bio-svgenes 0.3.1 → 0.3.2
Sign up to get free protection for your applications and to get access to all the features.
- data/README.md +88 -0
- data/VERSION +1 -1
- data/bio-svgenes.gemspec +131 -8
- data/doc/classes/Bio.html +131 -0
- data/doc/classes/Bio/Graphics.html +142 -0
- data/doc/classes/Bio/Graphics/Glyph.html +987 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000001.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000002.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000003.html +32 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000004.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000005.html +25 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000006.html +29 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000007.html +107 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000008.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000009.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000010.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000011.html +75 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000012.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000013.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000014.html +26 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000015.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000016.html +32 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000017.html +27 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000018.html +25 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000019.html +29 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000020.html +107 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000021.html +51 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000022.html +23 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000023.html +18 -0
- data/doc/classes/Bio/Graphics/Glyph.src/M000024.html +75 -0
- data/doc/classes/Bio/Graphics/MiniFeature.html +243 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000001.html +25 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000003.html +25 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000024.html +25 -0
- data/doc/classes/Bio/Graphics/Page.html +705 -0
- data/doc/classes/Bio/Graphics/Page.src/M000010.html +35 -0
- data/doc/classes/Bio/Graphics/Page.src/M000011.html +83 -0
- data/doc/classes/Bio/Graphics/Page.src/M000012.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000013.html +29 -0
- data/doc/classes/Bio/Graphics/Page.src/M000014.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000015.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000016.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000017.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000018.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000019.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000020.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000021.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000022.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000023.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000024.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000025.html +35 -0
- data/doc/classes/Bio/Graphics/Page.src/M000026.html +83 -0
- data/doc/classes/Bio/Graphics/Page.src/M000027.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000028.html +29 -0
- data/doc/classes/Bio/Graphics/Page.src/M000029.html +24 -0
- data/doc/classes/Bio/Graphics/Page.src/M000030.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000031.html +20 -0
- data/doc/classes/Bio/Graphics/Page.src/M000032.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000033.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000034.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000035.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000036.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000037.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000038.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000039.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000040.html +107 -0
- data/doc/classes/Bio/Graphics/Page.src/M000041.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000042.html +23 -0
- data/doc/classes/Bio/Graphics/Page.src/M000043.html +18 -0
- data/doc/classes/Bio/Graphics/Page.src/M000044.html +18 -0
- data/doc/classes/Bio/Graphics/Primitive.html +204 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000001.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000002.html +20 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000008.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000009.html +20 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000022.html +21 -0
- data/doc/classes/Bio/Graphics/Primitive.src/M000023.html +20 -0
- data/doc/classes/Bio/Graphics/SVGEE.html +290 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000002.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000003.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000004.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000005.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000006.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000007.html +21 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000008.html +27 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000009.html +23 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000016.html +24 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000017.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000018.html +18 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000019.html +21 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000020.html +27 -0
- data/doc/classes/Bio/Graphics/SVGEE.src/M000021.html +23 -0
- data/doc/classes/Bio/Graphics/Track.html +473 -0
