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>scale (Bio::Graphics::Glyph)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 337</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-identifier">first_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:start</span>]
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<span class="ruby-identifier">last_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:stop</span>]
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<span class="ruby-comment cmt">#(num.to_f / @nt_per_px_x.to_f)</span>
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<span class="ruby-identifier">full_dist</span> = <span class="ruby-identifier">last_mark</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span>
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<span class="ruby-identifier">interval_width</span> = <span class="ruby-identifier">full_dist</span> <span class="ruby-operator">/</span> (<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:number_of_intervals</span>] <span class="ruby-operator">-</span> <span class="ruby-value">1</span>)
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<span class="ruby-identifier">a</span> = [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:line</span>,
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<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
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<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
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<span class="ruby-identifier">:x1</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>, <span class="ruby-identifier">:x2</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:page_width</span>],<span class="ruby-comment cmt"># * 1.1, </span>
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<span class="ruby-identifier">:y1</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"20"</span>, <span class="ruby-identifier">:y2</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"20"</span> )]
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<span class="ruby-identifier">marks</span> = (<span class="ruby-identifier">first_mark</span><span class="ruby-operator">..</span><span class="ruby-identifier">last_mark</span>).<span class="ruby-identifier">step</span>(<span class="ruby-identifier">interval_width</span>).<span class="ruby-identifier">to_a</span>
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<span class="ruby-identifier">px_per_nt</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:page_width</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">full_dist</span>.<span class="ruby-identifier">to_f</span>
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<span class="ruby-identifier">marks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">mark</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">x</span> = (<span class="ruby-identifier">mark</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">px_per_nt</span>
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<span class="ruby-identifier">a</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>,
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<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
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<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-value">20</span>,
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<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
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<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
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<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
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<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value">5</span> )
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<span class="ruby-identifier">a</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:text</span>,
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<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
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<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-value">40</span>, <span class="ruby-identifier">:fill</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
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<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">mark</span>,
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<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"font-family:Arial;font-style:italic"</span>)
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<span class="ruby-keyword kw">end</span>
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">a</span>
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<span class="ruby-keyword kw">end</span></pre>
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<title>label (Bio::Graphics::Glyph)</title>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 382</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">label</span>(<span class="ruby-identifier">args</span>)
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[<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:text</span>,
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<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:text</span>],
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<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>],
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<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
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<span class="ruby-identifier">:fill</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"black"</span>,
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<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"font-family:monospace;"</span>)]
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<span class="ruby-keyword kw">end</span></pre>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 59</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-identifier">args</span> = {
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<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>,
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<span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'red'</span>,
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<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"black"</span>,
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<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
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<span class="ruby-identifier">:x_round</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
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<span class="ruby-identifier">:y_round</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
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<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"fill-opacity:0.4;"</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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[<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>, <span class="ruby-identifier">args</span>)]
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 103</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-identifier">args</span> = {
