is an abstract class extended by all validation reports</p>
-  </div>
-</div>
-<div class="tags">
-</div><div id="subclasses">
-  <h2>Direct Known Subclasses</h2>
-  <p class="children"><span class='object_link'><a href="AlignmentValidationOutput.html" title="AlignmentValidationOutput (class)">AlignmentValidationOutput</a></span>, <span class='object_link'><a href="BlastRFValidationOutput.html" title="BlastRFValidationOutput (class)">BlastRFValidationOutput</a></span>, <span class='object_link'><a href="DuplicationValidationOutput.html" title="DuplicationValidationOutput (class)">DuplicationValidationOutput</a></span>, <span class='object_link'><a href="GeneMergeValidationOutput.html" title="GeneMergeValidationOutput (class)">GeneMergeValidationOutput</a></span>, <span class='object_link'><a href="LengthClusterValidationOutput.html" title="LengthClusterValidationOutput (class)">LengthClusterValidationOutput</a></span>, <span class='object_link'><a href="LengthRankValidationOutput.html" title="LengthRankValidationOutput (class)">LengthRankValidationOutput</a></span>, <span class='object_link'><a href="ORFValidationOutput.html" title="ORFValidationOutput (class)">ORFValidationOutput</a></span></p>
-</div>
-  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
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-      <a href="#errors-instance_method" title="#errors (instance method)">- (Object) <strong>errors</strong> </a>
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-      <a href="#plot_files-instance_method" title="#plot_files (instance method)">- (Object) <strong>plot_files</strong> </a>
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-<p>Returns the value of attribute plot_files.</p>
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-      <a href="#result-instance_method" title="#result (instance method)">- (Object) <strong>result</strong> </a>
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-      <a href="#validation_result-instance_method" title="#validation_result (instance method)">- (Object) <strong>validation_result</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute validation_result.</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="#color-instance_method" title="#color (instance method)">- (Object) <strong>color</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>May return "success" or "error".</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (ValidationReport) <strong>initialize</strong>(message = &quot;Not enough evidence&quot;, validation_result = :no) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Initilizes the object Params:   <tt>message</tt>: result of the validation
-(to be displayed in the output) <tt>bg_color</tt>: background color of the
-table cell for the html output (nil by default).</p>
-</div></span>
-</li>
-        <li class="public ">
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-      <a href="#print-instance_method" title="#print (instance method)">- (Object) <strong>print</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#validation-instance_method" title="#validation (instance method)">- (Object) <strong>validation</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="ValidationReport (class)">ValidationReport</a></span></tt>) <strong>initialize</strong>(message = &quot;Not enough evidence&quot;, validation_result = :no)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Initilizes the object Params:   <tt>message</tt>: result of the validation
-(to be displayed in the output) <tt>bg_color</tt>: background color of the
-table cell for the html output (nil by default)</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/validation_output.rb', line 22</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_message'>message</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Not enough evidence</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_validation_result'>validation_result</span> <span class='op'>=</span> <span class='symbol'>:no</span><span class='rparen'>)</span>
-  <span class='ivar'>@message</span> <span class='op'>=</span> <span class='id identifier rubyid_message'>message</span>
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-  <span class='ivar'>@expected</span> <span class='op'>=</span> <span class='symbol'>:yes</span>
-  <span class='ivar'>@validation_result</span> <span class='op'>=</span> <span class='id identifier rubyid_validation_result'>validation_result</span>
-<span class='kw'>end</span></pre>
-    </td>
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-</div>
-</div>
-  <div id="instance_attr_details" class="attr_details">
-    <h2>Instance Attribute Details</h2>
-      <span id=""></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="bg_color-instance_method">
-    - (<tt>Object</tt>) <strong>bg_color</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute bg_color</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-10
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-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 10</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_bg_color'>bg_color</span>
-  <span class='ivar'>@bg_color</span>
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-</h3><div class="docstring">
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-<p>Returns the value of attribute errors</p>
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-<span class='kw'>def</span> <span class='id identifier rubyid_errors'>errors</span>
-  <span class='ivar'>@errors</span>
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-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 13</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_expected'>expected</span>
-  <span class='ivar'>@expected</span>
-<span class='kw'>end</span></pre>
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-      <span id=""></span>
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-</h3><div class="docstring">
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-<p>Returns the value of attribute message</p>
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-<div class="tags">
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-    <td>
-      <pre class="lines">
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-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 9</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_message'>message</span>
-  <span class='ivar'>@message</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
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-</div>
-      <span id=""></span>
-      <div class="method_details ">
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-    - (<tt>Object</tt>) <strong>plot_files</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute plot_files</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 11</span>
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-  <span class='ivar'>@plot_files</span>
-<span class='kw'>end</span></pre>
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-    - (<tt>Object</tt>) <strong>result</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute result</p>
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-<div class="tags">
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-    <td>
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-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 12</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_result'>result</span>
-  <span class='ivar'>@result</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="validation_result-instance_method">
-    - (<tt>Object</tt>) <strong>validation_result</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute validation_result</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/validation_output.rb', line 14</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_validation_result'>validation_result</span>
-  <span class='ivar'>@validation_result</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="color-instance_method">
-    - (<tt>Object</tt>) <strong>color</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>May return "success" or "error"</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-40
-41
-42
-43
-44
-45
-46
-47
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-49
-50
-51
-52
-53</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 40</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_color'>color</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_bg_color'>bg_color</span> <span class='op'>!=</span> <span class='kw'>nil</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_bg_color'>bg_color</span>
-  <span class='kw'>end</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_validation'>validation</span> <span class='op'>==</span> <span class='ivar'>@expected</span>
-    <span class='kw'>return</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='kw'>if</span> <span class='id identifier rubyid_validation'>validation</span> <span class='op'>==</span> <span class='symbol'>:warning</span>
-      <span class='kw'>return</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>warning</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>else</span>
-      <span class='kw'>return</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='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="print-instance_method">
-    - (<tt>Object</tt>) <strong>print</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-30
-31
-32</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 30</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_print'>print</span>
-  <span class='id identifier rubyid_message'>message</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="validation-instance_method">
-    - (<tt>Object</tt>) <strong>validation</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-34
-35
-36</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_output.rb', line 34</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_validation'>validation</span>
-  <span class='id identifier rubyid_validation_result'>validation_result</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:33 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>