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.
- 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
|
@@ -1,515 +0,0 @@
|
|
|
1
|
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
2
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
3
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
4
|
-
<head>
|
|
5
|
-
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
6
|
-
<title>
|
|
7
|
-
Class: LengthClusterValidationOutput
|
|
8
|
-
|
|
9
|
-
— Documentation by YARD 0.8.7.2
|
|
10
|
-
|
|
11
|
-
</title>
|
|
12
|
-
|
|
13
|
-
<link rel="stylesheet" href="css/style.css" type="text/css" charset="utf-8" />
|
|
14
|
-
|
|
15
|
-
<link rel="stylesheet" href="css/common.css" type="text/css" charset="utf-8" />
|
|
16
|
-
|
|
17
|
-
<script type="text/javascript" charset="utf-8">
|
|
18
|
-
hasFrames = window.top.frames.main ? true : false;
|
|
19
|
-
relpath = '';
|
|
20
|
-
framesUrl = "frames.html#!" + escape(window.location.href);
|
|
21
|
-
</script>
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
<script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
|
|
25
|
-
|
|
26
|
-
<script type="text/javascript" charset="utf-8" src="js/app.js"></script>
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
</head>
|
|
30
|
-
<body>
|
|
31
|
-
<div id="header">
|
|
32
|
-
<div id="menu">
|
|
33
|
-
|
|
34
|
-
<a href="_index.html">Index (L)</a> »
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
<span class="title">LengthClusterValidationOutput</span>
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
<div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
|
|
41
|
-
</div>
|
|
42
|
-
|
|
43
|
-
<div id="search">
|
|
44
|
-
|
|
45
|
-
<a class="full_list_link" id="class_list_link"
|
|
46
|
-
href="class_list.html">
|
|
47
|
-
Class List
|
|
48
|
-
</a>
|
|
49
|
-
|
|
50
|
-
<a class="full_list_link" id="method_list_link"
|
|
51
|
-
href="method_list.html">
|
|
52
|
-
Method List
|
|
53
|
-
</a>
|
|
54
|
-
|
|
55
|
-
<a class="full_list_link" id="file_list_link"
|
|
56
|
-
href="file_list.html">
|
|
57
|
-
File List
|
|
58
|
-
</a>
|
|
59
|
-
|
|
60
|
-
</div>
|
|
61
|
-
<div class="clear"></div>
|
|
62
|
-
</div>
|
|
63
|
-
|
|
64
|
-
<iframe id="search_frame"></iframe>
|
|
65
|
-
|
|
66
|
-
<div id="content"><h1>Class: LengthClusterValidationOutput
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
</h1>
|
|
71
|
-
|
|
72
|
-
<dl class="box">
|
|
73
|
-
|
|
74
|
-
<dt class="r1">Inherits:</dt>
|
|
75
|
-
<dd class="r1">
|
|
76
|
-
<span class="inheritName"><span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></span>
|
|
77
|
-
|
|
78
|
-
<ul class="fullTree">
|
|
79
|
-
<li>Object</li>
|
|
80
|
-
|
|
81
|
-
<li class="next"><span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></li>
|
|
82
|
-
|
|
83
|
-
<li class="next">LengthClusterValidationOutput</li>
|
|
84
|
-
|
|
85
|
-
</ul>
|
|
86
|
-
<a href="#" class="inheritanceTree">show all</a>
|
|
87
|
-
|
|
88
|
-
</dd>
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
<dt class="r2 last">Defined in:</dt>
|
|
99
|
-
<dd class="r2 last">lib/genevalidator/validation_length_cluster.rb</dd>
|
|
100
|
-
|
|
101
|
-
</dl>
|
|
102
|
-
<div class="clear"></div>
|
|
103
|
-
|
|
104
|
-
<h2>Overview</h2><div class="docstring">
|
|
105
|
-
<div class="discussion">
|
|
106
|
-
|
|
107
|
-
<p>Class that stores the validation output information</p>
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
</div>
|
