genevalidator 1.6.1 → 1.6.2

Sign up to get free protection for your applications and to get access to all the features.
Files changed (131) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +3 -1
  3. data/.travis.yml +2 -0
  4. data/README.md +78 -30
  5. data/Rakefile +11 -8
  6. data/aux/app_template_footer.erb +1 -6
  7. data/aux/app_template_header.erb +12 -32
  8. data/aux/files/css/style.css +2 -8
  9. data/aux/files/js/plots.js +564 -576
  10. data/aux/files/js/script.js +10 -0
  11. data/aux/json_footer.erb +8 -0
  12. data/aux/json_header.erb +19 -0
  13. data/aux/json_query.erb +14 -0
  14. data/aux/template_footer.erb +9 -58
  15. data/aux/template_header.erb +18 -58
  16. data/aux/template_query.erb +8 -36
  17. data/bin/genevalidator +45 -32
  18. data/genevalidator.gemspec +11 -7
  19. data/lib/genevalidator.rb +75 -455
  20. data/lib/genevalidator/arg_validation.rb +78 -107
  21. data/lib/genevalidator/blast.rb +57 -60
  22. data/lib/genevalidator/clusterization.rb +15 -15
  23. data/lib/genevalidator/exceptions.rb +32 -5
  24. data/lib/genevalidator/get_raw_sequences.rb +70 -33
  25. data/lib/genevalidator/hsp.rb +1 -4
  26. data/lib/genevalidator/json_to_gv_results.rb +109 -0
  27. data/lib/genevalidator/output.rb +177 -185
  28. data/lib/genevalidator/pool.rb +2 -1
  29. data/lib/genevalidator/sequences.rb +3 -3
  30. data/lib/genevalidator/tabular_parser.rb +24 -18
  31. data/lib/genevalidator/validation.rb +279 -0
  32. data/lib/genevalidator/validation_alignment.rb +31 -47
  33. data/lib/genevalidator/validation_blast_reading_frame.rb +19 -18
  34. data/lib/genevalidator/validation_duplication.rb +23 -19
  35. data/lib/genevalidator/validation_gene_merge.rb +30 -65
  36. data/lib/genevalidator/validation_length_cluster.rb +14 -53
  37. data/lib/genevalidator/validation_length_rank.rb +10 -11
  38. data/lib/genevalidator/validation_open_reading_frame.rb +18 -19
  39. data/lib/genevalidator/validation_report.rb +2 -5
  40. data/lib/genevalidator/validation_test.rb +8 -4
  41. data/lib/genevalidator/version.rb +1 -1
  42. data/test/test_all_validations.rb +51 -66
  43. data/test/test_blast.rb +68 -51
  44. data/test/test_clusterization.rb +1 -1
  45. data/test/test_clusterization_2d.rb +19 -13
  46. data/test/test_extended_array_methods.rb +1 -1
  47. data/test/test_files/all_validations_mrna/mrna.blast_tab6 +1806 -0
  48. data/test/test_files/all_validations_mrna/mrna.blast_tab7 +1865 -0
  49. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml → mrna.blast_xml} +18642 -1
  50. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.index → mrna.blast_xml.index} +300 -0
  51. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta → mrna.fa} +0 -0
  52. data/test/test_files/all_validations_mrna/mrna.raw_seq +3970 -0
  53. data/test/test_files/all_validations_mrna/{all_validations_mrna.fasta.blast_xml.raw_seq.idx → mrna.raw_seq.idx} +901 -1
  54. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_tab → prot.blast_tab6} +416 -0
  55. data/test/test_files/all_validations_prot/prot.blast_tab7 +2400 -0
  56. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml → prot.blast_xml} +18299 -6723
  57. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.index → prot.blast_xml.index} +408 -0
  58. data/test/test_files/all_validations_prot/{all_validations_prot.fasta → prot.fa} +0 -0
  59. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq → prot.raw_seq} +2735 -0
  60. data/test/test_files/all_validations_prot/{all_validations_prot.fasta.blast_xml.raw_seq.idx → prot.raw_seq.idx} +3032 -1808
  61. data/test/test_sequences.rb +46 -41
  62. data/test/test_validation_open_reading_frame.rb +318 -202
  63. data/test/test_validations.rb +48 -32
  64. metadata +76 -102
