bio-svgenes 0.2.3 → 0.3.0
Sign up to get free protection for your applications and to get access to all the features.
- data/.DS_Store +0 -0
- data/VERSION +1 -1
- data/bio-svgenes.gemspec +59 -4
- data/doc/.DS_Store +0 -0
- data/doc/Bio.html +141 -0
- data/doc/Bio/.DS_Store +0 -0
- data/doc/Bio/Graphics.html +147 -0
- data/doc/Bio/Graphics/Glyph.html +1061 -0
- data/doc/Bio/Graphics/MiniFeature.html +342 -0
- data/doc/Bio/Graphics/Page.html +1200 -0
- data/doc/Bio/Graphics/Primitive.html +278 -0
- data/doc/Bio/Graphics/SVGEE.html +471 -0
- data/doc/Bio/Graphics/Track.html +506 -0
- data/doc/LICENSE_txt.html +118 -0
- data/doc/created.rid +9 -0
- data/doc/images/add.png +0 -0
- data/doc/images/arrow_up.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
- data/doc/images/bullet_black.png +0 -0
- data/doc/images/bullet_toggle_minus.png +0 -0
- data/doc/images/bullet_toggle_plus.png +0 -0
- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
- data/doc/images/macFFBgHack.png +0 -0
- data/doc/images/package.png +0 -0
- data/doc/images/page_green.png +0 -0
- data/doc/images/page_white_text.png +0 -0
- data/doc/images/page_white_width.png +0 -0
- data/doc/images/plugin.png +0 -0
- data/doc/images/ruby.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/images/tag_green.png +0 -0
- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +94 -0
- data/doc/js/darkfish.js +155 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/rdoc.css +595 -0
- data/doc/table_of_contents.html +162 -0
- data/test/gene.gff +4 -0
- data/test/json_config.json +17 -0
- data/test/test_glyph.rb +33 -0
- data/test/test_mini_feature.rb +37 -0
- data/test/test_page.rb +127 -0
- data/test/test_primitive.rb +45 -0
- data/test/test_svgee.rb +73 -0
- data/test/test_track.rb +53 -0
- data/test/test_transcripts.gff +4 -0
- metadata +94 -14
|
@@ -0,0 +1,506 @@
|
|
|
1
|
+
<!DOCTYPE html>
|
|
2
|
+
|
|
3
|
+
<html>
|
|
4
|
+
<head>
|
|
5
|
+
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
|
|
6
|
+
|
|
7
|
+
<title>class Bio::Graphics::Track - RDoc Documentation</title>
|
|
8
|
+
|
|
9
|
+
<link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
|
|
10
|
+
|
|
11
|
+
<script type="text/javascript">
|
|
12
|
+
var rdoc_rel_prefix = "../../";
|
|
13
|
+
</script>
|
|
14
|
+
|
|
15
|
+
<script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
|
|
16
|
+
<script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
|
|
17
|
+
<script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
|
|
18
|
+
<script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
|
|
19
|
+
<script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
|
|
20
|
+
<script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
|
|
21
|
+
|
|
22
|
+
|
|
23
|
+
<body id="top" class="class">
|
|
24
|
+
<nav id="metadata">
|
|
25
|
+
<nav id="home-section" class="section">
|
|
26
|
+
<h3 class="section-header">
|
|
27
|
+
<a href="../../index.html">Home</a>
|
|
28
|
+
<a href="../../table_of_contents.html#classes">Classes</a>
|
|
29
|
+
<a href="../../table_of_contents.html#methods">Methods</a>
|
|
30
|
+
</h3>
|
|
31
|
+
</nav>
|
|
32
|
+
|
|
33
|
+
|
|
34
|
+
<nav id="search-section" class="section project-section" class="initially-hidden">
|
|
35
|
+
<form action="#" method="get" accept-charset="utf-8">
|
|
36
|
+
<h3 class="section-header">
|
|
37
|
+
<input type="text" name="search" placeholder="Search" id="search-field"
|
|
38
|
+
