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/Hsp.html DELETED

@@ -1,1485 +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: Hsp
-    &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 (H)</a> &raquo;
-    <span class="title">Hsp</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: Hsp
-</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">Hsp</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/genevalidator/hsp.rb</dd>
-</dl>
-<div class="clear"></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="#align_len-instance_method" title="#align_len (instance method)">- (Object) <strong>align_len</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute align_len.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#bit_score-instance_method" title="#bit_score (instance method)">- (Object) <strong>bit_score</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>positive (mis)matches with +, mismatches and gaps are with space.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#gaps-instance_method" title="#gaps (instance method)">- (Object) <strong>gaps</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute gaps.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#hit_alignment-instance_method" title="#hit_alignment (instance method)">- (Object) <strong>hit_alignment</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute hit_alignment.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#hit_from-instance_method" title="#hit_from (instance method)">- (Object) <strong>hit_from</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>references from the unaligned hit sequence.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#hit_to-instance_method" title="#hit_to (instance method)">- (Object) <strong>hit_to</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute hit_to.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#hsp_evalue-instance_method" title="#hsp_evalue (instance method)">- (Object) <strong>hsp_evalue</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute hsp_evalue.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#hsp_score-instance_method" title="#hsp_score (instance method)">- (Object) <strong>hsp_score</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute hsp_score.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#identity-instance_method" title="#identity (instance method)">- (Object) <strong>identity</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>number of conserved residues.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#match_query_from-instance_method" title="#match_query_from (instance method)">- (Object) <strong>match_query_from</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>references from the unaligned query sequence.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#match_query_to-instance_method" title="#match_query_to (instance method)">- (Object) <strong>match_query_to</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute match_query_to.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#middles-instance_method" title="#middles (instance method)">- (Object) <strong>middles</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>conserved residues are with letters,.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#pidentity-instance_method" title="#pidentity (instance method)">- (Object) <strong>pidentity</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>percentage of identical matches.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#positive-instance_method" title="#positive (instance method)">- (Object) <strong>positive</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>positive score for the (mis)match.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#query_alignment-instance_method" title="#query_alignment (instance method)">- (Object) <strong>query_alignment</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute query_alignment.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#query_reading_frame-instance_method" title="#query_reading_frame (instance method)">- (Object) <strong>query_reading_frame</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute query_reading_frame.</p>
-</div></span>
-</li>
-  </ul>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#init_tabular_attribute-instance_method" title="#init_tabular_attribute (instance method)">- (Object) <strong>init_tabular_attribute</strong>(column, value, type = :protein) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Initializes the corresponding attribute of the hsp with respect to the
-column name of the tabular blast output Params: <tt>column</tt>: String
-with column name <tt>value</tt>: Value of the column <tt>type</tt>: type of
-the sequences: :nucleotide or :protein.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (Hsp) <strong>initialize</strong> </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>A new instance of Hsp.</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="Hsp (class)">Hsp</a></span></tt>) <strong>initialize</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns a new instance of Hsp</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-25
-26
-27
-28</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 25</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span>
-  <span class='id identifier rubyid_query_alignment'>query_alignment</span> <span class='op'>=</span> <span class='kw'>nil</span>
-  <span class='id identifier rubyid_hit_alignment'>hit_alignment</span> <span class='op'>=</span> <span class='kw'>nil</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="align_len=-instance_method"></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="align_len-instance_method">
-    - (<tt>Object</tt>) <strong>align_len</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute align_len</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-23
-24
-25</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 23</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_align_len'>align_len</span>
-  <span class='ivar'>@align_len</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="bit_score=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="bit_score-instance_method">
-    - (<tt>Object</tt>) <strong>bit_score</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>positive (mis)matches with +, mismatches and gaps are with space</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-16
-17
-18</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 16</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_bit_score'>bit_score</span>
-  <span class='ivar'>@bit_score</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="gaps=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="gaps-instance_method">
-    - (<tt>Object</tt>) <strong>gaps</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute gaps</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-22
-23
-24</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 22</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_gaps'>gaps</span>
-  <span class='ivar'>@gaps</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="hit_alignment=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="hit_alignment-instance_method">
-    - (<tt>Object</tt>) <strong>hit_alignment</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute hit_alignment</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-11
-12
-13</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 11</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_hit_alignment'>hit_alignment</span>
-  <span class='ivar'>@hit_alignment</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="hit_from=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="hit_from-instance_method">
-    - (<tt>Object</tt>) <strong>hit_from</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>references from the unaligned hit sequence</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-6
-7
-8</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 6</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_hit_from'>hit_from</span>
-  <span class='ivar'>@hit_from</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="hit_to=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="hit_to-instance_method">
-    - (<tt>Object</tt>) <strong>hit_to</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute hit_to</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-7
-8
-9</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 7</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_hit_to'>hit_to</span>
-  <span class='ivar'>@hit_to</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="hsp_evalue=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="hsp_evalue-instance_method">
-    - (<tt>Object</tt>) <strong>hsp_evalue</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute hsp_evalue</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-18
-19
-20</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 18</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_hsp_evalue'>hsp_evalue</span>
-  <span class='ivar'>@hsp_evalue</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="hsp_score=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="hsp_score-instance_method">
-    - (<tt>Object</tt>) <strong>hsp_score</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute hsp_score</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-17
