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
- 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
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- 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
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- 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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<title>gradient (Bio::Graphics::Glyph)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 534</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">gradient</span>)
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<span class="ruby-identifier">type</span>, <span class="ruby-identifier">color</span> = <span class="ruby-keyword kw">case</span> <span class="ruby-identifier">gradient</span>
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:red_white_h</span>
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[<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">"red"</span>]
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:green_white_h</span>
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[<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">"green"</span>]
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:blue_white_h</span>
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[<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">"blue"</span>]
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:yellow_white_h</span>
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[<span class="ruby-identifier">:linear</span>, <span class="ruby-value str">"yellow"</span>]
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:red_white_radial</span>
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[<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">"red"</span>]
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:green_white_radial</span>
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[<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">"green"</span>]
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:blue_white_radial</span>
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[<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">"blue"</span>]
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:yellow_white_radial</span>
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[<span class="ruby-identifier">:radial</span>, <span class="ruby-value str">"yellow"</span>]
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">case</span> <span class="ruby-identifier">type</span>
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:linear</span>
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{<span class="ruby-identifier">:type</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:linear</span>,
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<span class="ruby-identifier">:id</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">gradient</span>,
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<span class="ruby-identifier">:x1</span> =<span class="ruby-operator">></span> <span class="ruby-value">0</span>, <span class="ruby-identifier">:y1</span> =<span class="ruby-operator">></span> <span class="ruby-value">0</span>,
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<span class="ruby-identifier">:x2</span> =<span class="ruby-operator">></span> <span class="ruby-value">0</span>, <span class="ruby-identifier">:y2</span> =<span class="ruby-operator">></span> <span class="ruby-value">100</span>,
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<span class="ruby-identifier">:stops</span> =<span class="ruby-operator">></span> [
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{
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<span class="ruby-identifier">:color</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">color</span>,
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<span class="ruby-identifier">:offset</span> =<span class="ruby-operator">></span> <span class="ruby-value">0</span>,
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<span class="ruby-identifier">:opacity=</span><span class="ruby-operator">></span> <span class="ruby-value">1</span>
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},
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{
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<span class="ruby-identifier">:color</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"white"</span>,
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<span class="ruby-identifier">:offset</span> =<span class="ruby-operator">></span> <span class="ruby-value">100</span>,
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<span class="ruby-identifier">:opacity=</span><span class="ruby-operator">></span> <span class="ruby-value">1</span>
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}
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]
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}
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<span class="ruby-keyword kw">when</span> <span class="ruby-identifier">:radial</span>
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{
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<span class="ruby-identifier">:type</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">:radial</span>,
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<span class="ruby-identifier">:id</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">gradient</span>,
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<span class="ruby-identifier">:cx</span> =<span class="ruby-operator">></span> <span class="ruby-value">50</span>, <span class="ruby-identifier">:cy</span> =<span class="ruby-operator">></span> <span class="ruby-value">50</span>,
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<span class="ruby-identifier">:r</span> =<span class="ruby-operator">></span> <span class="ruby-value">50</span>, <span class="ruby-identifier">:fx</span> =<span class="ruby-operator">></span> <span class="ruby-value">50</span>, <span class="ruby-identifier">:fy</span> =<span class="ruby-operator">></span> <span class="ruby-value">50</span>,
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<span class="ruby-identifier">:stops</span> =<span class="ruby-operator">></span> [
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{<span class="ruby-identifier">:offset</span> =<span class="ruby-operator">></span> <span class="ruby-value">0</span>,
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<span class="ruby-identifier">:color</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"white"</span>,
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<span class="ruby-identifier">:opacity</span> =<span class="ruby-operator">></span> <span class="ruby-value">0</span>
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},
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{
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<span class="ruby-identifier">:offset</span> =<span class="ruby-operator">></span> <span class="ruby-value">100</span>,
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<span class="ruby-identifier">:color</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">color</span>,
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<span class="ruby-identifier">:opacity</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>
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}
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]
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}
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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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<head>
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<title>Class: Bio::Graphics::MiniFeature</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<script type="text/javascript">
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// <![CDATA[
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// ]]>
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<div id="classHeader">
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<table class="header-table">
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<tr class="top-aligned-row">
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<td><strong>Class</strong></td>
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<td class="class-name-in-header">Bio::Graphics::MiniFeature</td>
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</tr>
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<tr class="top-aligned-row">
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<td><strong>In:</strong></td>
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<td>
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<a href="../../../files/lib/bio/graphics/mini_feature_rb.html">
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lib/bio/graphics/mini_feature.rb
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</a>
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<br />
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</td>
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A <a href="MiniFeature.html">Bio::Graphics::MiniFeature</a> object
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represents a single genomic feature (e.g. a gene, transcript, exon, start
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codon, etc), it is a lightweight object that holds the minimum information
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needed to do the render.