- data/doc/classes/Bio/Graphics/Track.src/M000001.html +35 -0
- data/doc/classes/Bio/Graphics/Track.src/M000002.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000003.html +28 -0
- data/doc/classes/Bio/Graphics/Track.src/M000004.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000010.html +35 -0
- data/doc/classes/Bio/Graphics/Track.src/M000011.html +18 -0
- data/doc/classes/Bio/Graphics/Track.src/M000012.html +28 -0
- data/doc/classes/Bio/Graphics/Track.src/M000013.html +18 -0
- data/doc/created.rid +1 -9
- data/doc/files/lib/bio-svgenes_rb.html +131 -0
- data/doc/files/lib/bio/graphics/glyph_rb.html +101 -0
- data/doc/files/lib/bio/graphics/mini_feature_rb.html +101 -0
- data/doc/files/lib/bio/graphics/page_rb.html +111 -0
- data/doc/files/lib/bio/graphics/primitive_rb.html +101 -0
- data/doc/files/lib/bio/graphics/svgee_rb.html +101 -0
- data/doc/files/lib/bio/graphics/track_rb.html +101 -0
- data/doc/fr_class_index.html +34 -0
- data/doc/fr_file_index.html +33 -0
- data/doc/fr_method_index.html +70 -0
- data/doc/index.html +21 -91
- data/doc/manual/bootstrap/css/bootstrap-responsive.css +1109 -0
- data/doc/manual/bootstrap/css/bootstrap-responsive.min.css +9 -0
- data/doc/manual/bootstrap/css/bootstrap.css +6158 -0
- data/doc/manual/bootstrap/css/bootstrap.min.css +9 -0
- data/doc/manual/bootstrap/img/glyphicons-halflings-white.png +0 -0
- data/doc/manual/bootstrap/img/glyphicons-halflings.png +0 -0
- data/doc/manual/bootstrap/js/bootstrap.js +2276 -0
- data/doc/manual/bootstrap/js/bootstrap.min.js +6 -0
- data/doc/manual/img/circle.png +0 -0
- data/doc/manual/img/directed.png +0 -0
- data/doc/manual/img/down_triangle.png +0 -0
- data/doc/manual/img/histogram.png +0 -0
- data/doc/manual/img/span.png +0 -0
- data/doc/manual/img/transcript.png +0 -0
- data/doc/manual/img/up_triangle.png +0 -0
- data/doc/manual/manual.html +360 -0
- data/doc/manual/manual.md +307 -0
- data/doc/rdoc-style.css +208 -0
- data/examples/example.rb +12 -8
- data/examples/{make_example.rb → example2.rb} +5 -16
- data/lib/bio/graphics/glyph.rb +293 -126
- data/lib/bio/graphics/mini_feature.rb +24 -17
- data/lib/bio/graphics/page.rb +112 -54
- data/lib/bio/graphics/primitive.rb +12 -9
- data/lib/bio/graphics/svgee.rb +9 -11
- data/lib/bio/graphics/track.rb +92 -10
- metadata +132 -9
- data/README.rdoc +0 -19
- data/examples/annotate_snps.rb +0 -86
- data/examples/eg2.rb +0 -40
- data/examples/get_coverage_in_windows.rb +0 -176
|
@@ -0,0 +1,987 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
+
<head>
|
|
8
|
+
<title>Class: Bio::Graphics::Glyph</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
+
<link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
+
<script type="text/javascript">
|
|
13
|
+
// <![CDATA[
|
|
14
|
+
|
|
15
|
+
function popupCode( url ) {
|
|
16
|
+
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
+
}
|
|
18
|
+
|
|
19
|
+
function toggleCode( id ) {
|
|
20
|
+
if ( document.getElementById )
|
|
21
|
+
elem = document.getElementById( id );
|
|
22
|
+
else if ( document.all )
|
|
23
|
+
elem = eval( "document.all." + id );
|
|
24
|
+
else
|
|
25
|
+
return false;
|
|
26
|
+
|
|
27
|
+
elemStyle = elem.style;
|
|
28
|
+
|
|
29
|
+
if ( elemStyle.display != "block" ) {
|
|
30
|
+
elemStyle.display = "block"
|
|
31
|
+
} else {
|
|
32
|
+
elemStyle.display = "none"
|
|
33
|
+
}
|
|
34
|
+
|
|
35
|
+
return true;
|
|
36
|
+
}
|
|
37
|
+
|
|
38
|
+
// Make codeblocks hidden by default
|
|
39
|
+
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
+
|
|
41
|
+
// ]]>
|
|
42
|
+
</script>
|
|
43
|
+
|
|
44
|
+
</head>
|
|
45
|
+
<body>
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
|
|
49
|
+
<div id="classHeader">
|
|
50
|
+
<table class="header-table">
|
|
51
|
+
<tr class="top-aligned-row">
|
|
52
|
+
<td><strong>Class</strong></td>
|
|
53
|
+
<td class="class-name-in-header">Bio::Graphics::Glyph</td>
|
|
54
|
+
</tr>
|
|
55
|
+
<tr class="top-aligned-row">
|
|
56
|
+
<td><strong>In:</strong></td>
|
|
57
|
+
<td>
|
|
58
|
+
<a href="../../../files/lib/bio/graphics/glyph_rb.html">
|
|
59
|
+
lib/bio/graphics/glyph.rb
|
|
60
|
+
</a>
|
|
61
|
+
<br />
|
|
62
|
+
</td>
|
|
63
|
+
</tr>
|
|
64
|
+
|
|
65
|
+
<tr class="top-aligned-row">
|
|
66
|
+
<td><strong>Parent:</strong></td>
|
|
67
|
+
<td>
|
|
68
|
+
Object
|
|
69
|
+
</td>
|
|
70
|
+
</tr>
|
|
71
|
+
</table>
|
|
72
|
+
</div>
|
|
73
|
+
<!-- banner header -->
|
|
74
|
+
|
|
75
|
+
<div id="bodyContent">
|
|
76
|
+
|
|
77
|
+
|
|
78
|
+
|
|
79
|
+
<div id="contextContent">
|
|
80
|
+
|
|
81
|
+
<div id="description">
|
|
82
|
+
<p>
|
|
83
|
+
A glyph is a particular shape that represents a genomic feature. <a
|
|
84
|
+
href="Glyph.html">Bio::Graphics::Glyph</a> objects represent glyphs.
|
|
85
|
+
Bio::Graphics::Glyphs are created internally according to specification
|
|
86
|
+
from the <a href="Track.html">Bio::Graphics::Track</a> and not instantiated
|
|
87
|
+
directly by the user. Internally, these are constructed as an array of <a
|
|
88
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects, which are
|
|
89
|
+
collections of simple shapes, combined appropriately to make a glyph
|
|
90
|
+
</p>
|
|
91
|
+
|
|
92
|
+
</div>
|
|
93
|
+
|
|
94
|
+
|
|
95
|
+
</div>
|
|
96
|
+
|
|
97
|
+
<div id="method-list">
|
|
98
|
+
<h3 class="section-bar">Methods</h3>
|
|
99
|
+
|
|
100
|
+
<div class="name-list">
|
|
101
|
+
<a href="#M000015">circle</a>
|
|
102
|
+
<a href="#M000016">directed</a>
|
|
103
|
+
<a href="#M000017">down_triangle</a>
|
|
104
|
+
<a href="#M000014">generic</a>
|
|
105
|
+
<a href="#M000024">gradient</a>
|
|
106
|
+
<a href="#M000023">gradients</a>
|
|
107
|
+
<a href="#M000022">label</a>
|
|
108
|
+
<a href="#M000021">scale</a>