|
111
|
-
</div>
|
|
112
|
-
<div class="tags">
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
</div>
|
|
116
|
-
|
|
117
|
-
|
|
118
|
-
|
|
119
|
-
<h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
|
|
120
|
-
<ul class="summary">
|
|
121
|
-
|
|
122
|
-
<li class="public ">
|
|
123
|
-
<span class="summary_signature">
|
|
124
|
-
|
|
125
|
-
<a href="#limits-instance_method" title="#limits (instance method)">- (Object) <strong>limits</strong> </a>
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
</span>
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
<span class="note title readonly">readonly</span>
|
|
135
|
-
|
|
136
|
-
|
|
137
|
-
|
|
138
|
-
|
|
139
|
-
|
|
140
|
-
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
|
|
144
|
-
<span class="summary_desc"><div class='inline'>
|
|
145
|
-
<p>Returns the value of attribute limits.</p>
|
|
146
|
-
</div></span>
|
|
147
|
-
|
|
148
|
-
</li>
|
|
149
|
-
|
|
150
|
-
|
|
151
|
-
<li class="public ">
|
|
152
|
-
<span class="summary_signature">
|
|
153
|
-
|
|
154
|
-
<a href="#prediction_len-instance_method" title="#prediction_len (instance method)">- (Object) <strong>prediction_len</strong> </a>
|
|
155
|
-
|
|
156
|
-
|
|
157
|
-
|
|
158
|
-
</span>
|
|
159
|
-
|
|
160
|
-
|
|
161
|
-
|
|
162
|
-
|
|
163
|
-
<span class="note title readonly">readonly</span>
|
|
164
|
-
|
|
165
|
-
|
|
166
|
-
|
|
167
|
-
|
|
168
|
-
|
|
169
|
-
|
|
170
|
-
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
<span class="summary_desc"><div class='inline'>
|
|
174
|
-
<p>Returns the value of attribute prediction_len.</p>
|
|
175
|
-
</div></span>
|
|
176
|
-
|
|
177
|
-
</li>
|
|
178
|
-
|
|
179
|
-
|
|
180
|
-
</ul>
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
|
|
184
|
-
|
|
185
|
-
|
|
186
|
-
<h3 class="inherited">Attributes inherited from <span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></h3>
|
|
187
|
-
<p class="inherited"><span class='object_link'><a href="ValidationReport.html#bg_color-instance_method" title="ValidationReport#bg_color (method)">#bg_color</a></span>, <span class='object_link'><a href="ValidationReport.html#errors-instance_method" title="ValidationReport#errors (method)">#errors</a></span>, <span class='object_link'><a href="ValidationReport.html#expected-instance_method" title="ValidationReport#expected (method)">#expected</a></span>, <span class='object_link'><a href="ValidationReport.html#message-instance_method" title="ValidationReport#message (method)">#message</a></span>, <span class='object_link'><a href="ValidationReport.html#plot_files-instance_method" title="ValidationReport#plot_files (method)">#plot_files</a></span>, <span class='object_link'><a href="ValidationReport.html#result-instance_method" title="ValidationReport#result (method)">#result</a></span>, <span class='object_link'><a href="ValidationReport.html#validation_result-instance_method" title="ValidationReport#validation_result (method)">#validation_result</a></span></p>
|
|
188
|
-
|
|
189
|
-
|
|
190
|
-
|
|
191
|
-
<h2>
|
|
192
|
-
Instance Method Summary
|
|
193
|
-
<small>(<a href="#" class="summary_toggle">collapse</a>)</small>
|
|
194
|
-
</h2>
|
|
195
|
-
|
|
196
|
-
<ul class="summary">
|
|
197
|
-
|
|
198
|
-
<li class="public ">
|
|
199
|
-
<span class="summary_signature">
|
|
200
|
-
|
|
201
|
-
<a href="#initialize-instance_method" title="#initialize (instance method)">- (LengthClusterValidationOutput) <strong>initialize</strong>(prediction_len, limits, expected = :yes) </a>