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<td class="context-item-name">start</td>
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Creates a <a href="MiniFeature.html#M000003">new</a> <a
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href="MiniFeature.html">MiniFeature</a>
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|
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<h2>args</h2>
|
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<ul>
|
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<li>:start = the start position of the feature
|
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|
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</li>
|
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<li>:end = the end position of the feature
|
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|
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</li>
|
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<li>:strand = the strand of the feature
|
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|
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</li>
|
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<li>:exons = an array of exon positions
|
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|
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|
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<li>:utrs = an array of utrs positions
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|
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|
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<li>:block_gaps = an array of regions with nothing to be drawn, e.g. introns
|
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|
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</li>
|
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<li>:id = the name for the feature such as the gene name or transcript ID
|
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|
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</li>
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<li>:segment_height = the height of the current feature
|
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|
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</li>
|
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|
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</ul>
|
|
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|
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<h2>Example usage</h2>
|
|
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|
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<pre>
|
|
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|
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mini1 = Bio::Graphics::MiniFeature.new(
|
|
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|
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:start=>3631,
|
|
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|
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:end=>5899,
|
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|
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:strand=>'+',
|
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|
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:exons=>[4000, 4500, 4700, 5000],
|
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:utrs=>[3631, 3650],
|
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|
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:segment_height=>5,
|
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|
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:id=>"AT1G01010"
|
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)
|
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|
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</pre>
|
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|
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<h3>MiniFeatures and Tracks</h3>
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<p>
|
|
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MiniFeatures are created and added to <a
|
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href="Track.html">Bio::Graphics::Track</a> objects which will take
|
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responsibility for positioning and syling them.#
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<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/mini_feature.rb, line 35</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">@start</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:start</span>]
|
|
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|
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<span class="ruby-ivar">@end</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:end</span>]
|
|
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|
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<span class="ruby-ivar">@strand</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>]
|
|
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|
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<span class="ruby-ivar">@exons</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>] <span class="ruby-operator">||</span> []
|
|
19
|
+
<span class="ruby-ivar">@utrs</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>] <span class="ruby-operator">||</span> [] <span class="ruby-comment cmt">#start, ennd, strand, arg[:exons], arg[:utrs]</span>
|
|
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|
+
<span class="ruby-ivar">@block_gaps</span> = []
|
|
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|
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<span class="ruby-ivar">@id</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:id</span>]
|
|
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|
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<span class="ruby-ivar">@segment_height</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:segment_height</span>]
|
|
23
|
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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/mini_feature.rb, line 35</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">@start</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:start</span>]
|
|
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|
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<span class="ruby-ivar">@end</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:end</span>]
|
|
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|
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<span class="ruby-ivar">@strand</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>]
|
|
18
|
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<span class="ruby-ivar">@exons</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>] <span class="ruby-operator">||</span> []
|
|
19
|
+
<span class="ruby-ivar">@utrs</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>] <span class="ruby-operator">||</span> [] <span class="ruby-comment cmt">#start, ennd, strand, arg[:exons], arg[:utrs]</span>
|
|
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|
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<span class="ruby-ivar">@block_gaps</span> = []
|
|
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|
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<span class="ruby-ivar">@id</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:id</span>]
|
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|
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<span class="ruby-ivar">@segment_height</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:segment_height</span>]
|
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/mini_feature.rb, line 35</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">@start</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:start</span>]
|
|
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|
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<span class="ruby-ivar">@end</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:end</span>]
|
|
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|
+
<span class="ruby-ivar">@strand</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>]
|
|
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|
+
<span class="ruby-ivar">@exons</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>] <span class="ruby-operator">||</span> []
|
|
19
|
+
<span class="ruby-ivar">@utrs</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>] <span class="ruby-operator">||</span> [] <span class="ruby-comment cmt">#start, ennd, strand, arg[:exons], arg[:utrs]</span>
|
|
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|
+
<span class="ruby-ivar">@block_gaps</span> = []
|
|
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|
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<span class="ruby-ivar">@id</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:id</span>]
|
|
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|
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|
|
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|
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<span class="ruby-keyword kw">end</span></pre>
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// <![CDATA[