|
|
109
|
+
<a href="#M000019">span</a>
|
|
110
|
+
<a href="#M000020">transcript</a>
|
|
111
|
+
<a href="#M000018">up_triangle</a>
|
|
112
|
+
</div>
|
|
113
|
+
</div>
|
|
114
|
+
|
|
115
|
+
</div>
|
|
116
|
+
|
|
117
|
+
|
|
118
|
+
<!-- if includes -->
|
|
119
|
+
|
|
120
|
+
<div id="section">
|
|
121
|
+
|
|
122
|
+
|
|
123
|
+
|
|
124
|
+
|
|
125
|
+
|
|
126
|
+
<div id="attribute-list">
|
|
127
|
+
<h3 class="section-bar">Attributes</h3>
|
|
128
|
+
|
|
129
|
+
<div class="name-list">
|
|
130
|
+
<table>
|
|
131
|
+
<tr class="top-aligned-row context-row">
|
|
132
|
+
<td class="context-item-name">glyphs</td>
|
|
133
|
+
<td class="context-item-value"> [R] </td>
|
|
134
|
+
<td class="context-item-desc">
|
|
135
|
+
The different type of Glyphs are:
|
|
136
|
+
|
|
137
|
+
<ul>
|
|
138
|
+
<li>:<a href="Glyph.html#M000014">generic</a>
|
|
139
|
+
|
|
140
|
+
</li>
|
|
141
|
+
<li>:<a href="Glyph.html#M000015">circle</a>
|
|
142
|
+
|
|
143
|
+
</li>
|
|
144
|
+
<li>:<a href="Glyph.html#M000016">directed</a>
|
|
145
|
+
|
|
146
|
+
</li>
|
|
147
|
+
<li>:<a href="Glyph.html#M000017">down_triangle</a>
|
|
148
|
+
|
|
149
|
+
</li>
|
|
150
|
+
<li>:<a href="Glyph.html#M000018">up_triangle</a>
|
|
151
|
+
|
|
152
|
+
</li>
|
|
153
|
+
<li>:<a href="Glyph.html#M000019">span</a>
|
|
154
|
+
|
|
155
|
+
</li>
|
|
156
|
+
<li>:<a href="Glyph.html#M000020">transcript</a>
|
|
157
|
+
|
|
158
|
+
</li>
|
|
159
|
+
<li>:<a href="Glyph.html#M000021">scale</a>
|
|
160
|
+
|
|
161
|
+
</li>
|
|
162
|
+
<li>:<a href="Glyph.html#M000022">label</a>
|
|
163
|
+
|
|
164
|
+
</li>
|
|
165
|
+
<li>:histogram
|
|
166
|
+
|
|
167
|
+
</li>
|
|
168
|
+
</ul>
|
|
169
|
+
</td>
|
|
170
|
+
</tr>
|
|
171
|
+
</table>
|
|
172
|
+
</div>
|
|
173
|
+
</div>
|
|
174
|
+
|
|
175
|
+
|
|
176
|
+
|
|
177
|
+
<!-- if method_list -->
|
|
178
|
+
<div id="methods">
|
|
179
|
+
<h3 class="section-bar">Public Class methods</h3>
|
|
180
|
+
|
|
181
|
+
<div id="method-M000015" class="method-detail">
|
|
182
|
+
<a name="M000015"></a>
|
|
183
|
+
|
|
184
|
+
<div class="method-heading">
|
|
185
|
+
<a href="Glyph.src/M000015.html" target="Code" class="method-signature"
|
|
186
|
+
onclick="popupCode('Glyph.src/M000015.html');return false;">
|
|
187
|
+
<span class="method-name">circle</span><span class="method-args">(args)</span>
|
|
188
|
+
</a>
|
|
189
|
+
</div>
|
|
190
|
+
|
|
191
|
+
<div class="method-description">
|
|
192
|
+
<p>
|
|
193
|
+
A circular glyph centered on the start of the feature it represents
|
|
194
|
+
</p>
|
|
195
|
+
<h2>args</h2>
|
|
196
|
+
<ul>
|
|
197
|
+
<li>:radius = the radius of the <a href="Glyph.html#M000015">circle</a>
|
|
198
|
+
(default = 10)
|
|
199
|
+
|
|
200
|
+
</li>
|
|
201
|
+
<li>:fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
|
|
202
|
+
(default = ‘red’), can be any SVG colour eg rgb(256,0,0) or
|
|
203
|
+
FF0000, or one of the built in <a href="Glyph.html#M000024">gradient</a>
|
|
204
|
+
types <a href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
205
|
+
|
|
206
|
+
</li>
|
|
207
|
+
</ul>
|
|
208
|
+
<pre>
|
|
209
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
210
|
+
</pre>
|
|
211
|
+
<p>
|
|
212
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
213
|
+
</p>
|
|
214
|
+
<pre>
|
|
215
|
+
{:type => :radial,
|
|
216
|
+
:id => :custom,
|
|
217
|
+
:cx => 5,
|
|
218
|
+
:cy => 5,
|
|
219
|
+
:r => 50,
|
|
220
|
+
:fx => 50,
|
|
221
|
+
:fy => 50,
|
|
222
|
+
:stops => [ {
|
|
223
|
+
:offset => 0,
|
|
224
|
+
:color => 'rgb(255,255,255)',
|
|
225
|
+
:opacity => 0
|
|
226
|
+
}, {
|
|
227
|
+
:offset => 100,
|
|
228
|
+
:color => 'rgb(0,127,200)',
|
|
229
|
+
:opacity => 1
|
|
230
|
+
}, ]
|
|
231
|
+
} #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
|
|
232
|
+
</pre>
|
|
233
|
+
<ul>
|
|
234
|
+
<li>:stroke_width = The width of the outline stroke (default = 1), can be any
|
|
235
|
+
SVG colour eg rgb(256,0,0) or FF0000
|
|
236
|
+
|
|
237
|
+
</li>
|
|
238
|
+
<li>:style = an arbitrary SVG compliant style string eg
|
|
239
|
+
"fill-opacity:0.4;"
|
|
240
|
+
|
|
241
|
+
</li>
|
|
242
|
+
<li>:x = base x coordinate of the feature in pixels, usually added by the <a
|
|
243
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
244
|
+
|
|
245
|
+
</li>
|
|
246
|
+
<li>:y = base y coordinate of the feature in pixels, usually added by the <a
|
|
247
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
248
|
+
|
|
249
|
+
</li>
|
|
250
|
+
</ul>
|
|
251
|
+
<h3>returns</h3>
|
|
252
|
+
<ul>
|
|
253
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
254
|
+
Bio::Graphic::Primitive objects
|
|
255
|
+
|
|
256
|
+
</li>
|
|
257
|
+
</ul>
|
|
258
|
+
</div>
|
|
259
|
+
</div>
|
|
260
|
+
|
|
261
|
+
<div id="method-M000016" class="method-detail">
|
|
262
|
+
<a name="M000016"></a>
|
|
263
|
+
|
|
264
|
+
<div class="method-heading">
|
|
265
|
+
<a href="Glyph.src/M000016.html" target="Code" class="method-signature"
|
|
266
|
+
onclick="popupCode('Glyph.src/M000016.html');return false;">
|
|
267
|
+
<span class="method-name">directed</span><span class="method-args">(args)</span>
|
|
268
|
+
</a>
|
|
269
|
+
</div>
|
|
270
|
+
|
|
271
|
+
<div class="method-description">
|
|
272
|
+
<p>
|
|
273
|
+
A polygon glyph with a point on the end that represents the features strand
|
|
274
|
+
and direction
|
|
275
|
+
</p>
|
|
276
|
+
<h2>args</h2>
|
|
277
|
+
<ul>
|
|
278
|
+
<li>:width = the width of the feature in px
|
|
279
|
+
|
|
280
|
+
</li>
|
|
281
|
+
<li>:fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
|
|
282
|
+
(default = ‘red’), can be any SVG colour eg rgb(256,0,0) or
|
|
283
|
+
FF0000, or one of the built in <a href="Glyph.html#M000024">gradient</a>
|
|
284
|
+