title="Type to search, Up and Down to navigate, Enter to load">
|
|
39
|
+
</h3>
|
|
40
|
+
</form>
|
|
41
|
+
|
|
42
|
+
<ul id="search-results" class="initially-hidden"></ul>
|
|
43
|
+
</nav>
|
|
44
|
+
|
|
45
|
+
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
<div id="file-metadata">
|
|
49
|
+
<nav id="file-list-section" class="section">
|
|
50
|
+
<h3 class="section-header">Defined In</h3>
|
|
51
|
+
<ul>
|
|
52
|
+
<li>lib/bio/graphics/track.rb
|
|
53
|
+
</ul>
|
|
54
|
+
</nav>
|
|
55
|
+
|
|
56
|
+
|
|
57
|
+
</div>
|
|
58
|
+
|
|
59
|
+
<div id="class-metadata">
|
|
60
|
+
|
|
61
|
+
<nav id="parent-class-section" class="section">
|
|
62
|
+
<h3 class="section-header">Parent</h3>
|
|
63
|
+
|
|
64
|
+
<p class="link">Object
|
|
65
|
+
|
|
66
|
+
</nav>
|
|
67
|
+
|
|
68
|
+
|
|
69
|
+
|
|
70
|
+
<!-- Method Quickref -->
|
|
71
|
+
<nav id="method-list-section" class="section">
|
|
72
|
+
<h3 class="section-header">Methods</h3>
|
|
73
|
+
|
|
74
|
+
<ul class="link-list">
|
|
75
|
+
|
|
76
|
+
<li ><a href="#method-c-new">::new</a>
|
|
77
|
+
|
|
78
|
+
<li ><a href="#method-i-add">#add</a>
|
|
79
|
+
|
|
80
|
+
<li ><a href="#method-i-get_rows">#get_rows</a>
|
|
81
|
+
|
|
82
|
+
<li ><a href="#method-i-overlaps">#overlaps</a>
|
|
83
|
+
|
|
84
|
+
</ul>
|
|
85
|
+
</nav>
|
|
86
|
+
|
|
87
|
+
</div>
|
|
88
|
+
|
|
89
|
+
<div id="project-metadata">
|
|
90
|
+
<nav id="fileindex-section" class="section project-section">
|
|
91
|
+
<h3 class="section-header">Pages</h3>
|
|
92
|
+
|
|
93
|
+
<ul>
|
|
94
|
+
|
|
95
|
+
<li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
|
|
96
|
+
|
|
97
|
+
</ul>
|
|
98
|
+
</nav>
|
|
99
|
+
|
|
100
|
+
<nav id="classindex-section" class="section project-section">
|
|
101
|
+
<h3 class="section-header">Class and Module Index</h3>
|
|
102
|
+
|
|
103
|
+
<ul class="link-list">
|
|
104
|
+
|
|
105
|
+
<li><a href="../../Bio.html">Bio</a>
|
|
106
|
+
|
|
107
|
+
<li><a href="../../Bio/Graphics.html">Bio::Graphics</a>
|
|
108
|
+
|
|
109
|
+
<li><a href="../../Bio/Graphics/Glyph.html">Bio::Graphics::Glyph</a>
|
|
110
|
+
|
|
111
|
+
<li><a href="../../Bio/Graphics/MiniFeature.html">Bio::Graphics::MiniFeature</a>
|
|
112
|
+
|
|
113
|
+
<li><a href="../../Bio/Graphics/Page.html">Bio::Graphics::Page</a>
|
|
114
|
+
|
|
115
|
+
<li><a href="../../Bio/Graphics/Primitive.html">Bio::Graphics::Primitive</a>
|
|
116
|
+
|
|
117
|
+
<li><a href="../../Bio/Graphics/SVGEE.html">Bio::Graphics::SVGEE</a>
|
|
118
|
+
|
|
119
|
+
<li><a href="../../Bio/Graphics/Track.html">Bio::Graphics::Track</a>
|
|
120
|
+
|
|
121
|
+
</ul>
|
|
122
|
+
</nav>
|
|
123
|
+
|
|
124
|
+
</div>
|
|
125
|
+
</nav>
|
|
126
|
+
|
|
127
|
+
<div id="documentation">
|
|
128
|
+
<h1 class="class">class Bio::Graphics::Track</h1>
|
|
129
|
+
|
|
130
|
+
<div id="description" class="description">
|
|
131
|
+
|
|
132
|
+
<p>The <a href="Track.html">Track</a> class holds and organises the features,
|
|
133
|
+
ordering them into different rows if they overlap</p>
|
|
134
|
+
|
|
135
|
+
</div><!-- description -->
|
|
136
|
+
|
|
137
|
+
|
|
138
|
+
|
|
139
|
+
|
|
140
|
+
<section id="5Buntitled-5D" class="documentation-section">
|
|
141
|
+
|
|
142
|
+
|
|
143
|
+
|
|
144
|
+
|
|
145
|
+
|
|
146
|
+
|
|
147
|
+
|
|
148
|
+
<!-- Attributes -->
|
|
149
|
+
<section id="attribute-method-details" class="method-section section">
|
|
150
|
+
<h3 class="section-header">Attributes</h3>
|
|
151
|
+
|
|
152
|
+
|
|
153