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[<span class="ruby-identifier">:x</span>, <span class="ruby-identifier">:y</span>].<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">e</span><span class="ruby-operator">|</span> <span class="ruby-identifier">args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">e</span>)}
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[<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:circle</span>, <span class="ruby-identifier">args</span>)]
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 151</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
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<span class="ruby-identifier">args</span> = {
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<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'-'</span>
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">"#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + args[:height] } #{args[:x]},#{args[:y] + (args[:height])} #{args[:x] - (args[:height] * 0.2)},#{args[:y] + (args[:height]/2)}"</span>
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<span class="ruby-keyword kw">else</span>
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">"#{args[:x]},#{args[:y]} #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + (args[:height]/2) } #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y] + args[:height]} #{args[:x]},#{args[:y] + args[:height]}"</span>
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 200</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">down_triangle</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
|
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<span class="ruby-identifier">args</span> = {
|
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|
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|
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|
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|
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|
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|
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">"#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{ args[:x] + (args[:width]/2) },#{(args[:y] + args[:height]) }"</span>
|
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|
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[<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:polygon</span>, <span class="ruby-identifier">args</span>)]
|
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|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 245</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">up_triangle</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment cmt">#:x, :y, :width :fill, :stroke :stroke_width, :style, :height</span>
|
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<span class="ruby-identifier">args</span> = {
|
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|
|
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|
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|
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|
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|
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:points</span>] = <span class="ruby-node">"#{args[:x]},#{args[:y] + args[:height]} #{args[:x] + args[:width]},#{args[:y] + args[:height]} #{ args[:x] + (args[:width]/2) },#{args[:y] }"</span>
|
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[<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:polygon</span>, <span class="ruby-identifier">args</span>)]
|
|
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|
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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/glyph.rb, line 289</span>
|
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">span</span>(<span class="ruby-identifier">args</span>)
|
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|
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|
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|
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|
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|
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|
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|
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|
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x2</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>] <span class="ruby-operator">+</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:width</span>]
|
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y1</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>]
|
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<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y2</span>] = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>]
|
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[<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:line</span>, <span class="ruby-identifier">args</span>)]
|
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 366</span>
|
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|
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">transcript</span>(<span class="ruby-identifier">args</span>)
|
|
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|
+
<span class="ruby-identifier">args</span> = {
|
|
16
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>,
|
|
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|
+
<span class="ruby-identifier">:utr_fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
|
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|
+
<span class="ruby-identifier">:utr_stroke</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"black"</span>,
|
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|
+
<span class="ruby-identifier">:utr_stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
|
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|
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<span class="ruby-identifier">:exon_fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'red'</span>,
|
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|
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<span class="ruby-identifier">:exon_stroke</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"black"</span>,
|
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|
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<span class="ruby-identifier">:exon_stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
|
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|
+
<span class="ruby-identifier">:line_color</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
|
|
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|
+
<span class="ruby-identifier">:line_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
|
|
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<span class="ruby-identifier">:exon_style</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"fill-opacity:0.4;"</span>,
|
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<span class="ruby-identifier">:utr_style</span> =<span class="ruby-operator">></span> <span class="ruby-value str">""</span>,
|
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|
