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

data/doc/AlignmentValidation.html DELETED

@@ -1,1687 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: AlignmentValidation
-    &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">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '';
-  framesUrl = "frames.html#!" + escape(window.location.href);
-</script>
-  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="_index.html">Index (A)</a> &raquo;
-    <span class="title">AlignmentValidation</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: AlignmentValidation
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName"><span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next"><span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></li>
-            <li class="next">AlignmentValidation</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>This class contains the methods necessary for validations based on multiple
-alignment</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="#filename-instance_method" title="#filename (instance method)">- (Object) <strong>filename</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</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="#index_file_name-instance_method" title="#index_file_name (instance method)">- (Object) <strong>index_file_name</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute index_file_name.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#mafft_path-instance_method" title="#mafft_path (instance method)">- (Object) <strong>mafft_path</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute mafft_path.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#multiple_alignment-instance_method" title="#multiple_alignment (instance method)">- (Object) <strong>multiple_alignment</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute multiple_alignment.</p>
-</div></span>
-</li>
-  </ul>
-  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="ValidationTest.html" title="ValidationTest (class)">ValidationTest</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="ValidationTest.html#cli_name-instance_method" title="ValidationTest#cli_name (method)">#cli_name</a></span>, <span class='object_link'><a href="ValidationTest.html#description-instance_method" title="ValidationTest#description (method)">#description</a></span>, <span class='object_link'><a href="ValidationTest.html#header-instance_method" title="ValidationTest#header (method)">#header</a></span>, <span class='object_link'><a href="ValidationTest.html#hits-instance_method" title="ValidationTest#hits (method)">#hits</a></span>, <span class='object_link'><a href="ValidationTest.html#prediction-instance_method" title="ValidationTest#prediction (method)">#prediction</a></span>, <span class='object_link'><a href="ValidationTest.html#running_time-instance_method" title="ValidationTest#running_time (method)">#running_time</a></span>, <span class='object_link'><a href="ValidationTest.html#short_header-instance_method" title="ValidationTest#short_header (method)">#short_header</a></span>, <span class='object_link'><a href="ValidationTest.html#type-instance_method" title="ValidationTest#type (method)">#type</a></span>, <span class='object_link'><a href="ValidationTest.html#validation_report-instance_method" title="ValidationTest#validation_report (method)">#validation_report</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="#consensus_validation-instance_method" title="#consensus_validation (instance method)">- (Object) <strong>consensus_validation</strong>(prediction_raw, consensus) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the percentage of consesnsus residues from the ma that are in the
-prediction  Params: <tt>prediction</tt>: <tt>String</tt> corresponding to
-the prediction sequence <tt>consensus</tt>: <tt>String</tt> corresponding
-to the statistical model Output: <tt>Fixnum</tt> with the score.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#extra_sequence_validation-instance_method" title="#extra_sequence_validation (instance method)">- (Object) <strong>extra_sequence_validation</strong>(prediction_raw, sm) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the percentage of extra sequences in the prediction  with respect
-to the statistical model Params: <tt>prediction</tt>: <tt>String</tt>
-corresponding to the prediction sequence <tt>sm</tt>: <tt>String</tt>
-corresponding to the statistical model Output: <tt>Fixnum</tt> with the
-score.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#gap_validation-instance_method" title="#gap_validation (instance method)">- (Object) <strong>gap_validation</strong>(prediction_raw, sm) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the percentage of gaps in the prediction  with respect to the
-statistical model Params: <tt>prediction</tt>: <tt>String</tt>
-corresponding to the prediction sequence <tt>sm</tt>: <tt>String</tt>
-corresponding to the statistical model Output: <tt>Fixnum</tt> with the
-score.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#get_consensus-instance_method" title="#get_consensus (instance method)">- (Object) <strong>get_consensus</strong>(ma = @multiple_alignment) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the consensus regions among  a set of multiple aligned sequences
-i.e positions where there is the same  element in all sequences Params:
-<tt>ma</tt>: array of <tt>String</tt>s, corresponding to the multiple aligned
-sequences Output: <tt>String</tt> with the consensus regions.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#get_sm_pssm-instance_method" title="#get_sm_pssm (instance method)">- (Object) <strong>get_sm_pssm</strong>(ma = @multiple_alignment, threshold = 0.7) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Builds a statistical model from  a set of multiple aligned sequences based
-on PSSM (Position Specific Matrix) Params: <tt>ma</tt>: array of <tt>String</tt>s,
-corresponding to the multiple aligned sequences <tt>threshold</tt>: the
-percentage of the genes that will be considered in the statistical model
-Output: <tt>String</tt> representing the statistical model.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (AlignmentValidation) <strong>initialize</strong>(type, prediction, hits, filename, mafft_path, index_file_name) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>A new instance of AlignmentValidation.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#isalpha-instance_method" title="#isalpha (instance method)">- (Object) <strong>isalpha</strong>(str) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns true if the string contains only letters and false otherwise.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#multiple_align_mafft-instance_method" title="#multiple_align_mafft (instance method)">- (Object) <strong>multiple_align_mafft</strong>(prediction = @prediction, hits = @hits, path = @mafft_path) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Builds the multiple alignment between  all the hits and the prediction
-using MAFFT tool Also creates a fasta file with the alignment Params:
-<tt>prediction</tt>: a <tt>Sequence</tt> object representing the blast
-query <tt>hits</tt>: a vector of <tt>Sequience</tt> objects (usually
-representig the blast hits) <tt>path</tt>: path of mafft installation
-Output: Array of <tt>String</tt>s, corresponding to the multiple aligned