|
+
<div id="attribute-i-args" class="method-detail">
|
|
154
|
+
<div class="method-heading attribute-method-heading">
|
|
155
|
+
<span class="method-name">args</span><span
|
|
156
|
+
class="attribute-access-type">[R]</span>
|
|
157
|
+
</div>
|
|
158
|
+
|
|
159
|
+
<div class="method-description">
|
|
160
|
+
|
|
161
|
+
|
|
162
|
+
|
|
163
|
+
</div>
|
|
164
|
+
</div>
|
|
165
|
+
|
|
166
|
+
<div id="attribute-i-feature_height" class="method-detail">
|
|
167
|
+
<div class="method-heading attribute-method-heading">
|
|
168
|
+
<span class="method-name">feature_height</span><span
|
|
169
|
+
class="attribute-access-type">[RW]</span>
|
|
170
|
+
</div>
|
|
171
|
+
|
|
172
|
+
<div class="method-description">
|
|
173
|
+
|
|
174
|
+
|
|
175
|
+
|
|
176
|
+
</div>
|
|
177
|
+
</div>
|
|
178
|
+
|
|
179
|
+
<div id="attribute-i-feature_rows" class="method-detail">
|
|
180
|
+
<div class="method-heading attribute-method-heading">
|
|
181
|
+
<span class="method-name">feature_rows</span><span
|
|
182
|
+
class="attribute-access-type">[RW]</span>
|
|
183
|
+
</div>
|
|
184
|
+
|
|
185
|
+
<div class="method-description">
|
|
186
|
+
|
|
187
|
+
|
|
188
|
+
|
|
189
|
+
</div>
|
|
190
|
+
</div>
|
|
191
|
+
|
|
192
|
+
<div id="attribute-i-features" class="method-detail">
|
|
193
|
+
<div class="method-heading attribute-method-heading">
|
|
194
|
+
<span class="method-name">features</span><span
|
|
195
|
+
class="attribute-access-type">[RW]</span>
|
|
196
|
+
</div>
|
|
197
|
+
|
|
198
|
+
<div class="method-description">
|
|
199
|
+
|
|
200
|
+
|
|
201
|
+
|
|
202
|
+
</div>
|
|
203
|
+
</div>
|
|
204
|
+
|
|
205
|
+
<div id="attribute-i-glyph" class="method-detail">
|
|
206
|
+
<div class="method-heading attribute-method-heading">
|
|
207
|
+
<span class="method-name">glyph</span><span
|
|
208
|
+
class="attribute-access-type">[R]</span>
|
|
209
|
+
</div>
|
|
210
|
+
|
|
211
|
+
<div class="method-description">
|
|
212
|
+
|
|
213
|
+
|
|
214
|
+
|
|
215
|
+
</div>
|
|
216
|
+
</div>
|
|
217
|
+
|
|
218
|
+
<div id="attribute-i-label" class="method-detail">
|
|
219
|
+
<div class="method-heading attribute-method-heading">
|
|
220
|
+
<span class="method-name">label</span><span
|
|
221
|
+
class="attribute-access-type">[R]</span>
|
|
222
|
+
</div>
|
|
223
|
+
|
|
224
|
+
<div class="method-description">
|
|
225
|
+
|
|
226
|
+
|
|
227
|
+
|
|
228
|
+
</div>
|
|
229
|
+
</div>
|
|
230
|
+
|
|
231
|
+
<div id="attribute-i-max_y" class="method-detail">
|
|
232
|
+
<div class="method-heading attribute-method-heading">
|
|
233
|
+
<span class="method-name">max_y</span><span
|
|
234
|
+
class="attribute-access-type">[R]</span>
|
|
235
|
+
</div>
|
|
236
|
+
|
|
237
|
+
<div class="method-description">
|
|
238
|
+
|
|
239
|
+
|
|
240
|
+
|
|
241
|
+
</div>
|
|
242
|
+
</div>
|
|
243
|
+
|
|
244
|
+
<div id="attribute-i-min_width" class="method-detail">
|
|
245
|
+
<div class="method-heading attribute-method-heading">
|
|
246
|
+
<span class="method-name">min_width</span><span
|
|
247
|
+
class="attribute-access-type">[R]</span>
|
|
248
|
+
</div>
|
|
249
|
+
|
|
250
|
+
<div class="method-description">
|
|
251
|
+
|
|
252
|
+
|
|
253
|
+
|
|
254
|
+
</div>
|
|
255
|
+
</div>
|
|
256
|
+
|
|
257
|
+
<div id="attribute-i-name" class="method-detail">
|
|
258
|
+
<div class="method-heading attribute-method-heading">
|
|
259
|
+
<span class="method-name">name</span><span
|
|
260
|
+
