bio-svgenes 0.2.3 → 0.3.0
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- data/.DS_Store +0 -0
- data/VERSION +1 -1
- data/bio-svgenes.gemspec +59 -4
- data/doc/.DS_Store +0 -0
- data/doc/Bio.html +141 -0
- data/doc/Bio/.DS_Store +0 -0
- data/doc/Bio/Graphics.html +147 -0
- data/doc/Bio/Graphics/Glyph.html +1061 -0
- data/doc/Bio/Graphics/MiniFeature.html +342 -0
- data/doc/Bio/Graphics/Page.html +1200 -0
- data/doc/Bio/Graphics/Primitive.html +278 -0
- data/doc/Bio/Graphics/SVGEE.html +471 -0
- data/doc/Bio/Graphics/Track.html +506 -0
- data/doc/LICENSE_txt.html +118 -0
- data/doc/created.rid +9 -0
- data/doc/images/add.png +0 -0
- data/doc/images/arrow_up.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
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- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
- data/doc/images/macFFBgHack.png +0 -0
- data/doc/images/package.png +0 -0
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- data/doc/images/ruby.png +0 -0
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- data/doc/images/tag_green.png +0 -0
- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +94 -0
- data/doc/js/darkfish.js +155 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/rdoc.css +595 -0
- data/doc/table_of_contents.html +162 -0
- data/test/gene.gff +4 -0
- data/test/json_config.json +17 -0
- data/test/test_glyph.rb +33 -0
- data/test/test_mini_feature.rb +37 -0
- data/test/test_page.rb +127 -0
- data/test/test_primitive.rb +45 -0
- data/test/test_svgee.rb +73 -0
- data/test/test_track.rb +53 -0
- data/test/test_transcripts.gff +4 -0
- metadata +94 -14
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<h1 class="class">class Bio::Graphics::MiniFeature</h1>
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<p>Creates a new <a href="MiniFeature.html">MiniFeature</a></p>
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<p><em>Arguments</em></p>
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<p>start = the start position of the feature</p>
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<h2 id="method-c-new-label-Example+usage">Example usage<span><a href="#method-c-new-label-Example+usage">¶</a> <a href="#documentation">↑</a></span></h2>
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<pre class="ruby"><span class="ruby-ivar">@mini1</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">MiniFeature</span>.<span class="ruby-identifier">new</span>(:<span class="ruby-identifier">start=</span><span class="ruby-operator">></span><span class="ruby-value">3631</span>, :<span class="ruby-keyword">end</span>=<span class="ruby-operator">></span><span class="ruby-value">5899</span>, :<span class="ruby-identifier">strand=</span><span class="ruby-operator">></span><span class="ruby-string">'+'</span>,
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:<span class="ruby-identifier">exons=</span><span class="ruby-operator">></span>[<span class="ruby-value">4000</span>, <span class="ruby-value">4500</span>, <span class="ruby-value">4700</span>, <span class="ruby-value">5000</span>], :<span class="ruby-identifier">utrs=</span><span class="ruby-operator">></span>[<span class="ruby-value">3631</span>, <span class="ruby-value">3650</span>], :<span class="ruby-identifier">segment_height=</span><span class="ruby-operator">></span><span class="ruby-value">5</span>, :<span class="ruby-identifier">id=</span><span class="ruby-operator">></span><span class="ruby-string">"AT1G01010"</span>)
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<h1 class="class">class Bio::Graphics::Page</h1>
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<p>Calculates the colour or gradient for the supplied <a
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href="Track.html">Bio::Graphics::Track</a> objects and adds them to the <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 138</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">args</span>)
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[<span class="ruby-value">:fill_color</span>, <span class="ruby-value">:exon_fill_color</span>, <span class="ruby-value">:utr_fill_color</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">colour_tag</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>])
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<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradient</span>(<span class="ruby-identifier">args</span>[<span class="ruby-identifier">colour_tag</span>]))
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<span class="ruby-keyword">end</span></pre>
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<p>Prints out the svg text</p>
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 332</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw</span>
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<span class="ruby-identifier">puts</span> <span class="ruby-identifier">get_markup</span>
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<span class="ruby-keyword">end</span></pre>
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<p><code>args</code> - an Array of <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 189</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_circle</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">circle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<span class="ruby-keyword">end</span></pre>
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<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
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<p><code>args</code> - an Array of <a
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 184</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_directed</span>(<span class="ruby-identifier">args</span>)
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<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">directed</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
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<span class="ruby-keyword">end</span></pre>
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</div><!-- draw_directed-method -->
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<div id="method-i-draw_down_triangle" class="method-detail ">
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<span class="method-name">draw_down_triangle</span><span
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class="method-args">(args)</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
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the <a href="SVGEE.html">SVGEE</a> object</p>
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<p><code>args</code> - an Array of <a
|
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href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
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type</p>
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<div class="method-source-code" id="draw_down_triangle-source">
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 209</span>
|
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+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_down_triangle</span>(<span class="ruby-identifier">args</span>)
|
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+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">down_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
