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/BlastReadingFrameValidation.html DELETED

@@ -1,370 +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: BlastReadingFrameValidation
-    &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 (B)</a> &raquo;
-    <span class="title">BlastReadingFrameValidation</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: BlastReadingFrameValidation
-</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">BlastReadingFrameValidation</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/validation_blast_reading_frame.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<p>This class contains the methods necessary for  reading frame validation
-based on BLAST output</p>
-  </div>
-</div>
-<div class="tags">
-</div>
-  <h2>Instance Attribute Summary</h2>
-  <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="#initialize-instance_method" title="#initialize (instance method)">- (BlastReadingFrameValidation) <strong>initialize</strong>(type, prediction, hits = nil) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>A new instance of BlastReadingFrameValidation.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#run-instance_method" title="#run (instance method)">- (Object) <strong>run</strong>(lst = @hits) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Check reading frame inconsistency Params: <tt>lst</tt>: vector of
-<tt>Sequence</tt> objects Output: <tt>BlastRFValidationOutput</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="BlastReadingFrameValidation (class)">BlastReadingFrameValidation</a></span></tt>) <strong>initialize</strong>(type, prediction, hits = nil)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns a new instance of BlastReadingFrameValidation</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_blast_reading_frame.rb', line 53</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='op'>=</span> <span class='kw'>nil</span><span class='rparen'>)</span>
-  <span class='kw'>super</span>
-  <span class='ivar'>@short_header</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Frame</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'>Reading Frame</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'>Check whether there is a single reading frame among BLAST</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'> hits. Otherwise there might be a reading frame shift in the query sequence.</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'> Meaning of the output displayed: (reading frame: no hsps)</span><span class='tstring_end'>&quot;</span></span>
-  <span class='ivar'>@cli_name</span>     <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>frame</span><span class='tstring_end'>&quot;</span></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="run-instance_method">
-    - (<tt>Object</tt>) <strong>run</strong>(lst = @hits)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Check reading frame inconsistency Params: <tt>lst</tt>: vector of
-<tt>Sequence</tt> objects Output: <tt>BlastRFValidationOutput</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_blast_reading_frame.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_lst'>lst</span> <span class='op'>=</span> <span class='ivar'>@hits</span><span class='rparen'>)</span>
-  <span class='kw'>begin</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'>nucleotide</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='int'>5</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_now'>now</span>
-    <span class='id identifier rubyid_rfs'>rfs</span> <span class='op'>=</span>  <span class='id identifier rubyid_lst'>lst</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_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</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_y'>y</span><span class='op'>|</span> <span class='id identifier rubyid_y'>y</span><span class='period'>.</span><span class='id identifier rubyid_query_reading_frame'>query_reading_frame</span><span class='rbrace'>}</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-    <span class='id identifier rubyid_frames_histo'>frames_histo</span> <span class='op'>=</span> <span class='const'>Hash</span><span class='lbracket'>[</span><span class='id identifier rubyid_rfs'>rfs</span><span class='period'>.</span><span class='id identifier rubyid_group_by'>group_by</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span> <span class='id identifier rubyid_x'>x</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_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_vs'>vs</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_vs'>vs</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span> <span class='rbrace'>}</span><span class='rbracket'>]</span>
-    <span class='comment'># get the main reading frame
-</span>    <span class='id identifier rubyid_main_rf'>main_rf</span> <span class='op'>=</span> <span class='id identifier rubyid_frames_histo'>frames_histo</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_k'>k</span><span class='comma'>,</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span>
-    <span class='ivar'>@prediction</span><span class='period'>.</span><span class='id identifier rubyid_nucleotide_rf'>nucleotide_rf</span> <span class='op'>=</span> <span class='id identifier rubyid_frames_histo'>frames_histo</span><span class='period'>.</span><span class='id identifier rubyid_select'>select</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span><span class='id identifier rubyid_v'>v</span><span class='op'>|</span> <span class='id identifier rubyid_v'>v</span><span class='op'>==</span><span class='id identifier rubyid_main_rf'>main_rf</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span>
-    <span class='ivar'>@validation_report</span> <span class='op'>=</span> <span class='const'>BlastRFValidationOutput</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_frames_histo'>frames_histo</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'>Exception</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'>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='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>

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-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: BlastUtils