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|
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function popupCode( url ) {
|
|
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|
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window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
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|
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}
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|
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function toggleCode( id ) {
|
|
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|
+
if ( document.getElementById )
|
|
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|
+
elem = document.getElementById( id );
|
|
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|
+
else if ( document.all )
|
|
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|
+
elem = eval( "document.all." + id );
|
|
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|
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else
|
|
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|
+
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|
|
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|
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|
|
27
|
+
elemStyle = elem.style;
|
|
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|
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|
|
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|
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if ( elemStyle.display != "block" ) {
|
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elemStyle.display = "block"
|
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} else {
|
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elemStyle.display = "none"
|
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}
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|
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return true;
|
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}
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|
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// Make codeblocks hidden by default
|
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|
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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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+
// ]]>
|
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</script>
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|
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</head>
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<body>
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<div id="classHeader">
|
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<table class="header-table">
|
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<tr class="top-aligned-row">
|
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|
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<td><strong>Class</strong></td>
|
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|
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<td class="class-name-in-header">Bio::Graphics::Page</td>
|
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|
+
</tr>
|
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|
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<tr class="top-aligned-row">
|
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|
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<td><strong>In:</strong></td>
|
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<td>
|
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<a href="../../../files/lib/bio/graphics/page_rb.html">
|
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lib/bio/graphics/page.rb
|
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+
</a>
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<br />
|
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</td>
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</tr>
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|
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<tr class="top-aligned-row">
|
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<td><strong>Parent:</strong></td>
|
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<td>
|
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Object
|
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|
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</td>
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</tr>
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</table>
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</div>
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<!-- banner header -->
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<div id="bodyContent">
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|
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|
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|
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|
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<div id="contextContent">
|
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|
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81
|
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<div id="description">
|
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|
+
<p>
|
|
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|
+
The <a href="Page.html">Bio::Graphics::Page</a> class represents the page
|
|
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|
+
of the final rendered SVG and is the top level container into which
|
|
85
|
+
Bio::Graphics::Tracks are added. It will contain a scale and all the tracks
|
|
86
|
+
along with their features. The scale is calculated will start at the
|
|
87
|
+
genomic co-ordinates of the start of the first feature and stop at the end
|
|
88
|
+
of the last feature)
|
|
89
|
+
</p>
|
|
90
|
+
|
|
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|
+
</div>
|
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|
+
|
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|
+
|
|
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|
+
</div>
|
|
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|
+
|
|
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|
+
<div id="method-list">
|
|
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|
+
<h3 class="section-bar">Methods</h3>
|
|
98
|
+
|
|
99
|
+
<div class="name-list">
|
|
100
|
+
<a href="#M000028">add_track</a>
|
|
101
|
+
<a href="#M000043">draw</a>
|
|
102
|
+
<a href="#M000034">draw_circle</a>
|
|
103
|
+
<a href="#M000033">draw_directed</a>
|
|
104
|
+
<a href="#M000038">draw_down_triangle</a>
|
|
105
|
+
<a href="#M000040">draw_features</a>
|
|
106
|
+
<a href="#M000032">draw_generic</a>
|
|
107
|
+
<a href="#M000036">draw_histogram</a>
|
|
108
|
+
<a href="#M000031">draw_label</a>
|
|
109
|
+
<a href="#M000030">draw_scale</a>
|
|
110
|
+
<a href="#M000039">draw_span</a>
|
|
111
|
+
<a href="#M000035">draw_transcript</a>
|
|
112
|
+
<a href="#M000037">draw_up_triangle</a>
|
|
113
|
+
<a href="#M000026">from_json</a>
|
|
114
|
+
<a href="#M000029">get_limits</a>
|
|
115
|
+
<a href="#M000042">get_markup</a>
|
|
116
|
+
<a href="#M000025">new</a>
|
|
117
|
+
<a href="#M000027">parse_gff</a>
|
|
118
|
+
<a href="#M000041">to_px</a>
|
|
119
|
+
<a href="#M000044">write</a>
|
|
120
|
+
</div>
|
|
121
|
+
</div>
|
|
122
|
+
|
|
123
|
+
</div>
|
|
124
|
+
|
|
125
|
+
|
|
126
|
+
<!-- if includes -->
|
|
127
|
+
|
|
128
|
+
<div id="section">
|
|
129
|
+
|
|
130
|
+
|
|
131
|
+
|
|
132
|
+
|
|
133
|
+
|
|
134
|
+
|
|
135
|
+
|
|
136
|
+
|
|
137
|
+
<!-- if method_list -->
|
|
138
|
+
<div id="methods">
|
|
139
|
+
<h3 class="section-bar">Public Class methods</h3>
|
|
140
|
+
|
|
141
|
+
<div id="method-M000026" class="method-detail">
|
|
142
|
+
<a name="M000026"></a>
|
|
143
|
+
|
|
144
|
+
<div class="method-heading">
|
|
145
|
+
<a href="Page.src/M000026.html" target="Code" class="method-signature"
|
|
146
|
+
onclick="popupCode('Page.src/M000026.html');return false;">
|
|
147
|
+
<span class="method-name">from_json</span><span class="method-args">(args)</span>
|
|
148
|
+
</a>
|
|
149
|
+
</div>
|
|
150
|
+
|
|
151
|
+
<div class="method-description">
|
|
152
|
+
<p>
|
|
153
|
+
Takes a custom-written json file and uses it to generate an SVG document
|
|
154
|
+
based on the information in that page.
|
|
155
|
+
</p>
|
|
156
|
+
<ul>
|
|
157
|
+
<li>:json a JSON file describing the parameters and files needed to build an
|
|
158
|
+
SVG document
|
|
159
|
+
|
|
160
|
+
</li>
|
|
161
|
+
</ul>
|
|
162
|
+
</div>
|
|
163
|
+
</div>
|
|
164
|
+
|
|
165
|
+
<div id="method-M000025" class="method-detail">
|
|
166
|
+
<a name="M000025"></a>
|
|
167
|
+
|
|
168
|
+
<div class="method-heading">
|
|
169
|
+
<a href="Page.src/M000025.html" target="Code" class="method-signature"
|
|
170
|
+
onclick="popupCode('Page.src/M000025.html');return false;">
|
|
171
|
+
<span class="method-name">new</span><span class="method-args">(args)</span>
|
|
172
|
+
</a>
|
|
173
|
+
</div>
|
|
174
|
+
|
|
175
|
+
<div class="method-description">
|
|
176
|
+
<p>
|
|
177
|
+
Creates a <a href="Page.html#M000025">new</a> <a href="Page.html">Page</a>
|
|
178
|
+
object.