class="attribute-access-type">[RW]</span>
|
|
261
|
+
</div>
|
|
262
|
+
|
|
263
|
+
<div class="method-description">
|
|
264
|
+
|
|
265
|
+
|
|
266
|
+
|
|
267
|
+
</div>
|
|
268
|
+
</div>
|
|
269
|
+
|
|
270
|
+
<div id="attribute-i-number_rows" class="method-detail">
|
|
271
|
+
<div class="method-heading attribute-method-heading">
|
|
272
|
+
<span class="method-name">number_rows</span><span
|
|
273
|
+
class="attribute-access-type">[RW]</span>
|
|
274
|
+
</div>
|
|
275
|
+
|
|
276
|
+
<div class="method-description">
|
|
277
|
+
|
|
278
|
+
|
|
279
|
+
|
|
280
|
+
</div>
|
|
281
|
+
</div>
|
|
282
|
+
|
|
283
|
+
<div id="attribute-i-scale" class="method-detail">
|
|
284
|
+
<div class="method-heading attribute-method-heading">
|
|
285
|
+
<span class="method-name">scale</span><span
|
|
286
|
+
class="attribute-access-type">[R]</span>
|
|
287
|
+
</div>
|
|
288
|
+
|
|
289
|
+
<div class="method-description">
|
|
290
|
+
|
|
291
|
+
|
|
292
|
+
|
|
293
|
+
</div>
|
|
294
|
+
</div>
|
|
295
|
+
|
|
296
|
+
<div id="attribute-i-track_height" class="method-detail">
|
|
297
|
+
<div class="method-heading attribute-method-heading">
|
|
298
|
+
<span class="method-name">track_height</span><span
|
|
299
|
+
class="attribute-access-type">[R]</span>
|
|
300
|
+
</div>
|
|
301
|
+
|
|
302
|
+
<div class="method-description">
|
|
303
|
+
|
|
304
|
+
|
|
305
|
+
|
|
306
|
+
</div>
|
|
307
|
+
</div>
|
|
308
|
+
|
|
309
|
+
</section><!-- attribute-method-details -->
|
|
310
|
+
|
|
311
|
+
|
|
312
|
+
<!-- Methods -->
|
|
313
|
+
|
|
314
|
+
<section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
|
|
315
|
+
<h3 class="section-header">Public Instance Methods</h3>
|
|
316
|
+
|
|
317
|
+
|
|
318
|
+
<div id="method-i-add" class="method-detail ">
|
|
319
|
+
|
|
320
|
+
<div class="method-heading">
|
|
321
|
+
<span class="method-name">add</span><span
|
|
322
|
+
class="method-args">(feature)</span>
|
|
323
|
+
|
|
324
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
325
|
+
|
|
326
|
+
</div>
|
|
327
|
+
|
|
328
|
+
|
|
329
|
+
<div class="method-description">
|
|
330
|
+
|
|
331
|
+
<p>Adds a new <a href="MiniFeature.html">MiniFeature</a> to the the @features
|
|
332
|
+
array</p>
|
|
333
|
+
|
|
334
|
+
|
|
335
|
+
|
|
336
|
+
|
|
337
|
+
<div class="method-source-code" id="add-source">
|
|
338
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 31</span>
|
|
339
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">feature</span>)
|
|
340
|
+
<span class="ruby-ivar">@features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">feature</span>
|
|
341
|
+
<span class="ruby-keyword">end</span></pre>
|
|
342
|
+
</div><!-- add-source -->
|
|
343
|
+
|
|
344
|
+
</div>
|
|
345
|
+
|
|
346
|
+
|
|
347
|
+
|
|
348
|
+
|
|
349
|
+
</div><!-- add-method -->
|
|
350
|
+
|
|
351
|
+
|
|
352
|
+
<div id="method-i-get_rows" class="method-detail ">
|
|
353
|
+
|
|
354
|
+
<div class="method-heading">
|
|
355
|
+
<span class="method-name">get_rows</span><span
|
|
356
|
+
class="method-args">()</span>
|
|
357
|
+
|
|
358
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
359
|
+
|
|
360
|
+
</div>
|
|
361
|
+
|
|
362
|
+
|
|
363
|
+
<div class="method-description">
|
|
364
|
+
|
|
365
|
+
<p>Calculates how many rows are needed per track for overlapping features and
|
|
366
|
+
which row each feature should be in</p>
|
|
367
|
+
|
|
368
|
+
|
|
369
|
+
|
|
370
|
+
|
|
371
|
+
<div class="method-source-code" id="get_rows-source">