-    &mdash; Documentation by YARD 0.8.7.2
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-      <div id="menu">
-    <a href="_index.html">Index (B)</a> &raquo;
-    <span class="title">BlastUtils</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>
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-        href="method_list.html">
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-        href="file_list.html">
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-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: BlastUtils
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName">Object</span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next">BlastUtils</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/blast.rb</dd>
-</dl>
-<div class="clear"></div>
-    <h2>
-      Class Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#call_blast_from_file-class_method" title="call_blast_from_file (class method)">+ (Object) <strong>call_blast_from_file</strong>(command, filename, gapopen, gapextend, db = &quot;nr -remote&quot;) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Calls blast from file with specific parameters Param: <tt>command</tt>:
-blast command in String format (e.g 'blastx' or 'blastp')
-<tt>filename</tt>: name of the FAST file <tt>query</tt>: <tt>String</tt>
-containing the the query in fasta format <tt>gapopen</tt>: gapopen blast
-parameter <tt>gapextend</tt>: gapextend blast parameter <tt>db</tt>:
-database Output: String with the blast xml output.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#call_blast_from_stdin-class_method" title="call_blast_from_stdin (class method)">+ (Object) <strong>call_blast_from_stdin</strong>(command, query, gapopen, gapextend, db = &quot;nr -remote&quot;) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Calls blast from standard input with specific parameters Params:
-<tt>command</tt>: blast command in String format (e.g 'blastx' or 'blastp')
-<tt>query</tt>: String containing the the query in fasta format
-<tt>gapopen</tt>: gapopen blast parameter <tt>gapextend</tt>: gapextend
-blast parameter <tt>db</tt>: database Output: String with the blast xml
-output.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#composition-class_method" title="composition (class method)">+ (Object) <strong>composition</strong>(sequence_string) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Method copied from sequenceserver/sequencehelpers.rb Params:
-sequence_string: String of which we mfind the composition Output: a Hash.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#guess_sequence_type-class_method" title="guess_sequence_type (class method)">+ (Object) <strong>guess_sequence_type</strong>(sequence_string) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Method copied from sequenceserver/sequencehelpers.rb Strips all non-letter
-characters.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#parse_next_query_xml-class_method" title="parse_next_query_xml (class method)">+ (Object) <strong>parse_next_query_xml</strong>(iterator, type) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Parses the next query from the blast xml output query Params:
-<tt>iterator</tt>: blast xml iterator for hits <tt>type</tt>: the type of
-the sequence: :nucleotide or :protein Outputs: Array of <tt>Sequence</tt>
-ojbects for hits.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#type_of_sequences-class_method" title="type_of_sequences (class method)">+ (Object) <strong>type_of_sequences</strong>(fasta_format_string) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Method copied from sequenceserver/sequencehelpers.rb Splits input at
-putative fasta definition lines (like "&gt;adsfadsf"), guesses sequence
-type for each sequence.</p>
-</div></span>
-</li>
-    </ul>
-  <div id="class_method_details" class="method_details_list">
-    <h2>Class Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="call_blast_from_file-class_method">
-    + (<tt>Object</tt>) <strong>call_blast_from_file</strong>(command, filename, gapopen, gapextend, db = &quot;nr -remote&quot;)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Calls blast from file with specific parameters Param: <tt>command</tt>:
-blast command in String format (e.g 'blastx' or 'blastp')
-<tt>filename</tt>: name of the FAST file <tt>query</tt>: <tt>String</tt>
-containing the the query in fasta format <tt>gapopen</tt>: gapopen blast
-parameter <tt>gapextend</tt>: gapextend blast parameter <tt>db</tt>:
-database Output: String with the blast xml output</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/blast.rb', line 66</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_call_blast_from_file'>call_blast_from_file</span><span class='lparen'>(</span><span class='id identifier rubyid_command'>command</span><span class='comma'>,</span> <span class='id identifier rubyid_filename'>filename</span><span class='comma'>,</span> <span class='id identifier rubyid_gapopen'>gapopen</span><span class='comma'>,</span> <span class='id identifier rubyid_gapextend'>gapextend</span><span class='comma'>,</span> <span class='id identifier rubyid_db'>db</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nr -remote</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>TypeError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_command'>command</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span> <span class='kw'>and</span> <span class='id identifier rubyid_filename'>filename</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span>
-    <span class='id identifier rubyid_evalue'>evalue</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>1e-5</span><span class='tstring_end'>&quot;</span></span>
-    <span class='comment'>#output = 5 (XML Blast output)