  65. data/doc/AliasDuplicationError.html +0 -134
  66. data/doc/AlignmentValidation.html +0 -1687
  67. data/doc/AlignmentValidationOutput.html +0 -659
  68. data/doc/Blast.html +0 -1905
  69. data/doc/BlastRFValidationOutput.html +0 -545
  70. data/doc/BlastReadingFrameValidation.html +0 -370
  71. data/doc/BlastUtils.html +0 -875
  72. data/doc/ClasspathError.html +0 -134
  73. data/doc/Cluster.html +0 -1316
  74. data/doc/DuplciationValidationOutput.html +0 -564
  75. data/doc/DuplicationValidation.html +0 -920
  76. data/doc/DuplicationValidationOutput.html +0 -564
  77. data/doc/FileNotFoundException.html +0 -134
  78. data/doc/GeneMergeValidation.html +0 -935
  79. data/doc/GeneMergeValidationOutput.html +0 -652
  80. data/doc/HierarchicalClusterization.html +0 -994
  81. data/doc/Hsp.html +0 -1485
  82. data/doc/InconsistentTabularFormat.html +0 -135
  83. data/doc/LengthClusterValidation.html +0 -982
  84. data/doc/LengthClusterValidationOutput.html +0 -515
  85. data/doc/LengthRankValidation.html +0 -496
  86. data/doc/LengthRankValidationOutput.html +0 -517
  87. data/doc/NoInternetError.html +0 -135
  88. data/doc/NoMafftInstallationError.html +0 -134
  89. data/doc/NoPIdentError.html +0 -134
  90. data/doc/NoValidationError.html +0 -134
  91. data/doc/NotEnoughHitsError.html +0 -135
  92. data/doc/ORFValidationOutput.html +0 -593
  93. data/doc/OpenReadingFrameValidation.html +0 -1107
  94. data/doc/OtherError.html +0 -123
  95. data/doc/Output.html +0 -1540
  96. data/doc/Pair.html +0 -309
  97. data/doc/PairCluster.html +0 -767
  98. data/doc/Plot.html +0 -837
  99. data/doc/QueryError.html +0 -134
  100. data/doc/ReportClassError.html +0 -135
  101. data/doc/Sequence.html +0 -1299
  102. data/doc/SequenceTypeError.html +0 -135
  103. data/doc/TabularEntry.html +0 -837
  104. data/doc/TabularParser.html +0 -1104
  105. data/doc/Validation.html +0 -2147
  106. data/doc/ValidationClassError.html +0 -134
  107. data/doc/ValidationOutput.html +0 -460
  108. data/doc/ValidationReport.html +0 -940
  109. data/doc/ValidationTest.html +0 -939
  110. data/doc/_index.html +0 -449
  111. data/doc/class_list.html +0 -54
  112. data/doc/css/common.css +0 -1
  113. data/doc/css/full_list.css +0 -57
  114. data/doc/css/style.css +0 -338
  115. data/doc/file.README.html +0 -151
  116. data/doc/file_list.html +0 -56
  117. data/doc/frames.html +0 -26
  118. data/doc/index.html +0 -151
  119. data/doc/js/app.js +0 -214
  120. data/doc/js/full_list.js +0 -178
  121. data/doc/js/jquery.js +0 -4
  122. data/doc/method_list.html +0 -1505
  123. data/doc/top-level-namespace.html +0 -112
  124. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab +0 -967
  125. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.index +0 -967
  126. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq +0 -4929
  127. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_tab.raw_seq.idx +0 -1006
  128. data/test/test_files/all_validations_mrna/all_validations_mrna.fasta.blast_xml.raw_seq +0 -2075
  129. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.index +0 -1864
  130. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq +0 -42411
  131. data/test/test_files/all_validations_prot/all_validations_prot.fasta.blast_tab.raw_seq.idx +0 -3751
data/doc/Pair.html DELETED
@@ -1,309 +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: Pair
8
-
9
- &mdash; 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 (P)</a> &raquo;
35
-
36
-
37
- <span class="title">Pair</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: Pair
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">Struct</span>
77
-
78
- <ul class="fullTree">
79
- <li>Object</li>
80
-
81
- <li class="next">Struct</li>
82
-
83
