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
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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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<title>get_rows (Bio::Graphics::Track)</title>
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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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<title>overlaps (Bio::Graphics::Track)</title>
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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
|
+
|
|
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|
+
|
|
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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<head>
|
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<title>add (Bio::Graphics::Track)</title>
|
|
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|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
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|
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|
|
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|
+
</head>
|
|
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|
+
<body class="standalone-code">
|
|
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|
+
<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 @@
|
|
|
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|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
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|
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<!DOCTYPE html
|
|
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|
+
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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|
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</head>
|
|
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|
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<body class="standalone-code">
|
|
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|
+
<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 @@
|
|
|
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|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
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|
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|
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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" />
|
|
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|
+
</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
|
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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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