|
|
179
|
+
</p>
|
|
180
|
+
<h2>args</h2>
|
|
181
|
+
<ul>
|
|
182
|
+
<li>:height = the minimum height of the rendered page
|
|
183
|
+
|
|
184
|
+
</li>
|
|
185
|
+
<li>:width = the minimum width of the rendered page
|
|
186
|
+
|
|
187
|
+
</li>
|
|
188
|
+
<li>:background_color = the background color of the page (default none), can be
|
|
189
|
+
any SVG colour eg rgb(256,0,0) or FF0000
|
|
190
|
+
|
|
191
|
+
</li>
|
|
192
|
+
</ul>
|
|
193
|
+
</div>
|
|
194
|
+
</div>
|
|
195
|
+
|
|
196
|
+
<div id="method-M000027" class="method-detail">
|
|
197
|
+
<a name="M000027"></a>
|
|
198
|
+
|
|
199
|
+
<div class="method-heading">
|
|
200
|
+
<a href="Page.src/M000027.html" target="Code" class="method-signature"
|
|
201
|
+
onclick="popupCode('Page.src/M000027.html');return false;">
|
|
202
|
+
<span class="method-name">parse_gff</span><span class="method-args">(gff_file)</span>
|
|
203
|
+
</a>
|
|
204
|
+
</div>
|
|
205
|
+
|
|
206
|
+
<div class="method-description">
|
|
207
|
+
<p>
|
|
208
|
+
Parses a GFF file into an Array of <a
|
|
209
|
+
href="http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html">Bio::GFF::GFF3::Record</a>
|
|
210
|
+
objects
|
|
211
|
+
</p>
|
|
212
|
+
<ul>
|
|
213
|
+
<li>gff_file - a GFF-formatted file
|
|
214
|
+
|
|
215
|
+
</li>
|
|
216
|
+
<li>returns - an Array of <a
|
|
217
|
+
href="http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html">Bio::GFF::GFF3::Record</a>
|
|
218
|
+
objects
|
|
219
|
+
|
|
220
|
+
</li>
|
|
221
|
+
</ul>
|
|
222
|
+
</div>
|
|
223
|
+
</div>
|
|
224
|
+
|
|
225
|
+
<h3 class="section-bar">Public Instance methods</h3>
|
|
226
|
+
|
|
227
|
+
<div id="method-M000028" class="method-detail">
|
|
228
|
+
<a name="M000028"></a>
|
|
229
|
+
|
|
230
|
+
<div class="method-heading">
|
|
231
|
+
<a href="Page.src/M000028.html" target="Code" class="method-signature"
|
|
232
|
+
onclick="popupCode('Page.src/M000028.html');return false;">
|
|
233
|
+
<span class="method-name">add_track</span><span class="method-args">(args)</span>
|
|
234
|
+
</a>
|
|
235
|
+
</div>
|
|
236
|
+
|
|
237
|
+
<div class="method-description">
|
|
238
|
+
<p>
|
|
239
|
+
adds a <a href="Page.html#M000025">new</a> <a
|
|
240
|
+
href="Track.html">Bio::Graphics::Track</a> object to the current <a
|
|
241
|
+
href="Page.html">Bio::Graphics::Page</a> object
|
|
242
|
+
</p>
|
|
243
|
+
<h2>args</h2>
|
|
244
|
+
<ul>
|
|
245
|
+
<li>:glyph = one of Bio::Graphics::Glyphs#glyphs currently
|
|
246
|
+
|
|
247
|
+
</li>
|
|
248
|
+
</ul>
|
|
249
|
+
<pre>
|
|
250
|
+
[:generic, :directed, :transcript, :scale, :label, :histogram, :circle, :down_triangle, :up_triangle, :span]
|
|
251
|
+
</pre>
|
|
252
|
+
<ul>
|
|
253
|
+
<li>:stroke_color = the outline colour of the glyphs in the track (default =
|
|
254
|
+
"black"), can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
255
|
+
|
|
256
|
+
</li>
|
|
257
|
+
<li>:fill_color = the fill colour of the glyphs in the track (default =
|
|
258
|
+
‘red’), can be any SVG colour eg rgb(256,0,0) or FF0000, or one
|
|
259
|
+
of the built in gradient types <a
|
|
260
|
+
href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
261
|
+
|
|
262
|
+
</li>
|
|
263
|
+
</ul>
|
|
264
|
+
<pre>
|
|
265
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
266
|
+
</pre>
|
|
267
|
+
<p>
|
|
268
|
+
or a custom definition of a gradient
|
|
269
|
+
</p>
|
|
270
|
+
<pre>
|
|
271
|
+
{:type => :radial,
|
|
272
|
+
:id => :custom,
|
|
273
|
+
:cx => 5,
|
|
274
|
+
:cy => 5,
|
|
275
|
+
:r => 50,
|
|
276
|
+
:fx => 50,
|
|
277
|
+
:fy => 50,
|
|
278
|
+
:stops => [ {
|
|
279
|
+
:offset => 0,
|
|
280
|
+
:color => 'rgb(255,255,255)',
|
|
281
|
+
:opacity => 0
|
|
282
|
+
}, {
|
|
283
|
+
:offset => 100,
|
|
284
|
+
:color => 'rgb(0,127,200)',
|
|
285