- <li class="next">Pair</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/clusterization.rb</dd>
100
-
101
- </dl>
102
- <div class="clear"></div>
103
-
104
-
105
-
106
-
107
-
108
- <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
109
- <ul class="summary">
110
-
111
- <li class="public ">
112
- <span class="summary_signature">
113
-
114
- <a href="#x-instance_method" title="#x (instance method)">- (Object) <strong>x</strong> </a>
115
-
116
-
117
-
118
- </span>
119
-
120
-
121
-
122
-
123
-
124
-
125
-
126
-
127
-
128
-
129
-
130
-
131
- <span class="summary_desc"><div class='inline'>
132
- <p>Returns the value of attribute x.</p>
133
- </div></span>
134
-
135
- </li>
136
-
137
-
138
- <li class="public ">
139
- <span class="summary_signature">
140
-
141
- <a href="#y-instance_method" title="#y (instance method)">- (Object) <strong>y</strong> </a>
142
-
143
-
144
-
145
- </span>
146
-
147
-
148
-
149
-
150
-
151
-
152
-
153
-
154
-
155
-
156
-
157
-
158
- <span class="summary_desc"><div class='inline'>
159
- <p>Returns the value of attribute y.</p>
160
- </div></span>
161
-
162
- </li>
163
-
164
-
165
- </ul>
166
-
167
-
168
-
169
-
170
-
171
-
172
- <div id="instance_attr_details" class="attr_details">
173
- <h2>Instance Attribute Details</h2>
174
-
175
-
176
- <span id="x=-instance_method"></span>
177
- <div class="method_details first">
178
- <h3 class="signature first" id="x-instance_method">
179
-
180
- - (<tt>Object</tt>) <strong>x</strong>
181
-
182
-
183
-
184
-
185
-
186
- </h3><div class="docstring">
187
- <div class="discussion">
188
-
189
- <p>Returns the value of attribute x</p>
190
-
191
-
192
- </div>
193
- </div>
194
- <div class="tags">
195
-
196
- <p class="tag_title">Returns:</p>
197
- <ul class="return">
198
-
199
- <li>
200
-
201
-
202
- <span class='type'>(<tt>Object</tt>)</span>
203
-
204
-
205
-
206
- &mdash;
207
- <div class='inline'>
208
- <p>the current value of x</p>
209
- </div>
210
-
211
- </li>
212
-
213
- </ul>
214
-
215
- </div><table class="source_code">
216
- <tr>
217
- <td>
218
- <pre class="lines">
219
-
220
-
221
- 3
222
- 4
223
- 5</pre>
224
- </td>
225
- <td>
226
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 3</span>
227
-
228
- <span class='kw'>def</span> <span class='id identifier rubyid_x'>x</span>
229
- <span class='ivar'>@x</span>
230
- <span class='kw'>end</span></pre>
231
- </td>
232
- </tr>
233
- </table>
234
- </div>
235
-
236
-
237
- <span id="y=-instance_method"></span>
238
- <div class="method_details ">
239
- <h3 class="signature " id="y-instance_method">
240
-
241
- - (<tt>Object</tt>) <strong>y</strong>
242
-
243
-
244
-
245
-
246
-
247
- </h3><div class="docstring">
248
- <div class="discussion">
249
-
250
- <p>Returns the value of attribute y</p>
251
-
252
-
253
- </div>
254
- </div>
255
- <div class="tags">
256
-
257
- <p class="tag_title">Returns:</p>
258
- <ul class="return">
259
-
260
- <li>
261
-
262
-
263
- <span class='type'>(<tt>Object</tt>)</span>
264
-
265
-
266
-
267
- &mdash;
268
- <div class='inline'>
269
- <p>the current value of y</p>
270
- </div>
271
-
272
- </li>
273
-
274
- </ul>
275
-
276
- </div><table class="source_code">
277
- <tr>
278
- <td>
279
- <pre class="lines">
280
-
281
-
282
- 3
283
- 4
284
- 5</pre>
285
- </td>
286
- <td>
287
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 3</span>
288
-
289
- <span class='kw'>def</span> <span class='id identifier rubyid_y'>y</span>
290
- <span class='ivar'>@y</span>
291
- <span class='kw'>end</span></pre>
292
- </td>
293
- </tr>
294
- </table>
295
- </div>
296
-
297
- </div>
298
-
299
-
300
- </div>
301
-
302
- <div id="footer">
303
- Generated on Sat Sep 28 07:01:32 2013 by
304
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
305
- 0.8.7.2 (ruby-1.9.3).