-</span>    <span class='id identifier rubyid_cmd'>cmd</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_command'>command</span><span class='rbrace'>}</span><span class='tstring_content'> -query </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_filename'>filename</span><span class='rbrace'>}</span><span class='tstring_content'> -db </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_content'> -evalue </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_evalue'>evalue</span><span class='rbrace'>}</span><span class='tstring_content'> -outfmt 5 -gapopen </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapopen'>gapopen</span><span class='rbrace'>}</span><span class='tstring_content'> -gapextend </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapextend'>gapextend</span><span class='rbrace'>}</span><span class='tstring_content'> </span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Executing \&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rbrace'>}</span><span class='tstring_content'>\&quot;...</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>This may take a while...</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_output'>output</span> <span class='op'>=</span> <span class='backtick'>%x[</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rbrace'>}</span><span class='tstring_content'>          if xml_file == nil
-          file = File.open(xml_file, &quot;rb&quot;).read
-          b.parse_xml_output(file)
-        end 2&gt;/dev/null</span><span class='tstring_end'>]</span></span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_output'>output</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
-      <span class='id identifier rubyid_raise'>raise</span> <span class='const'>ClasspathError</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_output'>output</span>
-  <span class='kw'>rescue</span> <span class='const'>TypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: one of the arguments of 'call_blast_from_file' method has not the proper type\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>rescue</span> <span class='const'>ClasspathError</span> <span class='op'>=&gt;</span><span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>BLAST error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</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'>\/([^\/]+:\d+):.*</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='rbrace'>}</span><span class='tstring_content'>. </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'>Did you add BLAST path to LOADPATH?\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="call_blast_from_stdin-class_method">
-    + (<tt>Object</tt>) <strong>call_blast_from_stdin</strong>(command, query, gapopen, gapextend, db = &quot;nr -remote&quot;)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Calls blast from standard input with specific parameters Params:
-<tt>command</tt>: blast command in String format (e.g 'blastx' or 'blastp')
-<tt>query</tt>: String containing the the query in fasta format
-<tt>gapopen</tt>: gapopen blast parameter <tt>gapextend</tt>: gapextend
-blast parameter <tt>db</tt>: database Output: String with the blast xml
-output</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/blast.rb', line 26</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_call_blast_from_stdin'>call_blast_from_stdin</span><span class='lparen'>(</span><span class='id identifier rubyid_command'>command</span><span class='comma'>,</span> <span class='id identifier rubyid_query'>query</span><span class='comma'>,</span> <span class='id identifier rubyid_gapopen'>gapopen</span><span class='comma'>,</span> <span class='id identifier rubyid_gapextend'>gapextend</span><span class='comma'>,</span> <span class='id identifier rubyid_db'>db</span><span class='op'>=</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>nr -remote</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>TypeError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_command'>command</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span> <span class='kw'>and</span> <span class='id identifier rubyid_query'>query</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>String</span>
-    <span class='id identifier rubyid_evalue'>evalue</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>1e-5</span><span class='tstring_end'>&quot;</span></span>
-    <span class='comment'>#output format = 5 (XML Blast output)
-</span>    <span class='id identifier rubyid_blast_cmd'>blast_cmd</span> <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_command'>command</span><span class='rbrace'>}</span><span class='tstring_content'> -db </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_db'>db</span><span class='rbrace'>}</span><span class='tstring_content'> -evalue </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_evalue'>evalue</span><span class='rbrace'>}</span><span class='tstring_content'> -outfmt 5 -gapopen </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapopen'>gapopen</span><span class='rbrace'>}</span><span class='tstring_content'> -gapextend </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_gapextend'>gapextend</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_cmd'>cmd</span>       <span class='op'>=</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>echo \&quot;</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_query'>query</span><span class='rbrace'>}</span><span class='tstring_content'>\&quot; | </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_blast_cmd'>blast_cmd</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_output'>output</span>    <span class='op'>=</span> <span class='backtick'>%x[</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_cmd'>cmd</span><span class='rbrace'>}</span><span class='tstring_content'> 2&gt;/dev/null</span><span class='tstring_end'>]</span></span>
-    <span class='kw'>if</span> <span class='id identifier rubyid_output'>output</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_raise'>raise</span> <span class='const'>ClasspathError</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_output'>output</span>
-  <span class='kw'>rescue</span> <span class='const'>TypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: one of the arguments of 'call_blast_from_file' method has not the proper type\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>rescue</span> <span class='const'>ClasspathError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>BLAST error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</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'>\/([^\/]+:\d+):.*</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='rbrace'>}</span><span class='tstring_content'>. </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'>Possible cause: BLAST installation path is not in the LOAD PATH.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit'>exit</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="composition-class_method">
