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Class: AlignmentValidationOutput
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<span class="title">AlignmentValidationOutput</span>
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<div id="content"><h1>Class: AlignmentValidationOutput
</h1>
<dl class="box">
<dt class="r1">Inherits:</dt>
<dd class="r1">
<span class="inheritName"><span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></span>
<ul class="fullTree">
<li>Object</li>
<li class="next"><span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></li>
<li class="next">AlignmentValidationOutput</li>
</ul>
<a href="#" class="inheritanceTree">show all</a>
</dd>
<dt class="r2 last">Defined in:</dt>
<dd class="r2 last">lib/genevalidator/validation_alignment.rb</dd>
</dl>
<div class="clear"></div>
<h2>Overview</h2><div class="docstring">
<div class="discussion">
<p>Class that stores the validation output information</p>
</div>
</div>
<div class="tags">
</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="#consensus-instance_method" title="#consensus (instance method)">- (Object) <strong>consensus</strong> </a>
</span>
<span class="note title readonly">readonly</span>
<span class="summary_desc"><div class='inline'>
<p>Returns the value of attribute consensus.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#extra_seq-instance_method" title="#extra_seq (instance method)">- (Object) <strong>extra_seq</strong> </a>
</span>
<span class="note title readonly">readonly</span>
<span class="summary_desc"><div class='inline'>
<p>Returns the value of attribute extra_seq.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#gaps-instance_method" title="#gaps (instance method)">- (Object) <strong>gaps</strong> </a>
</span>
<span class="note title readonly">readonly</span>
<span class="summary_desc"><div class='inline'>
<p>Returns the value of attribute gaps.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<a href="#threahsold-instance_method" title="#threahsold (instance method)">- (Object) <strong>threahsold</strong> </a>
</span>
<span class="note title readonly">readonly</span>
<span class="summary_desc"><div class='inline'>
<p>Returns the value of attribute threahsold.</p>
</div></span>
</li>
</ul>
<h3 class="inherited">Attributes inherited from <span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></h3>
<p class="inherited"><span class='object_link'><a href="ValidationReport.html#bg_color-instance_method" title="ValidationReport#bg_color (method)">#bg_color</a></span>, <span class='object_link'><a href="ValidationReport.html#errors-instance_method" title="ValidationReport#errors (method)">#errors</a></span>, <span class='object_link'><a href="ValidationReport.html#expected-instance_method" title="ValidationReport#expected (method)">#expected</a></span>, <span class='object_link'><a href="ValidationReport.html#message-instance_method" title="ValidationReport#message (method)">#message</a></span>, <span class='object_link'><a href="ValidationReport.html#plot_files-instance_method" title="ValidationReport#plot_files (method)">#plot_files</a></span>, <span class='object_link'><a href="ValidationReport.html#result-instance_method" title="ValidationReport#result (method)">#result</a></span>, <span class='object_link'><a href="ValidationReport.html#validation_result-instance_method" title="ValidationReport#validation_result (method)">#validation_result</a></span></p>
<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="#initialize-instance_method" title="#initialize (instance method)">- (AlignmentValidationOutput) <strong>initialize</strong>(gaps = 0, extra_seq = 0, consensus = 1, threshold = 0.2, expected = :yes) </a>
</span>
<span class="note title constructor">constructor</span>
<span class="summary_desc"><div class='inline'>
<p>A new instance of AlignmentValidationOutput.</p>
</div></span>
</li>
<li class="public ">
<span class="summary_signature">
<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>
<h3 class="inherited">Methods inherited from <span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></h3>
<p class="inherited"><span class='object_link'><a href="ValidationReport.html#color-instance_method" title="ValidationReport#color (method)">#color</a></span></p>
<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="AlignmentValidationOutput (class)">AlignmentValidationOutput</a></span></tt>) <strong>initialize</strong>(gaps = 0, extra_seq = 0, consensus = 1, threshold = 0.2, expected = :yes)
</h3><div class="docstring">
<div class="discussion">
<p>Returns a new instance of AlignmentValidationOutput</p>
</div>
</div>
<div class="tags">
</div><table class="source_code">
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<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 13</span>
<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span> <span class='lparen'>(</span><span class='id identifier rubyid_gaps'>gaps</span> <span class='op'>=</span> <span class='int'>0</span><span class='comma'>,</span> <span class='id identifier rubyid_extra_seq'>extra_seq</span> <span class='op'>=</span> <span class='int'>0</span><span class='comma'>,</span> <span class='id identifier rubyid_consensus'>consensus</span> <span class='op'>=</span> <span class='int'>1</span><span class='comma'>,</span> <span class='id identifier rubyid_threshold'>threshold</span> <span class='op'>=</span> <span class='float'>0.2</span><span class='comma'>,</span> <span class='id identifier rubyid_expected'>expected</span> <span class='op'>=</span> <span class='symbol'>:yes</span><span class='rparen'>)</span>
<span class='ivar'>@gaps</span> <span class='op'>=</span> <span class='id identifier rubyid_gaps'>gaps</span>
<span class='ivar'>@extra_seq</span> <span class='op'>=</span> <span class='id identifier rubyid_extra_seq'>extra_seq</span>
<span class='ivar'>@consensus</span> <span class='op'>=</span> <span class='id identifier rubyid_consensus'>consensus</span>