306
- </div>
307
-
308
- </body>
309
- </html>
data/doc/PairCluster.html DELETED
@@ -1,767 +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: PairCluster
8
-
9
- &mdash; 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 (P)</a> &raquo;
35
-
36
-
37
- <span class="title">PairCluster</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: PairCluster
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">Object</span>
77
-
78
- <ul class="fullTree">
79
- <li>Object</li>
80
-
81
- <li class="next">PairCluster</li>
82
-
83
- </ul>
84
- <a href="#" class="inheritanceTree">show all</a>
85
-
86
- </dd>
87
-
88
-
89
-
90
-
91
-
92
-
93
-
94
-
95
-
96
- <dt class="r2 last">Defined in:</dt>
97
- <dd class="r2 last">lib/genevalidator/clusterization.rb</dd>
98
-
99
- </dl>
100
- <div class="clear"></div>
101
-
102
-
103
-
104
-
105
-
106
- <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
107
- <ul class="summary">
108
-
109
- <li class="public ">
110
- <span class="summary_signature">
111
-
112
- <a href="#objects-instance_method" title="#objects (instance method)">- (Object) <strong>objects</strong> </a>
113
-
114
-
115
-
116
- </span>
117
-
118
-
119
-
120
-
121
-
122
-
123
-
124
-
125
-
126
-
127
-
128
-
129
- <span class="summary_desc"><div class='inline'>
130
- <p>a hash map containing the pair (object, no_occurences).</p>
131
- </div></span>
132
-
133
- </li>
134
-
135
-
136
- </ul>
137
-
138
-
139
-
140
-
141
-
142
- <h2>
143
- Instance Method Summary
144
- <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
145
- </h2>
146
-
147
- <ul class="summary">
148
-
149
- <li class="public ">
150
- <span class="summary_signature">
151
-
152
- <a href="#add-instance_method" title="#add (instance method)">- (Object) <strong>add</strong>(cluster) </a>
153
-
154
-
155
-
156
- </span>
157
-
158
-
159
-
160
-
161
-
162
-
163
-
164
-
165
-
166
- <span class="summary_desc"><div class='inline'>
167
- <p>Merges the current cluster with the one given as parameter
168
- <tt>clusters</tt> vector of Cluster objects.</p>
169
- </div></span>
170
-
171
- </li>
172
-
173
-
174
- <li class="public ">
175
- <span class="summary_signature">
176
-
177
- <a href="#density-instance_method" title="#density (instance method)">- (Object) <strong>density</strong> </a>
178
-
179
-
180
-
181
- </span>
182
-
183
-
184
-
185
-
186
-
187
-
188
-
189
-
190
-
191
- <span class="summary_desc"><div class='inline'>
192
- <p>Returns the density of the cluster: how many values it contains.</p>
193
- </div></span>
194
-
195
- </li>
196
-
197
-
198
- <li class="public ">
199
- <span class="summary_signature">
200
-
201
- <a href="#distance-instance_method" title="#distance (instance method)">- (Object) <strong>distance</strong>(cluster, method = 0) </a>
202
-
203
-
204
-
205
- </span>
206
-
207
-
208
-
209
-
210
-
211
-
212
-
213
-
214
-
215
- <span class="summary_desc"><div class='inline'>
216
- <p>Returns the euclidian distance between the current cluster and the one
217
- given as parameter Params: <tt>cluster</tt>: Cluster object
218
- <tt>method</tt>: 0 or 1 method = 0: do not into condseideration duplicate
219
- values method = 1: average linkage clusterization.</p>
220
- </div></span>
221
-
222
- </li>
223
-
224
-
225
- <li class="public ">
226
- <span class="summary_signature">
227
-
228
- <a href="#initialize-instance_method" title="#initialize (instance method)">- (PairCluster) <strong>initialize</strong>(objects) </a>
229
-
230
-
231
-
232
- </span>
233
-
234
-
235
- <span class="note title constructor">constructor</span>
236
-
237
-
238
-
239
-
240
-
241
-
242
-
243
-
244
- <span class="summary_desc"><div class='inline'>
245
- <p>A new instance of PairCluster.</p>
246
- </div></span>
247
-
248
- </li>
249
-
250
-
251
- <li class="public ">
252
- <span class="summary_signature">
253
-
254
- <a href="#mean-instance_method" title="#mean (instance method)">- (Object) <strong>mean</strong> </a>
255
-
256
-
257
-
258
- </span>
259
-
260
-
261
-
262
-
263
-
264
-
265
-
266
-
267
-
268
- <span class="summary_desc"><div class='inline'>
269
- <p>Returns the weighted mean value of the cluster.</p>
270
- </div></span>