-    + (<tt>Object</tt>) <strong>composition</strong>(sequence_string)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Method copied from sequenceserver/sequencehelpers.rb Params:
-sequence_string: String of which we mfind the composition Output: a Hash</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/blast.rb', line 185</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_composition'>composition</span><span class='lparen'>(</span><span class='id identifier rubyid_sequence_string'>sequence_string</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_count'>count</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_sequence_string'>sequence_string</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='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_x'>x</span><span class='op'>|</span>
-    <span class='id identifier rubyid_count'>count</span><span class='lbracket'>[</span><span class='id identifier rubyid_x'>x</span><span class='rbracket'>]</span> <span class='op'>+=</span> <span class='int'>1</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_count'>count</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="guess_sequence_type-class_method">
-    + (<tt>Object</tt>) <strong>guess_sequence_type</strong>(sequence_string)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Method copied from sequenceserver/sequencehelpers.rb Strips all non-letter
-characters. guestimates sequence based on that. If less than 10 useable
-characters... returns nil If more than 90% ACGTU returns :nucleotide. else
-returns :protein Params: <tt>sequence_string</tt>: String to validate
-Output: nil, :nucleotide or :protein</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/blast.rb', line 202</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_sequence_string'>sequence_string</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span> <span class='op'>=</span> <span class='id identifier rubyid_sequence_string'>sequence_string</span><span class='period'>.</span><span class='id identifier rubyid_gsub'>gsub</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>[^A-Z]</span><span class='regexp_end'>/i</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='comment'># removing non-letter characters
-</span>  <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span><span class='period'>.</span><span class='id identifier rubyid_gsub!'>gsub!</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>[NX]</span><span class='regexp_end'>/i</span></span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_end'>'</span></span><span class='rparen'>)</span> <span class='comment'># removing ambiguous characters
-</span>
-  <span class='kw'>return</span> <span class='kw'>nil</span> <span class='kw'>if</span> <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>&lt;</span> <span class='int'>10</span> <span class='comment'># conservative
-</span>
-  <span class='id identifier rubyid_composition'>composition</span> <span class='op'>=</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_composition'>composition</span><span class='lparen'>(</span><span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_composition_NAs'>composition_NAs</span> <span class='op'>=</span> <span class='id identifier rubyid_composition'>composition</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_character'>character</span><span class='comma'>,</span> <span class='id identifier rubyid_count'>count</span><span class='op'>|</span><span class='id identifier rubyid_character'>character</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'>[ACGTU]</span><span class='regexp_end'>/i</span></span><span class='rparen'>)</span> <span class='rbrace'>}</span> <span class='comment'># only putative NAs
-</span>  <span class='id identifier rubyid_putative_NA_counts'>putative_NA_counts</span> <span class='op'>=</span> <span class='id identifier rubyid_composition_NAs'>composition_NAs</span><span class='period'>.</span><span class='id identifier rubyid_collect'>collect</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_key_value_array'>key_value_array</span><span class='op'>|</span> <span class='id identifier rubyid_key_value_array'>key_value_array</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='rbrace'>}</span> <span class='comment'># only count, not char
-</span>  <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span> <span class='op'>=</span> <span class='id identifier rubyid_putative_NA_counts'>putative_NA_counts</span><span class='period'>.</span><span class='id identifier rubyid_inject'>inject</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_sum'>sum</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='id identifier rubyid_sum'>sum</span> <span class='op'>+</span> <span class='id identifier rubyid_n'>n</span> <span class='rbrace'>}</span> <span class='comment'># count of all putative NA
-</span>  <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span> <span class='op'>=</span> <span class='int'>0</span> <span class='kw'>if</span> <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_putative_NA_sum'>putative_NA_sum</span> <span class='op'>&gt;</span> <span class='lparen'>(</span><span class='float'>0.9</span> <span class='op'>*</span> <span class='id identifier rubyid_cleaned_sequence'>cleaned_sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rparen'>)</span>
-    <span class='kw'>return</span> <span class='symbol'>:nucleotide</span>
-  <span class='kw'>else</span>
-    <span class='kw'>return</span> <span class='symbol'>:protein</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="parse_next_query_xml-class_method">
-    + (<tt>Object</tt>) <strong>parse_next_query_xml</strong>(iterator, type)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Parses the next query from the blast xml output query Params:
-<tt>iterator</tt>: blast xml iterator for hits <tt>type</tt>: the type of