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<span class="ruby-identifier">:block_gaps</span> =<span class="ruby-operator">></span> <span class="ruby-value str">""</span>,
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<span class="ruby-identifier">:gap_marker</span> =<span class="ruby-operator">></span> <span class="ruby-value str">""</span>
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}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">args</span>)
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|
+
|
|
32
|
+
<span class="ruby-identifier">composite</span> = []
|
|
33
|
+
|
|
34
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">empty?</span> <span class="ruby-comment cmt">##draw the utr as terminal element...##terminal utr is the one with the point on...</span>
|
|
35
|
+
<span class="ruby-identifier">x</span>,<span class="ruby-identifier">width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'-'</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">shift</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">pop</span>
|
|
36
|
+
<span class="ruby-identifier">composite</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
37
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
|
|
38
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
39
|
+
<span class="ruby-identifier">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>],
|
|
40
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
|
|
41
|
+
<span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_fill_color</span>],
|
|
42
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke</span>],
|
|
43
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke_width</span>],
|
|
44
|
+
<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_style</span>] )
|
|
45
|
+
<span class="ruby-comment cmt">##draw the other(s!) </span>
|
|
46
|
+
<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utrs</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">utr</span><span class="ruby-operator">|</span>
|
|
47
|
+
<span class="ruby-identifier">composite</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>, {
|
|
48
|
+
<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">first</span>,
|
|
49
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">last</span>,
|
|
50
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
|
|
51
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
|
|
52
|
+
<span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_fill_color</span>],
|
|
53
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke</span>],
|
|
54
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_stroke_width</span>],
|
|
55
|
+
<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:utr_style</span>]} )
|
|
56
|
+
<span class="ruby-keyword kw">end</span>
|
|
57
|
+
<span class="ruby-keyword kw">else</span> <span class="ruby-comment cmt">## draw the terminal exon as terminal element </span>
|
|
58
|
+
<span class="ruby-identifier">points</span> = <span class="ruby-keyword kw">nil</span>
|
|
59
|
+
<span class="ruby-identifier">x</span>,<span class="ruby-identifier">width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">'-'</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>].<span class="ruby-identifier">shift</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>].<span class="ruby-identifier">pop</span>
|
|
60
|
+
<span class="ruby-identifier">composite</span> <span class="ruby-operator">+=</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
61
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
|
|
62
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
63
|
+
<span class="ruby-identifier">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:strand</span>],
|
|
64
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
|
|
65
|
+
<span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_fill_color</span>],
|
|
66
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke</span>],
|
|
67
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke_width</span>],
|
|
68
|
+
<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_style</span>] )
|
|
69
|
+
<span class="ruby-keyword kw">end</span>
|
|
70
|
+
<span class="ruby-comment cmt">#draw any remaining exons</span>
|
|
71
|
+
<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exons</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">exon</span><span class="ruby-operator">|</span>
|
|
72
|
+
<span class="ruby-identifier">composite</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>, {
|
|
73
|
+
<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>],
|
|
74
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">exon</span>[<span class="ruby-value">1</span>],
|
|
75
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>],
|
|
76
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>],
|
|
77
|
+
<span class="ruby-identifier">:fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_fill_color</span>],
|
|
78
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span><span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke</span>],
|
|
79
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_stroke_width</span>],
|
|
80
|
+
<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:exon_style</span>]} )
|
|
81
|
+
<span class="ruby-keyword kw">end</span>
|
|
82
|
+
<span class="ruby-keyword kw">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:gap_marker</span>] <span class="ruby-operator">==</span> <span class="ruby-value str">"angled"</span> <span class="ruby-keyword kw">and</span> <span class="ruby-keyword kw">not</span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:block_gaps</span>].<span class="ruby-identifier">empty?</span>
|
|
83
|
+
<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:block_gaps</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gap</span><span class="ruby-operator">|</span>
|
|
84
|
+
<span class="ruby-identifier">points</span> = <span class="ruby-node">"#{gap.first},#{args[:y] + (args[:height]/2) } #{gap.first + (gap.last/2)},#{args[:y]} #{gap.first + gap.last},#{args[:y] + (args[:height]/2)}"</span>
|
|
85
|
+
<span class="ruby-identifier">composite</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:polyline</span>, {
|
|
86
|
+
<span class="ruby-identifier">:points</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">points</span>,
|
|
87
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_color</span>],
|
|
88
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_width</span>],
|
|
89
|
+
<span class="ruby-identifier">:fill</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"none"</span>,
|
|
90
|
+
<span class="ruby-identifier">:line_style</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_style</span>]})
|
|
91
|
+
<span class="ruby-keyword kw">end</span>
|
|
92
|
+
<span class="ruby-keyword kw">else</span>
|
|
93
|
+
<span class="ruby-comment cmt">#add line</span>
|
|
94
|
+
<span class="ruby-identifier">composite</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:line</span>, {
|
|
95
|
+
<span class="ruby-identifier">:x1</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:x</span>],
|
|
96
|
+
<span class="ruby-identifier">:x2</span> =<span class="ruby-operator">></span> <span class="ruby-node">"#{args[:x] + args[:width]}"</span>,
|
|
97
|
+