-sequences.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#plot_alignment-instance_method" title="#plot_alignment (instance method)">- (Object) <strong>plot_alignment</strong>(output = &quot;#{@filename}_ma.json&quot;, ma = @multiple_alignment, prediction = @prediction, sm) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Generates a json file cotaining data used for plotting lines for multiple
-hits alignment, prediction and statistical model Params: <tt>output</tt>:
-filneme of the json file <tt>ma</tt>: <tt>String</tt> array with the
-multiple alignmened hits and prediction <tt>prediction</tt>:
-<tt>Sequence</tt> object <tt>sm</tt>: <tt>String</tt> with the statistical
-model.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#remove_isolated_residues-instance_method" title="#remove_isolated_residues (instance method)">- (Object) <strong>remove_isolated_residues</strong>(seq, len = 2) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Remove isolated residues inside long gaps  from a given sequence Params:
-<tt>seq</tt>:<tt>String</tt>: sequence of residues
-<tt>len</tt>:<tt>Fixnum</tt>: number of isolated residues to be removed
-Output: <tt>String</tt>: the new sequence.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#run-instance_method" title="#run (instance method)">- (Object) <strong>run</strong>(n = 10) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Find gaps/extra regions based on the multiple alignment  of the first n
-hits Output: <tt>AlignmentValidationOutput</tt> object.</p>
-</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="AlignmentValidation (class)">AlignmentValidation</a></span></tt>) <strong>initialize</strong>(type, prediction, hits, filename, mafft_path, index_file_name)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns a new instance of AlignmentValidation</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-47
-48
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-62</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 47</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_type'>type</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span><span class='comma'>,</span> <span class='id identifier rubyid_filename'>filename</span><span class='comma'>,</span> <span class='id identifier rubyid_mafft_path'>mafft_path</span><span class='comma'>,</span> <span class='id identifier rubyid_index_file_name'>index_file_name</span><span class='rparen'>)</span>
-  <span class='kw'>super</span>
-  <span class='ivar'>@filename</span>        <span class='op'>=</span> <span class='id identifier rubyid_filename'>filename</span>
-  <span class='ivar'>@mafft_path</span>      <span class='op'>=</span> <span class='id identifier rubyid_mafft_path'>mafft_path</span>
-  <span class='ivar'>@index_file_name</span> <span class='op'>=</span> <span class='id identifier rubyid_index_file_name'>index_file_name</span>
-  <span class='ivar'>@short_header</span>    <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>MA</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@header</span>          <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Missing/Extra sequences</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@description</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Finds missing and extra sequences in the prediction, based</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> on the multiple alignment of the best hits. Also counts the percentahe of</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> the conserved regions that appear in the prediction. Meaning of the output:</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> the percentages of the missing/extra sequences with respect to the multiple</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> alignment. Validation fails if one of these values is higher than 20%.</span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-  <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'> Percentage of the conserved residues.</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@multiple_alignment</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-  <span class='ivar'>@cli_name</span>           <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>align</span><span class='tstring_end'>&quot;</span></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=""></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="filename-instance_method">
-    - (<tt>Object</tt>) <strong>filename</strong>  <span class="extras">(readonly)</span>
-</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">
-42
-43
-44</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 42</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=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="index_file_name-instance_method">
-    - (<tt>Object</tt>) <strong>index_file_name</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute index_file_name</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-45
-46
-47</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 45</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_index_file_name'>index_file_name</span>
-  <span class='ivar'>@index_file_name</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="mafft_path-instance_method">
-    - (<tt>Object</tt>) <strong>mafft_path</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute mafft_path</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-44
-45
-46</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 44</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_mafft_path'>mafft_path</span>
-  <span class='ivar'>@mafft_path</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="multiple_alignment-instance_method">
-    - (<tt>Object</tt>) <strong>multiple_alignment</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute multiple_alignment</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-43
-44
-45</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 43</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_multiple_alignment'>multiple_alignment</span>
-  <span class='ivar'>@multiple_alignment</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="consensus_validation-instance_method">
-    - (<tt>Object</tt>) <strong>consensus_validation</strong>(prediction_raw, consensus)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the percentage of consesnsus residues from the ma that are in the
-prediction  Params: <tt>prediction</tt>: <tt>String</tt> corresponding to
-the prediction sequence <tt>consensus</tt>: <tt>String</tt> corresponding
-to the statistical model Output: <tt>Fixnum</tt> with the score</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_alignment.rb', line 253</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_consensus_validation'>consensus_validation</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='comma'>,</span> <span class='id identifier rubyid_consensus'>consensus</span><span class='rparen'>)</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>!=</span> <span class='id identifier rubyid_consensus'>consensus</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-    <span class='kw'>return</span> <span class='int'>1</span>
-  <span class='kw'>end</span>
-  <span class='comment'># find consnsus that are in the ma
-</span>  <span class='comment'># but not in the prediction