types <a href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
285
|
+
|
|
286
|
+
</li>
|
|
287
|
+
</ul>
|
|
288
|
+
<pre>
|
|
289
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
290
|
+
</pre>
|
|
291
|
+
<p>
|
|
292
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
293
|
+
</p>
|
|
294
|
+
<pre>
|
|
295
|
+
{:type => :radial,
|
|
296
|
+
:id => :custom,
|
|
297
|
+
:cx => 5,
|
|
298
|
+
:cy => 5,
|
|
299
|
+
:r => 50,
|
|
300
|
+
:fx => 50,
|
|
301
|
+
:fy => 50,
|
|
302
|
+
:stops => [ {
|
|
303
|
+
:offset => 0,
|
|
304
|
+
:color => 'rgb(255,255,255)',
|
|
305
|
+
:opacity => 0
|
|
306
|
+
}, {
|
|
307
|
+
:offset => 100,
|
|
308
|
+
:color => 'rgb(0,127,200)',
|
|
309
|
+
:opacity => 1
|
|
310
|
+
}, ]
|
|
311
|
+
}
|
|
312
|
+
</pre>
|
|
313
|
+
<ul>
|
|
314
|
+
<li>:stroke = the outline colour of the <a href="Glyph.html">Glyph</a> (default
|
|
315
|
+
= "black"), can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
316
|
+
|
|
317
|
+
</li>
|
|
318
|
+
<li>:stroke_width = The width of the outline stroke (default = 1), can be any
|
|
319
|
+
SVG colour eg rgb(256,0,0) or FF0000
|
|
320
|
+
|
|
321
|
+
</li>
|
|
322
|
+
<li>:style = an arbitrary SVG compliant style string eg
|
|
323
|
+
"fill-opacity:0.4;"
|
|
324
|
+
|
|
325
|
+
</li>
|
|
326
|
+
<li>:strand = the strand on which the feature is located. May be
|
|
327
|
+
’+’ or ’-’
|
|
328
|
+
|
|
329
|
+
</li>
|
|
330
|
+
<li>:points = the x and y axis coordinates that make up the corners of the
|
|
331
|
+
polygon, calculated and added by the <a
|
|
332
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
333
|
+
|
|
334
|
+
</li>
|
|
335
|
+
<li>:x = base x coordinate of the feature in pixels, usually added by the <a
|
|
336
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
337
|
+
|
|
338
|
+
</li>
|
|
339
|
+
<li>:y = base y coordinate of the feature in pixels, usually added by the <a
|
|
340
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
341
|
+
|
|
342
|
+
</li>
|
|
343
|
+
</ul>
|
|
344
|
+
<p>
|
|
345
|
+
The points of the polygon are calculated form the +:x+ and +:y+
|
|
346
|
+
co-ordinates
|
|
347
|
+
</p>
|
|
348
|
+
<h3>returns</h3>
|
|
349
|
+
<ul>
|
|
350
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
351
|
+
Bio::Graphic::Primitive objects
|
|
352
|
+
|
|
353
|
+
</li>
|
|
354
|
+
</ul>
|
|
355
|
+
</div>
|
|
356
|
+
</div>
|
|
357
|
+
|
|
358
|
+
<div id="method-M000017" class="method-detail">
|
|
359
|
+
<a name="M000017"></a>
|
|
360
|
+
|
|
361
|
+
<div class="method-heading">
|
|
362
|
+
<a href="Glyph.src/M000017.html" target="Code" class="method-signature"
|
|
363
|
+
onclick="popupCode('Glyph.src/M000017.html');return false;">
|
|
364
|
+
<span class="method-name">down_triangle</span><span class="method-args">(args)</span>
|
|
365
|
+
</a>
|
|
366
|
+
</div>
|
|
367
|
+
|
|
368
|
+
<div class="method-description">
|
|
369
|
+
<p>
|
|
370
|
+
A downward-pointing triangle glyph
|
|
371
|
+
</p>
|
|
372
|
+
<h2>args</h2>
|
|
373
|
+
<ul>
|
|
374
|
+
<li>:height = the height of the <a href="Glyph.html">Glyph</a> (default = 10)
|
|
375
|
+
|
|
376
|
+
</li>
|
|
377
|
+
<li>:fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
|
|
378
|
+
(default = ‘red’), can be any SVG colour eg rgb(256,0,0) or
|
|
379
|
+
FF0000, or one of the built in <a href="Glyph.html#M000024">gradient</a>
|
|
380
|
+
types <a href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
381
|
+
|
|
382
|
+
</li>
|
|
383
|
+
</ul>
|
|
384
|
+
<pre>
|
|
385
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
386
|
+
</pre>
|
|
387
|
+
<p>
|
|
388
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
389
|
+
</p>
|
|
390
|
+
<pre>
|
|
391
|
+
{:type => :radial,
|
|
392
|
+
:id => :custom,
|
|
393
|
+
:cx => 5,
|
|
394
|
+
:cy => 5,
|
|
395
|
+
:r => 50,
|
|
396
|
+
:fx => 50,
|
|
397
|
+
:fy => 50,
|
|
398
|
+
:stops => [ {
|
|
399
|
+
:offset => 0,
|
|
400
|
+
:color => 'rgb(255,255,255)',
|
|
401
|
+
:opacity => 0
|
|
402
|
+
}, {
|
|
403
|
+
:offset => 100,
|
|
404
|
+
:color => 'rgb(0,127,200)',
|
|
405
|
+
:opacity => 1
|
|
406
|
+
}, ]
|
|
407
|
+
} #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
|
|
408
|
+
</pre>
|
|
409
|
+
<ul>
|
|
410
|
+
<li>:stroke_width = The width of the outline stroke (default = 1), can be any
|
|
411
|
+
SVG colour eg rgb(256,0,0) or FF0000
|
|
412
|
+
|
|
413
|
+
</li>
|
|
414
|
+
<li>:style = an arbitrary SVG compliant style string eg
|
|
415
|
+
"fill-opacity:0.4;"
|
|
416
|
+
|
|
417
|
+
</li>
|
|
418
|
+
<li>:x = x coordinate of the feature in pixels, usually added by the <a
|
|
419
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
420
|
+
|
|
421
|
+
</li>
|
|
422
|
+
<li>:y = y coordinate of the feature in pixels, usually added by the <a
|
|
423
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
424
|
+
|
|
425
|
+
</li>
|
|
426
|
+
</ul>
|
|
427
|
+
<h3>returns</h3>
|
|
428
|
+
<ul>
|
|
429
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
430
|
+
Bio::Graphic::Primitive objects
|
|
431
|
+
|
|
432
|
+
</li>
|
|
433
|
+
</ul>
|
|
434
|
+
</div>
|
|
435
|
+
</div>
|
|
436
|
+
|
|
437
|
+
<div id="method-M000014" class="method-detail">
|
|
438
|
+
<a name="M000014"></a>
|
|
439
|
+
|
|
440
|
+
<div class="method-heading">
|
|
441
|
+
<a href="Glyph.src/M000014.html" target="Code" class="method-signature"
|
|
442
|
+
onclick="popupCode('Glyph.src/M000014.html');return false;">
|
|
443
|
+
<span class="method-name">generic</span><span class="method-args">(args)</span>
|
|
444
|
+
</a>
|
|
445
|
+
</div>
|
|
446
|
+
|
|
447
|
+
<div class="method-description">
|
|
448
|
+
<p>
|
|
449
|
+
A <a href="Glyph.html#M000014">generic</a> glyph is a block of colour that
|
|
450
|
+
displays no specific directional information attached.
