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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<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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<title>Class: Bio::Graphics::MiniFeature</title>
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// <![CDATA[
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// ]]>
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</script>
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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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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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|
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<h2>args</h2>
|
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|
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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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</li>
|
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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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|
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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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|
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</pre>
|
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|
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<h3>MiniFeatures and Tracks</h3>
|
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|
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<p>
|
|
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|
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MiniFeatures are created and added to <a
|
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|
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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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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/mini_feature.rb, line 35</span>
|
|
14
|
+
<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>]
|
|
16
|
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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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|
+
<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
|
+
<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
|
+
<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>
|
|
20
|
+
<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>
|
|
14
|
+
<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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|
+
<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>]
|
|
18
|
+
<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>
|
|
20
|
+
<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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|
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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 ) {
|
|
20
|
+
if ( document.getElementById )
|
|
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|
+
elem = document.getElementById( id );
|
|
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|
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else if ( document.all )
|
|
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|
+
elem = eval( "document.all." + id );
|
|
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|
+
else
|
|
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|
+
return false;
|
|
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|
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|
|
27
|
+
elemStyle = elem.style;
|
|
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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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|
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<td>
|
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|
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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
|
+
<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>
|
|
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|
+
|
|
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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