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<span class="ruby-keyword">end</span></pre>
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</div>
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</div><!-- draw_down_triangle-method -->
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<div id="method-i-draw_features" class="method-detail ">
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<div class="method-heading">
|
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<span class="method-name">draw_features</span><span
|
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+
class="method-args">(track)</span>
|
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|
|
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<span class="method-click-advice">click to toggle source</span>
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|
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</div>
|
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|
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|
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<div class="method-description">
|
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|
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|
|
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|
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<p>Takes a <a href="Track.html">Bio::Graphics::Track</a> object and sorts out
|
|
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|
+
the input information into a user friendly format.</p>
|
|
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|
+
|
|
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|
+
<p>It examines the the type of track and calculates the required parameters</p>
|
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<ul><li>
|
|
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|
+
<p><code>args</code> - an Array of <a
|
|
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|
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href="Track.html">Bio::Graphics::Track</a> object</p>
|
|
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|
+
</li></ul>
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<div class="method-source-code" id="draw_features-source">
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<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 222</span>
|
|
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|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_features</span>(<span class="ruby-identifier">track</span>)
|
|
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|
+
<span class="ruby-keyword">if</span> [<span class="ruby-value">:histogram</span>, <span class="ruby-string">"histogram"</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">glyph</span>) <span class="ruby-comment">#do different stuff for data tracks...</span>
|
|
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|
+
|
|
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|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>)
|
|
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|
+
<span class="ruby-identifier">max</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">max_y</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">max_y</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span>, <span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">segment_height</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">segment_height</span> }.<span class="ruby-identifier">last</span>.<span class="ruby-identifier">segment_height</span>
|
|
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|
+
<span class="ruby-identifier">min</span> = <span class="ruby-value">0</span>
|
|
427
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">label</span>
|
|
428
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">name</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> <span class="ruby-value">30</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-value">3</span>)
|
|
429
|
+
<span class="ruby-keyword">end</span>
|
|
430
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">max</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">to_px</span>(<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">+</span> <span class="ruby-value">5</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>)
|
|
431
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">min</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">to_px</span>(<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">+</span> <span class="ruby-value">5</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>)
|
|
432
|
+
<span class="ruby-identifier">data_interval</span> = <span class="ruby-identifier">max</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">min</span>
|
|
433
|
+
<span class="ruby-identifier">data_per_px</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">data_interval</span>.<span class="ruby-identifier">to_f</span>
|
|
434
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span>
|
|
435
|
+
<span class="ruby-identifier">x</span> = <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>)
|
|
436
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">f</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))
|
|
437
|
+
<span class="ruby-identifier">height</span> = <span class="ruby-identifier">f</span>.<span class="ruby-identifier">segment_height</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">data_per_px</span>
|
|
438
|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">height</span> <span class="ruby-operator">+</span> <span class="ruby-value">5</span>
|
|
439
|
+
<span class="ruby-comment">#$stderr.puts f.segment_height, data_per_px, data_interval, max, min, "------"</span>
|
|
440
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">send</span>(<span class="ruby-node">"draw_#{track.glyph}"</span>, {<span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
441
|
+
<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>,
|
|
442
|
+
<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
443
|
+
<span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">height</span>}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">args</span>))
|
|
444
|
+
<span class="ruby-keyword">end</span>
|
|
445
|
+
<span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">track_height</span>) <span class="ruby-operator">+</span> <span class="ruby-value">20</span>
|
|
446
|
+
<span class="ruby-keyword">else</span> <span class="ruby-comment">##following stuff for the features</span>
|
|
447
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">label</span>
|
|
448
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">name</span>, <span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> <span class="ruby-value">30</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-value">3</span>)
|
|
449
|
+
<span class="ruby-keyword">end</span>
|
|
450
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">get_rows</span> <span class="ruby-comment">##work out how many rows and which features belong in each row...</span>
|
|
451
|
+
<span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">f</span>, <span class="ruby-identifier">index</span><span class="ruby-operator">|</span>
|
|
452
|
+
<span class="ruby-identifier">x</span> = <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-comment">#bottom left of feature</span>
|
|
453
