bio-svgenes 0.3.1 → 0.3.2
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- 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
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- data/doc/classes/Bio/Graphics/MiniFeature.html +243 -0
- data/doc/classes/Bio/Graphics/MiniFeature.src/M000001.html +25 -0
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- data/doc/classes/Bio/Graphics/SVGEE.html +290 -0
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- 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
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- 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
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 93</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-ivar">@args</span> = {<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:generic</span>,
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<span class="ruby-identifier">:name</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"feature_track"</span>,
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<span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>,
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<span class="ruby-identifier">:feature_height</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>,
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<span class="ruby-identifier">:track_height</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">nil</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:glyph</span>]
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<span class="ruby-ivar">@name</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:name</span>]
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<span class="ruby-ivar">@label</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:label</span>]
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<span class="ruby-ivar">@track_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:track_height</span>]
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<span class="ruby-ivar">@features</span> = []
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<span class="ruby-ivar">@feature_rows</span> = []
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<span class="ruby-ivar">@scale</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:scale</span>]
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<span class="ruby-ivar">@feature_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:feature_height</span>]
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<span class="ruby-ivar">@number_of_rows</span> = <span class="ruby-value">1</span>
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<span class="ruby-ivar">@max_y</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:max_y</span>]
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<span class="ruby-ivar">@min_width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:min_width</span>]
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<span class="ruby-keyword kw">end</span></pre>
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<title>add (Bio::Graphics::Track)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 115</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">feature</span>)
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<span class="ruby-ivar">@features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">feature</span>
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 121</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_rows</span>
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<span class="ruby-identifier">current_row</span> = <span class="ruby-value">1</span>
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<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>)
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f1</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
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<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f2</span>, <span class="ruby-identifier">j</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">j</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">j</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">i</span>
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>,<span class="ruby-identifier">f2</span>)
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<span class="ruby-ivar">@feature_rows</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-ivar">@number_rows</span> = <span class="ruby-ivar">@feature_rows</span>.<span class="ruby-identifier">max</span>
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 140</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>, <span class="ruby-identifier">f2</span>)
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(<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 kw">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 kw">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 kw">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>)
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 93</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
|
|
15
|
+
<span class="ruby-ivar">@args</span> = {<span class="ruby-identifier">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:generic</span>,
|
|
16
|
+
<span class="ruby-identifier">:name</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"feature_track"</span>,
|
|
17
|
+
<span class="ruby-identifier">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">true</span>,
|
|
18
|
+
<span class="ruby-identifier">:feature_height</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>,
|
|
19
|
+
<span class="ruby-identifier">:track_height</span> =<span class="ruby-operator">></span> <span class="ruby-keyword kw">nil</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
|
|
20
|
+
<span class="ruby-ivar">@glyph</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:glyph</span>]
|
|
21
|
+
<span class="ruby-ivar">@name</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:name</span>]
|
|
22
|
+
<span class="ruby-ivar">@label</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:label</span>]
|
|
23
|
+
<span class="ruby-ivar">@track_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:track_height</span>]
|
|
24
|
+
<span class="ruby-ivar">@features</span> = []
|
|
25
|
+
<span class="ruby-ivar">@feature_rows</span> = []
|
|
26
|
+
<span class="ruby-ivar">@scale</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:scale</span>]
|
|
27
|
+
<span class="ruby-ivar">@feature_height</span> = <span class="ruby-ivar">@args</span>[<span class="ruby-identifier">:feature_height</span>]
|
|
28
|
+
<span class="ruby-ivar">@number_of_rows</span> = <span class="ruby-value">1</span>
|
|
29
|
+
<span class="ruby-ivar">@max_y</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:max_y</span>]
|
|
30
|
+
<span class="ruby-ivar">@min_width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:min_width</span>]
|
|
31
|
+
|
|
32
|
+
|
|
33
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
34
|
+
</body>
|
|
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|
+
</html>
|
|
@@ -0,0 +1,18 @@
|
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|
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|
+
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|
|
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<html>
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|
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<head>
|
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+
<title>add (Bio::Graphics::Track)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
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|