-</span>  <span class='id identifier rubyid_no_conserved_pred'>no_conserved_pred</span> <span class='op'>=</span> <span class='int'>0</span>
-  <span class='id identifier rubyid_no_conserved_residues'>no_conserved_residues</span> <span class='op'>=</span> <span class='int'>0</span>
-  <span class='lparen'>(</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_consensus'>consensus</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</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_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_consensus'>consensus</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>!=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span>
-      <span class='id identifier rubyid_no_conserved_residues'>no_conserved_residues</span> <span class='op'>+=</span> <span class='int'>1</span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_consensus'>consensus</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>!=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span> <span class='kw'>and</span> <span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>==</span> <span class='id identifier rubyid_consensus'>consensus</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span>
-      <span class='id identifier rubyid_no_conserved_pred'>no_conserved_pred</span>  <span class='op'>+=</span> <span class='int'>1</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='kw'>return</span> <span class='id identifier rubyid_no_conserved_pred'>no_conserved_pred</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_no_conserved_residues'>no_conserved_residues</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="extra_sequence_validation-instance_method">
-    - (<tt>Object</tt>) <strong>extra_sequence_validation</strong>(prediction_raw, sm)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the percentage of extra sequences in the prediction  with respect
-to the statistical model Params: <tt>prediction</tt>: <tt>String</tt>
-corresponding to the prediction sequence <tt>sm</tt>: <tt>String</tt>
-corresponding to the statistical model Output: <tt>Fixnum</tt> with the
-score</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_alignment.rb', line 229</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_extra_sequence_validation'>extra_sequence_validation</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='comma'>,</span> <span class='id identifier rubyid_sm'>sm</span><span class='rparen'>)</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>!=</span> <span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-    <span class='kw'>return</span> <span class='int'>1</span>
-  <span class='kw'>end</span>
-  <span class='comment'># find residues that are in the prediction
-</span>  <span class='comment'># but not in the statistical model
-</span>  <span class='id identifier rubyid_no_insertions'>no_insertions</span> <span class='op'>=</span> <span class='int'>0</span>
-  <span class='lparen'>(</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</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_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>!=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span> <span class='kw'>and</span>  <span class='id identifier rubyid_sm'>sm</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>==</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span>
-      <span class='id identifier rubyid_no_insertions'>no_insertions</span> <span class='op'>+=</span> <span class='int'>1</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_no_insertions'>no_insertions</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>+</span><span class='float'>0.0</span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="gap_validation-instance_method">
-    - (<tt>Object</tt>) <strong>gap_validation</strong>(prediction_raw, sm)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the percentage of gaps in the prediction  with respect to the
-statistical model Params: <tt>prediction</tt>: <tt>String</tt>
-corresponding to the prediction sequence <tt>sm</tt>: <tt>String</tt>
-corresponding to the statistical model Output: <tt>Fixnum</tt> with the
-score</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-219</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 206</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_gap_validation'>gap_validation</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='comma'>,</span> <span class='id identifier rubyid_sm'>sm</span><span class='rparen'>)</span>
-  <span class='comment'># find gaps in the prediction and
-</span>  <span class='comment'># not in the statistical model
-</span>  <span class='kw'>if</span> <span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>!=</span> <span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-    <span class='kw'>return</span> <span class='int'>1</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_no_gaps'>no_gaps</span> <span class='op'>=</span> <span class='int'>0</span>
-  <span class='lparen'>(</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</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_i'>i</span><span class='op'>|</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span> <span class='kw'>and</span>  <span class='id identifier rubyid_sm'>sm</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='op'>!=</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span>
-      <span class='id identifier rubyid_no_gaps'>no_gaps</span> <span class='op'>+=</span> <span class='int'>1</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_no_gaps'>no_gaps</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>+</span><span class='float'>0.0</span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="get_consensus-instance_method">
-    - (<tt>Object</tt>) <strong>get_consensus</strong>(ma = @multiple_alignment)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the consensus regions among  a set of multiple aligned sequences
-i.e positions where there is the same  element in all sequences Params:
-<tt>ma</tt>: array of <tt>String</tt>s, corresponding to the multiple aligned
-sequences Output: <tt>String</tt> with the consensus regions</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-194
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 193</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_get_consensus'>get_consensus</span><span class='lparen'>(</span><span class='id identifier rubyid_ma'>ma</span> <span class='op'>=</span> <span class='ivar'>@multiple_alignment</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_align'>align</span> <span class='op'>=</span> <span class='const'>Bio</span><span class='op'>::</span><span class='const'>Alignment</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_ma'>ma</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_consensus'>consensus</span> <span class='op'>=</span> <span class='id identifier rubyid_align'>align</span><span class='period'>.</span><span class='id identifier rubyid_consensus'>consensus</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="get_sm_pssm-instance_method">
-    - (<tt>Object</tt>) <strong>get_sm_pssm</strong>(ma = @multiple_alignment, threshold = 0.7)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Builds a statistical model from  a set of multiple aligned sequences based