|
+
<span class="ruby-identifier">all_sub_blocks</span> = []
|
|
454
|
+
|
|
455
|
+
<span class="ruby-comment">#convert the exon and utr start stops to px start stops and px widths</span>
|
|
456
|
+
<span class="ruby-identifier">exons</span> = []
|
|
457
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>
|
|
458
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>.<span class="ruby-identifier">each_slice</span>(<span class="ruby-value">2</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">exon</span><span class="ruby-operator">|</span>
|
|
459
|
+
<span class="ruby-identifier">all_sub_blocks</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">exon</span>
|
|
460
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">exon</span>.<span class="ruby-identifier">nil?</span>
|
|
461
|
+
<span class="ruby-identifier">exons</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">exon</span>[<span class="ruby-value">1</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">exon</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
462
|
+
<span class="ruby-keyword">end</span>
|
|
463
|
+
<span class="ruby-keyword">end</span>
|
|
464
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span> = <span class="ruby-identifier">exons</span>
|
|
465
|
+
|
|
466
|
+
<span class="ruby-identifier">utrs</span> = []
|
|
467
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>
|
|
468
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>.<span class="ruby-identifier">each_slice</span>(<span class="ruby-value">2</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">utr</span><span class="ruby-operator">|</span>
|
|
469
|
+
<span class="ruby-identifier">all_sub_blocks</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">utr</span>
|
|
470
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">utr</span>.<span class="ruby-identifier">nil?</span>
|
|
471
|
+
<span class="ruby-identifier">utrs</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">utr</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">utr</span>[<span class="ruby-value">1</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">utr</span>[<span class="ruby-value">0</span>] <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
472
|
+
<span class="ruby-keyword">end</span>
|
|
473
|
+
<span class="ruby-keyword">end</span>
|
|
474
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span> = <span class="ruby-identifier">utrs</span>
|
|
475
|
+
|
|
476
|
+
<span class="ruby-comment">#if there are any intron like gaps.. get where they would be</span>
|
|
477
|
+
<span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">empty?</span>
|
|
478
|
+
<span class="ruby-identifier">all_sub_blocks</span> = <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span>, <span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">first</span> }
|
|
479
|
+
<span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">each_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
|
|
480
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">all_sub_blocks</span>.<span class="ruby-identifier">length</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">>=</span> <span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">first</span> <span class="ruby-comment">#skip if there is no gap</span>
|
|
481
|
+
<span class="ruby-identifier">f</span>.<span class="ruby-identifier">block_gaps</span> <span class="ruby-operator"><<</span> [<span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>), <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>].<span class="ruby-identifier">first</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">all_sub_blocks</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">last</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))]
|
|
482
|
+
<span class="ruby-keyword">end</span>
|
|
483
|
+
<span class="ruby-keyword">end</span>
|
|
484
|
+
|
|
485
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">to_px</span>((<span class="ruby-identifier">f</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>) <span class="ruby-operator">-</span> (<span class="ruby-identifier">f</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>))
|
|
486
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span> <span class="ruby-keyword">and</span> <span class="ruby-identifier">width</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span>
|
|
487
|
+
<span class="ruby-identifier">width</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">min_width</span>
|
|
488
|
+
<span class="ruby-keyword">end</span>
|
|
489
|
+
<span class="ruby-identifier">y</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_rows</span>[<span class="ruby-identifier">index</span>] <span class="ruby-operator">*</span> <span class="ruby-value">2</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span>)
|
|
490
|
+
|
|
491
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">send</span>(<span class="ruby-node">"draw_#{track.glyph}"</span>, {<span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span>,
|
|
492
|
+
<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>,
|
|
493
|
+
<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">width</span>,
|
|
494
|
+
<span class="ruby-value">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">strand</span>,
|
|
495
|
+
<span class="ruby-value">:exons</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">exons</span>,
|
|
496
|
+
<span class="ruby-value">:utrs</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">utrs</span>,
|
|
497
|
+
<span class="ruby-value">:block_gaps</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">block_gaps</span>,
|
|
498
|
+
<span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span>
|
|
499
|
+
}.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">track</span>.<span class="ruby-identifier">args</span>))
|
|
500
|
+
|
|
501
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">id</span>
|
|
502
|
+
<span class="ruby-identifier">draw_label</span>(<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">y</span>, <span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">x</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">width</span> <span class="ruby-value">+2</span>, <span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">id</span>)
|
|
503
|
+
<span class="ruby-keyword">end</span>
|
|
504
|
+
<span class="ruby-keyword">end</span>
|
|
505
|
+
<span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+=</span> (<span class="ruby-identifier">track</span>.<span class="ruby-identifier">feature_height</span> <span class="ruby-operator">*</span> <span class="ruby-identifier">track</span>.<span class="ruby-identifier">number_rows</span> <span class="ruby-operator">*</span> <span class="ruby-value">2</span>) <span class="ruby-operator">+</span> <span class="ruby-value">20</span>
|
|
506
|
+
<span class="ruby-keyword">end</span>
|
|
507
|
+
|
|
508
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-ivar">@track_top</span> <span class="ruby-operator">+</span> <span class="ruby-value">100</span> <span class="ruby-comment">#fudge...</span>
|
|
509
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">update_height</span>(<span class="ruby-ivar">@height</span>)
|
|
510
|
+
<span class="ruby-comment">#@svg.update_width(@width + 200)</span>
|
|
511
|
+
|
|
512
|
+
<span class="ruby-keyword">end</span></pre>
|
|
513
|
+