-the sequence: :nucleotide or :protein Outputs: Array of <tt>Sequence</tt>
-ojbects for hits</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/blast.rb', line 105</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_parse_next_query_xml'>parse_next_query_xml</span><span class='lparen'>(</span><span class='id identifier rubyid_iterator'>iterator</span><span class='comma'>,</span> <span class='id identifier rubyid_type'>type</span><span class='rparen'>)</span>
-  <span class='kw'>begin</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>TypeError</span> <span class='kw'>unless</span> <span class='id identifier rubyid_iterator'>iterator</span><span class='period'>.</span><span class='id identifier rubyid_is_a?'>is_a?</span> <span class='const'>Enumerator</span>
-    <span class='id identifier rubyid_hits'>hits</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='id identifier rubyid_predicted_seq'>predicted_seq</span> <span class='op'>=</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-    <span class='id identifier rubyid_iter'>iter</span> <span class='op'>=</span> <span class='id identifier rubyid_iterator'>iterator</span><span class='period'>.</span><span class='id identifier rubyid_next'>next</span>
-    <span class='comment'># parse blast the xml output and get the hits
-</span>    <span class='comment'># hits obtained are proteins! (we use only blastp and blastx)
-</span>    <span class='id identifier rubyid_iter'>iter</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_hit'>hit</span> <span class='op'>|</span>
-      <span class='id identifier rubyid_seq'>seq</span> <span class='op'>=</span> <span class='const'>Sequence</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_length_protein'>length_protein</span> <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_len'>len</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-      <span class='id identifier rubyid_seq'>seq</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_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_identifier'>identifier</span>     <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hit_id'>hit_id</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_definition'>definition</span>     <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hit_def'>hit_def</span>
-      <span class='comment'>#puts seq.identifier
-</span>      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_accession_no'>accession_no</span> <span class='op'>=</span> <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_accession'>accession</span>
-      <span class='comment'># get all high-scoring segment pairs (hsp)
-</span>      <span class='id identifier rubyid_hsps'>hsps</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
-      <span class='id identifier rubyid_hit'>hit</span><span class='period'>.</span><span class='id identifier rubyid_hsps'>hsps</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_hsp'>hsp</span><span class='op'>|</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span>            <span class='op'>=</span> <span class='const'>Hsp</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hsp_evalue'>hsp_evalue</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_evalue'>evalue</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_from'>hit_from</span>         <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_from'>hit_from</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_to'>hit_to</span>           <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_to'>hit_to</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_from'>query_from</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span>   <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_to'>query_to</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='kw'>if</span> <span class='id identifier rubyid_type'>type</span> <span class='op'>==</span> <span class='symbol'>:nucleotide</span>
-          <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span> <span class='op'>=</span>  <span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_from'>match_query_from</span> <span class='op'>/</span> <span class='int'>3</span><span class='rparen'>)</span> <span class='op'>+</span> <span class='int'>1</span>
-          <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span>   <span class='op'>=</span>  <span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_match_query_to'>match_query_to</span> <span class='op'>/</span> <span class='int'>3</span><span class='rparen'>)</span> <span class='op'>+</span> <span class='int'>1</span>
-        <span class='kw'>end</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_reading_frame'>query_reading_frame</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_frame'>query_frame</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_alignment'>hit_alignment</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_hseq'>hseq</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span>
-        <span class='kw'>if</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_hit_alignment'>hit_alignment</span><span class='rparen'>)</span> <span class='op'>!=</span> <span class='symbol'>:protein</span>
-          <span class='id identifier rubyid_raise'>raise</span> <span class='const'>SequenceTypeError</span>
-        <span class='kw'>end</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_alignment'>query_alignment</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_qseq'>qseq</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span>
-        <span class='kw'>if</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_query_alignment'>query_alignment</span><span class='rparen'>)</span> <span class='op'>!=</span> <span class='symbol'>:protein</span>
-          <span class='id identifier rubyid_raise'>raise</span> <span class='const'>SequenceTypeError</span>