-on PSSM (Position Specific Matrix) Params: <tt>ma</tt>: array of <tt>String</tt>s,
-corresponding to the multiple aligned sequences <tt>threshold</tt>: the
-percentage of the genes that will be considered in the statistical model
-Output: <tt>String</tt> representing the statistical model</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_alignment.rb', line 281</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_get_sm_pssm'>get_sm_pssm</span><span class='lparen'>(</span><span class='id identifier rubyid_ma'>ma</span> <span class='op'>=</span> <span class='ivar'>@multiple_alignment</span><span class='comma'>,</span> <span class='id identifier rubyid_threshold'>threshold</span> <span class='op'>=</span> <span class='float'>0.7</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_sm'>sm</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span>
-  <span class='lparen'>(</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_ma'>ma</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</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_i'>i</span><span class='op'>|</span>
-    <span class='id identifier rubyid_freqs'>freqs</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='int'>0</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_ma'>ma</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_seq'>seq</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_i'>i</span><span class='rbracket'>]</span><span class='rbrace'>}</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_res'>res</span><span class='op'>|</span> <span class='id identifier rubyid_freqs'>freqs</span><span class='lbracket'>[</span><span class='id identifier rubyid_res'>res</span><span class='rbracket'>]</span> <span class='op'>+=</span> <span class='int'>1</span><span class='rbrace'>}</span>
-    <span class='comment'># get the residue with the highest frequency
-</span>    <span class='id identifier rubyid_max_freq'>max_freq</span> <span class='op'>=</span> <span class='id identifier rubyid_freqs'>freqs</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_res'>res</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='id identifier rubyid_n'>n</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_max_freq'>max_freq</span><span class='op'>/</span><span class='lparen'>(</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>+</span><span class='float'>0.0</span><span class='rparen'>)</span> <span class='op'>&gt;=</span> <span class='id identifier rubyid_threshold'>threshold</span>
-      <span class='id identifier rubyid_residue'>residue</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_freqs'>freqs</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_res'>res</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='id identifier rubyid_n'>n</span> <span class='op'>==</span> <span class='id identifier rubyid_max_freq'>max_freq</span> <span class='op'>?</span> <span class='id identifier rubyid_res'>res</span> <span class='op'>:</span> <span class='lbracket'>[</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span>
-      <span class='id identifier rubyid_sm'>sm</span> <span class='op'>&lt;&lt;</span> <span class='id identifier rubyid_residue'>residue</span>
-    <span class='kw'>else</span>
-      <span class='id identifier rubyid_sm'>sm</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='kw'>end</span>
-  <span class='id identifier rubyid_sm'>sm</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="isalpha-instance_method">
-    - (<tt>Object</tt>) <strong>isalpha</strong>(str)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns true if the string contains only letters and false otherwise</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_alignment.rb', line 333</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_isalpha'>isalpha</span><span class='lparen'>(</span><span class='id identifier rubyid_str'>str</span><span class='rparen'>)</span>
-  <span class='op'>!</span><span class='id identifier rubyid_str'>str</span><span class='period'>.</span><span class='id identifier rubyid_match'>match</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>[^A-Za-z]</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="multiple_align_mafft-instance_method">
-    - (<tt>Object</tt>) <strong>multiple_align_mafft</strong>(prediction = @prediction, hits = @hits, path = @mafft_path)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Builds the multiple alignment between  all the hits and the prediction
-using MAFFT tool Also creates a fasta file with the alignment Params:
-<tt>prediction</tt>: a <tt>Sequence</tt> object representing the blast
-query <tt>hits</tt>: a vector of <tt>Sequience</tt> objects (usually
-representig the blast hits) <tt>path</tt>: path of mafft installation
-Output: Array of <tt>String</tt>s, corresponding to the multiple aligned sequences</p>
-  </div>
-</div>
-<div class="tags">
-<p class="tag_title">Raises:</p>
-<ul class="raise">
-    <li>
-        <span class='type'>(<tt>Exception</tt>)</span>
-    </li>
-</ul>
-</div><table class="source_code">
-  <tr>
-    <td>
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/validation_alignment.rb', line 159</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_multiple_align_mafft'>multiple_align_mafft</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='ivar'>@hits</span><span class='comma'>,</span> <span class='id identifier rubyid_path'>path</span> <span class='op'>=</span> <span class='ivar'>@mafft_path</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_raise'>raise</span> <span class='const'>Exception</span> <span class='kw'>unless</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span> <span class='kw'>and</span> <span class='id identifier rubyid_hits'>hits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span>
-    <span class='id identifier rubyid_options'>options</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>--maxiterate</span><span class='tstring_end'>'</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>1000</span><span class='tstring_end'>'</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>--localpair</span><span class='tstring_end'>'</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>--quiet</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span>
-    <span class='id identifier rubyid_mafft'>mafft</span> <span class='op'>=</span> <span class='const'>Bio</span><span class='op'>::</span><span class='const'>MAFFT</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_path'>path</span><span class='comma'>,</span> <span class='id identifier rubyid_options'>options</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_sequences'>sequences</span> <span class='op'>=</span> <span class='id identifier rubyid_hits'>hits</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_hit'>hit</span><span class='op'>|</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='rbrace'>}</span>
-    <span class='id identifier rubyid_sequences'>sequences</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_report'>report</span> <span class='op'>=</span> <span class='id identifier rubyid_mafft'>mafft</span><span class='period'>.</span><span class='id identifier rubyid_query_align'>query_align</span><span class='lparen'>(</span><span class='id identifier rubyid_sequences'>sequences</span><span class='rparen'>)</span>
-    <span class='comment'># Accesses the actual alignment.