</div><!-- draw_features-source -->
|
|
514
|
+
|
|
515
|
+
</div>
|
|
516
|
+
|
|
517
|
+
|
|
518
|
+
|
|
519
|
+
|
|
520
|
+
</div><!-- draw_features-method -->
|
|
521
|
+
|
|
522
|
+
|
|
523
|
+
<div id="method-i-draw_generic" class="method-detail ">
|
|
524
|
+
|
|
525
|
+
<div class="method-heading">
|
|
526
|
+
<span class="method-name">draw_generic</span><span
|
|
527
|
+
class="method-args">(args)</span>
|
|
528
|
+
|
|
529
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
530
|
+
|
|
531
|
+
</div>
|
|
532
|
+
|
|
533
|
+
|
|
534
|
+
<div class="method-description">
|
|
535
|
+
|
|
536
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
537
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
538
|
+
<ul><li>
|
|
539
|
+
<p><code>args</code> - an Array of <a
|
|
540
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
541
|
+
type</p>
|
|
542
|
+
</li></ul>
|
|
543
|
+
|
|
544
|
+
|
|
545
|
+
|
|
546
|
+
|
|
547
|
+
<div class="method-source-code" id="draw_generic-source">
|
|
548
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 179</span>
|
|
549
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_generic</span>(<span class="ruby-identifier">args</span>) <span class="ruby-comment">#remember presentation info comes from track@args when the track is defined</span>
|
|
550
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
551
|
+
<span class="ruby-keyword">end</span></pre>
|
|
552
|
+
</div><!-- draw_generic-source -->
|
|
553
|
+
|
|
554
|
+
</div>
|
|
555
|
+
|
|
556
|
+
|
|
557
|
+
|
|
558
|
+
|
|
559
|
+
</div><!-- draw_generic-method -->
|
|
560
|
+
|
|
561
|
+
|
|
562
|
+
<div id="method-i-draw_histogram" class="method-detail ">
|
|
563
|
+
|
|
564
|
+
<div class="method-heading">
|
|
565
|
+
<span class="method-name">draw_histogram</span><span
|
|
566
|
+
class="method-args">(args)</span>
|
|
567
|
+
|
|
568
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
569
|
+
|
|
570
|
+
</div>
|
|
571
|
+
|
|
572
|
+
|
|
573
|
+
<div class="method-description">
|
|
574
|
+
|
|
575
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
576
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
577
|
+
<ul><li>
|
|
578
|
+
<p><code>args</code> - an Array of <a
|
|
579
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
580
|
+
type</p>
|
|
581
|
+
</li></ul>
|
|
582
|
+
|
|
583
|
+
|
|
584
|
+
|
|
585
|
+
|
|
586
|
+
<div class="method-source-code" id="draw_histogram-source">
|
|
587
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 199</span>
|
|
588
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_histogram</span>(<span class="ruby-identifier">args</span>)
|
|
589
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">generic</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
590
|
+
<span class="ruby-keyword">end</span></pre>
|
|
591
|
+
</div><!-- draw_histogram-source -->
|
|
592
|
+
|
|
593
|
+
</div>
|
|
594
|
+
|
|
595
|
+
|
|
596
|
+
|
|
597
|
+
|
|
598
|
+
</div><!-- draw_histogram-method -->
|
|
599
|
+
|
|
600
|
+
|
|
601
|
+
<div id="method-i-draw_label" class="method-detail ">
|
|
602
|
+
|
|
603
|
+
<div class="method-heading">
|
|
604
|
+
<span class="method-name">draw_label</span><span
|
|
605
|
+
class="method-args">(args)</span>
|
|
606
|
+
|
|
607
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
608
|
+
|
|
609
|
+
</div>
|
|
610
|
+
|
|
611
|
+
|
|
612
|
+
<div class="method-description">
|
|
613
|
+
|
|
614
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
615
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
616
|
+
<ul><li>
|
|
617
|
+
<p><code>args</code> - an Array of <a
|
|
618
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> object</p>
|
|
619
|
+
</li></ul>
|
|
620
|
+
|
|
621
|
+
|
|
622
|
+
|
|
623
|
+
|
|
624
|
+
<div class="method-source-code" id="draw_label-source">
|
|
625
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 172</span>
|
|
626
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_label</span>(<span class="ruby-identifier">args</span>)
|
|
627
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">label</span>(<span class="ruby-value">:text</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:text</span>],
|
|
628
|
+
<span class="ruby-value">:x</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:x</span>],
|
|
629
|
+
<span class="ruby-value">:y</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:y</span>]).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
630
|
+
<span class="ruby-keyword">end</span></pre>
|
|
631
|
+
</div><!-- draw_label-source -->
|
|
632
|
+
|
|
633
|
+
</div>
|
|
634
|
+
|
|
635
|
+
|
|
636
|
+
|
|
637
|
+
|
|
638
|
+
</div><!-- draw_label-method -->
|
|
639
|
+
|
|
640
|
+
|
|
641
|
+
<div id="method-i-draw_scale" class="method-detail ">
|
|
642
|
+
|
|
643
|
+
<div class="method-heading">
|
|
644
|
+
<span class="method-name">draw_scale</span><span
|
|
645
|
+
class="method-args">()</span>
|
|
646
|
+
|
|
647
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
648
|
+
|
|
649
|
+
</div>
|
|
650
|
+
|
|
651
|
+
|
|
652
|
+
<div class="method-description">
|
|
653
|
+
|
|
654
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
655
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
656
|
+
|
|
657
|
+
|
|
658
|
+
|
|
659
|
+
|
|
660
|
+
<div class="method-source-code" id="draw_scale-source">
|
|
661
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 165</span>
|
|
662
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_scale</span>
|
|
663
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">scale</span>(<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_start</span>,
|
|
664
|
+
<span class="ruby-value">:stop</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>,
|
|
665
|
+
<span class="ruby-value">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@num_intervals</span>, <span class="ruby-value">:page_width</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@width</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
666
|
+
<span class="ruby-keyword">end</span></pre>
|
|
667
|
+
</div><!-- draw_scale-source -->
|
|
668
|
+
|
|
669
|
+
</div>
|
|
670
|
+
|
|
671
|
+
|
|
672
|
+
|
|
673
|
+
|
|
674
|
+
</div><!-- draw_scale-method -->
|
|
675
|
+
|
|
676
|
+
|
|
677
|
+
<div id="method-i-draw_span" class="method-detail ">
|
|
678
|
+
|
|
679
|
+
<div class="method-heading">
|
|
680
|
+
<span class="method-name">draw_span</span><span
|
|
681
|
+
class="method-args">(args)</span>
|
|
682
|
+
|
|
683
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
684
|
+
|
|
685
|
+
</div>
|
|
686
|
+
|
|
687
|
+
|
|
688
|
+
<div class="method-description">
|
|
689
|
+
|
|
690
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
691
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
692
|
+
<ul><li>
|
|
693
|
+
<p><code>args</code> - an Array of <a
|
|
694
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
695
|
+
type</p>
|
|
696
|
+
</li></ul>
|
|
697
|
+
|
|
698
|
+
|
|
699
|
+
|
|
700
|
+
|
|
701
|
+
<div class="method-source-code" id="draw_span-source">
|
|
702
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 214</span>
|
|
703
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_span</span>(<span class="ruby-identifier">args</span>)
|
|
704
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">span</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
705
|
+
<span class="ruby-keyword">end</span></pre>