271
-
272
- </li>
273
-
274
-
275
- <li class="public ">
276
- <span class="summary_signature">
277
-
278
- <a href="#print-instance_method" title="#print (instance method)">- (Object) <strong>print</strong> </a>
279
-
280
-
281
-
282
- </span>
283
-
284
-
285
-
286
-
287
-
288
-
289
-
290
-
291
-
292
- <span class="summary_desc"><div class='inline'></div></span>
293
-
294
- </li>
295
-
296
-
297
- <li class="public ">
298
- <span class="summary_signature">
299
-
300
- <a href="#wss-instance_method" title="#wss (instance method)">- (Object) <strong>wss</strong>(objects = nil) </a>
301
-
302
-
303
-
304
- </span>
305
-
306
-
307
-
308
-
309
-
310
-
311
-
312
-
313
-
314
- <span class="summary_desc"><div class='inline'>
315
- <p>Returns within cluster sum of squares.</p>
316
- </div></span>
317
-
318
- </li>
319
-
320
-
321
- </ul>
322
-
323
-
324
- <div id="constructor_details" class="method_details_list">
325
- <h2>Constructor Details</h2>
326
-
327
- <div class="method_details first">
328
- <h3 class="signature first" id="initialize-instance_method">
329
-
330
- - (<tt><span class='object_link'><a href="" title="PairCluster (class)">PairCluster</a></span></tt>) <strong>initialize</strong>(objects)
331
-
332
-
333
-
334
-
335
-
336
- </h3><div class="docstring">
337
- <div class="discussion">
338
-
339
- <p>Returns a new instance of PairCluster</p>
340
-
341
-
342
- </div>
343
- </div>
344
- <div class="tags">
345
-
346
-
347
- </div><table class="source_code">
348
- <tr>
349
- <td>
350
- <pre class="lines">
351
-
352
-
353
- 70
354
- 71
355
- 72</pre>
356
- </td>
357
- <td>
358
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 70</span>
359
-
360
- <span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_objects'>objects</span><span class='rparen'>)</span>
361
- <span class='ivar'>@objects</span> <span class='op'>=</span> <span class='id identifier rubyid_objects'>objects</span>
362
- <span class='kw'>end</span></pre>
363
- </td>
364
- </tr>
365
- </table>
366
- </div>
367
-
368
- </div>
369
-
370
- <div id="instance_attr_details" class="attr_details">
371
- <h2>Instance Attribute Details</h2>
372
-
373
-
374
- <span id="objects=-instance_method"></span>
375
- <div class="method_details first">
376
- <h3 class="signature first" id="objects-instance_method">
377
-
378
- - (<tt>Object</tt>) <strong>objects</strong>
379
-
380
-
381
-
382
-
383
-
384
- </h3><div class="docstring">
385
- <div class="discussion">
386
-
387
- <p>a hash map containing the pair (object, no_occurences)</p>
388
-
389
-
390
- </div>
391
- </div>
392
- <div class="tags">
393
-
394
-
395
- </div><table class="source_code">
396
- <tr>
397
- <td>
398
- <pre class="lines">
399
-
400
-
401
- 68
402
- 69
403
- 70</pre>
404
- </td>
405
- <td>
406
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 68</span>
407
-
408
- <span class='kw'>def</span> <span class='id identifier rubyid_objects'>objects</span>
409
- <span class='ivar'>@objects</span>
410
- <span class='kw'>end</span></pre>
411
- </td>
412
- </tr>
413
- </table>
414
- </div>
415
-
416
- </div>
417
-
418
-
419
- <div id="instance_method_details" class="method_details_list">
420
- <h2>Instance Method Details</h2>
421
-
422
-
423
- <div class="method_details first">
424
- <h3 class="signature first" id="add-instance_method">
425
-
426
- - (<tt>Object</tt>) <strong>add</strong>(cluster)
427
-
428
-
429
-
430
-
431
-
432
- </h3><div class="docstring">
433
- <div class="discussion">
434
-
435
- <p>Merges the current cluster with the one given as parameter
436
- <tt>clusters</tt> vector of Cluster objects</p>
437
-
438
-
439
- </div>
440
- </div>
441
- <div class="tags">
442
-
443
-
444
- </div><table class="source_code">
445
- <tr>
446
- <td>
447
- <pre class="lines">
448
-
449
-
450
- 154
451
- 155
452
- 156
453
- 157
454
- 158</pre>
455
- </td>
456
- <td>
457
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 154</span>
458
-
459
- <span class='kw'>def</span> <span class='id identifier rubyid_add'>add</span><span class='lparen'>(</span><span class='id identifier rubyid_cluster'>cluster</span><span class='rparen'>)</span>
460