-</span>    <span class='id identifier rubyid_align'>align</span> <span class='op'>=</span> <span class='id identifier rubyid_report'>report</span><span class='period'>.</span><span class='id identifier rubyid_alignment'>alignment</span>
-    <span class='comment'># Prints each sequence to a file.
-</span>    <span class='id identifier rubyid_f'>f</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='embexpr_beg'>#{</span><span class='ivar'>@filename</span><span class='rbrace'>}</span><span class='tstring_content'>_ma.fasta</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'>w</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_align'>align</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_s'>s</span><span class='comma'>,</span><span class='id identifier rubyid_i'>i</span><span class='op'>|</span>
-       <span class='ivar'>@multiple_alignment</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_s'>s</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='rparen'>)</span>
-       <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>&gt;seq</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_i'>i</span><span class='rbrace'>}</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-       <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='id identifier rubyid_s'>s</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='rparen'>)</span>
-       <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</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='rparen'>)</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
-    <span class='kw'>return</span> <span class='ivar'>@multiple_alignment</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="plot_alignment-instance_method">
-    - (<tt>Object</tt>) <strong>plot_alignment</strong>(output = &quot;#{@filename}_ma.json&quot;, ma = @multiple_alignment, prediction = @prediction, sm)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Generates a json file cotaining data used for plotting lines for multiple
-hits alignment, prediction and statistical model Params: <tt>output</tt>:
-filneme of the json file <tt>ma</tt>: <tt>String</tt> array with the
-multiple alignmened hits and prediction <tt>prediction</tt>:
-<tt>Sequence</tt> object <tt>sm</tt>: <tt>String</tt> with the statistical
-model</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_alignment.rb', line 344</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_plot_alignment'>plot_alignment</span> <span class='lparen'>(</span><span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='ivar'>@filename</span><span class='rbrace'>}</span><span class='tstring_content'>_ma.json</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='id identifier rubyid_ma'>ma</span> <span class='op'>=</span> <span class='ivar'>@multiple_alignment</span><span class='comma'>,</span> <span class='id identifier rubyid_prediction'>prediction</span> <span class='op'>=</span> <span class='ivar'>@prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_sm'>sm</span><span class='rparen'>)</span>
-    <span class='comment'># get indeces of consensus in the multiple alignment
-</span>    <span class='id identifier rubyid_consensus'>consensus</span> <span class='op'>=</span> <span class='id identifier rubyid_get_consensus'>get_consensus</span><span class='lparen'>(</span><span class='ivar'>@multiple_alignment</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='ivar'>@multiple_alignment</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_consensus_idxs'>consensus_idxs</span> <span class='op'>=</span> <span class='id identifier rubyid_consensus'>consensus</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_index'>each_index</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_j'>j</span><span class='op'>|</span> <span class='id identifier rubyid_isalpha'>isalpha</span><span class='lparen'>(</span><span class='id identifier rubyid_consensus'>consensus</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span>
-    <span class='id identifier rubyid_len'>len</span> <span class='op'>=</span> <span class='id identifier rubyid_ma'>ma</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
-    <span class='id identifier rubyid_f'>f</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='id identifier rubyid_output'>output</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='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_write'>write</span><span class='lparen'>(</span><span class='lparen'>(</span><span class='id identifier rubyid_ma'>ma</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_seq'>seq</span><span class='comma'>,</span> <span class='id identifier rubyid_j'>j</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='id identifier rubyid_j'>j</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_len'>len</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>red</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span> <span class='op'>+</span>
-    <span class='id identifier rubyid_ma'>ma</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_seq'>seq</span><span class='comma'>,</span> <span class='id identifier rubyid_j'>j</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_index'>each_index</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_j'>j</span><span class='op'>|</span> <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span><span class='rbrace'>}</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_gap'>gap</span><span class='op'>|</span> <span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='id identifier rubyid_j'>j</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_gap'>gap</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_gap'>gap</span><span class='op'>+</span><span class='int'>1</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>black</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span> <span class='op'>+</span>
-    <span class='id identifier rubyid_ma'>ma</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_each_with_index'>each_with_index</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_seq'>seq</span><span class='comma'>,</span> <span class='id identifier rubyid_j'>j</span><span class='op'>|</span> <span class='id identifier rubyid_consensus_idxs'>consensus_idxs</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_con'>con</span><span class='op'>|</span><span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='id identifier rubyid_j'>j</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_con'>con</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_con'>con</span><span class='op'>+</span><span class='int'>1</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>yellow</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span> <span class='op'>+</span>
-    <span class='comment'>#plot prediction