|
|
202
|
-
|
|
203
|
-
|
|
204
|
-
|
|
205
|
-
</span>
|
|
206
|
-
|
|
207
|
-
|
|
208
|
-
<span class="note title constructor">constructor</span>
|
|
209
|
-
|
|
210
|
-
|
|
211
|
-
|
|
212
|
-
|
|
213
|
-
|
|
214
|
-
|
|
215
|
-
|
|
216
|
-
|
|
217
|
-
<span class="summary_desc"><div class='inline'>
|
|
218
|
-
<p>A new instance of LengthClusterValidationOutput.</p>
|
|
219
|
-
</div></span>
|
|
220
|
-
|
|
221
|
-
</li>
|
|
222
|
-
|
|
223
|
-
|
|
224
|
-
<li class="public ">
|
|
225
|
-
<span class="summary_signature">
|
|
226
|
-
|
|
227
|
-
<a href="#print-instance_method" title="#print (instance method)">- (Object) <strong>print</strong> </a>
|
|
228
|
-
|
|
229
|
-
|
|
230
|
-
|
|
231
|
-
</span>
|
|
232
|
-
|
|
233
|
-
|
|
234
|
-
|
|
235
|
-
|
|
236
|
-
|
|
237
|
-
|
|
238
|
-
|
|
239
|
-
|
|
240
|
-
|
|
241
|
-
<span class="summary_desc"><div class='inline'></div></span>
|
|
242
|
-
|
|
243
|
-
</li>
|
|
244
|
-
|
|
245
|
-
|
|
246
|
-
<li class="public ">
|
|
247
|
-
<span class="summary_signature">
|
|
248
|
-
|
|
249
|
-
<a href="#validation-instance_method" title="#validation (instance method)">- (Object) <strong>validation</strong> </a>
|
|
250
|
-
|
|
251
|
-
|
|
252
|
-
|
|
253
|
-
</span>
|
|
254
|
-
|
|
255
|
-
|
|
256
|
-
|
|
257
|
-
|
|
258
|
-
|
|
259
|
-
|
|
260
|
-
|
|
261
|
-
|
|
262
|
-
|
|
263
|
-
<span class="summary_desc"><div class='inline'></div></span>
|
|
264
|
-
|
|
265
|
-
</li>
|
|
266
|
-
|
|
267
|
-
|
|
268
|
-
</ul>
|
|
269
|
-
|
|
270
|
-
|
|
271
|
-
|
|
272
|
-
|
|
273
|
-
|
|
274
|
-
|
|
275
|
-
|
|
276
|
-
|
|
277
|
-
|
|
278
|
-
|
|
279
|
-
|
|
280
|
-
<h3 class="inherited">Methods inherited from <span class='object_link'><a href="ValidationReport.html" title="ValidationReport (class)">ValidationReport</a></span></h3>
|
|
281
|
-
<p class="inherited"><span class='object_link'><a href="ValidationReport.html#color-instance_method" title="ValidationReport#color (method)">#color</a></span></p>
|
|
282
|
-
<div id="constructor_details" class="method_details_list">
|
|
283
|
-
<h2>Constructor Details</h2>
|
|
284
|
-
|
|
285
|
-
<div class="method_details first">
|
|
286
|
-
<h3 class="signature first" id="initialize-instance_method">
|
|
287
|
-
|
|
288
|
-
- (<tt><span class='object_link'><a href="" title="LengthClusterValidationOutput (class)">LengthClusterValidationOutput</a></span></tt>) <strong>initialize</strong>(prediction_len, limits, expected = :yes)
|
|
289
|
-
|
|
290
|
-
|
|
291
|
-
|
|
292
|
-
|
|
293
|
-
|
|
294
|
-
</h3><div class="docstring">
|
|
295
|
-
<div class="discussion">
|
|
296
|
-
|
|
297
|
-
<p>Returns a new instance of LengthClusterValidationOutput</p>
|
|
298
|
-
|
|
299
|
-
|
|
300
|
-
</div>
|
|
301
|
-
</div>
|
|
302
|
-
<div class="tags">
|
|
303
|
-
|
|
304
|
-
|
|
305
|
-
</div><table class="source_code">
|
|
306
|
-
<tr>
|
|
307
|
-
<td>
|
|
308
|
-
<pre class="lines">
|
|
309
|
-
|
|
310
|
-
|
|
311
|
-
13
|
|
312
|
-
14
|
|
313
|
-
15
|
|
314
|
-
16
|
|
315
|
-
17
|
|
316
|
-
18
|
|
317
|
-
19</pre>
|
|
318
|
-
</td>
|
|
319
|
-
<td>
|
|
320
|
-
<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 13</span>
|
|
321
|
-
|
|
322
|
-