|
+
:opacity => 1
|
|
286
|
+
}, ]
|
|
287
|
+
}
|
|
288
|
+
</pre>
|
|
289
|
+
<ul>
|
|
290
|
+
<li>:track_height = minimum height for the track, will be modified
|
|
291
|
+
automatically if more space is needed e.g for overlapping features (default
|
|
292
|
+
= auto),
|
|
293
|
+
|
|
294
|
+
</li>
|
|
295
|
+
<li>:name = a displayed name for the track (default =
|
|
296
|
+
‘feature_track’)
|
|
297
|
+
|
|
298
|
+
</li>
|
|
299
|
+
<li>:label = display the name given to the track (default = true),
|
|
300
|
+
|
|
301
|
+
</li>
|
|
302
|
+
<li>:stroke_width = width in pixels of the outline of the glyphs (default=1)
|
|
303
|
+
|
|
304
|
+
</li>
|
|
305
|
+
<li>:x_round = x radius of the ellipse used to round off the corners of
|
|
306
|
+
rectangles (default = 1)
|
|
307
|
+
|
|
308
|
+
</li>
|
|
309
|
+
<li>:y_round = y radius of the ellipse used to round off the corners of
|
|
310
|
+
rectangles (default = 1)
|
|
311
|
+
|
|
312
|
+
</li>
|
|
313
|
+
</ul>
|
|
314
|
+
<p>
|
|
315
|
+
:utr_fill_color = the fill colour of the utr part of the glyph (default =
|
|
316
|
+
‘black’), can be any SVG colour eg rgb(256,0,0) or FF0000, or
|
|
317
|
+
one of the built in gradient types <a
|
|
318
|
+
href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a>
|
|
319
|
+
</p>
|
|
320
|
+
<pre>
|
|
321
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
322
|
+
</pre>
|
|
323
|
+
<p>
|
|
324
|
+
or a custom definition of a gradient
|
|
325
|
+
</p>
|
|
326
|
+
<pre>
|
|
327
|
+
{:type => :radial,
|
|
328
|
+
:id => :custom,
|
|
329
|
+
:cx => 5,
|
|
330
|
+
:cy => 5,
|
|
331
|
+
:r => 50,
|
|
332
|
+
:fx => 50,
|
|
333
|
+
:fy => 50,
|
|
334
|
+
:stops => [ {
|
|
335
|
+
:offset => 0,
|
|
336
|
+
:color => 'rgb(255,255,255)',
|
|
337
|
+
:opacity => 0
|
|
338
|
+
}, {
|
|
339
|
+
:offset => 100,
|
|
340
|
+
:color => 'rgb(0,127,200)',
|
|
341
|
+
:opacity => 1
|
|
342
|
+
}, ]
|
|
343
|
+
}
|
|
344
|
+
</pre>
|
|
345
|
+
<ul>
|
|
346
|
+
<li>:utr_stroke = the outline colour of the utr part of the glyph (default =
|
|
347
|
+
"black"), can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
348
|
+
|
|
349
|
+
</li>
|
|
350
|
+
<li>:utr_stroke_width = The width of the outline stroke for the utr part of the
|
|
351
|
+
glyph (default = 1)
|
|
352
|
+
|
|
353
|
+
</li>
|
|
354
|
+
<li>:exon_fill_color = the fill colour of the utr part of the glyph (default =
|
|
355
|
+
‘red’), can be any SVG colour eg rgb(256,0,0) or FF0000, or one
|
|
356
|
+
of the built in gradient types <a
|
|
357
|
+
href="Glyph.html#M000023">Bio::Graphics::Glyph#gradients</a> or a custom
|
|
358
|
+
definition of a gradient
|
|
359
|
+
|
|
360
|
+
</li>
|
|
361
|
+
</ul>
|
|
362
|
+
<pre>
|
|
363
|
+
[:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
|
|
364
|
+
</pre>
|
|
365
|
+
<p>
|
|
366
|
+
or a custom definition of a gradient
|
|
367
|
+
</p>
|
|
368
|
+
<pre>
|
|
369
|
+
{:type => :radial,
|
|
370
|
+
:id => :custom,
|
|
371
|
+
:cx => 5,
|
|
372
|
+
:cy => 5,
|
|
373
|
+
:r => 50,
|
|
374
|
+
:fx => 50,
|
|
375
|
+
:fy => 50,
|
|
376
|
+
:stops => [ {
|
|
377
|
+
:offset => 0,
|
|
378
|
+
:color => 'rgb(255,255,255)',
|
|
379
|
+
:opacity => 0
|
|
380
|
+
}, {
|
|
381
|
+
:offset => 100,
|
|
382
|
+
:color => 'rgb(0,127,200)',
|
|
383
|
+
:opacity => 1
|
|
384
|
+
}, ]
|
|
385
|
+
</pre>
|
|
386
|
+
<ul>
|
|
387
|
+
<li>:exon_stroke = the outline colour of the exon part of the glyph (default =
|
|
388
|
+
"black") can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
389
|
+
|
|
390
|
+
</li>
|
|
391
|
+
<li>:exon_stroke_width = The width of the outline stroke for the exon part of
|
|
392
|
+
the glyph (default = 1)
|
|
393
|
+
|
|
394
|
+
</li>
|
|
395
|
+
<li>:line_color = the colour for the line part that joins the blocks (default =