-        <span class='kw'>end</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_align_len'>align_len</span> <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_align_len'>align_len</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_identity'>identity</span>  <span class='op'>=</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_identity'>identity</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-        <span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='period'>.</span><span class='id identifier rubyid_pidentity'>pidentity</span> <span class='op'>=</span> <span class='int'>100</span> <span class='op'>*</span> <span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_identity'>identity</span> <span class='op'>/</span> <span class='lparen'>(</span><span class='id identifier rubyid_hsp'>hsp</span><span class='period'>.</span><span class='id identifier rubyid_align_len'>align_len</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
-        <span class='id identifier rubyid_hsps'>hsps</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_current_hsp'>current_hsp</span><span class='rparen'>)</span>
-      <span class='kw'>end</span>
-      <span class='id identifier rubyid_seq'>seq</span><span class='period'>.</span><span class='id identifier rubyid_hsp_list'>hsp_list</span> <span class='op'>=</span> <span class='id identifier rubyid_hsps'>hsps</span>
-      <span class='id identifier rubyid_hits'>hits</span><span class='period'>.</span><span class='id identifier rubyid_push'>push</span><span class='lparen'>(</span><span class='id identifier rubyid_seq'>seq</span><span class='rparen'>)</span>
-    <span class='kw'>end</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_hits'>hits</span>
-  <span class='kw'>rescue</span> <span class='const'>TypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_scan'>scan</span><span class='lparen'>(</span><span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>\/([^\/]+:\d+):.*</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_content'>. </span><span class='tstring_end'>&quot;</span></span><span class='op'>&lt;&lt;</span>
-      <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Possible cause: you didn't call parse method first!\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>SequenceTypeError</span> <span class='op'>=&gt;</span> <span class='id identifier rubyid_error'>error</span>
-    <span class='gvar'>$stderr</span><span class='period'>.</span><span class='id identifier rubyid_print'>print</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Sequence Type error at </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_error'>error</span><span class='period'>.</span><span class='id identifier rubyid_backtrace'>backtrace</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</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'>\/([^\/]+:\d+):.*</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='rbrace'>}</span><span class='tstring_content'>. </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'>Possible cause: the blast output was not obtained against a protein database.\n</span><span class='tstring_end'>&quot;</span></span>
-    <span class='id identifier rubyid_exit!'>exit!</span>
-  <span class='kw'>rescue</span> <span class='const'>StopIteration</span>
-    <span class='kw'>nil</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="type_of_sequences-class_method">
-    + (<tt>Object</tt>) <strong>type_of_sequences</strong>(fasta_format_string)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Method copied from sequenceserver/sequencehelpers.rb Splits input at
-putative fasta definition lines (like "&gt;adsfadsf"), guesses sequence
-type for each sequence. If not enough sequence to determine, returns nil.
-If 2 kinds of sequence mixed together, raises ArgumentError Otherwise,
-returns :nucleotide or :protein Params: <tt>sequence_string</tt>: String to
-validate Output: nil, :nucleotide or :protein</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/blast.rb', line 231</span>
-<span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_type_of_sequences'>type_of_sequences</span><span class='lparen'>(</span><span class='id identifier rubyid_fasta_format_string'>fasta_format_string</span><span class='rparen'>)</span>
-  <span class='comment'># the first sequence does not need to have a fasta definition line
-</span>  <span class='id identifier rubyid_sequences'>sequences</span> <span class='op'>=</span> <span class='id identifier rubyid_fasta_format_string'>fasta_format_string</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='tstring_content'>^&gt;.*$</span><span class='regexp_end'>/</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_delete_if'>delete_if</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='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span> <span class='rbrace'>}</span>
-  <span class='comment'># get all sequence types
-</span>  <span class='id identifier rubyid_sequence_types'>sequence_types</span> <span class='op'>=</span> <span class='id identifier rubyid_sequences'>sequences</span><span class='period'>.</span><span class='id identifier rubyid_collect'>collect</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_seq'>seq</span><span class='op'>|</span> <span class='const'>BlastUtils</span><span class='period'>.</span><span class='id identifier rubyid_guess_sequence_type'>guess_sequence_type</span><span class='lparen'>(</span><span class='id identifier rubyid_seq'>seq</span><span class='rparen'>)</span> <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_uniq'>uniq</span><span class='period'>.</span><span class='id identifier rubyid_compact'>compact</span>
-  <span class='kw'>return</span> <span class='kw'>nil</span> <span class='kw'>if</span> <span class='id identifier rubyid_sequence_types'>sequence_types</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
-  <span class='kw'>if</span> <span class='id identifier rubyid_sequence_types'>sequence_types</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>==</span> <span class='int'>1</span>
-    <span class='kw'>return</span> <span class='id identifier rubyid_sequence_types'>sequence_types</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span> <span class='comment'># there is only one (but yes its an array)
-</span>  <span class='kw'>else</span>
-    <span class='id identifier rubyid_raise'>raise</span> <span class='const'>SequenceTypeError</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Sat Sep 28 07:01:32 2013 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.2 (ruby-1.9.3).
-</div>
-  </body>
-</html>