-</span>    <span class='lbracket'>[</span><span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>1</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_len'>len</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>green</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbracket'>]</span> <span class='op'>+</span>
-    <span class='id identifier rubyid_ma'>ma</span><span class='lbracket'>[</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_index'>each_index</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_j'>j</span><span class='op'>|</span> <span class='id identifier rubyid_ma'>ma</span><span class='lbracket'>[</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span><span class='rbrace'>}</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_gap'>gap</span><span class='op'>|</span><span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>1</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_gap'>gap</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_gap'>gap</span><span class='op'>+</span><span class='int'>1</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>black</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span> <span class='op'>+</span>
-    <span class='comment'>#plot statistical model
-</span>    <span class='lbracket'>[</span><span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_len'>len</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>red</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbracket'>]</span> <span class='op'>+</span>
-    <span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_index'>each_index</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_j'>j</span><span class='op'>|</span> <span class='id identifier rubyid_isalpha'>isalpha</span><span class='lparen'>(</span><span class='id identifier rubyid_sm'>sm</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</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_con'>con</span><span class='op'>|</span><span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_con'>con</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_con'>con</span><span class='op'>+</span><span class='int'>1</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>orange</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span> <span class='op'>+</span>
-    <span class='id identifier rubyid_sm'>sm</span><span class='period'>.</span><span class='id identifier rubyid_split'>split</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_index'>each_index</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_j'>j</span><span class='op'>|</span> <span class='id identifier rubyid_sm'>sm</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span><span class='rbrace'>}</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_gap'>gap</span><span class='op'>|</span><span class='lbrace'>{</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>y</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='int'>0</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>start</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_gap'>gap</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>stop</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='id identifier rubyid_gap'>gap</span><span class='op'>+</span><span class='int'>1</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>color</span><span class='tstring_end'>&quot;</span></span><span class='op'>=&gt;</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>black</span><span class='tstring_end'>&quot;</span></span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_to_json'>to_json</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_f'>f</span><span class='period'>.</span><span class='id identifier rubyid_close'>close</span>
-    <span class='id identifier rubyid_yAxisValues'>yAxisValues</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sm, pred</span><span class='tstring_end'>&quot;</span></span>
-    <span class='lparen'>(</span><span class='int'>1</span><span class='op'>..</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</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_i'>i</span><span class='op'>|</span>
-       <span class='id identifier rubyid_yAxisValues'>yAxisValues</span> <span class='op'>&lt;&lt;</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>, hit</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>-</span> <span class='id identifier rubyid_i'>i</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='const'>Plot</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_output'>output</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='comma'>,</span>
-                              <span class='symbol'>:lines</span><span class='comma'>,</span>
-                              <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Multiple alignment and Statistical model of blast hits</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'>gaps, black;consensus, yellow;mismatches, red;prediction, green;statistical model,orange</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'>alignment length</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'>idx</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span>
-                              <span class='id identifier rubyid_ma'>ma</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>+</span><span class='int'>1</span><span class='comma'>,</span>
-                              <span class='id identifier rubyid_yAxisValues'>yAxisValues</span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="remove_isolated_residues-instance_method">
-    - (<tt>Object</tt>) <strong>remove_isolated_residues</strong>(seq, len = 2)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Remove isolated residues inside long gaps  from a given sequence Params:
-<tt>seq</tt>:<tt>String</tt>: sequence of residues
-<tt>len</tt>:<tt>Fixnum</tt>: number of isolated residues to be removed
-Output: <tt>String</tt>: the new sequence</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_alignment.rb', line 306</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_remove_isolated_residues'>remove_isolated_residues</span><span class='lparen'>(</span><span class='id identifier rubyid_seq'>seq</span><span class='comma'>,</span> <span class='id identifier rubyid_len'>len</span> <span class='op'>=</span> <span class='int'>2</span><span class='rparen'>)</span>
-  <span class='comment'>#puts seq
-</span>  <span class='id identifier rubyid_gap_starts'>gap_starts</span> <span class='op'>=</span> <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_to_enum'>to_enum</span><span class='lparen'>(</span><span class='symbol'>:scan</span><span class='comma'>,</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>(-\w{1,</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_len'>len</span><span class='rbrace'>}</span><span class='tstring_content'>}-)</span><span class='regexp_end'>/i</span></span><span class='rparen'>)</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_m'>m</span><span class='op'>|</span> <span class='backref'>$`</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span> <span class='op'>+</span> <span class='int'>1</span><span class='rbrace'>}</span>