<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span> <span class='lparen'>(</span><span class='id identifier rubyid_prediction_len'>prediction_len</span><span class='comma'>,</span> <span class='id identifier rubyid_limits'>limits</span><span class='comma'>,</span> <span class='id identifier rubyid_expected'>expected</span> <span class='op'>=</span> <span class='symbol'>:yes</span><span class='rparen'>)</span>
|
|
323
|
-
<span class='ivar'>@limits</span> <span class='op'>=</span> <span class='id identifier rubyid_limits'>limits</span>
|
|
324
|
-
<span class='ivar'>@prediction_len</span> <span class='op'>=</span> <span class='id identifier rubyid_prediction_len'>prediction_len</span>
|
|
325
|
-
<span class='ivar'>@expected</span> <span class='op'>=</span> <span class='id identifier rubyid_expected'>expected</span>
|
|
326
|
-
<span class='ivar'>@result</span> <span class='op'>=</span> <span class='id identifier rubyid_validation'>validation</span>
|
|
327
|
-
<span class='ivar'>@plot_files</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='rbracket'>]</span>
|
|
328
|
-
<span class='kw'>end</span></pre>
|
|
329
|
-
</td>
|
|
330
|
-
</tr>
|
|
331
|
-
</table>
|
|
332
|
-
</div>
|
|
333
|
-
|
|
334
|
-
</div>
|
|
335
|
-
|
|
336
|
-
<div id="instance_attr_details" class="attr_details">
|
|
337
|
-
<h2>Instance Attribute Details</h2>
|
|
338
|
-
|
|
339
|
-
|
|
340
|
-
<span id=""></span>
|
|
341
|
-
<div class="method_details first">
|
|
342
|
-
<h3 class="signature first" id="limits-instance_method">
|
|
343
|
-
|
|
344
|
-
- (<tt>Object</tt>) <strong>limits</strong> <span class="extras">(readonly)</span>
|
|
345
|
-
|
|
346
|
-
|
|
347
|
-
|
|
348
|
-
|
|
349
|
-
|
|
350
|
-
</h3><div class="docstring">
|
|
351
|
-
<div class="discussion">
|
|
352
|
-
|
|
353
|
-
<p>Returns the value of attribute limits</p>
|
|
354
|
-
|
|
355
|
-
|
|
356
|
-
</div>
|
|
357
|
-
</div>
|
|
358
|
-
<div class="tags">
|
|
359
|
-
|
|
360
|
-
|
|
361
|
-
</div><table class="source_code">
|
|
362
|
-
<tr>
|
|
363
|
-
<td>
|
|
364
|
-
<pre class="lines">
|
|
365
|
-
|
|
366
|
-
|
|
367
|
-
11
|
|
368
|
-
12
|
|
369
|
-
13</pre>
|
|
370
|
-
</td>
|
|
371
|
-
<td>
|
|
372
|
-
<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 11</span>
|
|
373
|
-
|
|
374
|
-
<span class='kw'>def</span> <span class='id identifier rubyid_limits'>limits</span>
|
|
375
|
-
<span class='ivar'>@limits</span>
|
|
376
|
-
<span class='kw'>end</span></pre>
|
|
377
|
-
</td>
|
|
378
|
-
</tr>
|
|
379
|
-
</table>
|
|
380
|
-
</div>
|
|
381
|
-
|
|
382
|
-
|
|
383
|
-
<span id=""></span>
|
|
384
|
-
<div class="method_details ">
|
|
385
|
-
<h3 class="signature " id="prediction_len-instance_method">
|
|
386
|
-
|
|
387
|
-
- (<tt>Object</tt>) <strong>prediction_len</strong> <span class="extras">(readonly)</span>
|
|
388
|
-
|
|
389
|
-
|
|
390
|
-
|
|
391
|
-
|
|
392
|
-
|
|
393
|
-
</h3><div class="docstring">
|
|
394
|
-
<div class="discussion">
|
|
395
|
-
|
|
396
|
-
<p>Returns the value of attribute prediction_len</p>
|
|
397
|
-
|
|
398
|
-
|
|
399
|
-
</div>
|
|
400
|
-
</div>
|
|
401
|
-
<div class="tags">
|
|
402
|
-
|
|
403
|
-
|
|
404
|
-
</div><table class="source_code">
|
|
405
|
-
<tr>
|
|
406
|
-
<td>
|
|
407
|
-
<pre class="lines">
|
|
408
|
-
|
|
409
|
-
|
|
410
|
-
10
|
|
411
|
-
11
|
|
412
|
-
12</pre>
|
|
413
|
-
</td>
|
|
414
|
-
<td>
|
|
415
|
-
<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 10</span>
|
|
416
|
-
|
|
417
|
-
<span class='kw'>def</span> <span class='id identifier rubyid_prediction_len'>prediction_len</span>
|
|
418
|
-
<span class='ivar'>@prediction_len</span>
|
|
419
|
-