-18
-19</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 17</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_hsp_score'>hsp_score</span>
-  <span class='ivar'>@hsp_score</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="identity=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="identity-instance_method">
-    - (<tt>Object</tt>) <strong>identity</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>number of conserved residues</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-19
-20
-21</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 19</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_identity'>identity</span>
-  <span class='ivar'>@identity</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="match_query_from=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="match_query_from-instance_method">
-    - (<tt>Object</tt>) <strong>match_query_from</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>references from the unaligned query sequence</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-8
-9
-10</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 8</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_match_query_from'>match_query_from</span>
-  <span class='ivar'>@match_query_from</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="match_query_to=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="match_query_to-instance_method">
-    - (<tt>Object</tt>) <strong>match_query_to</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute match_query_to</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-9
-10
-11</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 9</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_match_query_to'>match_query_to</span>
-  <span class='ivar'>@match_query_to</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="middles=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="middles-instance_method">
-    - (<tt>Object</tt>) <strong>middles</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>conserved residues are with letters,</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-13
-14
-15</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 13</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_middles'>middles</span>
-  <span class='ivar'>@middles</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="pidentity=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="pidentity-instance_method">
-    - (<tt>Object</tt>) <strong>pidentity</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>percentage of identical matches</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-20
-21
-22</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 20</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_pidentity'>pidentity</span>
-  <span class='ivar'>@pidentity</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="positive=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="positive-instance_method">
-    - (<tt>Object</tt>) <strong>positive</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>positive score for the (mis)match</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-21
-22
-23</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 21</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_positive'>positive</span>
-  <span class='ivar'>@positive</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="query_alignment=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="query_alignment-instance_method">
-    - (<tt>Object</tt>) <strong>query_alignment</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute query_alignment</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-12
-13
-14</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 12</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_query_alignment'>query_alignment</span>
-  <span class='ivar'>@query_alignment</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="query_reading_frame=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="query_reading_frame-instance_method">
-    - (<tt>Object</tt>) <strong>query_reading_frame</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute query_reading_frame</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-10
-11
-12</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 10</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_query_reading_frame'>query_reading_frame</span>
-  <span class='ivar'>@query_reading_frame</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="init_tabular_attribute-instance_method">
-    - (<tt>Object</tt>) <strong>init_tabular_attribute</strong>(column, value, type = :protein)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Initializes the corresponding attribute of the hsp with respect to the
-column name of the tabular blast output Params: <tt>column</tt>: String
-with column name <tt>value</tt>: Value of the column <tt>type</tt>: type of
-the sequences: :nucleotide or :protein</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-37
-38
-39
-40
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-42
-43
-44
-45
-46
-47
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-49
-50
-51
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-53
-54
-55
-56
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-61
-62
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-64
-65
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-67
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-69
-70
-71
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-75
-76</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/genevalidator/hsp.rb', line 37</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_init_tabular_attribute'>init_tabular_attribute</span><span class='lparen'>(</span><span class='id identifier rubyid_column'>column</span><span class='comma'>,</span> <span class='id identifier rubyid_value'>value</span><span class='comma'>,</span> <span class='id identifier rubyid_type'>type</span><span class='op'>=</span><span class='symbol'>:protein</span><span class='rparen'>)</span>
-  <span class='kw'>case</span> <span class='id identifier rubyid_column'>column</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>qstart</span><span class='tstring_end'>&quot;</span></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='ivar'>@match_query_from</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</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'>else</span>
-        <span class='ivar'>@match_query_from</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-      <span class='kw'>end</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>qend</span><span class='tstring_end'>&quot;</span></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='ivar'>@match_query_to</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</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'>else</span>
-        <span class='ivar'>@match_query_to</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-      <span class='kw'>end</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>qframe</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@query_reading_frame</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sstart</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@hit_from</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>send</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@hit_to</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>qseq</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@query_alignment</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span>
-      <span class='id identifier rubyid_seq_type'>seq_type</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_value'>value</span><span class='rparen'>)</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_seq_type'>seq_type</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_seq_type'>seq_type</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='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>sseq</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@hit_alignment</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span>
-      <span class='id identifier rubyid_seq_type'>seq_type</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_value'>value</span><span class='rparen'>)</span>
-      <span class='kw'>if</span> <span class='id identifier rubyid_seq_type'>seq_type</span> <span class='op'>!=</span> <span class='kw'>nil</span> <span class='kw'>and</span> <span class='id identifier rubyid_seq_type'>seq_type</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='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>length</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@align_len</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_i'>to_i</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>pident</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@pidentity</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</span>
-    <span class='kw'>when</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>evalue</span><span class='tstring_end'>&quot;</span></span>
-      <span class='ivar'>@hsp_evalue</span> <span class='op'>=</span> <span class='id identifier rubyid_value'>value</span><span class='period'>.</span><span class='id identifier rubyid_to_f'>to_f</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>