|
|
396
|
+
‘black’) can be any SVG colour eg rgb(256,0,0) or FF0000
|
|
397
|
+
|
|
398
|
+
</li>
|
|
399
|
+
<li>:line_width = the width ffor the line part that joins the blocks (default =
|
|
400
|
+
1)
|
|
401
|
+
|
|
402
|
+
</li>
|
|
403
|
+
<li>:exon_style = an arbitrary SVG compliant style string eg
|
|
404
|
+
"fill-opacity:0.4;"
|
|
405
|
+
|
|
406
|
+
</li>
|
|
407
|
+
<li>:utr_style = an arbitrary SVG compliant style string eg
|
|
408
|
+
"fill-opacity:0.4;"
|
|
409
|
+
|
|
410
|
+
</li>
|
|
411
|
+
<li>:line_style = an arbitrary SVG compliant style string eg
|
|
412
|
+
"fill-opacity:0.4;"
|
|
413
|
+
|
|
414
|
+
</li>
|
|
415
|
+
<li>:gap_marker = style of the line between blocks - either angled or straight
|
|
416
|
+
|
|
417
|
+
</li>
|
|
418
|
+
</ul>
|
|
419
|
+
<h3>returns</h3>
|
|
420
|
+
<pre>
|
|
421
|
+
a new Bio::Graphics::Track object
|
|
422
|
+
</pre>
|
|
423
|
+
</div>
|
|
424
|
+
</div>
|
|
425
|
+
|
|
426
|
+
<div id="method-M000043" class="method-detail">
|
|
427
|
+
<a name="M000043"></a>
|
|
428
|
+
|
|
429
|
+
<div class="method-heading">
|
|
430
|
+
<a href="Page.src/M000043.html" target="Code" class="method-signature"
|
|
431
|
+
onclick="popupCode('Page.src/M000043.html');return false;">
|
|
432
|
+
<span class="method-name">draw</span><span class="method-args">()</span>
|
|
433
|
+
</a>
|
|
434
|
+
</div>
|
|
435
|
+
|
|
436
|
+
<div class="method-description">
|
|
437
|
+
<p>
|
|
438
|
+
Prints the svg text to STDOUT
|
|
439
|
+
</p>
|
|
440
|
+
</div>
|
|
441
|
+
</div>
|
|
442
|
+
|
|
443
|
+
<div id="method-M000034" class="method-detail">
|
|
444
|
+
<a name="M000034"></a>
|
|
445
|
+
|
|
446
|
+
<div class="method-heading">
|
|
447
|
+
<a href="Page.src/M000034.html" target="Code" class="method-signature"
|
|
448
|
+
onclick="popupCode('Page.src/M000034.html');return false;">
|
|
449
|
+
<span class="method-name">draw_circle</span><span class="method-args">(args)</span>
|
|
450
|
+
</a>
|
|
451
|
+
</div>
|
|
452
|
+
|
|
453
|
+
<div class="method-description">
|
|
454
|
+
</div>
|
|
455
|
+
</div>
|
|
456
|
+
|
|
457
|
+
<div id="method-M000033" class="method-detail">
|
|
458
|
+
<a name="M000033"></a>
|
|
459
|
+
|
|
460
|
+
<div class="method-heading">
|
|
461
|
+
<a href="Page.src/M000033.html" target="Code" class="method-signature"
|
|
462
|
+
onclick="popupCode('Page.src/M000033.html');return false;">
|
|
463
|
+
<span class="method-name">draw_directed</span><span class="method-args">(args)</span>
|
|
464
|
+
</a>
|
|
465
|
+
</div>
|
|
466
|
+
|
|
467
|
+
<div class="method-description">
|
|
468
|
+
</div>
|
|
469
|
+
</div>
|
|
470
|
+
|
|
471
|
+
<div id="method-M000038" class="method-detail">
|
|
472
|
+
<a name="M000038"></a>
|
|
473
|
+
|
|
474
|
+
<div class="method-heading">
|
|
475
|
+
<a href="Page.src/M000038.html" target="Code" class="method-signature"
|
|
476
|
+
onclick="popupCode('Page.src/M000038.html');return false;">
|
|
477
|
+
<span class="method-name">draw_down_triangle</span><span class="method-args">(args)</span>
|
|
478
|
+
</a>
|
|
479
|
+
</div>
|
|
480
|
+
|
|
481
|
+
<div class="method-description">
|
|
482
|
+
</div>
|
|
483
|
+
</div>
|
|
484
|
+
|
|
485
|
+
<div id="method-M000040" class="method-detail">
|
|
486
|
+
<a name="M000040"></a>
|
|
487
|
+
|
|
488
|
+
<div class="method-heading">
|
|
489
|
+
<a href="Page.src/M000040.html" target="Code" class="method-signature"
|
|
490
|
+
onclick="popupCode('Page.src/M000040.html');return false;">
|
|
491
|
+
<span class="method-name">draw_features</span><span class="method-args">(track)</span>
|
|
492
|
+
</a>
|
|
493
|
+
</div>
|
|
494
|
+
|
|
495
|
+
<div class="method-description">
|
|
496
|
+
<p>
|
|
497
|
+
Takes a <a href="Track.html">Bio::Graphics::Track</a> object and does the
|
|
498
|