<span class='ivar'>@threshold</span> <span class='op'>=</span> <span class='id identifier rubyid_threshold'>threshold</span>
<span class='ivar'>@result</span> <span class='op'>=</span> <span class='id identifier rubyid_validation'>validation</span>
<span class='ivar'>@expected</span> <span class='op'>=</span> <span class='id identifier rubyid_expected'>expected</span>
<span class='ivar'>@plot_files</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
<span class='kw'>end</span></pre>
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<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="consensus-instance_method">
- (<tt>Object</tt>) <strong>consensus</strong> <span class="extras">(readonly)</span>
</h3><div class="docstring">
<div class="discussion">
<p>Returns the value of attribute consensus</p>
</div>
</div>
<div class="tags">
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<td>
<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 10</span>
<span class='kw'>def</span> <span class='id identifier rubyid_consensus'>consensus</span>
<span class='ivar'>@consensus</span>
<span class='kw'>end</span></pre>
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</div>
<span id=""></span>
<div class="method_details ">
<h3 class="signature " id="extra_seq-instance_method">
- (<tt>Object</tt>) <strong>extra_seq</strong> <span class="extras">(readonly)</span>
</h3><div class="docstring">
<div class="discussion">
<p>Returns the value of attribute extra_seq</p>
</div>
</div>
<div class="tags">
</div><table class="source_code">
<tr>
<td>
<pre class="lines">
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<td>
<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 9</span>
<span class='kw'>def</span> <span class='id identifier rubyid_extra_seq'>extra_seq</span>
<span class='ivar'>@extra_seq</span>
<span class='kw'>end</span></pre>
</td>
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</table>
</div>
<span id=""></span>
<div class="method_details ">
<h3 class="signature " id="gaps-instance_method">
- (<tt>Object</tt>) <strong>gaps</strong> <span class="extras">(readonly)</span>
</h3><div class="docstring">
<div class="discussion">
<p>Returns the value of attribute gaps</p>
</div>
</div>
<div class="tags">
</div><table class="source_code">
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<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 8</span>
<span class='kw'>def</span> <span class='id identifier rubyid_gaps'>gaps</span>
<span class='ivar'>@gaps</span>
<span class='kw'>end</span></pre>
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</div>
<span id=""></span>
<div class="method_details ">
<h3 class="signature " id="threahsold-instance_method">
- (<tt>Object</tt>) <strong>threahsold</strong> <span class="extras">(readonly)</span>
</h3><div class="docstring">
<div class="discussion">
<p>Returns the value of attribute threahsold</p>
</div>
</div>
<div class="tags">
</div><table class="source_code">
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<pre class="lines">
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<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 11</span>
<span class='kw'>def</span> <span class='id identifier rubyid_threahsold'>threahsold</span>
<span class='ivar'>@threahsold</span>
<span class='kw'>end</span></pre>
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</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="print-instance_method">
- (<tt>Object</tt>) <strong>print</strong>
</h3><table class="source_code">
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<pre class="lines">
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<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 23</span>
<span class='kw'>def</span> <span class='id identifier rubyid_print'>print</span>
<span class='tstring'><span class='tstring_beg'>"</span><span class='embexpr_beg'>#{</span><span class='lparen'>(</span><span class='id identifier rubyid_gaps'>gaps</span><span class='op'>*</span><span class='int'>100</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='rbrace'>}</span><span class='tstring_content'>% missing, </span><span class='embexpr_beg'>#{</span><span class='lparen'>(</span><span class='id identifier rubyid_extra_seq'>extra_seq</span><span class='op'>*</span><span class='int'>100</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='rbrace'>}</span><span class='tstring_content'>% extra, </span><span class='embexpr_beg'>#{</span><span class='lparen'>(</span><span class='id identifier rubyid_consensus'>consensus</span><span class='op'>*</span><span class='int'>100</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='rbrace'>}</span><span class='tstring_content'>% conserved</span><span class='tstring_end'>"</span></span>
<span class='kw'>end</span></pre>
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<div class="method_details ">
<h3 class="signature " id="validation-instance_method">
- (<tt>Object</tt>) <strong>validation</strong>
</h3><table class="source_code">
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<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 27</span>
<span class='kw'>def</span> <span class='id identifier rubyid_validation'>validation</span>
<span class='kw'>if</span> <span class='id identifier rubyid_gaps'>gaps</span> <span class='op'><</span> <span class='ivar'>@threshold</span> <span class='kw'>and</span> <span class='id identifier rubyid_extra_seq'>extra_seq</span> <span class='op'><</span> <span class='ivar'>@threshold</span> <span class='comment'>#and consensus < @threshold
</span> <span class='symbol'>:yes</span>
<span class='kw'>else</span>
<span class='symbol'>:no</span>
<span class='kw'>end</span>
<span class='kw'>end</span></pre>
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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).
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