|
|
451
|
+
</p>
|
|
452
|
+
<h2>args</h2>
|
|
453
|
+
<ul>
|
|
454
|
+
<li>:height = the height of the <a href="Glyph.html">Glyph</a> (default = 10)
|
|
455
|
+
|
|
456
|
+
</li>
|
|
457
|
+
<li>:fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
|
|
458
|
+
(default = ‘red’), can be any SVG colour eg rgb(256,0,0) or
|
|
459
|
+
FF0000, or one of the built in <a href="Glyph.html#M000024">gradient</a>
|
|
460
|
+
types <a href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
461
|
+
|
|
462
|
+
</li>
|
|
463
|
+
</ul>
|
|
464
|
+
<pre>
|
|
465
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
466
|
+
</pre>
|
|
467
|
+
<p>
|
|
468
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
469
|
+
</p>
|
|
470
|
+
<pre>
|
|
471
|
+
{:type => :radial,
|
|
472
|
+
:id => :custom,
|
|
473
|
+
:cx => 5,
|
|
474
|
+
:cy => 5,
|
|
475
|
+
:r => 50,
|
|
476
|
+
:fx => 50,
|
|
477
|
+
:fy => 50,
|
|
478
|
+
:stops => [ {
|
|
479
|
+
:offset => 0,
|
|
480
|
+
:color => 'rgb(255,255,255)',
|
|
481
|
+
:opacity => 0
|
|
482
|
+
}, {
|
|
483
|
+
:offset => 100,
|
|
484
|
+
:color => 'rgb(0,127,200)',
|
|
485
|
+
:opacity => 1
|
|
486
|
+
}, ]
|
|
487
|
+
} #* :stroke = the outline colour of the Glyph (default = "black"), can be any SVG colour eg rgb(256,0,0) or #FF0000
|
|
488
|
+
</pre>
|
|
489
|
+
<ul>
|
|
490
|
+
<li>:stroke_width = The width of the outline stroke (default = 1), can be any
|
|
491
|
+
SVG colour eg rgb(256,0,0) or FF0000
|
|
492
|
+
|
|
493
|
+
</li>
|
|
494
|
+
<li>:x_round = x-axis radius of the ellipse used to round off the corners of
|
|
495
|
+
the rectangle (default = 1)
|
|
496
|
+
|
|
497
|
+
</li>
|
|
498
|
+
<li>:y_round = y-axis radius of the ellipse used to round off the corners of
|
|
499
|
+
the rectangle (default = 1)
|
|
500
|
+
|
|
501
|
+
</li>
|
|
502
|
+
<li>:style = an arbitrary SVG compliant style string eg
|
|
503
|
+
"fill-opacity:0.4;"
|
|
504
|
+
|
|
505
|
+
</li>
|
|
506
|
+
<li>:x = x coordinate of the feature in pixels, usually added by the <a
|
|
507
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
508
|
+
|
|
509
|
+
</li>
|
|
510
|
+
<li>:y = y coordinate of the feature in pixels, usually added by the <a
|
|
511
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
512
|
+
|
|
513
|
+
</li>
|
|
514
|
+
</ul>
|
|
515
|
+
<h3>returns</h3>
|
|
516
|
+
<ul>
|
|
517
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
518
|
+
Bio::Graphic::Primitive objects
|
|
519
|
+
|
|
520
|
+
</li>
|
|
521
|
+
</ul>
|
|
522
|
+
</div>
|
|
523
|
+
</div>
|
|
524
|
+
|
|
525
|
+
<div id="method-M000024" class="method-detail">
|
|
526
|
+
<a name="M000024"></a>
|
|
527
|
+
|
|
528
|
+
<div class="method-heading">
|
|
529
|
+
<a href="Glyph.src/M000024.html" target="Code" class="method-signature"
|
|
530
|
+
onclick="popupCode('Glyph.src/M000024.html');return false;">
|
|
531
|
+
<span class="method-name">gradient</span><span class="method-args">(gradient)</span>
|
|
532
|
+
</a>
|
|
533
|
+
</div>
|
|
534
|
+
|
|
535
|
+
<div class="method-description">
|
|
536
|
+
<p>
|
|
537
|
+
Sets the the type (linear or radial) and colours for a pre-defined <a
|
|
538
|
+
href="Glyph.html#M000024">gradient</a>
|
|
539
|
+
</p>
|
|
540
|
+
<h2>args</h2>
|
|
541
|
+
<ul>
|
|
542
|
+
<li><a href="Glyph.html#M000024">gradient</a> = a pre-defined <a
|
|
543
|
+
href="Glyph.html#M000024">gradient</a> type, one of
|
|
544
|
+
|
|
545
|
+
</li>
|
|
546
|
+
</ul>
|
|
547
|
+
<pre>
|
|
548
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
549
|
+
</pre>
|
|
550
|
+
</div>
|
|
551
|
+
</div>
|
|
552
|
+
|
|
553
|
+
<div id="method-M000023" class="method-detail">
|
|
554
|
+
<a name="M000023"></a>
|
|
555
|
+
|
|
556
|
+
<div class="method-heading">
|
|
557
|
+
<a href="Glyph.src/M000023.html" target="Code" class="method-signature"
|
|
558
|
+
onclick="popupCode('Glyph.src/M000023.html');return false;">
|
|
559
|
+
<span class="method-name">gradients</span><span class="method-args">(</span>
|
|
560
|
+
</a>
|
|
561
|
+
</div>
|
|
562
|
+
|
|
563
|
+
<div class="method-description">
|
|
564
|
+
<p>
|
|
565
|
+
The list of pre-defined <a href="Glyph.html#M000023">gradients</a>
|
|
566
|
+
</p>
|
|
567
|
+
</div>
|
|
568
|
+
</div>
|
|
569
|
+
|
|
570
|
+
<div id="method-M000022" class="method-detail">
|
|
571
|
+
<a name="M000022"></a>
|
|
572
|
+
|
|
573
|
+
<div class="method-heading">
|
|
574
|
+
<a href="Glyph.src/M000022.html" target="Code" class="method-signature"
|
|
575
|
+
onclick="popupCode('Glyph.src/M000022.html');return false;">
|
|
576
|
+
<span class="method-name">label</span><span class="method-args">(args)</span>
|
|
577
|
+
</a>
|
|
578
|
+
</div>
|
|
579
|
+
|
|
580
|
+
<div class="method-description">