-  <span class='comment'>#puts gap_starts.to_s
-</span>  <span class='comment'># remove isolated residues
-</span>  <span class='id identifier rubyid_gap_starts'>gap_starts</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_i'>i</span><span class='op'>|</span>
-    <span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span><span class='op'>..</span><span class='id identifier rubyid_i'>i</span><span class='op'>+</span><span class='id identifier rubyid_len'>len</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</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_j'>j</span><span class='op'>|</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_isalpha'>isalpha</span><span class='lparen'>(</span><span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-        <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='comment'>#remove isolated gaps
-</span>  <span class='id identifier rubyid_res_starts'>res_starts</span> <span class='op'>=</span> <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_to_enum'>to_enum</span><span class='lparen'>(</span><span class='symbol'>:scan</span><span class='comma'>,</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>([?\w]-{1,2}[?\w])</span><span class='regexp_end'>/i</span></span><span class='rparen'>)</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_m'>m</span><span class='op'>|</span> <span class='backref'>$`</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span> <span class='op'>+</span> <span class='int'>1</span><span class='rbrace'>}</span>
-  <span class='id identifier rubyid_res_starts'>res_starts</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_i'>i</span><span class='op'>|</span>
-    <span class='lparen'>(</span><span class='id identifier rubyid_i'>i</span><span class='op'>..</span><span class='id identifier rubyid_i'>i</span><span class='op'>+</span><span class='id identifier rubyid_len'>len</span><span class='op'>-</span><span class='int'>1</span><span class='rparen'>)</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_j'>j</span><span class='op'>|</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>-</span><span class='tstring_end'>'</span></span>
-        <span class='id identifier rubyid_seq'>seq</span><span class='lbracket'>[</span><span class='id identifier rubyid_j'>j</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>?</span><span class='tstring_end'>'</span></span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_seq'>seq</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="run-instance_method">
-    - (<tt>Object</tt>) <strong>run</strong>(n = 10)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Find gaps/extra regions based on the multiple alignment  of the first n
-hits Output: <tt>AlignmentValidationOutput</tt> object</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_alignment.rb', line 69</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_run'>run</span><span class='lparen'>(</span><span class='id identifier rubyid_n'>n</span><span class='op'>=</span><span class='int'>10</span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_n'>n</span> <span class='op'>&gt;</span> <span class='int'>50</span>
-      <span class='id identifier rubyid_n'>n</span> <span class='op'>=</span> <span class='int'>50</span>
-    <span class='kw'>end</span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_type'>type</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span> <span class='op'>!=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>protein</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:unapplicable</span><span class='rparen'>)</span>
-      <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NotEnoughHitsError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&gt;=</span> <span class='id identifier rubyid_n'>n</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>Exception</span> <span class='kw'>unless</span> <span class='id identifier rubyid_prediction'>prediction</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span> <span class='kw'>and</span> <span class='id identifier rubyid_hits'>hits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Sequence</span>
-    <span class='id identifier rubyid_start'>start</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='comment'># get the first n hits
-</span>    <span class='id identifier rubyid_less_hits'>less_hits</span> <span class='op'>=</span> <span class='ivar'>@hits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='lbracket'>[</span><span class='id identifier rubyid_n'>n</span><span class='op'>-</span><span class='int'>1</span><span class='comma'>,</span><span class='ivar'>@hits</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_useless_hits'>useless_hits</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-    <span class='kw'>begin</span>
-      <span class='comment'># get raw sequences for less_hits
-</span>      <span class='id identifier rubyid_less_hits'>less_hits</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_hit'>hit</span><span class='op'>|</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</span> <span class='op'>==</span> <span class='kw'>nil</span>
-          <span class='comment'>#get gene by accession number
-</span>          <span class='kw'>if</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_type'>type</span> <span class='op'>==</span> <span class='symbol'>:protein</span>
-            <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_get_sequence_by_accession_no'>get_sequence_by_accession_no</span><span class='lparen'>(</span><span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_accession_no'>accession_no</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>protein</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-          <span class='kw'>else</span>
-            <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_get_sequence_by_accession_no'>get_sequence_by_accession_no</span><span class='lparen'>(</span><span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_accession_no'>accession_no</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nucleotide</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-          <span class='kw'>end</span>
-          <span class='kw'>if</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_raw_sequence'>raw_sequence</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_useless_hits'>useless_hits</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_hit'>hit</span><span class='rparen'>)</span>