<span class="ruby-identifier">:y1</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>] <span class="ruby-operator">+</span> (<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>]<span class="ruby-operator">/</span><span class="ruby-value">2</span>),
|
|
98
|
+
<span class="ruby-identifier">:y2</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:y</span>] <span class="ruby-operator">+</span> (<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:height</span>]<span class="ruby-operator">/</span><span class="ruby-value">2</span>),
|
|
99
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_color</span>],
|
|
100
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_width</span>],
|
|
101
|
+
<span class="ruby-identifier">:line_style</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:line_style</span>]})
|
|
102
|
+
|
|
103
|
+
<span class="ruby-keyword kw">end</span>
|
|
104
|
+
<span class="ruby-identifier">composite</span>
|
|
105
|
+
<span class="ruby-keyword kw">end</span></pre>
|
|
106
|
+
</body>
|
|
107
|
+
</html>
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
|
|
6
|
+
<html>
|
|
7
|
+
<head>
|
|
8
|
+
<title>scale (Bio::Graphics::Glyph)</title>
|
|
9
|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
+
<link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
+
</head>
|
|
12
|
+
<body class="standalone-code">
|
|
13
|
+
<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 470</span>
|
|
14
|
+
<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-identifier">args</span>)
|
|
15
|
+
<span class="ruby-identifier">first_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:start</span>]
|
|
16
|
+
<span class="ruby-identifier">last_mark</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:stop</span>]
|
|
17
|
+
<span class="ruby-comment cmt">#(num.to_f / @nt_per_px_x.to_f)</span>
|
|
18
|
+
<span class="ruby-identifier">full_dist</span> = <span class="ruby-identifier">last_mark</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span>
|
|
19
|
+
<span class="ruby-identifier">interval_width</span> = <span class="ruby-identifier">full_dist</span> <span class="ruby-operator">/</span> (<span class="ruby-identifier">args</span>[<span class="ruby-identifier">:number_of_intervals</span>] <span class="ruby-operator">-</span> <span class="ruby-value">1</span>)
|
|
20
|
+
|
|
21
|
+
|
|
22
|
+
<span class="ruby-identifier">a</span> = [<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:line</span>,
|
|
23
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
|
|
24
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
|
|
25
|
+
<span class="ruby-identifier">:x1</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>, <span class="ruby-identifier">:x2</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:page_width</span>],<span class="ruby-comment cmt"># * 1.1, </span>
|
|
26
|
+
<span class="ruby-identifier">:y1</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"20"</span>, <span class="ruby-identifier">:y2</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"20"</span> )]
|
|
27
|
+
|
|
28
|
+
|
|
29
|
+
<span class="ruby-identifier">marks</span> = (<span class="ruby-identifier">first_mark</span><span class="ruby-operator">..</span><span class="ruby-identifier">last_mark</span>).<span class="ruby-identifier">step</span>(<span class="ruby-identifier">interval_width</span>).<span class="ruby-identifier">to_a</span>
|
|
30
|
+
|
|
31
|
+
<span class="ruby-identifier">px_per_nt</span> = <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:page_width</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">full_dist</span>.<span class="ruby-identifier">to_f</span>
|
|
32
|
+
<span class="ruby-identifier">marks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">mark</span><span class="ruby-operator">|</span>
|
|
33
|
+
<span class="ruby-identifier">x</span> = (<span class="ruby-identifier">mark</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">first_mark</span> ).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">px_per_nt</span>
|
|
34
|
+
<span class="ruby-identifier">a</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:rectangle</span>,
|
|
35
|
+
<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
36
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-value">20</span>,
|
|
37
|
+
<span class="ruby-identifier">:stroke</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
|
|
38
|
+
<span class="ruby-identifier">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
|
|
39
|
+
<span class="ruby-identifier">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
|
|
40
|
+
<span class="ruby-identifier">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value">5</span> )
|
|
41
|
+
|
|
42
|
+
<span class="ruby-identifier">a</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:text</span>,
|
|
43
|
+
<span class="ruby-identifier">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
44
|
+
<span class="ruby-identifier">:y</span> =<span class="ruby-operator">></span> <span class="ruby-value">40</span>, <span class="ruby-identifier">:fill</span> =<span class="ruby-operator">></span> <span class="ruby-value str">'black'</span>,
|
|
45
|
+
<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">mark</span>,
|
|
46
|
+
<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"font-family:Arial;font-style:italic"</span>)
|
|
47
|
+
<span class="ruby-keyword kw">end</span>
|
|
48
|
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<span class="ruby-keyword kw">return</span> <span class="ruby-identifier">a</span>
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 515</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">label</span>(<span class="ruby-identifier">args</span>)
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[<span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Primitive</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:text</span>,
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<span class="ruby-identifier">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-identifier">:text</span>],
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<span class="ruby-identifier">:fill</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"black"</span>,
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<span class="ruby-identifier">:style</span> =<span class="ruby-operator">></span> <span class="ruby-value str">"font-family:monospace;"</span>)]
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<pre><span class="ruby-comment cmt"># File lib/bio/graphics/glyph.rb, line 525</span>
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<span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">gradients</span> <span class="ruby-comment cmt">#needs to know which of its gradients are predefined</span>
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[<span class="ruby-identifier">:red_white_h</span>, <span class="ruby-identifier">:green_white_h</span>, <span class="ruby-identifier">:blue_white_h</span>, <span class="ruby-identifier">:yellow_white_h</span>, <span class="ruby-identifier">:red_white_radial</span>, <span class="ruby-identifier">:green_white_radial</span>, <span class="ruby-identifier">:blue_white_radial</span>, <span class="ruby-identifier">:yellow_white_radial</span> ]
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