|
|
706
|
+
</div><!-- draw_span-source -->
|
|
707
|
+
|
|
708
|
+
</div>
|
|
709
|
+
|
|
710
|
+
|
|
711
|
+
|
|
712
|
+
|
|
713
|
+
</div><!-- draw_span-method -->
|
|
714
|
+
|
|
715
|
+
|
|
716
|
+
<div id="method-i-draw_transcript" class="method-detail ">
|
|
717
|
+
|
|
718
|
+
<div class="method-heading">
|
|
719
|
+
<span class="method-name">draw_transcript</span><span
|
|
720
|
+
class="method-args">(args)</span>
|
|
721
|
+
|
|
722
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
723
|
+
|
|
724
|
+
</div>
|
|
725
|
+
|
|
726
|
+
|
|
727
|
+
<div class="method-description">
|
|
728
|
+
|
|
729
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
730
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
731
|
+
<ul><li>
|
|
732
|
+
<p><code>args</code> - an Array of <a
|
|
733
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
734
|
+
type</p>
|
|
735
|
+
</li></ul>
|
|
736
|
+
|
|
737
|
+
|
|
738
|
+
|
|
739
|
+
|
|
740
|
+
<div class="method-source-code" id="draw_transcript-source">
|
|
741
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 194</span>
|
|
742
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_transcript</span>(<span class="ruby-identifier">args</span>)
|
|
743
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">transcript</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
744
|
+
<span class="ruby-keyword">end</span></pre>
|
|
745
|
+
</div><!-- draw_transcript-source -->
|
|
746
|
+
|
|
747
|
+
</div>
|
|
748
|
+
|
|
749
|
+
|
|
750
|
+
|
|
751
|
+
|
|
752
|
+
</div><!-- draw_transcript-method -->
|
|
753
|
+
|
|
754
|
+
|
|
755
|
+
<div id="method-i-draw_up_triangle" class="method-detail ">
|
|
756
|
+
|
|
757
|
+
<div class="method-heading">
|
|
758
|
+
<span class="method-name">draw_up_triangle</span><span
|
|
759
|
+
class="method-args">(args)</span>
|
|
760
|
+
|
|
761
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
762
|
+
|
|
763
|
+
</div>
|
|
764
|
+
|
|
765
|
+
|
|
766
|
+
<div class="method-description">
|
|
767
|
+
|
|
768
|
+
<p>Adds the <a href="Primitive.html">Bio::Graphics::Primitive</a> objects to
|
|
769
|
+
the <a href="SVGEE.html">SVGEE</a> object</p>
|
|
770
|
+
<ul><li>
|
|
771
|
+
<p><code>args</code> - an Array of <a
|
|
772
|
+
href="Primitive.html">Bio::Graphics::Primitive</a> objects of the stated
|
|
773
|
+
type</p>
|
|
774
|
+
</li></ul>
|
|
775
|
+
|
|
776
|
+
|
|
777
|
+
|
|
778
|
+
|
|
779
|
+
<div class="method-source-code" id="draw_up_triangle-source">
|
|
780
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 204</span>
|
|
781
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">draw_up_triangle</span>(<span class="ruby-identifier">args</span>)
|
|
782
|
+
<span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">up_triangle</span>(<span class="ruby-identifier">args</span>).<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">g</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">add_primitive</span>(<span class="ruby-identifier">g</span>) }
|
|
783
|
+
<span class="ruby-keyword">end</span></pre>
|
|
784
|
+
</div><!-- draw_up_triangle-source -->
|
|
785
|
+
|
|
786
|
+
</div>
|
|
787
|
+
|
|
788
|
+
|
|
789
|
+
|
|
790
|
+
|
|
791
|
+
</div><!-- draw_up_triangle-method -->
|
|
792
|
+
|
|
793
|
+
|
|
794
|
+
<div id="method-i-get_limits" class="method-detail ">
|
|
795
|
+
|
|
796
|
+
<div class="method-heading">
|
|
797
|
+
<span class="method-name">get_limits</span><span
|
|
798
|
+
class="method-args">()</span>
|
|
799
|
+
|
|
800
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
801
|
+
|
|
802
|
+
</div>
|
|
803
|
+
|
|
804
|
+
|
|
805
|
+
<div class="method-description">
|
|
806
|
+
|
|
807
|
+
<p>Calculates the <a href="Page.html">Page</a> scale-start and scale-stop
|
|
808
|
+
position and the nucleotides per pixel for the current <a
|
|
809
|
+
href="Page.html">Page</a></p>
|
|
810
|
+
|
|
811
|
+
|
|
812
|
+
|
|
813
|
+
|
|
814
|
+
<div class="method-source-code" id="get_limits-source">
|
|
815
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 154</span>
|
|
816
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">get_limits</span>
|
|
817
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
818
|
+
<span class="ruby-identifier">lowest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">start</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">start</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">start</span>
|
|
819
|
+
<span class="ruby-identifier">highest</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">features</span>.<span class="ruby-identifier">sort</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">x</span>, <span class="ruby-identifier">y</span><span class="ruby-operator">|</span> <span class="ruby-identifier">y</span>.<span class="ruby-identifier">end</span> <span class="ruby-operator"><=></span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">end</span> }.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">end</span>
|
|
820
|
+
<span class="ruby-ivar">@scale_start</span> = <span class="ruby-identifier">lowest</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">lowest</span> <span class="ruby-operator"><</span> <span class="ruby-ivar">@scale_start</span>
|
|
821
|
+
<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-identifier">highest</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">highest</span> <span class="ruby-operator">></span> <span class="ruby-ivar">@scale_stop</span>
|
|
822
|
+
<span class="ruby-ivar">@nt_per_px_x</span> = (<span class="ruby-ivar">@scale_stop</span> <span class="ruby-operator">-</span> <span class="ruby-ivar">@scale_start</span>).<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@width</span>.<span class="ruby-identifier">to_f</span>
|
|
823
|
+
<span class="ruby-keyword">end</span>
|
|
824
|
+
<span class="ruby-keyword">end</span></pre>
|
|
825
|
+
</div><!-- get_limits-source -->
|
|
826
|
+
|
|
827
|
+
</div>
|
|
828
|
+
|
|
829
|
+
|
|
830
|
+
|
|
831
|
+
|
|
832
|
+
</div><!-- get_limits-method -->
|
|
833
|
+
|
|
834
|
+
|
|
835
|
+
<div id="method-i-get_markup" class="method-detail ">
|
|
836
|
+
|
|
837
|
+
<div class="method-heading">
|
|
838
|
+
<span class="method-name">get_markup</span><span
|
|
839
|
+
class="method-args">()</span>
|
|
840
|
+
|
|
841
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
842
|
+
|
|
843
|
+
</div>
|
|
844
|
+
|
|
845
|
+
|
|
846
|
+
<div class="method-description">
|
|
847
|
+
|
|
848
|
+
<p>Pulls together all track information to create svg text which will draw all
|
|
849
|
+
the features on the page to scale Uses the methods <code>get_limits</code>
|
|
850
|
+
and <code>draw_scale</code> and then <code>draw_feature</code> for each
|
|
851
|
+
track on the page</p>
|
|
852
|
+
|
|
853
|
+
|
|
854
|
+
|
|
855
|
+
|
|
856
|
+
<div class="method-source-code" id="get_markup-source">
|
|
857
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 323</span>
|
|
858
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">get_markup</span>
|
|
859
|
+
<span class="ruby-identifier">get_limits</span>
|
|
860
|
+
<span class="ruby-identifier">draw_scale</span>
|
|
861
|
+
<span class="ruby-ivar">@tracks</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
862
|
+
<span class="ruby-identifier">draw_features</span>(<span class="ruby-identifier">track</span>)
|
|
863
|
+
<span class="ruby-keyword">end</span>