+
work to <a href="Page.html#M000043">draw</a> features
|
|
499
|
+
</p>
|
|
500
|
+
<p>
|
|
501
|
+
It examines the the type of track and calculates the required parameters
|
|
502
|
+
</p>
|
|
503
|
+
<ul>
|
|
504
|
+
<li><tt>args</tt> - an Array of <a href="Track.html">Bio::Graphics::Track</a>
|
|
505
|
+
object
|
|
506
|
+
|
|
507
|
+
</li>
|
|
508
|
+
</ul>
|
|
509
|
+
</div>
|
|
510
|
+
</div>
|
|
511
|
+
|
|
512
|
+
<div id="method-M000032" class="method-detail">
|
|
513
|
+
<a name="M000032"></a>
|
|
514
|
+
|
|
515
|
+
<div class="method-heading">
|
|
516
|
+
<a href="Page.src/M000032.html" target="Code" class="method-signature"
|
|
517
|
+
onclick="popupCode('Page.src/M000032.html');return false;">
|
|
518
|
+
<span class="method-name">draw_generic</span><span class="method-args">(args)</span>
|
|
519
|
+
</a>
|
|
520
|
+
</div>
|
|
521
|
+
|
|
522
|
+
<div class="method-description">
|
|
523
|
+
</div>
|
|
524
|
+
</div>
|
|
525
|
+
|
|
526
|
+
<div id="method-M000036" class="method-detail">
|
|
527
|
+
<a name="M000036"></a>
|
|
528
|
+
|
|
529
|
+
<div class="method-heading">
|
|
530
|
+
<a href="Page.src/M000036.html" target="Code" class="method-signature"
|
|
531
|
+
onclick="popupCode('Page.src/M000036.html');return false;">
|
|
532
|
+
<span class="method-name">draw_histogram</span><span class="method-args">(args)</span>
|
|
533
|
+
</a>
|
|
534
|
+
</div>
|
|
535
|
+
|
|
536
|
+
<div class="method-description">
|
|
537
|
+
</div>
|
|
538
|
+
</div>
|
|
539
|
+
|
|
540
|
+
<div id="method-M000031" class="method-detail">
|
|
541
|
+
<a name="M000031"></a>
|
|
542
|
+
|
|
543
|
+
<div class="method-heading">
|
|
544
|
+
<a href="Page.src/M000031.html" target="Code" class="method-signature"
|
|
545
|
+
onclick="popupCode('Page.src/M000031.html');return false;">
|
|
546
|
+
<span class="method-name">draw_label</span><span class="method-args">(args)</span>
|
|
547
|
+
</a>
|
|
548
|
+
</div>
|
|
549
|
+
|
|
550
|
+
<div class="method-description">
|
|
551
|
+
<p>
|
|
552
|
+
Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
553
|
+
the <a href="SVGEE.html">SVGEE</a> object
|
|
554
|
+
</p>
|
|
555
|
+
<ul>
|
|
556
|
+
<li><tt>args</tt> - an Array of <a
|
|
557
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> object
|
|
558
|
+
|
|
559
|
+
</li>
|
|
560
|
+
</ul>
|
|
561
|
+
</div>
|
|
562
|
+
</div>
|
|
563
|
+
|
|
564
|
+
<div id="method-M000030" class="method-detail">
|
|
565
|
+
<a name="M000030"></a>
|
|
566
|
+
|
|
567
|
+
<div class="method-heading">
|
|
568
|
+
<a href="Page.src/M000030.html" target="Code" class="method-signature"
|
|
569
|
+
onclick="popupCode('Page.src/M000030.html');return false;">
|
|
570
|
+
<span class="method-name">draw_scale</span><span class="method-args">()</span>
|
|
571
|
+
</a>
|
|
572
|
+
</div>
|
|
573
|
+
|
|
574
|
+
<div class="method-description">
|
|
575
|
+
<p>
|
|
576
|
+
Adds scale bar to the list of objects to be rendered in the final
|
|
577
|
+
</p>
|
|
578
|
+
</div>
|
|
579
|
+
</div>
|
|
580
|
+
|
|
581
|
+
<div id="method-M000039" class="method-detail">
|
|
582
|
+
<a name="M000039"></a>
|
|
583
|
+
|
|
584
|
+
<div class="method-heading">
|
|
585
|
+
<a href="Page.src/M000039.html" target="Code" class="method-signature"
|
|
586
|
+
onclick="popupCode('Page.src/M000039.html');return false;">
|
|
587
|
+
<span class="method-name">draw_span</span><span class="method-args">(args)</span>
|
|
588
|
+
</a>
|
|
589
|
+
</div>
|
|
590
|
+
|
|
591
|
+
<div class="method-description">
|
|
592
|
+
</div>
|
|
593
|
+
</div>
|
|
594
|
+
|
|
595
|
+
<div id="method-M000035" class="method-detail">
|
|
596
|
+
<a name="M000035"></a>
|
|
597
|
+
|
|
598
|
+
<div class="method-heading">
|
|
599
|
+
<a href="Page.src/M000035.html" target="Code" class="method-signature"