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<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
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|
+
</head>
|
|
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|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 115</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">feature</span>)
|
|
15
|
+
<span class="ruby-ivar">@features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">feature</span>
|
|
16
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
17
|
+
</body>
|
|
18
|
+
</html>
|
|
@@ -0,0 +1,28 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
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|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
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|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>get_rows (Bio::Graphics::Track)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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|
+
</head>
|
|
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|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 121</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_rows</span>
|
|
15
|
+
<span class="ruby-identifier">current_row</span> = <span class="ruby-value">1</span>
|
|
16
|
+
<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>)
|
|
17
|
+
<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f1</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
18
|
+
<span class="ruby-ivar">@features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f2</span>, <span class="ruby-identifier">j</span><span class="ruby-operator">|</span>
|
|
19
|
+
<span class="ruby-keyword kw">next</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">j</span> <span class="ruby-keyword kw">or</span> <span class="ruby-identifier">j</span> <span class="ruby-operator"><=</span> <span class="ruby-identifier">i</span>
|
|
20
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>,<span class="ruby-identifier">f2</span>)
|
|
21
|
+
<span class="ruby-ivar">@feature_rows</span>[<span class="ruby-identifier">i</span>] <span class="ruby-operator">+=</span> <span class="ruby-value">1</span>
|
|
22
|
+
<span class="ruby-keyword kw">end</span>
|
|
23
|
+
<span class="ruby-keyword kw">end</span>
|
|
24
|
+
<span class="ruby-ivar">@number_rows</span> = <span class="ruby-ivar">@feature_rows</span>.<span class="ruby-identifier">max</span>
|
|
25
|
+
<span class="ruby-keyword kw">end</span>
|
|
26
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
27
|
+
</body>
|
|
28
|
+
</html>
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
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|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
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|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>overlaps (Bio::Graphics::Track)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/track.rb, line 140</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">overlaps</span>(<span class="ruby-identifier">f1</span>, <span class="ruby-identifier">f2</span>)
|
|
15
|
+
(<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 kw">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 kw">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 kw">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>)
|
|
16
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
17
|
+
</body>
|
|
18
|
+
</html>
|
data/doc/created.rid
CHANGED
|
@@ -1,9 +1 @@
|
|
|
1
|
-
|
|
2
|
-
./lib/bio/graphics/primitive.rb Fri, 01 Mar 2013 13:01:51 +0000
|
|
3
|
-
./lib/bio/graphics/svgee.rb Fri, 01 Mar 2013 14:31:26 +0000
|
|
4
|
-
./lib/bio-svgenes.rb Tue, 12 Feb 2013 12:53:21 +0000
|
|
5
|
-
./lib/bio/graphics/track.rb Fri, 01 Mar 2013 15:38:24 +0000
|
|
6
|
-
./lib/bio/graphics/glyph.rb Fri, 01 Mar 2013 14:55:52 +0000
|
|
7
|
-
./LICENSE.txt Tue, 12 Feb 2013 12:53:20 +0000
|
|
8
|
-
./lib/bio/graphics/mini_feature.rb Fri, 01 Mar 2013 15:52:40 +0000
|
|
9
|
-
./lib/bio/graphics/page.rb Fri, 01 Mar 2013 14:34:28 +0000
|
|
1
|
+
Thu, 04 Apr 2013 16:23:02 +0100
|
|
@@ -0,0 +1,131 @@
|
|
|
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>File: bio-svgenes.rb</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="fileHeader">
|
|
50
|
+
<h1>bio-svgenes.rb</h1>
|
|
51
|
+
<table class="header-table">
|
|
52
|
+
<tr class="top-aligned-row">
|
|
53
|
+
<td><strong>Path:</strong></td>
|
|
54
|
+
<td>lib/bio-svgenes.rb
|
|
55
|
+
</td>
|
|
56
|
+
</tr>
|
|
57
|
+
<tr class="top-aligned-row">
|
|
58
|
+
<td><strong>Last Update:</strong></td>
|
|
59
|
+
<td>Mon Mar 04 12:51:41 +0000 2013</td>
|
|
60
|
+
</tr>
|
|
61
|
+
</table>
|
|
62
|
+
</div>
|
|
63
|
+
<!-- banner header -->
|
|
64
|
+
|
|
65
|
+
<div id="bodyContent">
|
|
66
|
+
|
|
67
|
+
|
|
68
|
+
|
|
69
|
+
<div id="contextContent">
|
|
70
|
+
|
|
71
|
+
<div id="description">
|
|
72
|
+
<p>
|
|
73
|
+
Please require your code below, respecting the bioruby directory tree. For
|
|
74
|
+
instance, perhaps the only uncommented line in this file might be something
|
|
75
|
+
like this:
|
|
76
|
+
</p>
|
|
77
|
+
<pre>
|
|
78
|
+
require 'bio/sequence/awesome_sequence_plugin_thingy'
|
|
79
|
+
</pre>
|
|
80
|
+
<p>
|
|
81
|
+
and then create the ruby file
|
|
82
|
+
‘lib/bio/sequence/awesome_sequence_thingy.rb’ and put your
|
|
83
|
+
plugin‘s code there. It is bad practice to write other code directly
|
|
84
|
+
into this file, because doing so causes confusion if this biogem was ever
|
|
85
|
+
to get merged into the main bioruby tree.
|
|
86
|
+
</p>
|
|
87
|
+
|
|
88
|
+
</div>
|
|
89
|
+
|
|
90
|
+
<div id="requires-list">
|
|
91
|
+
<h3 class="section-bar">Required files</h3>
|
|
92
|
+
|
|
93
|
+
<div class="name-list">
|
|
94
|
+
bio/graphics/svgee
|
|
95
|
+
bio/graphics/glyph
|
|
96
|
+
bio/graphics/page
|
|
97
|
+
bio/graphics/track
|
|
98
|
+
bio/graphics/mini_feature
|
|
99
|
+
bio/graphics/primitive
|
|
100
|
+
</div>
|
|
101
|
+
</div>
|
|
102
|
+
|
|
103
|
+
</div>
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
</div>
|
|
107
|
+
|
|
108
|
+
|
|
109
|
+
<!-- if includes -->
|
|
110
|
+
|
|
111
|
+
<div id="section">
|
|
112
|
+
|
|
113
|
+
|
|
114
|
+
|
|
115
|
+
|
|
116
|
+
|
|
117
|
+
|
|
118
|
+
|
|
119
|
+
|
|
120
|
+
<!-- if method_list -->
|
|
121
|
+
|
|
122
|
+
|
|
123
|
+
</div>
|
|
124
|
+
|
|
125
|
+
|
|
126
|
+
<div id="validator-badges">
|
|
127
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
128
|
+
</div>
|
|
129
|
+
|
|
130
|
+
</body>
|
|
131
|
+
</html>
|
|
@@ -0,0 +1,101 @@
|
|
|
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>File: glyph.rb</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
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+
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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// ]]>
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<h1>glyph.rb</h1>
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<table class="header-table">
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<tr class="top-aligned-row">
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<td><strong>Path:</strong></td>
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<td>lib/bio/graphics/glyph.rb
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</td>
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<td><strong>Last Update:</strong></td>
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<td>Thu Apr 04 15:40:52 +0100 2013</td>
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<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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