|
|
372
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 38</span>
|
|
373
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">get_rows</span>
|
|
374
|
+
<span class="ruby-identifier">current_row</span> = <span class="ruby-value">1</span>
|
|
375
|
+
<span class="ruby-ivar">@feature_rows</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">length</span>,<span class="ruby-value">1</span>)
|
|
376
|
+
<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f1</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
377
|
+
<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f2</span>, <span class="ruby-identifier">j</span><span class="ruby-operator">|</span>
|
|
378
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">j</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">j</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">i</span>
|
|
379
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>,<span class="ruby-identifier">f2</span>)
|
|
380
|
+
<span class="ruby-ivar">@feature_rows</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
|
|
381
|
+
<span class="ruby-keyword">end</span>
|
|
382
|
+
<span class="ruby-keyword">end</span>
|
|
383
|
+
<span class="ruby-ivar">@number_rows</span> = <span class="ruby-ivar">@feature_rows</span>.<span class="ruby-identifier">max</span>
|
|
384
|
+
<span class="ruby-keyword">end</span>
|
|
385
|
+
<span class="ruby-keyword">end</span></pre>
|
|
386
|
+
</div><!-- get_rows-source -->
|
|
387
|
+
|
|
388
|
+
</div>
|
|
389
|
+
|
|
390
|
+
|
|
391
|
+
|
|
392
|
+
|
|
393
|
+
</div><!-- get_rows-method -->
|
|
394
|
+
|
|
395
|
+
|
|
396
|
+
<div id="method-i-overlaps" class="method-detail ">
|
|
397
|
+
|
|
398
|
+
<div class="method-heading">
|
|
399
|
+
<span class="method-name">overlaps</span><span
|
|
400
|
+
class="method-args">(f1, f2)</span>
|
|
401
|
+
|
|
402
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
403
|
+
|
|
404
|
+
</div>
|
|
405
|
+
|
|
406
|
+
|
|
407
|
+
<div class="method-description">
|
|
408
|
+
|
|
409
|
+
<p>Calculates if two <a href="MiniFeature.html">MiniFeature</a> objects
|
|
410
|
+
overlap by examining their start and end positions. If two features overlap
|
|
411
|
+
then then will be placed on separate rows of the track</p>
|
|
412
|
+
|
|
413
|
+
<p><code>args</code></p>
|
|
414
|
+
<ul><li>
|
|
415
|
+
<p>f1 - a <a href="MiniFeature.html">MiniFeature</a> object</p>
|
|
416
|
+
</li><li>
|
|
417
|
+
<p>f2 - a <a href="MiniFeature.html">MiniFeature</a> object</p>
|
|
418
|
+
</li></ul>
|
|
419
|
+
|
|
420
|
+
|
|
421
|
+
|
|
422
|
+
|
|
423
|
+
<div class="method-source-code" id="overlaps-source">
|
|
424
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 58</span>
|
|
425
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>, <span class="ruby-identifier">f2</span>)
|
|
426
|
+
(<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>) <span class="ruby-keyword">or</span> (<span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">start</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">f1</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">f2</span>.<span class="ruby-identifier">end</span>)
|
|
427
|
+
<span class="ruby-keyword">end</span></pre>
|
|
428
|
+
</div><!-- overlaps-source -->
|
|
429
|
+
|
|
430
|
+
</div>
|
|
431
|
+
|
|
432
|
+
|
|
433
|
+
|
|
434
|
+
|
|
435
|
+
</div><!-- overlaps-method -->
|
|
436
|
+
|
|
437
|
+
|
|
438
|
+