- <span class='id identifier rubyid_cluster'>cluster</span><span class='period'>.</span><span class='id identifier rubyid_objects'>objects</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_elem'>elem</span><span class='op'>|</span>
461
- <span class='id identifier rubyid_objects'>objects</span><span class='lbracket'>[</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
462
- <span class='kw'>end</span>
463
- <span class='kw'>end</span></pre>
464
- </td>
465
- </tr>
466
- </table>
467
- </div>
468
-
469
- <div class="method_details ">
470
- <h3 class="signature " id="density-instance_method">
471
-
472
- - (<tt>Object</tt>) <strong>density</strong>
473
-
474
-
475
-
476
-
477
-
478
- </h3><div class="docstring">
479
- <div class="discussion">
480
-
481
- <p>Returns the density of the cluster: how many values it contains</p>
482
-
483
-
484
- </div>
485
- </div>
486
- <div class="tags">
487
-
488
-
489
- </div><table class="source_code">
490
- <tr>
491
- <td>
492
- <pre class="lines">
493
-
494
-
495
- 99
496
- 100
497
- 101
498
- 102
499
- 103
500
- 104
501
- 105
502
- 106</pre>
503
- </td>
504
- <td>
505
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 99</span>
506
-
507
- <span class='kw'>def</span> <span class='id identifier rubyid_density'>density</span>
508
- <span class='id identifier rubyid_d'>d</span> <span class='op'>=</span> <span class='int'>0</span>
509
- <span class='id identifier rubyid_objects'>objects</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_elem'>elem</span><span class='op'>|</span>
510
- <span class='id identifier rubyid_d'>d</span> <span class='op'>+=</span> <span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
511
- <span class='kw'>end</span>
512
- <span class='id identifier rubyid_d'>d</span>
513
-
514
- <span class='kw'>end</span></pre>
515
- </td>
516
- </tr>
517
- </table>
518
- </div>
519
-
520
- <div class="method_details ">
521
- <h3 class="signature " id="distance-instance_method">
522
-
523
- - (<tt>Object</tt>) <strong>distance</strong>(cluster, method = 0)
524
-
525
-
526
-
527
-
528
-
529
- </h3><div class="docstring">
530
- <div class="discussion">
531
-
532
- <p>Returns the euclidian distance between the current cluster and the one
533
- given as parameter Params: <tt>cluster</tt>: Cluster object
534
- <tt>method</tt>: 0 or 1 method = 0: do not into condseideration duplicate
535
- values method = 1: average linkage clusterization</p>
536
-
537
-
538
- </div>
539
- </div>
540
- <div class="tags">
541
-
542
-
543
- </div><table class="source_code">
544
- <tr>
545
- <td>
546
- <pre class="lines">
547
-
548
-
549
- 114
550
- 115
551
- 116
552
- 117
553
- 118
554
- 119
555
- 120
556
- 121
557
- 122
558
- 123
559
- 124
560
- 125
561
- 126
562
- 127
563
- 128
564
- 129
565
- 130
566
- 131
567
- 132
568
- 133</pre>
569
- </td>
570
- <td>
571
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 114</span>
572
-
573
- <span class='kw'>def</span> <span class='id identifier rubyid_distance'>distance</span><span class='lparen'>(</span><span class='id identifier rubyid_cluster'>cluster</span><span class='comma'>,</span> <span class='id identifier rubyid_method'>method</span> <span class='op'>=</span> <span class='int'>0</span><span class='rparen'>)</span>
574
- <span class='id identifier rubyid_d'>d</span> <span class='op'>=</span> <span class='int'>0</span>
575
- <span class='id identifier rubyid_norm'>norm</span> <span class='op'>=</span> <span class='int'>0</span>
576
-
577
- <span class='id identifier rubyid_cluster'>cluster</span><span class='period'>.</span><span class='id identifier rubyid_objects'>objects</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_elem1'>elem1</span><span class='op'>|</span>
578
- <span class='id identifier rubyid_objects'>objects</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_elem2'>elem2</span><span class='op'>|</span>
579
- <span class='kw'>if</span> <span class='id identifier rubyid_method'>method</span> <span class='op'>==</span> <span class='int'>1</span>
580
