bio-svgenes 0.3.1 → 0.3.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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>
|