-          <span class='kw'>end</span>
-        <span class='kw'>end</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_useless_hits'>useless_hits</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_hit'>hit</span><span class='op'>|</span> <span class='id identifier rubyid_less_hits'>less_hits</span><span class='period'>.</span><span class='id identifier rubyid_delete'>delete</span><span class='lparen'>(</span><span class='id identifier rubyid_hit'>hit</span><span class='rparen'>)</span><span class='rbrace'>}</span>
-    <span class='kw'>begin</span>
-      <span class='comment'># multiple align sequences from  less_hits with the prediction
-</span>      <span class='id identifier rubyid_multiple_align_mafft'>multiple_align_mafft</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction'>prediction</span><span class='comma'>,</span> <span class='id identifier rubyid_less_hits'>less_hits</span><span class='rparen'>)</span>
-    <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-      <span class='id identifier rubyid_raise'>raise</span> <span class='const'>NoInternetError</span>
-    <span class='kw'>end</span>
-    <span class='id identifier rubyid_sm'>sm</span>  <span class='op'>=</span> <span class='id identifier rubyid_get_sm_pssm'>get_sm_pssm</span><span class='lparen'>(</span><span class='ivar'>@multiple_alignment</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='ivar'>@multiple_alignment</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-    <span class='comment'># remove isolated residues from the predicted sequence
-</span>    <span class='id identifier rubyid_prediction_raw'>prediction_raw</span> <span class='op'>=</span> <span class='id identifier rubyid_remove_isolated_residues'>remove_isolated_residues</span><span class='lparen'>(</span><span class='ivar'>@multiple_alignment</span><span class='lbracket'>[</span><span class='ivar'>@multiple_alignment</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>1</span><span class='rbracket'>]</span><span class='rparen'>)</span>
-    <span class='comment'># remove isolated residues from the statistical model
-</span>    <span class='id identifier rubyid_sm'>sm</span> <span class='op'>=</span> <span class='id identifier rubyid_remove_isolated_residues'>remove_isolated_residues</span><span class='lparen'>(</span><span class='id identifier rubyid_sm'>sm</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_plot1'>plot1</span>     <span class='op'>=</span> <span class='id identifier rubyid_plot_alignment'>plot_alignment</span><span class='lparen'>(</span><span class='id identifier rubyid_sm'>sm</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_gaps'>gaps</span>      <span class='op'>=</span> <span class='id identifier rubyid_gap_validation'>gap_validation</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='comma'>,</span> <span class='id identifier rubyid_sm'>sm</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_extra_seq'>extra_seq</span> <span class='op'>=</span> <span class='id identifier rubyid_extra_sequence_validation'>extra_sequence_validation</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='comma'>,</span> <span class='id identifier rubyid_sm'>sm</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_consensus'>consensus</span> <span class='op'>=</span> <span class='id identifier rubyid_consensus_validation'>consensus_validation</span><span class='lparen'>(</span><span class='id identifier rubyid_prediction_raw'>prediction_raw</span><span class='comma'>,</span> <span class='id identifier rubyid_get_consensus'>get_consensus</span><span class='lparen'>(</span><span class='ivar'>@multiple_alignment</span><span class='lbracket'>[</span><span class='int'>0</span><span class='op'>..</span><span class='ivar'>@multiple_alignment</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='op'>-</span><span class='int'>2</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rparen'>)</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>AlignmentValidationOutput</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_gaps'>gaps</span><span class='comma'>,</span> <span class='id identifier rubyid_extra_seq'>extra_seq</span><span class='comma'>,</span> <span class='id identifier rubyid_consensus'>consensus</span><span class='rparen'>)</span>
-    <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_plot_files'>plot_files</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_plot1'>plot1</span><span class='rparen'>)</span>
-    <span class='ivar'>@running_time</span> <span class='op'>=</span> <span class='const'>Time</span><span class='period'>.</span><span class='id identifier rubyid_now'>now</span> <span class='op'>-</span> <span class='id identifier rubyid_start'>start</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='comment'># Exception is raised when blast founds no hits
-</span>  <span class='kw'>rescue</span>  <span class='const'>NotEnoughHitsError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</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='symbol'>:warning</span><span class='rparen'>)</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='kw'>rescue</span> <span class='const'>NoMafftInstallationError</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Mafft error</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:error</span><span class='rparen'>)</span>
-    <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>NoMafftInstallationError</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='kw'>rescue</span> <span class='const'>NoInternetError</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Internet error</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:error</span><span class='rparen'>)</span>
-    <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>NoInternetError</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</span>
-  <span class='kw'>rescue</span> <span class='const'>Exception</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unexpected Error</span><span class='tstring_end'>&quot;</span></span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>ValidationReport</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unexpected error</span><span class='tstring_end'>&quot;</span></span><span class='comma'>,</span> <span class='symbol'>:error</span><span class='rparen'>)</span>
-    <span class='ivar'>@validation_report</span><span class='period'>.</span><span class='id identifier rubyid_errors'>errors</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span> <span class='const'>OtherError</span>
-    <span class='kw'>return</span> <span class='ivar'>@validation_report</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 07:01:33 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>