|
|
864
|
+
<span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">draw</span>
|
|
865
|
+
<span class="ruby-keyword">end</span></pre>
|
|
866
|
+
</div><!-- get_markup-source -->
|
|
867
|
+
|
|
868
|
+
</div>
|
|
869
|
+
|
|
870
|
+
|
|
871
|
+
|
|
872
|
+
|
|
873
|
+
</div><!-- get_markup-method -->
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
<div id="method-i-to_px" class="method-detail ">
|
|
877
|
+
|
|
878
|
+
<div class="method-heading">
|
|
879
|
+
<span class="method-name">to_px</span><span
|
|
880
|
+
class="method-args">(num)</span>
|
|
881
|
+
|
|
882
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
883
|
+
|
|
884
|
+
</div>
|
|
885
|
+
|
|
886
|
+
|
|
887
|
+
<div class="method-description">
|
|
888
|
+
|
|
889
|
+
<p>Provides the number of pixels required for a given number of nucleotides,
|
|
890
|
+
e.g the length of a certain exon</p>
|
|
891
|
+
<ul><li>
|
|
892
|
+
<p><code>num</code> - the number of nucleotides</p>
|
|
893
|
+
</li><li>
|
|
894
|
+
<p><code>returns</code> - the required number of pixels to draw the object</p>
|
|
895
|
+
</li></ul>
|
|
896
|
+
|
|
897
|
+
|
|
898
|
+
|
|
899
|
+
|
|
900
|
+
<div class="method-source-code" id="to_px-source">
|
|
901
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 317</span>
|
|
902
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">to_px</span>(<span class="ruby-identifier">num</span>)
|
|
903
|
+
(<span class="ruby-identifier">num</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-ivar">@nt_per_px_x</span>.<span class="ruby-identifier">to_f</span>)
|
|
904
|
+
<span class="ruby-keyword">end</span></pre>
|
|
905
|
+
</div><!-- to_px-source -->
|
|
906
|
+
|
|
907
|
+
</div>
|
|
908
|
+
|
|
909
|
+
|
|
910
|
+
|
|
911
|
+
|
|
912
|
+
</div><!-- to_px-method -->
|
|
913
|
+
|
|
914
|
+
|
|
915
|
+
<div id="method-i-write" class="method-detail ">
|
|
916
|
+
|
|
917
|
+
<div class="method-heading">
|
|
918
|
+
<span class="method-name">write</span><span
|
|
919
|
+
class="method-args">(file)</span>
|
|
920
|
+
|
|
921
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
922
|
+
|
|
923
|
+
</div>
|
|
924
|
+
|
|
925
|
+
|
|
926
|
+
<div class="method-description">
|
|
927
|
+
|
|
928
|
+
<p>Writes the svg text to a file</p>
|
|
929
|
+
<ul><li>
|
|
930
|
+
<p><code>file</code> - the file to which the svg text should be written</p>
|
|
931
|
+
</li></ul>
|
|
932
|
+
|
|
933
|
+
|
|
934
|
+
|
|
935
|
+
|
|
936
|
+
<div class="method-source-code" id="write-source">
|
|
937
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 338</span>
|
|
938
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">write</span>(<span class="ruby-identifier">file</span>)
|
|
939
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">file</span>, <span class="ruby-string">'w'</span>).<span class="ruby-identifier">write</span>(<span class="ruby-identifier">get_markup</span>)
|
|
940
|
+
<span class="ruby-keyword">end</span></pre>
|
|
941
|
+
</div><!-- write-source -->
|
|
942
|
+
|
|
943
|
+
</div>
|
|
944
|
+
|
|
945
|
+
|
|
946
|
+
|
|
947
|
+
|
|
948
|
+
</div><!-- write-method -->
|
|
949
|
+
|
|
950
|
+
|
|
951
|
+
</section><!-- public-instance-method-details -->
|
|
952
|
+
|
|
953
|
+
<section id="public-class-5Buntitled-5D-method-details" class="method-section section">
|
|
954
|
+
<h3 class="section-header">Public Class Methods</h3>
|
|
955
|
+
|
|
956
|
+
|
|
957
|
+
<div id="method-c-from_json" class="method-detail ">
|
|
958
|
+
|
|
959
|
+
<div class="method-heading">
|
|
960
|
+
<span class="method-name">from_json</span><span
|
|
961
|
+
class="method-args">(args)</span>
|
|
962
|
+
|
|
963
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
964
|
+
|
|
965
|
+
</div>
|
|
966
|
+
|
|
967
|
+
|
|
968
|
+
<div class="method-description">
|
|
969
|
+
|
|
970
|
+
<p>Takes a custom-written json file and writes an svg page to file which will
|
|
971
|
+
contain the given features described within the json file.</p>
|
|
972
|
+
<ul><li>
|
|
973
|
+
<p><code>args</code> - a custom-written json file describing the parameters
|
|
974
|
+
and resources needed for a new page</p>
|
|
975
|
+
</li></ul>
|
|
976
|
+
|
|
977
|
+
|
|
978
|
+
|
|
979
|
+
|
|
980
|
+
<div class="method-source-code" id="from_json-source">
|
|
981
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 53</span>
|
|
982
|
+
<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">from_json</span>(<span class="ruby-identifier">args</span>)
|
|
983
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'rubygems'</span>
|
|
984
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'json'</span>
|
|
985
|
+
<span class="ruby-identifier">data</span> = <span class="ruby-constant">JSON</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">args</span>[<span class="ruby-value">:json</span>], <span class="ruby-string">'r'</span>).<span class="ruby-identifier">read</span>)
|
|
986
|
+
<span class="ruby-identifier">p</span> = <span class="ruby-constant">Page</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-string">"Page"</span>][<span class="ruby-string">"width"</span>],
|
|
987
|
+
<span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-string">"Page"</span>][<span class="ruby-string">"height"</span>],
|
|
988
|
+
<span class="ruby-value">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">data</span>[<span class="ruby-string">"Page"</span>][<span class="ruby-string">"intervals"</span>])
|
|
989
|
+
<span class="ruby-identifier">data</span>[<span class="ruby-string">"Tracks"</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">track</span><span class="ruby-operator">|</span>
|
|
990
|
+
<span class="ruby-comment">#prep the track args</span>
|
|
991
|
+
<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track</span>.<span class="ruby-identifier">dup</span>
|
|
992
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-string">"file"</span>)
|
|
993
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-string">"file_type"</span>)
|
|
994
|
+
<span class="ruby-identifier">track_args</span> = <span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">inject</span>({}) { <span class="ruby-operator">|</span><span class="ruby-identifier">memo</span>, (<span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span>)<span class="ruby-operator">|</span> <span class="ruby-identifier">memo</span>[<span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_sym</span>] = <span class="ruby-identifier">v</span>; <span class="ruby-identifier">memo</span> }
|
|
995
|
+
<span class="ruby-comment">##convert any of the pre-made gradient strings in the keys to symbol</span>
|
|
996
|
+
<span class="ruby-identifier">track_args</span>.<span class="ruby-identifier">each_key</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
|
|
997
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">respond_to?</span>(<span class="ruby-value">:to_sym</span>)
|
|
998
|
+
<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>] = <span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span> <span class="ruby-keyword">if</span> <span class="ruby-constant">Glyph</span>.<span class="ruby-identifier">gradients</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">track_args</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">to_sym</span>)
|
|
999
|
+
<span class="ruby-keyword">end</span>
|
|
1000
|
+
|
|
1001
|
+