</section><!-- public-instance-method-details -->
|
|
439
|
+
|
|
440
|
+
<section id="public-class-5Buntitled-5D-method-details" class="method-section section">
|
|
441
|
+
<h3 class="section-header">Public Class Methods</h3>
|
|
442
|
+
|
|
443
|
+
|
|
444
|
+
<div id="method-c-new" class="method-detail ">
|
|
445
|
+
|
|
446
|
+
<div class="method-heading">
|
|
447
|
+
<span class="method-name">new</span><span
|
|
448
|
+
class="method-args">(args)</span>
|
|
449
|
+
|
|
450
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
451
|
+
|
|
452
|
+
</div>
|
|
453
|
+
|
|
454
|
+
|
|
455
|
+
<div class="method-description">
|
|
456
|
+
|
|
457
|
+
<p>Creates a new <a href="Track.html">Track</a></p>
|
|
458
|
+
|
|
459
|
+
|
|
460
|
+
|
|
461
|
+
|
|
462
|
+
<div class="method-source-code" id="new-source">
|
|
463
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/track.rb, line 9</span>
|
|
464
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
|
|
465
|
+
<span class="ruby-ivar">@args</span> = {<span class="ruby-value">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-value">:generic</span>,
|
|
466
|
+
<span class="ruby-value">:name</span> =<span class="ruby-operator">></span> <span class="ruby-string">"feature_track"</span>,
|
|
467
|
+
<span class="ruby-value">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">true</span>,
|
|
468
|
+
<span class="ruby-value">:feature_height</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>,
|
|
469
|
+
<span class="ruby-value">:track_height</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">nil</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
|
|
470
|
+
<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:glyph</span>]
|
|
471
|
+
<span class="ruby-ivar">@name</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:name</span>]
|
|
472
|
+
<span class="ruby-ivar">@label</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:label</span>]
|
|
473
|
+
<span class="ruby-ivar">@track_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:track_height</span>]
|
|
474
|
+
<span class="ruby-ivar">@features</span> = []
|
|
475
|
+
<span class="ruby-ivar">@feature_rows</span> = []
|
|
476
|
+
<span class="ruby-ivar">@scale</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:scale</span>]
|
|
477
|
+
<span class="ruby-ivar">@feature_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-value">:feature_height</span>]
|
|
478
|
+
<span class="ruby-ivar">@number_of_rows</span> = <span class="ruby-value">1</span>
|
|
479
|
+
<span class="ruby-ivar">@max_y</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:max_y</span>]
|
|
480
|
+
<span class="ruby-ivar">@min_width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:min_width</span>]
|
|
481
|
+
|
|
482
|
+
|
|
483
|
+
<span class="ruby-keyword">end</span></pre>
|
|
484
|
+
</div><!-- new-source -->
|
|
485
|
+
|
|
486
|
+
</div>
|
|
487
|
+
|
|
488
|
+
|
|
489
|
+
|
|
490
|
+
|
|
491
|
+
</div><!-- new-method -->
|
|
492
|
+
|
|
493
|
+
|
|
494
|
+
</section><!-- public-class-method-details -->
|
|
495
|
+
|
|
496
|
+
</section><!-- 5Buntitled-5D -->
|
|
497
|
+
|
|
498
|
+
</div><!-- documentation -->
|
|
499
|
+
|
|
500
|
+
|
|
501
|
+
<footer id="validator-badges">
|
|
502
|
+
<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
|
|
503
|
+
<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
|
|
504
|
+
<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
|
|
505
|
+
</footer>
|
|
506
|
+
|