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

genevalidator 1.6.1 → 1.6.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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
-49
-50
-51
-52
-53
-54
-55
-56
-57
-58
-59
-60
-61
-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
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-    </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
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-    </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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-    </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>