<span class="ruby-identifier">svg_track</span> = <span class="ruby-identifier">p</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-identifier">track_args</span>)
|
|
1002
|
+
<span class="ruby-identifier">features</span> = [] <span class="ruby-comment">##set up the features...</span>
|
|
1003
|
+
|
|
1004
|
+
<span class="ruby-keyword">case</span> <span class="ruby-identifier">track</span>[<span class="ruby-string">"file_type"</span>] <span class="ruby-comment">##deal with the gff and data files</span>
|
|
1005
|
+
<span class="ruby-keyword">when</span> <span class="ruby-string">"gff"</span>
|
|
1006
|
+
<span class="ruby-identifier">groups</span> = {}
|
|
1007
|
+
<span class="ruby-identifier">parentless_features</span> = []
|
|
1008
|
+
<span class="ruby-constant">Page</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">track</span>[<span class="ruby-string">"file"</span>]).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">gff</span><span class="ruby-operator">|</span> <span class="ruby-comment">#gets features in a list and links their children to them as members of the array at the key</span>
|
|
1009
|
+
<span class="ruby-identifier">parent_id</span> = <span class="ruby-identifier">gff</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-string">'Parent'</span> }
|
|
1010
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">empty?</span>
|
|
1011
|
+
<span class="ruby-identifier">parentless_features</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
1012
|
+
<span class="ruby-keyword">else</span>
|
|
1013
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>].<span class="ruby-identifier">nil?</span>
|
|
1014
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] = []
|
|
1015
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
1016
|
+
<span class="ruby-keyword">else</span>
|
|
1017
|
+
<span class="ruby-identifier">groups</span>[<span class="ruby-identifier">parent_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>] <span class="ruby-operator"><<</span> <span class="ruby-identifier">gff</span>
|
|
1018
|
+
<span class="ruby-keyword">end</span>
|
|
1019
|
+
<span class="ruby-keyword">end</span>
|
|
1020
|
+
<span class="ruby-keyword">end</span>
|
|
1021
|
+
<span class="ruby-comment">#now flick through the parentless features and add any exons / UTRs</span>
|
|
1022
|
+
<span class="ruby-identifier">parentless_features</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">plf</span><span class="ruby-operator">|</span>
|
|
1023
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'pp'</span>
|
|
1024
|
+
<span class="ruby-comment">#pp parentless_features</span>
|
|
1025
|
+
<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">attributes</span>.<span class="ruby-identifier">select</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">first</span> <span class="ruby-operator">==</span> <span class="ruby-string">'ID'</span> }
|
|
1026
|
+
<span class="ruby-identifier">gff_id</span> = <span class="ruby-identifier">gff_id</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">last</span>
|
|
1027
|
+
<span class="ruby-identifier">exons</span> = []
|
|
1028
|
+
<span class="ruby-identifier">utrs</span> = []
|
|
1029
|
+
<span class="ruby-identifier">children</span> = <span class="ruby-identifier">groups</span>[<span class="ruby-identifier">gff_id</span>] <span class="ruby-operator">||</span> <span class="ruby-identifier">children</span> = []
|
|
1030
|
+
<span class="ruby-identifier">children</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">child</span><span class="ruby-operator">|</span>
|
|
1031
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-string">'exon'</span> <span class="ruby-keyword">or</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">==</span> <span class="ruby-string">'CDS'</span>
|
|
1032
|
+
<span class="ruby-identifier">exons</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
|
|
1033
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">child</span>.<span class="ruby-identifier">feature</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp">/utr/</span>
|
|
1034
|
+
<span class="ruby-identifier">utrs</span> <span class="ruby-operator">+=</span> [<span class="ruby-identifier">child</span>.<span class="ruby-identifier">start</span>, <span class="ruby-identifier">child</span>.<span class="ruby-identifier">end</span>]
|
|
1035
|
+
<span class="ruby-keyword">end</span>
|
|
1036
|
+
<span class="ruby-keyword">end</span>
|
|
1037
|
+
<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">start</span>, <span class="ruby-value">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">end</span>, <span class="ruby-value">:exons</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">exons</span>, <span class="ruby-value">:utrs</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">utrs</span>, <span class="ruby-value">:strand</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">plf</span>.<span class="ruby-identifier">strand</span>, <span class="ruby-value">:id</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">gff_id</span>)
|
|
1038
|
+
<span class="ruby-keyword">end</span> <span class="ruby-comment">#parentless features end</span>
|
|
1039
|
+
<span class="ruby-keyword">when</span> <span class="ruby-string">"data"</span>
|
|
1040
|
+
<span class="ruby-comment">##each line is a data feature</span>
|
|
1041
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">track</span>[<span class="ruby-string">"file"</span>], <span class="ruby-string">"r"</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
1042
|
+
<span class="ruby-identifier">start</span>, <span class="ruby-identifier">stop</span>, <span class="ruby-identifier">value</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
|
|
1043
|
+
<span class="ruby-identifier">features</span> <span class="ruby-operator"><<</span> <span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">start</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:end</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">stop</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:segment_height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">value</span>.<span class="ruby-identifier">to_f</span>)
|
|
1044
|
+
<span class="ruby-keyword">end</span>
|
|
1045
|
+
<span class="ruby-keyword">end</span> <span class="ruby-comment">#data end</span>
|
|
1046
|
+
<span class="ruby-identifier">features</span>.<span class="ruby-identifier">each</span> { <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">svg_track</span>.<span class="ruby-identifier">add</span>(<span class="ruby-identifier">f</span>) }
|
|
1047
|
+
<span class="ruby-keyword">end</span> <span class="ruby-comment">#track end</span>
|
|
1048
|
+
<span class="ruby-identifier">p</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">args</span>[<span class="ruby-value">:outfile</span>])
|
|
1049
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1050
|
+
</div><!-- from_json-source -->
|
|
1051
|
+
|
|
1052
|
+
</div>
|
|
1053
|
+
|
|
1054
|
+
|
|
1055
|
+
|
|
1056
|
+
|
|
1057
|
+
</div><!-- from_json-method -->
|
|
1058
|
+
|
|
1059
|
+
|
|
1060
|
+
<div id="method-c-new" class="method-detail ">
|
|
1061
|
+
|
|
1062
|
+
<div class="method-heading">
|
|
1063
|
+
<span class="method-name">new</span><span
|
|
1064
|
+
class="method-args">(args)</span>
|
|
1065
|
+
|
|
1066
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1067