- <span class='id identifier rubyid_d'>d</span> <span class='op'>+=</span> <span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>*</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>*</span> <span class='lparen'>(</span><span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_abs'>abs</span>
581
- <span class='id identifier rubyid_norm'>norm</span> <span class='op'>+=</span> <span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span> <span class='op'>*</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span>
582
- <span class='kw'>else</span>
583
- <span class='id identifier rubyid_d'>d</span> <span class='op'>+=</span> <span class='lparen'>(</span><span class='id identifier rubyid_elem1'>elem1</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span> <span class='op'>-</span> <span class='id identifier rubyid_elem2'>elem2</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_abs'>abs</span>
584
- <span class='id identifier rubyid_norm'>norm</span> <span class='op'>=</span> <span class='id identifier rubyid_cluster'>cluster</span><span class='period'>.</span><span class='id identifier rubyid_objects'>objects</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span> <span class='op'>*</span> <span class='id identifier rubyid_objects'>objects</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span>
585
- <span class='kw'>end</span>
586
- <span class='kw'>end</span>
587
- <span class='kw'>end</span>
588
-
589
- <span class='comment'>#group average distance
590
- </span> <span class='id identifier rubyid_d'>d</span> <span class='op'>/=</span> <span class='lparen'>(</span><span class='id identifier rubyid_norm'>norm</span> <span class='op'>+</span> <span class='float'>0.0</span><span class='rparen'>)</span>
591
-
592
- <span class='kw'>end</span></pre>
593
- </td>
594
- </tr>
595
- </table>
596
- </div>
597
-
598
- <div class="method_details ">
599
- <h3 class="signature " id="mean-instance_method">
600
-
601
- - (<tt>Object</tt>) <strong>mean</strong>
602
-
603
-
604
-
605
-
606
-
607
- </h3><div class="docstring">
608
- <div class="discussion">
609
-
610
- <p>Returns the weighted mean value of the cluster</p>
611
-
612
-
613
- </div>
614
- </div>
615
- <div class="tags">
616
-
617
-
618
- </div><table class="source_code">
619
- <tr>
620
- <td>
621
- <pre class="lines">
622
-
623
-
624
- 83
625
- 84
626
- 85
627
- 86
628
- 87
629
- 88
630
- 89
631
- 90
632
- 91
633
- 92
634
- 93
635
- 94
636
- 95</pre>
637
- </td>
638
- <td>
639
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 83</span>
640
-
641
- <span class='kw'>def</span> <span class='id identifier rubyid_mean'>mean</span>
642
- <span class='id identifier rubyid_mean'>mean</span> <span class='op'>=</span> <span class='const'>Pair</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='int'>0</span><span class='comma'>,</span><span class='int'>0</span><span class='rparen'>)</span>
643
- <span class='id identifier rubyid_weight'>weight</span> <span class='op'>=</span> <span class='int'>0</span>
644
-
645
- <span class='id identifier rubyid_objects'>objects</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_object'>object</span><span class='comma'>,</span> <span class='id identifier rubyid_n'>n</span><span class='op'>|</span>
646
- <span class='id identifier rubyid_object'>object</span> <span class='op'>*</span> <span class='id identifier rubyid_n'>n</span>
647
- <span class='id identifier rubyid_mean'>mean</span> <span class='op'>+</span> <span class='id identifier rubyid_object'>object</span>
648
- <span class='id identifier rubyid_weight'>weight</span> <span class='op'>+=</span> <span class='id identifier rubyid_n'>n</span>
649
- <span class='kw'>end</span>
650
- <span class='id identifier rubyid_mean'>mean</span> <span class='op'>/</span> <span class='id identifier rubyid_weight'>weight</span>
651
- <span class='kw'>return</span> <span class='id identifier rubyid_mean'>mean</span>
652
-
653
- <span class='kw'>end</span></pre>
654
- </td>
655
- </tr>
656
- </table>
657
- </div>
658
-
659
- <div class="method_details ">
660
- <h3 class="signature " id="print-instance_method">
661
-
662
- - (<tt>Object</tt>) <strong>print</strong>
663
-
664
-
665
-
666
-
667
-
668
- </h3><table class="source_code">
669
- <tr>
670
- <td>
671