<span class='kw'>end</span></pre>
|
|
420
|
-
</td>
|
|
421
|
-
</tr>
|
|
422
|
-
</table>
|
|
423
|
-
</div>
|
|
424
|
-
|
|
425
|
-
</div>
|
|
426
|
-
|
|
427
|
-
|
|
428
|
-
<div id="instance_method_details" class="method_details_list">
|
|
429
|
-
<h2>Instance Method Details</h2>
|
|
430
|
-
|
|
431
|
-
|
|
432
|
-
<div class="method_details first">
|
|
433
|
-
<h3 class="signature first" id="print-instance_method">
|
|
434
|
-
|
|
435
|
-
- (<tt>Object</tt>) <strong>print</strong>
|
|
436
|
-
|
|
437
|
-
|
|
438
|
-
|
|
439
|
-
|
|
440
|
-
|
|
441
|
-
</h3><table class="source_code">
|
|
442
|
-
<tr>
|
|
443
|
-
<td>
|
|
444
|
-
<pre class="lines">
|
|
445
|
-
|
|
446
|
-
|
|
447
|
-
21
|
|
448
|
-
22
|
|
449
|
-
23</pre>
|
|
450
|
-
</td>
|
|
451
|
-
<td>
|
|
452
|
-
<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 21</span>
|
|
453
|
-
|
|
454
|
-
<span class='kw'>def</span> <span class='id identifier rubyid_print'>print</span>
|
|
455
|
-
<span class='tstring'><span class='tstring_beg'>"</span><span class='embexpr_beg'>#{</span><span class='ivar'>@prediction_len</span><span class='rbrace'>}</span><span class='tstring_content'> </span><span class='embexpr_beg'>#{</span><span class='ivar'>@limits</span><span class='period'>.</span><span class='id identifier rubyid_to_s'>to_s</span><span class='rbrace'>}</span><span class='tstring_end'>"</span></span>
|
|
456
|
-
<span class='kw'>end</span></pre>
|
|
457
|
-
</td>
|
|
458
|
-
</tr>
|
|
459
|
-
</table>
|
|
460
|
-
</div>
|
|
461
|
-
|
|
462
|
-
<div class="method_details ">
|
|
463
|
-
<h3 class="signature " id="validation-instance_method">
|
|
464
|
-
|
|
465
|
-
- (<tt>Object</tt>) <strong>validation</strong>
|
|
466
|
-
|
|
467
|
-
|
|
468
|
-
|
|
469
|
-
|
|
470
|
-
|
|
471
|
-
</h3><table class="source_code">
|
|
472
|
-
<tr>
|
|
473
|
-
<td>
|
|
474
|
-
<pre class="lines">
|
|
475
|
-
|
|
476
|
-
|
|
477
|
-
25
|
|
478
|
-
26
|
|
479
|
-
27
|
|
480
|
-
28
|
|
481
|
-
29
|
|
482
|
-
30
|
|
483
|
-
31
|
|
484
|
-
32
|
|
485
|
-
33</pre>
|
|
486
|
-
</td>
|
|
487
|
-
<td>
|
|
488
|
-
<pre class="code"><span class="info file"># File 'lib/genevalidator/validation_length_cluster.rb', line 25</span>
|
|
489
|
-
|
|
490
|
-
<span class='kw'>def</span> <span class='id identifier rubyid_validation'>validation</span>
|
|
491
|
-
<span class='kw'>if</span> <span class='ivar'>@limits</span> <span class='op'>!=</span> <span class='kw'>nil</span>
|
|
492
|
-
<span class='kw'>if</span> <span class='ivar'>@prediction_len</span> <span class='op'>>=</span> <span class='ivar'>@limits</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='kw'>and</span> <span class='ivar'>@prediction_len</span> <span class='op'><=</span> <span class='ivar'>@limits</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
|
|
493
|
-
<span class='symbol'>:yes</span>
|
|
494
|
-
<span class='kw'>else</span>
|
|
495
|
-
<span class='symbol'>:no</span>
|
|
496
|
-
<span class='kw'>end</span>
|
|
497
|
-
<span class='kw'>end</span>
|
|
498
|
-
<span class='kw'>end</span></pre>
|
|
499
|
-
</td>
|
|
500
|
-
</tr>
|
|
501
|
-
</table>
|
|
502
|
-
</div>
|
|
503
|
-
|
|
504
|
-
</div>
|
|
505
|
-
|
|
506
|
-
</div>
|
|
507
|
-
|
|
508
|
-
<div id="footer">
|
|
509
|
-
Generated on Sat Sep 28 07:01:33 2013 by
|
|
510
|
-
<a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
|
|
511
|
-
0.8.7.2 (ruby-1.9.3).
|
|
512
|
-
</div>
|
|
513
|
-
|
|
514
|
-
</body>
|
|
515
|
-
</html>
|