|
|
581
|
+
<p>
|
|
582
|
+
Creates a <a href="Glyph.html#M000022">label</a> <a
|
|
583
|
+
href="Glyph.html">Glyph</a> to write text
|
|
584
|
+
</p>
|
|
585
|
+
<p>
|
|
586
|
+
<tt>args</tt>
|
|
587
|
+
</p>
|
|
588
|
+
<ul>
|
|
589
|
+
<li>:text = the text to write
|
|
590
|
+
|
|
591
|
+
</li>
|
|
592
|
+
<li>:fill = the colour of the text ("black")
|
|
593
|
+
|
|
594
|
+
</li>
|
|
595
|
+
<li>:style = the style of writing ("font-family:monospace;")
|
|
596
|
+
|
|
597
|
+
</li>
|
|
598
|
+
<li>:x = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the x-axis
|
|
599
|
+
|
|
600
|
+
</li>
|
|
601
|
+
<li>:y = the co-ordinates of the <a href="Glyph.html">Glyph</a> for the y-axis
|
|
602
|
+
|
|
603
|
+
</li>
|
|
604
|
+
</ul>
|
|
605
|
+
</div>
|
|
606
|
+
</div>
|
|
607
|
+
|
|
608
|
+
<div id="method-M000021" class="method-detail">
|
|
609
|
+
<a name="M000021"></a>
|
|
610
|
+
|
|
611
|
+
<div class="method-heading">
|
|
612
|
+
<a href="Glyph.src/M000021.html" target="Code" class="method-signature"
|
|
613
|
+
onclick="popupCode('Glyph.src/M000021.html');return false;">
|
|
614
|
+
<span class="method-name">scale</span><span class="method-args">(args)</span>
|
|
615
|
+
</a>
|
|
616
|
+
</div>
|
|
617
|
+
|
|
618
|
+
<div class="method-description">
|
|
619
|
+
<p>
|
|
620
|
+
<a href="Glyph.html">Glyph</a> for the <a
|
|
621
|
+
href="Glyph.html#M000021">scale</a> across the top of the rendered page
|
|
622
|
+
</p>
|
|
623
|
+
<h2>args</h2>
|
|
624
|
+
<ul>
|
|
625
|
+
<li>:start = the start of the <a href="Glyph.html#M000021">scale</a>, usually
|
|
626
|
+
added by the <a href="Page.html">Bio::Graphics::Page</a> object
|
|
627
|
+
|
|
628
|
+
</li>
|
|
629
|
+
<li>:stop = the end of the <a href="Glyph.html#M000021">scale</a>, usually
|
|
630
|
+
added by the <a href="Page.html">Bio::Graphics::Page</a> object
|
|
631
|
+
|
|
632
|
+
</li>
|
|
633
|
+
<li>:number_of_intervals = the number of tick-marks the <a
|
|
634
|
+
href="Glyph.html#M000021">scale</a> will marked with
|
|
635
|
+
|
|
636
|
+
</li>
|
|
637
|
+
<li>:page_width = the minimum width of the page, usually updated by the <a
|
|
638
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
639
|
+
|
|
640
|
+
</li>
|
|
641
|
+
</ul>
|
|
642
|
+
<p>
|
|
643
|
+
<tt>returns</tt>
|
|
644
|
+
</p>
|
|
645
|
+
<ul>
|
|
646
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
647
|
+
Bio::Graphic::Primitive objects (of type ‘line’,
|
|
648
|
+
‘rectangle’ and ‘text’)
|
|
649
|
+
|
|
650
|
+
</li>
|
|
651
|
+
</ul>
|
|
652
|
+
</div>
|
|
653
|
+
</div>
|
|
654
|
+
|
|
655
|
+
<div id="method-M000019" class="method-detail">
|
|
656
|
+
<a name="M000019"></a>
|
|
657
|
+
|
|
658
|
+
<div class="method-heading">
|
|
659
|
+
<a href="Glyph.src/M000019.html" target="Code" class="method-signature"
|
|
660
|
+
onclick="popupCode('Glyph.src/M000019.html');return false;">
|
|
661
|
+
<span class="method-name">span</span><span class="method-args">(args)</span>
|
|
662
|
+
</a>
|
|
663
|
+
</div>
|
|
664
|
+
|
|
665
|
+
<div class="method-description">
|
|
666
|
+
<p>
|
|
667
|
+
A line (<a href="Glyph.html#M000019">span</a>) glyph
|
|
668
|
+
</p>
|
|
669
|
+
<p>
|
|
670
|
+
<tt>args</tt>
|
|
671
|
+
</p>
|
|
672
|
+
<ul>
|
|
673
|
+
<li>:height = the height of the <a href="Glyph.html">Glyph</a> (default = 10)
|
|
674
|
+
|
|
675
|
+
</li>
|
|
676
|
+
<li>:fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
|
|
677
|
+
(default = ‘red’), can be any SVG colour eg rgb(256,0,0) or
|
|
678
|
+
FF0000, or one of the built in <a href="Glyph.html#M000024">gradient</a>
|
|
679
|
+
types <a href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
680
|
+
|
|
681
|
+
</li>
|
|
682
|
+
</ul>
|
|
683
|
+
<pre>
|
|
684
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
685
|
+
</pre>
|
|
686
|
+
<p>
|
|
687
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
688
|
+
</p>
|
|
689
|
+
<pre>
|
|
690
|
+
{:type => :radial,
|
|
691
|
+
:id => :custom,
|
|
692
|
+
:cx => 5,
|
|
693
|
+
:cy => 5,
|
|
694
|
+
:r => 50,
|
|
695
|
+
:fx => 50,
|
|
696
|
+
:fy => 50,
|
|
697
|
+
:stops => [ {
|
|
698
|
+
:offset => 0,
|
|
699
|
+
:color => 'rgb(255,255,255)',
|
|
700
|
+
:opacity => 0
|
|
701
|
+
}, {
|
|
702
|
+
:offset => 100,
|
|
703
|
+
:color => 'rgb(0,127,200)',
|
|
704
|
+
:opacity => 1
|
|
705
|
+
}, ]
|
|
706
|
+
}
|
|
707
|
+
</pre>
|
|
708
|
+
<ul>
|
|
709
|
+
<li>:stroke = the outline colour of the <a href="Glyph.html">Glyph</a> (default
|
|
710
|
+
= "black"), can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
711
|
+
|
|
712
|
+
</li>
|
|
713
|
+
<li>:stroke_width = The width of the outline stroke (default = 1)
|
|
714
|
+
|
|
715
|
+
</li>
|
|
716
|
+