|
|
600
|
+
onclick="popupCode('Page.src/M000035.html');return false;">
|
|
601
|
+
<span class="method-name">draw_transcript</span><span class="method-args">(args)</span>
|
|
602
|
+
</a>
|
|
603
|
+
</div>
|
|
604
|
+
|
|
605
|
+
<div class="method-description">
|
|
606
|
+
</div>
|
|
607
|
+
</div>
|
|
608
|
+
|
|
609
|
+
<div id="method-M000037" class="method-detail">
|
|
610
|
+
<a name="M000037"></a>
|
|
611
|
+
|
|
612
|
+
<div class="method-heading">
|
|
613
|
+
<a href="Page.src/M000037.html" target="Code" class="method-signature"
|
|
614
|
+
onclick="popupCode('Page.src/M000037.html');return false;">
|
|
615
|
+
<span class="method-name">draw_up_triangle</span><span class="method-args">(args)</span>
|
|
616
|
+
</a>
|
|
617
|
+
</div>
|
|
618
|
+
|
|
619
|
+
<div class="method-description">
|
|
620
|
+
</div>
|
|
621
|
+
</div>
|
|
622
|
+
|
|
623
|
+
<div id="method-M000029" class="method-detail">
|
|
624
|
+
<a name="M000029"></a>
|
|
625
|
+
|
|
626
|
+
<div class="method-heading">
|
|
627
|
+
<a href="Page.src/M000029.html" target="Code" class="method-signature"
|
|
628
|
+
onclick="popupCode('Page.src/M000029.html');return false;">
|
|
629
|
+
<span class="method-name">get_limits</span><span class="method-args">()</span>
|
|
630
|
+
</a>
|
|
631
|
+
</div>
|
|
632
|
+
|
|
633
|
+
<div class="method-description">
|
|
634
|
+
<p>
|
|
635
|
+
Calculates the <a href="Page.html">Page</a> scale-start and scale-stop
|
|
636
|
+
position and the nucleotides per pixel for the current <a
|
|
637
|
+
href="Page.html">Page</a>
|
|
638
|
+
</p>
|
|
639
|
+
</div>
|
|
640
|
+
</div>
|
|
641
|
+
|
|
642
|
+
<div id="method-M000042" class="method-detail">
|
|
643
|
+
<a name="M000042"></a>
|
|
644
|
+
|
|
645
|
+
<div class="method-heading">
|
|
646
|
+
<a href="Page.src/M000042.html" target="Code" class="method-signature"
|
|
647
|
+
onclick="popupCode('Page.src/M000042.html');return false;">
|
|
648
|
+
<span class="method-name">get_markup</span><span class="method-args">()</span>
|
|
649
|
+
</a>
|
|
650
|
+
</div>
|
|
651
|
+
|
|
652
|
+
<div class="method-description">
|
|
653
|
+
<p>
|
|
654
|
+
generates the SVG text
|
|
655
|
+
</p>
|
|
656
|
+
</div>
|
|
657
|
+
</div>
|
|
658
|
+
|
|
659
|
+
<div id="method-M000041" class="method-detail">
|
|
660
|
+
<a name="M000041"></a>
|
|
661
|
+
|
|
662
|
+
<div class="method-heading">
|
|
663
|
+
<a href="Page.src/M000041.html" target="Code" class="method-signature"
|
|
664
|
+
onclick="popupCode('Page.src/M000041.html');return false;">
|
|
665
|
+
<span class="method-name">to_px</span><span class="method-args">(num)</span>
|
|
666
|
+
</a>
|
|
667
|
+
</div>
|
|
668
|
+
|
|
669
|
+
<div class="method-description">
|
|
670
|
+
<p>
|
|
671
|
+
Calculates the pixel value for a given number
|
|
672
|
+
</p>
|
|
673
|
+
</div>
|
|
674
|
+
</div>
|
|
675
|
+
|
|
676
|
+
<div id="method-M000044" class="method-detail">
|
|
677
|
+
<a name="M000044"></a>
|
|
678
|
+
|
|
679
|
+
<div class="method-heading">
|
|
680
|
+
<a href="Page.src/M000044.html" target="Code" class="method-signature"
|
|
681
|
+
onclick="popupCode('Page.src/M000044.html');return false;">
|
|
682
|
+
<span class="method-name">write</span><span class="method-args">(file)</span>
|
|
683
|
+
</a>
|
|
684
|
+
</div>
|
|
685
|
+
|
|
686
|
+
<div class="method-description">
|
|
687
|
+
<p>
|
|
688
|
+
Writes the SVG text to a file
|
|
689
|
+
</p>
|
|
690
|
+
</div>
|
|
691
|
+
</div>
|
|
692
|
+
|
|
693
|
+
|
|
694
|
+
</div>
|
|
695
|
+
|
|
696
|
+
|
|
697
|
+
</div>
|
|
698
|
+
|
|
699
|
+
|
|
700
|
+
<div id="validator-badges">
|
|
701
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
702
|
+
</div>
|
|
703
|
+
|
|
704
|
+
</body>
|
|
705
|
+
</html>
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