|
+
|
|
1068
|
+
</div>
|
|
1069
|
+
|
|
1070
|
+
|
|
1071
|
+
<div class="method-description">
|
|
1072
|
+
|
|
1073
|
+
<p>Creates a new <a href="Page.html">Page</a> object.</p>
|
|
1074
|
+
|
|
1075
|
+
<p>A new <a href="Page.html">Page</a> contains the following arguments:</p>
|
|
1076
|
+
<ul><li>
|
|
1077
|
+
<p>height = the height of the page</p>
|
|
1078
|
+
</li><li>
|
|
1079
|
+
<p>width = the width of the page</p>
|
|
1080
|
+
</li><li>
|
|
1081
|
+
<p>style = includes the a background colour</p>
|
|
1082
|
+
</li><li>
|
|
1083
|
+
<p>svg = a new <a href="SVGEE.html">SVGEE</a> object</p>
|
|
1084
|
+
</li><li>
|
|
1085
|
+
<p>scale_start = the scale-start of the page (1.0/0.0)</p>
|
|
1086
|
+
</li><li>
|
|
1087
|
+
<p>scale_stop = the scale-stop of the page (-1.0/0.0)</p>
|
|
1088
|
+
</li><li>
|
|
1089
|
+
<p>tracks = an array of track objects with loads of features in it…</p>
|
|
1090
|
+
</li><li>
|
|
1091
|
+
<p>nt_per_percent = the number of nucleotides that are represented by 1% of
|
|
1092
|
+
the page (1);</p>
|
|
1093
|
+
</li><li>
|
|
1094
|
+
<p>num_intervals = the number of intervals</p>
|
|
1095
|
+
</li><li>
|
|
1096
|
+
<p>track_top = the position of the top of the first track (30)</p>
|
|
1097
|
+
</li></ul>
|
|
1098
|
+
|
|
1099
|
+
<p>A new page maybe set up as follows:</p>
|
|
1100
|
+
|
|
1101
|
+
<pre class="ruby"><span class="ruby-ivar">@page</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">Page</span>.<span class="ruby-identifier">new</span>(:<span class="ruby-identifier">width</span> =<span class="ruby-operator">></span> <span class="ruby-value">800</span>,
|
|
1102
|
+
:<span class="ruby-identifier">height</span> =<span class="ruby-operator">></span> <span class="ruby-value">110</span>, :<span class="ruby-identifier">number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>)
|
|
1103
|
+
</pre>
|
|
1104
|
+
|
|
1105
|
+
|
|
1106
|
+
|
|
1107
|
+
|
|
1108
|
+
<div class="method-source-code" id="new-source">
|
|
1109
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 30</span>
|
|
1110
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
|
|
1111
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:height</span>]
|
|
1112
|
+
<span class="ruby-ivar">@width</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:width</span>]
|
|
1113
|
+
<span class="ruby-identifier">args</span>[<span class="ruby-value">:style</span>] = <span class="ruby-node">"background-color:#{args[:background_color]};"</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">args</span>[<span class="ruby-value">:background_color</span>]
|
|
1114
|
+
<span class="ruby-ivar">@svg</span> = <span class="ruby-constant">SVGEE</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">args</span>)
|
|
1115
|
+
<span class="ruby-ivar">@scale_start</span> = <span class="ruby-value">1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0.0</span>
|
|
1116
|
+
<span class="ruby-ivar">@scale_stop</span> = <span class="ruby-value">-1.0</span><span class="ruby-operator">/</span><span class="ruby-value">0.0</span>
|
|
1117
|
+
<span class="ruby-ivar">@tracks</span> = [] <span class="ruby-comment">#array of track objects with loads of features in it...</span>
|
|
1118
|
+
<span class="ruby-ivar">@nt_per_percent</span> = <span class="ruby-value">1</span>;
|
|
1119
|
+
<span class="ruby-ivar">@num_intervals</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:number_of_intervals</span>]
|
|
1120
|
+
<span class="ruby-ivar">@track_top</span> = <span class="ruby-value">30</span>
|
|
1121
|
+
|
|
1122
|
+
<span class="ruby-keyword">def</span> <span class="ruby-ivar">@svg</span>.<span class="ruby-identifier">update_height</span>(<span class="ruby-identifier">height</span>)
|
|
1123
|
+
<span class="ruby-ivar">@height</span> = <span class="ruby-identifier">height</span>
|
|
1124
|
+
<span class="ruby-keyword">end</span>
|
|
1125
|
+
|
|
1126
|
+
<span class="ruby-comment">#def @svg.update_width(width)</span>
|
|
1127
|
+
<span class="ruby-comment"># @width = width</span>
|
|
1128
|
+
<span class="ruby-comment">#end</span>
|
|
1129
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1130
|
+
</div><!-- new-source -->
|
|
1131
|
+
|
|
1132
|
+
</div>
|
|
1133
|
+
|
|
1134
|
+
|
|
1135
|
+
|
|
1136
|
+
|
|
1137
|
+
</div><!-- new-method -->
|
|
1138
|
+
|
|
1139
|
+
|
|
1140
|
+
<div id="method-c-parse_gff" class="method-detail ">
|
|
1141
|
+
|
|
1142
|
+
<div class="method-heading">
|
|
1143
|
+
<span class="method-name">parse_gff</span><span
|
|
1144
|
+
class="method-args">(gff_file)</span>
|
|
1145
|
+
|
|
1146
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1147
|
+
|
|
1148
|
+
</div>
|
|
1149
|
+
|
|
1150
|
+
|
|
1151
|
+
<div class="method-description">
|
|
1152
|
+
|
|
1153
|
+
<p>Parses a GFF file into an Array of <a
|
|
1154
|
+
href="http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html">Bio::GFF::GFF3::Record</a>
|
|
1155
|
+
objects</p>
|
|
1156
|
+
<ul><li>
|
|
1157
|
+
<p><code>gff_file</code> - a GFF-formatted file</p>
|
|
1158
|
+
</li><li>
|
|
1159
|
+
<p><code>returns</code> - an Array of <a
|
|
1160
|
+
href="http://bioruby.org/rdoc/Bio/GFF/GFF3/Record.html">Bio::GFF::GFF3::Record</a>
|
|
1161
|
+
objects</p>
|
|
1162
|
+
</li></ul>
|
|
1163
|
+
|
|
1164
|
+
|
|
1165
|
+
|
|
1166
|
+
|
|
1167
|
+
<div class="method-source-code" id="parse_gff-source">
|
|
1168
|
+
<pre><span class="ruby-comment"># File lib/bio/graphics/page.rb, line 125</span>
|
|
1169
|
+
<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">parse_gff</span>(<span class="ruby-identifier">gff_file</span>)
|
|
1170
|
+
<span class="ruby-identifier">require</span> <span class="ruby-string">'bio'</span>
|
|
1171
|
+
<span class="ruby-identifier">a</span> = []
|
|
1172
|
+
<span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">gff_file</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
1173
|
+
<span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">=~</span> <span class="ruby-node">/^#/</span>
|
|
1174
|
+
<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">GFF</span><span class="ruby-operator">::</span><span class="ruby-constant">GFF3</span><span class="ruby-operator">::</span><span class="ruby-constant">Record</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
|
|
1175
|
+
<span class="ruby-keyword">end</span>
|
|
1176
|
+
<span class="ruby-identifier">a</span>
|
|
1177
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1178
|
+
</div><!-- parse_gff-source -->
|
|
1179
|
+
|
|
1180
|
+
</div>
|
|
1181
|
+
|
|
1182
|
+
|
|
1183
|
+
|
|
1184
|
+
|
|
1185
|
+
</div><!-- parse_gff-method -->
|
|
1186
|
+
|
|
1187
|
+
|
|
1188
|
+
</section><!-- public-class-method-details -->
|
|
1189
|
+
|
|
1190
|
+
</section><!-- 5Buntitled-5D -->
|
|
1191
|
+
|
|
1192
|
+
</div><!-- documentation -->
|
|
1193
|
+
|
|
1194
|
+
|
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1195
|
+
<footer id="validator-badges">
|
|
1196
|
+
<p><a href="http://validator.w3.org/check/referer">[Validate]</a>
|
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1197
|
+
<p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.rc.2.1.
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1198
|
+
<p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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</footer>
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