<li>:style = an arbitrary SVG compliant style string eg
|
|
717
|
+
"fill-opacity:0.4;"
|
|
718
|
+
|
|
719
|
+
</li>
|
|
720
|
+
<li>:x = x coordinate of the feature in pixels, usually added by the <a
|
|
721
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
722
|
+
|
|
723
|
+
</li>
|
|
724
|
+
<li>:y = y coordinate of the feature in pixels, usually added by the <a
|
|
725
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
726
|
+
|
|
727
|
+
</li>
|
|
728
|
+
</ul>
|
|
729
|
+
<h3>returns</h3>
|
|
730
|
+
<ul>
|
|
731
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
732
|
+
Bio::Graphic::Primitive objects
|
|
733
|
+
|
|
734
|
+
</li>
|
|
735
|
+
</ul>
|
|
736
|
+
</div>
|
|
737
|
+
</div>
|
|
738
|
+
|
|
739
|
+
<div id="method-M000020" class="method-detail">
|
|
740
|
+
<a name="M000020"></a>
|
|
741
|
+
|
|
742
|
+
<div class="method-heading">
|
|
743
|
+
<a href="Glyph.src/M000020.html" target="Code" class="method-signature"
|
|
744
|
+
onclick="popupCode('Glyph.src/M000020.html');return false;">
|
|
745
|
+
<span class="method-name">transcript</span><span class="method-args">(args)</span>
|
|
746
|
+
</a>
|
|
747
|
+
</div>
|
|
748
|
+
|
|
749
|
+
<div class="method-description">
|
|
750
|
+
<p>
|
|
751
|
+
Creates a <a href="Glyph.html#M000020">transcript</a> glyph, which is a
|
|
752
|
+
composite glyph containing <a href="Glyph.html#M000014">generic</a> glyphs
|
|
753
|
+
for the exons/utrs and a <a href="Glyph.html#M000016">directed</a> glyph at
|
|
754
|
+
the end. The glyphs are joined by lines.
|
|
755
|
+
</p>
|
|
756
|
+
<h2>args</h2>
|
|
757
|
+
<ul>
|
|
758
|
+
<li>:height = the height of the <a href="Glyph.html">Glyph</a> (default = 10)
|
|
759
|
+
|
|
760
|
+
</li>
|
|
761
|
+
<li>:utr_fill_color = the fill colour of the utr part of the glyph (default =
|
|
762
|
+
‘black’), can be any SVG colour eg rgb(256,0,0) or FF0000, or
|
|
763
|
+
one of the built in <a href="Glyph.html#M000024">gradient</a> types <a
|
|
764
|
+
href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
765
|
+
|
|
766
|
+
</li>
|
|
767
|
+
</ul>
|
|
768
|
+
<pre>
|
|
769
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
770
|
+
</pre>
|
|
771
|
+
<p>
|
|
772
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
773
|
+
</p>
|
|
774
|
+
<pre>
|
|
775
|
+
{:type => :radial,
|
|
776
|
+
:id => :custom,
|
|
777
|
+
:cx => 5,
|
|
778
|
+
:cy => 5,
|
|
779
|
+
:r => 50,
|
|
780
|
+
:fx => 50,
|
|
781
|
+
:fy => 50,
|
|
782
|
+
:stops => [ {
|
|
783
|
+
:offset => 0,
|
|
784
|
+
:color => 'rgb(255,255,255)',
|
|
785
|
+
:opacity => 0
|
|
786
|
+
}, {
|
|
787
|
+
:offset => 100,
|
|
788
|
+
:color => 'rgb(0,127,200)',
|
|
789
|
+
:opacity => 1
|
|
790
|
+
}, ]
|
|
791
|
+
}
|
|
792
|
+
</pre>
|
|
793
|
+
<ul>
|
|
794
|
+
<li>:utr_stroke = the outline colour of the utr part of the glyph (default =
|
|
795
|
+
"black"), can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
796
|
+
|
|
797
|
+
</li>
|
|
798
|
+
<li>:utr_stroke_width = The width of the outline stroke for the utr part of the
|
|
799
|
+
glyph (default = 1)
|
|
800
|
+
|
|
801
|
+
</li>
|
|
802
|
+
<li>:exon_fill_color = the fill colour of the utr part of the glyph (default =
|
|
803
|
+
‘red’), can be any SVG colour eg rgb(256,0,0) or FF0000, or one
|
|
804
|
+
of the built in <a href="Glyph.html#M000024">gradient</a> types <a
|
|
805
|
+
href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a> or a custom
|
|
806
|
+
definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
807
|
+
|
|
808
|
+
</li>
|
|
809
|
+
</ul>
|
|
810
|
+
<pre>
|
|
811
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
812
|
+
</pre>
|
|
813
|
+
<p>
|
|
814
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
815
|
+
</p>
|
|
816
|
+
<pre>
|
|
817
|
+
{:type => :radial,
|
|
818
|
+
:id => :custom,
|
|
819
|
+
:cx => 5,
|
|
820
|
+
:cy => 5,
|
|
821
|
+
:r => 50,
|
|
822
|
+
:fx => 50,
|
|
823
|
+
:fy => 50,
|
|
824
|
+
:stops => [ {
|
|
825
|
+
:offset => 0,
|
|
826
|
+
:color => 'rgb(255,255,255)',
|
|
827
|
+
:opacity => 0
|
|
828
|
+
}, {
|
|
829
|
+
:offset => 100,
|
|
830
|
+
:color => 'rgb(0,127,200)',
|
|
831
|
+
:opacity => 1
|
|
832
|
+
}, ]
|
|
833
|
+
}
|
|
834
|
+
</pre>
|
|
835
|
+
<ul>
|
|
836
|
+
<li>:exon_stroke = the outline colour of the exon part of the glyph (default =
|
|
837
|
+
"black") can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
838
|
+
|
|
839
|
+
</li>
|
|
840
|
+
<li>:exon_stroke_width = The width of the outline stroke for the exon part of
|
|
841
|
+
the glyph (default = 1)
|
|
842
|
+
|
|
843
|
+
</li>
|
|
844
|
+
<li>:line_color = the colour for the line part that joins the blocks (default =
|
|
845
|
+
‘black’) can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