- <pre class="lines">
672
-
673
-
674
- 74
675
- 75
676
- 76
677
- 77
678
- 78
679
- 79</pre>
680
- </td>
681
- <td>
682
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 74</span>
683
-
684
- <span class='kw'>def</span> <span class='id identifier rubyid_print'>print</span>
685
- <span class='id identifier rubyid_objects'>objects</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_elem'>elem</span><span class='op'>|</span>
686
- <span class='id identifier rubyid_puts'>puts</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>(</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_x'>x</span><span class='rbrace'>}</span><span class='tstring_content'>,</span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_y'>y</span><span class='rbrace'>}</span><span class='tstring_content'>): </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_elem'>elem</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span>
687
- <span class='kw'>end</span>
688
-
689
- <span class='kw'>end</span></pre>
690
- </td>
691
- </tr>
692
- </table>
693
- </div>
694
-
695
- <div class="method_details ">
696
- <h3 class="signature " id="wss-instance_method">
697
-
698
- - (<tt>Object</tt>) <strong>wss</strong>(objects = nil)
699
-
700
-
701
-
702
-
703
-
704
- </h3><div class="docstring">
705
- <div class="discussion">
706
-
707
- <p>Returns within cluster sum of squares</p>
708
-
709
-
710
- </div>
711
- </div>
712
- <div class="tags">
713
-
714
-
715
- </div><table class="source_code">
716
- <tr>
717
- <td>
718
- <pre class="lines">
719
-
720
-
721
- 137
722
- 138
723
- 139
724
- 140
725
- 141
726
- 142
727
- 143
728
- 144
729
- 145
730
- 146
731
- 147
732
- 148
733
- 149</pre>
734
- </td>
735
- <td>
736
- <pre class="code"><span class="info file"># File 'lib/genevalidator/clusterization.rb', line 137</span>
737
-
738
- <span class='kw'>def</span> <span class='id identifier rubyid_wss'>wss</span><span class='lparen'>(</span><span class='id identifier rubyid_objects'>objects</span> <span class='op'>=</span> <span class='kw'>nil</span><span class='rparen'>)</span>
739
- <span class='kw'>if</span> <span class='id identifier rubyid_objects'>objects</span> <span class='op'>==</span> <span class='kw'>nil</span>
740
- <span class='id identifier rubyid_objects'>objects</span> <span class='op'>=</span> <span class='ivar'>@objects</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_a'>a</span> <span class='op'>=</span> <span class='const'>Array</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>1</span><span class='rbracket'>]</span><span class='comma'>,</span><span class='id identifier rubyid_x'>x</span><span class='lbracket'>[</span><span class='int'>0</span><span class='rbracket'>]</span><span class='rparen'>)</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
741
- <span class='kw'>end</span>
742
-
743
- <span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>=</span> <span class='id identifier rubyid_mean'>mean</span>
744
- <span class='id identifier rubyid_ss'>ss</span> <span class='op'>=</span> <span class='int'>0</span>
745
- <span class='id identifier rubyid_objects'>objects</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_object'>object</span><span class='op'>|</span>
746
- <span class='id identifier rubyid_ss'>ss</span> <span class='op'>+=</span> <span class='lparen'>(</span><span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>-</span> <span class='id identifier rubyid_object'>object</span><span class='rparen'>)</span> <span class='op'>*</span> <span class='lparen'>(</span><span class='id identifier rubyid_cluster_mean'>cluster_mean</span> <span class='op'>-</span> <span class='id identifier rubyid_object'>object</span><span class='rparen'>)</span>
747
- <span class='kw'>end</span>
748
- <span class='id identifier rubyid_ss'>ss</span>
749
-
750
- <span class='kw'>end</span></pre>
751
- </td>
752
- </tr>
753
- </table>
754
- </div>
755
-
756
- </div>
757
-
758
- </div>
759
-
760
- <div id="footer">
761
- Generated on Sat Sep 28 07:01:32 2013 by
762
- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
763
- 0.8.7.2 (ruby-1.9.3).
764
- </div>
765
-
766
- </body>
767
- </html>