846
|
+
|
|
847
|
+
</li>
|
|
848
|
+
<li>:line_width = the width ffor the line part that joins the blocks (default =
|
|
849
|
+
1)
|
|
850
|
+
|
|
851
|
+
</li>
|
|
852
|
+
<li>:exon_style = an arbitrary SVG compliant style string eg
|
|
853
|
+
"fill-opacity:0.4;"
|
|
854
|
+
|
|
855
|
+
</li>
|
|
856
|
+
<li>:utr_style = an arbitrary SVG compliant style string eg
|
|
857
|
+
"fill-opacity:0.4;"
|
|
858
|
+
|
|
859
|
+
</li>
|
|
860
|
+
<li>:line_style = an arbitrary SVG compliant style string eg
|
|
861
|
+
"fill-opacity:0.4;"
|
|
862
|
+
|
|
863
|
+
</li>
|
|
864
|
+
<li>:block_gaps = gaps between the rendered blocks - calculated internally by
|
|
865
|
+
<a href="Page.html">Bio::Graphics::Page</a> object
|
|
866
|
+
|
|
867
|
+
</li>
|
|
868
|
+
<li>:gap_marker = style of the line between blocks - either angled or straight
|
|
869
|
+
|
|
870
|
+
</li>
|
|
871
|
+
<li>:x = x coordinate of the feature in pixels, usually added by the <a
|
|
872
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
873
|
+
|
|
874
|
+
</li>
|
|
875
|
+
<li>:y = y coordinate of the feature in pixels, usually added by the <a
|
|
876
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
877
|
+
|
|
878
|
+
</li>
|
|
879
|
+
</ul>
|
|
880
|
+
<p>
|
|
881
|
+
<tt>returns</tt>
|
|
882
|
+
</p>
|
|
883
|
+
<ul>
|
|
884
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
885
|
+
Bio::Graphic::Primitive objects
|
|
886
|
+
|
|
887
|
+
</li>
|
|
888
|
+
</ul>
|
|
889
|
+
</div>
|
|
890
|
+
</div>
|
|
891
|
+
|
|
892
|
+
<div id="method-M000018" class="method-detail">
|
|
893
|
+
<a name="M000018"></a>
|
|
894
|
+
|
|
895
|
+
<div class="method-heading">
|
|
896
|
+
<a href="Glyph.src/M000018.html" target="Code" class="method-signature"
|
|
897
|
+
onclick="popupCode('Glyph.src/M000018.html');return false;">
|
|
898
|
+
<span class="method-name">up_triangle</span><span class="method-args">(args)</span>
|
|
899
|
+
</a>
|
|
900
|
+
</div>
|
|
901
|
+
|
|
902
|
+
<div class="method-description">
|
|
903
|
+
<p>
|
|
904
|
+
An upward-pointing triangle glyph
|
|
905
|
+
</p>
|
|
906
|
+
<h2>args</h2>
|
|
907
|
+
<ul>
|
|
908
|
+
<li>:height = the height of the <a href="Glyph.html">Glyph</a> (default = 10)
|
|
909
|
+
|
|
910
|
+
</li>
|
|
911
|
+
<li>:fill_color = the fill colour of the <a href="Glyph.html">Glyph</a>
|
|
912
|
+
(default = ‘red’), can be any SVG colour eg rgb(256,0,0) or
|
|
913
|
+
FF0000, or one of the built in <a href="Glyph.html#M000024">gradient</a>
|
|
914
|
+
types <a href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
915
|
+
|
|
916
|
+
</li>
|
|
917
|
+
</ul>
|
|
918
|
+
<pre>
|
|
919
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
920
|
+
</pre>
|
|
921
|
+
<p>
|
|
922
|
+
or a custom definition of a <a href="Glyph.html#M000024">gradient</a>
|
|
923
|
+
</p>
|
|
924
|
+
<pre>
|
|
925
|
+
{:type => :radial,
|
|
926
|
+
:id => :custom,
|
|
927
|
+
:cx => 5,
|
|
928
|
+
:cy => 5,
|
|
929
|
+
:r => 50,
|
|
930
|
+
:fx => 50,
|
|
931
|
+
:fy => 50,
|
|
932
|
+
:stops => [ {
|
|
933
|
+
:offset => 0,
|
|
934
|
+
:color => 'rgb(255,255,255)',
|
|
935
|
+
:opacity => 0
|
|
936
|
+
}, {
|
|
937
|
+
:offset => 100,
|
|
938
|
+
:color => 'rgb(0,127,200)',
|
|
939
|
+
:opacity => 1
|
|
940
|
+
}, ]
|
|
941
|
+
}
|
|
942
|
+
</pre>
|
|
943
|
+
<ul>
|
|
944
|
+
<li>:stroke = the outline colour of the <a href="Glyph.html">Glyph</a> (default
|
|
945
|
+
= "black"), can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
946
|
+
|
|
947
|
+
</li>
|
|
948
|
+
<li>:stroke_width = The width of the outline stroke (default = 1), can be any
|
|
949
|
+
SVG colour eg rgb(256,0,0) or FF0000
|
|
950
|
+
|
|
951
|
+
</li>
|
|
952
|
+
<li>:style = an arbitrary SVG compliant style string eg
|
|
953
|
+
"fill-opacity:0.4;"
|
|
954
|
+
|
|
955
|
+
</li>
|
|
956
|
+
<li>:x = x coordinate of the feature in pixels, usually added by the <a
|
|
957
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
958
|
+
|
|
959
|
+
</li>
|
|
960
|
+
<li>:y = y coordinate of the feature in pixels, usually added by the <a
|
|
961
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
962
|
+
|
|
963
|
+
</li>
|
|
964
|
+
</ul>
|
|
965
|
+
<h3>returns</h3>
|
|
966
|
+
<ul>
|
|
967
|
+
<li>An <a href="http://www.ruby-doc.org/core-2.0/Array.html">Array</a> of
|
|
968
|
+
Bio::Graphic::Primitive objects
|
|
969
|
+
|
|
970
|
+
</li>
|
|
971
|
+
</ul>
|
|
972
|
+
</div>
|
|
973
|
+
</div>
|
|
974
|
+
|
|
975
|
+
|
|
976
|
+
</div>
|
|
977
|
+
|
|
978
|
+
|
|
979
|
+
</div>
|
|
980
|
+
|
|
981
|
+
|
|
982
|
+
<div id="validator-badges">
|
|
983
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
984
|
+
</div>
|
|
985
|
+
|
|
986
|
+
</body>
|
|
987
|
+
</html>
|